Proteomic similarity of the Littorinid snails in the evolutionary context
Background The introduction of DNA-based molecular markers made a revolution in biological systematics. However, in cases of very recent divergence events, the neutral divergence may be too slow, and the analysis of adaptive part of the genome is more informative to reconstruct the recent evolutiona...
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PeerJ Inc.
2020-02-01
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| Online Access: | https://peerj.com/articles/8546.pdf |
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| author | Arina L. Maltseva Marina A. Varfolomeeva Arseniy A. Lobov Polina Tikanova Marina Panova Natalia A. Mikhailova Andrei I. Granovitch |
| author_facet | Arina L. Maltseva Marina A. Varfolomeeva Arseniy A. Lobov Polina Tikanova Marina Panova Natalia A. Mikhailova Andrei I. Granovitch |
| author_sort | Arina L. Maltseva |
| collection | DOAJ |
| description | Background The introduction of DNA-based molecular markers made a revolution in biological systematics. However, in cases of very recent divergence events, the neutral divergence may be too slow, and the analysis of adaptive part of the genome is more informative to reconstruct the recent evolutionary history of young species. The advantage of proteomics is its ability to reflect the biochemical machinery of life. It may help both to identify rapidly evolving genes and to interpret their functions. Methods Here we applied a comparative gel-based proteomic analysis to several species from the gastropod family Littorinidae. Proteomes were clustered to assess differences related to species, geographic location, sex and body part, using data on presence/absence of proteins in samples and data on protein occurrence frequency in samples of different species. Cluster support was assessed using multiscale bootstrap resampling and the stability of clustering—using cluster-wise index of cluster stability. Taxon-specific protein markers were derived using IndVal method. Proteomic trees were compared to consensus phylogenetic tree (based on neutral genetic markers) using estimates of the Robinson–Foulds distance, the Fowlkes–Mallows index and cophenetic correlation. Results Overall, the DNA-based phylogenetic tree and the proteomic similarity tree had consistent topologies. Further, we observed some interesting deviations of the proteomic littorinid tree from the neutral expectations. (1) There were signs of molecular parallelism in two Littoraria species that phylogenetically are quite distant, but live in similar habitats. (2) Proteome divergence was unexpectedly high between very closely related Littorina fabalis and L. obtusata, possibly reflecting their ecology-driven divergence. (3) Conservative house-keeping proteins were usually identified as markers for cryptic species groups (“saxatilis” and “obtusata” groups in the Littorina genus) and for genera (Littoraria and Echinolittorina species pairs), while metabolic enzymes and stress-related proteins (both potentially adaptively important) were often identified as markers supporting species branches. (4) In all five Littorina species British populations were separated from the European mainland populations, possibly reflecting their recent phylogeographic history. Altogether our study shows that proteomic data, when interpreted in the context of DNA-based phylogeny, can bring additional information on the evolutionary history of species. |
| first_indexed | 2024-03-09T06:49:40Z |
| format | Article |
| id | doaj.art-d0c81e8556594010843641f9d033d7eb |
| institution | Directory Open Access Journal |
| issn | 2167-8359 |
| language | English |
| last_indexed | 2024-03-09T06:49:40Z |
| publishDate | 2020-02-01 |
| publisher | PeerJ Inc. |
| record_format | Article |
| series | PeerJ |
| spelling | doaj.art-d0c81e8556594010843641f9d033d7eb2023-12-03T10:31:15ZengPeerJ Inc.PeerJ2167-83592020-02-018e854610.7717/peerj.8546Proteomic similarity of the Littorinid snails in the evolutionary contextArina L. Maltseva0Marina A. Varfolomeeva1Arseniy A. Lobov2Polina Tikanova3Marina Panova4Natalia A. Mikhailova5Andrei I. Granovitch6Department of Invertebrate Zoology, St. Petersburg State University, St. Petersburg, RussiaDepartment of Invertebrate Zoology, St. Petersburg State University, St. Petersburg, RussiaDepartment of Invertebrate Zoology, St. Petersburg State University, St. Petersburg, RussiaDepartment of Invertebrate Zoology, St. Petersburg State University, St. Petersburg, RussiaDepartment of Invertebrate Zoology, St. Petersburg State University, St. Petersburg, RussiaDepartment of Invertebrate Zoology, St. Petersburg State University, St. Petersburg, RussiaDepartment of Invertebrate Zoology, St. Petersburg State University, St. Petersburg, RussiaBackground The introduction of DNA-based molecular markers made a revolution in biological systematics. However, in cases of very recent divergence events, the neutral divergence may be too slow, and the analysis of adaptive part of the genome is more informative to reconstruct the recent evolutionary history of young species. The advantage of proteomics is its ability to reflect the biochemical machinery of life. It may help both to identify rapidly evolving genes and to interpret their functions. Methods Here we applied a comparative gel-based proteomic analysis to several species from the gastropod family Littorinidae. Proteomes were clustered to assess differences related to species, geographic location, sex and body part, using data on presence/absence of proteins in samples and data on protein occurrence frequency in samples of different species. Cluster support was assessed using multiscale bootstrap resampling and the stability of clustering—using cluster-wise index of cluster stability. Taxon-specific protein markers were derived using IndVal method. Proteomic trees were compared to consensus phylogenetic tree (based on neutral genetic markers) using estimates of the Robinson–Foulds distance, the Fowlkes–Mallows index and cophenetic correlation. Results Overall, the DNA-based phylogenetic tree and the proteomic similarity tree had consistent topologies. Further, we observed some interesting deviations of the proteomic littorinid tree from the neutral expectations. (1) There were signs of molecular parallelism in two Littoraria species that phylogenetically are quite distant, but live in similar habitats. (2) Proteome divergence was unexpectedly high between very closely related Littorina fabalis and L. obtusata, possibly reflecting their ecology-driven divergence. (3) Conservative house-keeping proteins were usually identified as markers for cryptic species groups (“saxatilis” and “obtusata” groups in the Littorina genus) and for genera (Littoraria and Echinolittorina species pairs), while metabolic enzymes and stress-related proteins (both potentially adaptively important) were often identified as markers supporting species branches. (4) In all five Littorina species British populations were separated from the European mainland populations, possibly reflecting their recent phylogeographic history. Altogether our study shows that proteomic data, when interpreted in the context of DNA-based phylogeny, can bring additional information on the evolutionary history of species.https://peerj.com/articles/8546.pdfTaxonomyCryptic speciesPhylogenetic markersOutliersProteomicsLittorinidae |
| spellingShingle | Arina L. Maltseva Marina A. Varfolomeeva Arseniy A. Lobov Polina Tikanova Marina Panova Natalia A. Mikhailova Andrei I. Granovitch Proteomic similarity of the Littorinid snails in the evolutionary context PeerJ Taxonomy Cryptic species Phylogenetic markers Outliers Proteomics Littorinidae |
| title | Proteomic similarity of the Littorinid snails in the evolutionary context |
| title_full | Proteomic similarity of the Littorinid snails in the evolutionary context |
| title_fullStr | Proteomic similarity of the Littorinid snails in the evolutionary context |
| title_full_unstemmed | Proteomic similarity of the Littorinid snails in the evolutionary context |
| title_short | Proteomic similarity of the Littorinid snails in the evolutionary context |
| title_sort | proteomic similarity of the littorinid snails in the evolutionary context |
| topic | Taxonomy Cryptic species Phylogenetic markers Outliers Proteomics Littorinidae |
| url | https://peerj.com/articles/8546.pdf |
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