Proteomic similarity of the Littorinid snails in the evolutionary context

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In: PeerJ, Vol. 8, No. 2, e8546, 13.02.2020.

Research output: Contribution to journal › Article › peer-review

BibTeX

@article{5bc0f2fd872341dea0bfa102a1b337c5,

title = "Proteomic similarity of the Littorinid snails in the evolutionary context",

abstract = "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.",

keywords = "taxonomy, cryptic species, phylogenetic markers, outliers, proteomics, Littorinidae, taxon-specific proteomic markers, ecological divergence, phylogeny, IndVal, taxonomy, Cryptic Species, phylogenetic markers, outliers, Proteomics, Littorinidae, taxon-specific proteomic markers, ecological divergence, Phylogeny, IndVal, Taxonomy, Taxon-specific proteomic markers, Outliers, Ecological divergence, Cryptic species, Phylogenetic markers, SPECIES COMPLEX, PROTEIN, GENUS LITTORINA, SPECIATION, SPATIAL-DISTRIBUTION, MAXIMUM-LIKELIHOOD-ESTIMATION, LITTORARIA-ARDOUINIANA, OF-THE-ART, GEL-ELECTROPHORESIS, MOLECULAR MARKERS",

author = "Maltseva, {Arina L.} and Varfolomeeva, {Marina A.} and Lobov, {Arseniy A.} and Polina Tikanova and Marina Panova and Mikhailova, {Natalia A.} and Granovitch, {Andrei I.}",

note = "Publisher Copyright: {\textcopyright} 2020 Maltseva et al.",

year = "2020",

month = feb,

day = "13",

doi = "10.7717/peerj.8546",

language = "English",

volume = "8",

journal = "PeerJ",

issn = "2167-8359",

publisher = "PeerJ",

number = "2",

}

RIS

TY - JOUR

T1 - Proteomic similarity of the Littorinid snails in the evolutionary context

AU - Maltseva, Arina L.

AU - Varfolomeeva, Marina A.

AU - Lobov, Arseniy A.

AU - Tikanova, Polina

AU - Panova, Marina

AU - Mikhailova, Natalia A.

AU - Granovitch, Andrei I.

PY - 2020/2/13

Y1 - 2020/2/13

N2 - 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.

AB - 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.

KW - taxonomy

KW - cryptic species

KW - phylogenetic markers

KW - outliers

KW - proteomics

KW - Littorinidae

KW - taxon-specific proteomic markers

KW - ecological divergence

KW - phylogeny

KW - IndVal

KW - taxonomy

KW - Cryptic Species

KW - phylogenetic markers

KW - outliers

KW - Proteomics

KW - Littorinidae

KW - taxon-specific proteomic markers

KW - ecological divergence

KW - Phylogeny

KW - IndVal

KW - Taxonomy

KW - Taxon-specific proteomic markers

KW - Outliers

KW - Ecological divergence

KW - Cryptic species

KW - Phylogenetic markers

KW - SPECIES COMPLEX

KW - PROTEIN

KW - GENUS LITTORINA

KW - SPECIATION

KW - SPATIAL-DISTRIBUTION

KW - MAXIMUM-LIKELIHOOD-ESTIMATION

KW - LITTORARIA-ARDOUINIANA

KW - OF-THE-ART

KW - GEL-ELECTROPHORESIS

KW - MOLECULAR MARKERS

UR - http://www.scopus.com/inward/record.url?scp=85079608552&partnerID=8YFLogxK

UR - https://www.mendeley.com/catalogue/166c6f41-32e3-30f0-ace1-ed522a7b45fd/

U2 - 10.7717/peerj.8546

DO - 10.7717/peerj.8546

M3 - Article

C2 - 32095363

VL - 8

JO - PeerJ

JF - PeerJ

SN - 2167-8359

IS - 2

M1 - e8546

ER -

ID: 51252943