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Contrasting rates of molecular evolution and patterns of selection among gymnosperms and flowering plants

(2017) MOLECULAR BIOLOGY AND EVOLUTION. 34(6). p.1363-1377
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Bioinformatics: from nucleotids to networks (N2N)
Abstract
The majority of variation in rates of molecular evolution among seed plants remains both unexplored and unexplained. Although some attention has been given to flowering plants, reports of molecular evolutionary rates for their sister plant clade (gymnosperms) are scarce, and to our knowledge differences in molecular evolution among seed plant clades have never been tested in a phylogenetic framework. Angiosperms and gymnosperms differ in a number of features, of which contrasting reproductive biology, life spans, and population sizes are the most prominent. The highly conserved morphology of gymnosperms evidenced by similarity of extant species to fossil records and the high levels of macrosynteny at the genomic level have led scientists to believe that gymnosperms are slow-evolving plants, although some studies have offered contradictory results. Here, we used 31,968 nucleotide sites obtained from orthologous genes across a wide taxonomic sampling that includes representatives of most conifers, cycads, ginkgo, and many angiosperms with a sequenced genome. Our results suggest that angiosperms and gymnosperms differ considerably in their rates of molecular evolution per unit time, with gymnosperm rates being, on average, seven times lower than angiosperm species. Longer generation times and larger genome sizes are some of the factors explaining the slow rates of molecular evolution found in gymnosperms. In contrast to their slow rates of molecular evolution, gymnosperms possess higher substitution rate ratios than angiosperm taxa. Finally, our study suggests stronger and more efficient purifying and diversifying selection in gymnosperm than in angiosperm species, probably in relation to larger effective population sizes.
Keywords
gymnosperms, angiosperms, substitution rates, selection, mutation, life-history traits, EFFECTIVE POPULATION-SIZE, MULTIPLE SEQUENCE ALIGNMENT, CODON-SUBSTITUTION MODELS, DELETERIOUS MUTATION-RATE, PINE PINUS-TAEDA, AMINO-ACID SITES, LOBLOLLY-PINE, NUCLEOTIDE SUBSTITUTION, PHYLOGENETIC ANALYSIS, POSITIVE SELECTION

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Citation

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Chicago
De La Torre, Amanda R, Zhen Li, Yves Van de Peer, and Pär K Ingvarsson. 2017. “Contrasting Rates of Molecular Evolution and Patterns of Selection Among Gymnosperms and Flowering Plants.” Molecular Biology and Evolution 34 (6): 1363–1377.
APA
De La Torre, A. R., Li, Z., Van de Peer, Y., & Ingvarsson, P. K. (2017). Contrasting rates of molecular evolution and patterns of selection among gymnosperms and flowering plants. MOLECULAR BIOLOGY AND EVOLUTION, 34(6), 1363–1377.
Vancouver
1.
De La Torre AR, Li Z, Van de Peer Y, Ingvarsson PK. Contrasting rates of molecular evolution and patterns of selection among gymnosperms and flowering plants. MOLECULAR BIOLOGY AND EVOLUTION. 2017;34(6):1363–77.
MLA
De La Torre, Amanda R, Zhen Li, Yves Van de Peer, et al. “Contrasting Rates of Molecular Evolution and Patterns of Selection Among Gymnosperms and Flowering Plants.” MOLECULAR BIOLOGY AND EVOLUTION 34.6 (2017): 1363–1377. Print.
@article{8523498,
  abstract     = {The majority of variation in rates of molecular evolution among seed plants remains both unexplored and unexplained. Although some attention has been given to flowering plants, reports of molecular evolutionary rates for their sister plant clade (gymnosperms) are scarce, and to our knowledge differences in molecular evolution among seed plant clades have never been tested in a phylogenetic framework. Angiosperms and gymnosperms differ in a number of features, of which contrasting reproductive biology, life spans, and population sizes are the most prominent. The highly conserved morphology of gymnosperms evidenced by similarity of extant species to fossil records and the high levels of macrosynteny at the genomic level have led scientists to believe that gymnosperms are slow-evolving plants, although some studies have offered contradictory results. Here, we used 31,968 nucleotide sites obtained from orthologous genes across a wide taxonomic sampling that includes representatives of most conifers, cycads, ginkgo, and many angiosperms with a sequenced genome. Our results suggest that angiosperms and gymnosperms differ considerably in their rates of molecular evolution per unit time, with gymnosperm rates being, on average, seven times lower than angiosperm species. Longer generation times and larger genome sizes are some of the factors explaining the slow rates of molecular evolution found in gymnosperms. In contrast to their slow rates of molecular evolution, gymnosperms possess higher substitution rate ratios than angiosperm taxa. Finally, our study suggests stronger and more efficient purifying and diversifying selection in gymnosperm than in angiosperm species, probably in relation to larger effective population sizes.},
  author       = {De La Torre, Amanda R and Li, Zhen and Van de Peer, Yves and Ingvarsson, P{\"a}r K},
  issn         = {0737-4038},
  journal      = {MOLECULAR BIOLOGY AND EVOLUTION},
  keyword      = {gymnosperms,angiosperms,substitution rates,selection,mutation,life-history traits,EFFECTIVE POPULATION-SIZE,MULTIPLE SEQUENCE ALIGNMENT,CODON-SUBSTITUTION MODELS,DELETERIOUS MUTATION-RATE,PINE PINUS-TAEDA,AMINO-ACID SITES,LOBLOLLY-PINE,NUCLEOTIDE SUBSTITUTION,PHYLOGENETIC ANALYSIS,POSITIVE SELECTION},
  language     = {eng},
  number       = {6},
  pages        = {1363--1377},
  title        = {Contrasting rates of molecular evolution and patterns of selection among gymnosperms and flowering plants},
  url          = {http://dx.doi.org/10.1093/molbev/msx069},
  volume       = {34},
  year         = {2017},
}

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