publication . Article . Other literature type . 2019

Resolution of the ordinal phylogeny of mosses using targeted exons from organellar and nuclear genomes

Yang Liu; Matthew G. Johnson; Cymon J. Cox; Rafael Medina; Nicolas Devos; Alain Vanderpoorten; Lars Hedenäs; Neil E. Bell; James R. Shevock; Blanka Aguero; ...
Open Access English
  • Published: 01 Apr 2019 Journal: Nature Communications (issn: 2041-1723, Copyright policy)
  • Publisher: Nature Publishing Group
Abstract
Mosses are a highly diverse lineage of land plants, whose diversification, spanning at least 400 million years, remains phylogenetically ambiguous due to the lack of fossils, massive early extinctions, late radiations, limited morphological variation, and conflicting signal among previously used markers. Here, we present phylogenetic reconstructions based on complete organellar exomes and a comparable set of nuclear genes for this major lineage of land plants. Our analysis of 142 species representing 29 of the 30 moss orders reveals that relative average rates of non-synonymous substitutions in nuclear versus plastid genes are much higher in mosses than in seed ...
Subjects
Medical Subject Headings: food and beverages
free text keywords: Bryophyta, Embryophyta, Spermatophyta, : Phytobiology (plant sciences, forestry, mycology...) [Life sciences], : Biologie végétale (sciences végétales, sylviculture, mycologie...) [Sciences du vivant], Science, Q, Article, General Biochemistry, Genetics and Molecular Biology, General Physics and Astronomy, General Chemistry, Phylogenetic tree, Evolutionary biology, Taxon, Biology, Genome, Plastid, Moss, biology.organism_classification, Nuclear gene, Genetics, Phylogenetics, Biodiversity
Related Organizations
85 references, page 1 of 6

Clarke, JT, Warnock, R, Donoghue, PC. Establishing a time-scale for plant evolution. New Phytol.. 2011; 192: 266-301 [OpenAIRE] [PubMed] [DOI]

Laenen, B. Extant diversity of bryophytes emerged from successive post-Mesozoic diversification bursts. Nat. Commun.. 2014; 5: 6134 [OpenAIRE] [DOI]

Cardona-Correa, C. Peat moss–like vegetative remains from ordovician carbonates. Int. J. Plant Sci.. 2016; 177: 523-538 [OpenAIRE] [DOI]

Goffinet, B, Buck, WR. The evolution of body form in bryophytes. Annu. Plant Rev.. 2013; 45: 51-89

La Farge-England, C. Growth form, branching pattern, and perichaetial position in mosses: cladocarpy and pleurocarpy redefined. Bryologist. 1996; 99: 170-186 [OpenAIRE] [DOI]

6.Goffinet, B., Buck, W. R. & Shaw A. J. in Bryophyte Biology, 2nd edn. (eds Goffinet, B. & Shaw, A. J.) (Cambridge University Press, New York, NY USA, 2009).

Proctor, MC. The bryophyte paradox: tolerance of desiccation, evasion of drought. Plant Ecol.. 2000; 151: 41-49 [DOI]

Deane-Coe, KK, Stanton, D. Functional ecology of cryptogams: scaling from bryophyte, lichen, and soil crust traits to ecosystem processes. New Phytol.. 2017; 213: 993-995 [OpenAIRE] [PubMed] [DOI]

Yu, Z. Northern peatland carbon stocks and dynamics: a review. Biogeosciences. 2012; 9: 4071-4085 [OpenAIRE] [DOI]

Shaw, AJ. Peatmoss (Sphagnum) diversification associated with Miocene Northern Hemisphere climatic cooling?. Mol. Phylogen. Evol.. 2010; 55: 1139-1145 [OpenAIRE] [DOI]

Johnson, MG. HybPiper: Extracting coding sequence and introns for phylogenetics from high-throughput sequencing reads using target enrichment. Appl. Plant Sci.. 2016; 4: 1600016 [OpenAIRE] [DOI]

Newton, AE. Evolution of the major moss lineages: phylogenetic analyses based on multiple gene sequences and morphology. Bryologist. 2000; 103: 187-211 [DOI]

Cox, CJ, Goffinet, B, Shaw, AJ, Boles, SB. Phylogenetic relationships among the mosses based on heterogeneous Bayesian analysis of multiple genes from multiple genomic compartments. Syst. Bot.. 2004; 29: 234-250 [OpenAIRE] [DOI]

Qiu, YL. The deepest divergences in land plants inferred from phylogenomic evidence. Proc. Natl Acad. Sci. USA. 2006; 103: 15511-15516 [OpenAIRE] [PubMed] [DOI]

Chang, Y, Graham, SW. Inferring the higher-order phylogeny of mosses (Bryophyta) and relatives using a large, multigene plastid data set. Am. J. Bot.. 2011; 98: 839-849 [OpenAIRE] [PubMed] [DOI]

85 references, page 1 of 6
Abstract
Mosses are a highly diverse lineage of land plants, whose diversification, spanning at least 400 million years, remains phylogenetically ambiguous due to the lack of fossils, massive early extinctions, late radiations, limited morphological variation, and conflicting signal among previously used markers. Here, we present phylogenetic reconstructions based on complete organellar exomes and a comparable set of nuclear genes for this major lineage of land plants. Our analysis of 142 species representing 29 of the 30 moss orders reveals that relative average rates of non-synonymous substitutions in nuclear versus plastid genes are much higher in mosses than in seed ...
Subjects
Medical Subject Headings: food and beverages
free text keywords: Bryophyta, Embryophyta, Spermatophyta, : Phytobiology (plant sciences, forestry, mycology...) [Life sciences], : Biologie végétale (sciences végétales, sylviculture, mycologie...) [Sciences du vivant], Science, Q, Article, General Biochemistry, Genetics and Molecular Biology, General Physics and Astronomy, General Chemistry, Phylogenetic tree, Evolutionary biology, Taxon, Biology, Genome, Plastid, Moss, biology.organism_classification, Nuclear gene, Genetics, Phylogenetics, Biodiversity
Related Organizations
85 references, page 1 of 6

Clarke, JT, Warnock, R, Donoghue, PC. Establishing a time-scale for plant evolution. New Phytol.. 2011; 192: 266-301 [OpenAIRE] [PubMed] [DOI]

Laenen, B. Extant diversity of bryophytes emerged from successive post-Mesozoic diversification bursts. Nat. Commun.. 2014; 5: 6134 [OpenAIRE] [DOI]

Cardona-Correa, C. Peat moss–like vegetative remains from ordovician carbonates. Int. J. Plant Sci.. 2016; 177: 523-538 [OpenAIRE] [DOI]

Goffinet, B, Buck, WR. The evolution of body form in bryophytes. Annu. Plant Rev.. 2013; 45: 51-89

La Farge-England, C. Growth form, branching pattern, and perichaetial position in mosses: cladocarpy and pleurocarpy redefined. Bryologist. 1996; 99: 170-186 [OpenAIRE] [DOI]

6.Goffinet, B., Buck, W. R. & Shaw A. J. in Bryophyte Biology, 2nd edn. (eds Goffinet, B. & Shaw, A. J.) (Cambridge University Press, New York, NY USA, 2009).

Proctor, MC. The bryophyte paradox: tolerance of desiccation, evasion of drought. Plant Ecol.. 2000; 151: 41-49 [DOI]

Deane-Coe, KK, Stanton, D. Functional ecology of cryptogams: scaling from bryophyte, lichen, and soil crust traits to ecosystem processes. New Phytol.. 2017; 213: 993-995 [OpenAIRE] [PubMed] [DOI]

Yu, Z. Northern peatland carbon stocks and dynamics: a review. Biogeosciences. 2012; 9: 4071-4085 [OpenAIRE] [DOI]

Shaw, AJ. Peatmoss (Sphagnum) diversification associated with Miocene Northern Hemisphere climatic cooling?. Mol. Phylogen. Evol.. 2010; 55: 1139-1145 [OpenAIRE] [DOI]

Johnson, MG. HybPiper: Extracting coding sequence and introns for phylogenetics from high-throughput sequencing reads using target enrichment. Appl. Plant Sci.. 2016; 4: 1600016 [OpenAIRE] [DOI]

Newton, AE. Evolution of the major moss lineages: phylogenetic analyses based on multiple gene sequences and morphology. Bryologist. 2000; 103: 187-211 [DOI]

Cox, CJ, Goffinet, B, Shaw, AJ, Boles, SB. Phylogenetic relationships among the mosses based on heterogeneous Bayesian analysis of multiple genes from multiple genomic compartments. Syst. Bot.. 2004; 29: 234-250 [OpenAIRE] [DOI]

Qiu, YL. The deepest divergences in land plants inferred from phylogenomic evidence. Proc. Natl Acad. Sci. USA. 2006; 103: 15511-15516 [OpenAIRE] [PubMed] [DOI]

Chang, Y, Graham, SW. Inferring the higher-order phylogeny of mosses (Bryophyta) and relatives using a large, multigene plastid data set. Am. J. Bot.. 2011; 98: 839-849 [OpenAIRE] [PubMed] [DOI]

85 references, page 1 of 6
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publication . Article . Other literature type . 2019

Resolution of the ordinal phylogeny of mosses using targeted exons from organellar and nuclear genomes

Yang Liu; Matthew G. Johnson; Cymon J. Cox; Rafael Medina; Nicolas Devos; Alain Vanderpoorten; Lars Hedenäs; Neil E. Bell; James R. Shevock; Blanka Aguero; ...