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Organellomic data sets confirm a cryptic consensus on (unrooted) land-plant relationships and provide new insights into bryophyte molecular evolution.

Publication ,  Journal Article
Bell, D; Lin, Q; Gerelle, WK; Joya, S; Chang, Y; Taylor, ZN; Rothfels, CJ; Larsson, A; Villarreal, JC; Li, F-W; Pokorny, L; Szövényi, P ...
Published in: American journal of botany
January 2020

Phylogenetic trees of bryophytes provide important evolutionary context for land plants. However, published inferences of overall embryophyte relationships vary considerably. We performed phylogenomic analyses of bryophytes and relatives using both mitochondrial and plastid gene sets, and investigated bryophyte plastome evolution.We employed diverse likelihood-based analyses to infer large-scale bryophyte phylogeny for mitochondrial and plastid data sets. We tested for changes in purifying selection in plastid genes of a mycoheterotrophic liverwort (Aneura mirabilis) and a putatively mycoheterotrophic moss (Buxbaumia), and compared 15 bryophyte plastomes for major structural rearrangements.Overall land-plant relationships conflict across analyses, generally weakly. However, an underlying (unrooted) four-taxon tree is consistent across most analyses and published studies. Despite gene coverage patchiness, relationships within mosses, liverworts, and hornworts are largely congruent with previous studies, with plastid results generally better supported. Exclusion of RNA edit sites restores cases of unexpected non-monophyly to monophyly for Takakia and two hornwort genera. Relaxed purifying selection affects multiple plastid genes in mycoheterotrophic Aneura but not Buxbaumia. Plastid genome structure is nearly invariant across bryophytes, but the tufA locus, presumed lost in embryophytes, is unexpectedly retained in several mosses.A common unrooted tree underlies embryophyte phylogeny, [(liverworts, mosses), (hornworts, vascular plants)]; rooting inconsistency across studies likely reflects substantial distance to algal outgroups. Analyses combining genomic and transcriptomic data may be misled locally for heavily RNA-edited taxa. The Buxbaumia plastome lacks hallmarks of relaxed selection found in mycoheterotrophic Aneura. Autotrophic bryophyte plastomes, including Buxbaumia, hardly vary in overall structure.

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Published In

American journal of botany

DOI

EISSN

1537-2197

ISSN

1537-2197

Publication Date

January 2020

Volume

107

Issue

1

Start / End Page

91 / 115

Related Subject Headings

  • Phylogeny
  • Likelihood Functions
  • Evolutionary Biology
  • Evolution, Molecular
  • Consensus
  • Bryophyta
  • 3108 Plant biology
  • 3104 Evolutionary biology
  • 3103 Ecology
  • 0607 Plant Biology
 

Citation

APA
Chicago
ICMJE
MLA
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Bell, D., Lin, Q., Gerelle, W. K., Joya, S., Chang, Y., Taylor, Z. N., … Graham, S. W. (2020). Organellomic data sets confirm a cryptic consensus on (unrooted) land-plant relationships and provide new insights into bryophyte molecular evolution. American Journal of Botany, 107(1), 91–115. https://doi.org/10.1002/ajb2.1397
Bell, David, Qianshi Lin, Wesley K. Gerelle, Steve Joya, Ying Chang, Z Nathan Taylor, Carl J. Rothfels, et al. “Organellomic data sets confirm a cryptic consensus on (unrooted) land-plant relationships and provide new insights into bryophyte molecular evolution.American Journal of Botany 107, no. 1 (January 2020): 91–115. https://doi.org/10.1002/ajb2.1397.
Bell D, Lin Q, Gerelle WK, Joya S, Chang Y, Taylor ZN, et al. Organellomic data sets confirm a cryptic consensus on (unrooted) land-plant relationships and provide new insights into bryophyte molecular evolution. American journal of botany. 2020 Jan;107(1):91–115.
Bell, David, et al. “Organellomic data sets confirm a cryptic consensus on (unrooted) land-plant relationships and provide new insights into bryophyte molecular evolution.American Journal of Botany, vol. 107, no. 1, Jan. 2020, pp. 91–115. Epmc, doi:10.1002/ajb2.1397.
Bell D, Lin Q, Gerelle WK, Joya S, Chang Y, Taylor ZN, Rothfels CJ, Larsson A, Villarreal JC, Li F-W, Pokorny L, Szövényi P, Crandall-Stotler B, DeGironimo L, Floyd SK, Beerling DJ, Deyholos MK, von Konrat M, Ellis S, Shaw AJ, Chen T, Wong GK-S, Stevenson DW, Palmer JD, Graham SW. Organellomic data sets confirm a cryptic consensus on (unrooted) land-plant relationships and provide new insights into bryophyte molecular evolution. American journal of botany. 2020 Jan;107(1):91–115.

Published In

American journal of botany

DOI

EISSN

1537-2197

ISSN

1537-2197

Publication Date

January 2020

Volume

107

Issue

1

Start / End Page

91 / 115

Related Subject Headings

  • Phylogeny
  • Likelihood Functions
  • Evolutionary Biology
  • Evolution, Molecular
  • Consensus
  • Bryophyta
  • 3108 Plant biology
  • 3104 Evolutionary biology
  • 3103 Ecology
  • 0607 Plant Biology