publication . Other literature type . Article . 2020 . Embargo end date: 07 Feb 2020

A phylogenomic perspective on evolution and discordance in the alpine-arctic plant clade Micranthes (Saxifragaceae)

Stubbs, Rebecca L.; Folk, Ryan A.; Xiang, Chun-Lei; Chen, Shichao; Soltis, Douglas E.; Cellinese, Nico;
Open Access
  • Published: 01 Feb 2020
  • Publisher: Frontiers Research Foundation
  • Country: Switzerland
Abstract
The increased availability of large phylogenomic datasets is often accompanied by difficulties in disentangling and harnessing the data. These difficulties may be enhanced for species resulting from reticulate evolution and/or rapid radiations producing large-scale discordance. As a result, there is a need for methods to investigate discordance, and in turn, use this conflict to inform and aid in downstream analyses. Therefore, we drew upon multiple analytical tools to investigate the evolution of Micranthes (Saxifragaceae), a clade of primarily arctic-alpine herbs impacted by reticulate and rapid radiations. To elucidate the evolution of Micranthes we sought ne...
Subjects
free text keywords: Department of Systematic and Evolutionary Botany, Zurich-Basel Plant Science Center, 580 Plants (Botany), Plant Science, Original Research, arctic, alpine, diversification, coalescent, gene tree conflict, phylogenomics, incongruence, Saxifragaceae
72 references, page 1 of 5

Baduel P.Bray S.Vallejo-Marin M.KolářF.Yant L. (2018). The “Polyploid Hop”: shifting challenges and opportunities over the evolutionary lifespan of genome duplications. Front. Ecol. Evol. 6, 1–19. 10.3389/fevo.2018.00117 [OpenAIRE] [DOI]

Borowiec M. L. (2016). AMAS: a fast tool for alignment manipulation and computing of summary statistics. PeerJ 4, e1660. 10.7717/peerj.1660 26835189 [OpenAIRE] [PubMed] [DOI]

Brouillet L.Elvander P. E. (2009 a). “Micranthes,” in Flora of North America North of Mexico (New York: Oxford University Press).

Brouillet L.Elvander P. E. (2009 b). “Saxifraga L,” in Flora of North America north of Mexico Magnoliophyta: Paeoniaceae to Ericaceae (New York: Oxford University Press), 132–146.

Brown J. W.Walker J. F.Smith S. A. (2017). Phyx: phylogenetic tools for unix. Bioinformatics 33, 1886–1888. 10.1093/bioinformatics/btx063 28174903 [OpenAIRE] [PubMed] [DOI]

Chamala S.García N.Godden G. T.Krishnakumar V.Jordon-Thaden I. E.Smet R. D. (2015). MarkerMiner 1.0: a new application for phylogenetic marker development using angiosperm transcriptomes. Appl. Plant Sci. 3, 1400115. 10.3732/apps.1400115 [OpenAIRE] [DOI]

Crowl A. A.Myers C.Cellinese N. (2017). Embracing discordance: phylogenomic analyses provide evidence for allopolyploidy leading to cryptic diversity in a mediterranean Campanula (Campanulaceae) clade: cryptic diversity in a meditteranean campanula CAMPANULA. Evolution 71, 913–922. 10.1111/evo.13203 28186341 [OpenAIRE] [PubMed] [DOI]

De Smet R.Adams K. L.Vandepoele K.Van Montagu M. C.Maere S.Van de Peer Y. (2013). Convergent gene loss following gene and genome duplications creates single-copy families in flowering plants. Proc. Natl. Acad. Sci. 110, 2898–2903. 10.1073/pnas.1300127110 23382190 [OpenAIRE] [PubMed] [DOI]

Don D. (1822). Monograph of the genus Saxifraga (London: Trans. Linn. Soc. London). Available at: http://www.biodiversitylibrary.org/item/13692.

Doyle J. J.Doyle J. L. (1987). A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem. bull 19, 11–15.

Drummond A. J.Suchard M. A.Xie D.Rambaut A. (2012). Bayesian Phylogenetics with BEAUti and the BEAST 1.7. Mol. Biol. Evol. 29, 1969–1973. 10.1093/molbev/mss075 22367748 [OpenAIRE] [PubMed] [DOI]

Ebersbach J.Muellner-Riehl A. N.Michalak I.Tkach N.Hoffmann M. H.Röser M. (2016). In and out of the Qinghai-Tibet Plateau: divergence time estimation and historical biogeography of the large arctic-alpine genus Saxifraga L. J. Biogeogr. 44, 900–910. 10.1111/jbi.12899 [OpenAIRE] [DOI]

Elvander P. E. (1984). The taxonomy of Saxifraga (Saxifragaceae), section Boraphila, subsection Integrifoliae in western North America. Syst. Bot. Mono. 3, 1–44. 10.2307/25027593 [OpenAIRE] [DOI]

Emms D. M.Kelly S. (2015). OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy. Genome Biol. 16, 1–14. 10.1186/s13059-015-0721-2 25583448 [OpenAIRE] [PubMed] [DOI]

Folk R. A.Mandel J. R.Freudenstein J. V. (2015). A protocol for targeted enrichment of intron-containing sequence markers for recent radiations: a phylogenomic example from Heuchera (Saxifragaceae). Appl. Plant Sci. 3, 1500039. 10.3732/apps.1500039 [OpenAIRE] [DOI]

72 references, page 1 of 5
Abstract
The increased availability of large phylogenomic datasets is often accompanied by difficulties in disentangling and harnessing the data. These difficulties may be enhanced for species resulting from reticulate evolution and/or rapid radiations producing large-scale discordance. As a result, there is a need for methods to investigate discordance, and in turn, use this conflict to inform and aid in downstream analyses. Therefore, we drew upon multiple analytical tools to investigate the evolution of Micranthes (Saxifragaceae), a clade of primarily arctic-alpine herbs impacted by reticulate and rapid radiations. To elucidate the evolution of Micranthes we sought ne...
Subjects
free text keywords: Department of Systematic and Evolutionary Botany, Zurich-Basel Plant Science Center, 580 Plants (Botany), Plant Science, Original Research, arctic, alpine, diversification, coalescent, gene tree conflict, phylogenomics, incongruence, Saxifragaceae
72 references, page 1 of 5

Baduel P.Bray S.Vallejo-Marin M.KolářF.Yant L. (2018). The “Polyploid Hop”: shifting challenges and opportunities over the evolutionary lifespan of genome duplications. Front. Ecol. Evol. 6, 1–19. 10.3389/fevo.2018.00117 [OpenAIRE] [DOI]

Borowiec M. L. (2016). AMAS: a fast tool for alignment manipulation and computing of summary statistics. PeerJ 4, e1660. 10.7717/peerj.1660 26835189 [OpenAIRE] [PubMed] [DOI]

Brouillet L.Elvander P. E. (2009 a). “Micranthes,” in Flora of North America North of Mexico (New York: Oxford University Press).

Brouillet L.Elvander P. E. (2009 b). “Saxifraga L,” in Flora of North America north of Mexico Magnoliophyta: Paeoniaceae to Ericaceae (New York: Oxford University Press), 132–146.

Brown J. W.Walker J. F.Smith S. A. (2017). Phyx: phylogenetic tools for unix. Bioinformatics 33, 1886–1888. 10.1093/bioinformatics/btx063 28174903 [OpenAIRE] [PubMed] [DOI]

Chamala S.García N.Godden G. T.Krishnakumar V.Jordon-Thaden I. E.Smet R. D. (2015). MarkerMiner 1.0: a new application for phylogenetic marker development using angiosperm transcriptomes. Appl. Plant Sci. 3, 1400115. 10.3732/apps.1400115 [OpenAIRE] [DOI]

Crowl A. A.Myers C.Cellinese N. (2017). Embracing discordance: phylogenomic analyses provide evidence for allopolyploidy leading to cryptic diversity in a mediterranean Campanula (Campanulaceae) clade: cryptic diversity in a meditteranean campanula CAMPANULA. Evolution 71, 913–922. 10.1111/evo.13203 28186341 [OpenAIRE] [PubMed] [DOI]

De Smet R.Adams K. L.Vandepoele K.Van Montagu M. C.Maere S.Van de Peer Y. (2013). Convergent gene loss following gene and genome duplications creates single-copy families in flowering plants. Proc. Natl. Acad. Sci. 110, 2898–2903. 10.1073/pnas.1300127110 23382190 [OpenAIRE] [PubMed] [DOI]

Don D. (1822). Monograph of the genus Saxifraga (London: Trans. Linn. Soc. London). Available at: http://www.biodiversitylibrary.org/item/13692.

Doyle J. J.Doyle J. L. (1987). A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem. bull 19, 11–15.

Drummond A. J.Suchard M. A.Xie D.Rambaut A. (2012). Bayesian Phylogenetics with BEAUti and the BEAST 1.7. Mol. Biol. Evol. 29, 1969–1973. 10.1093/molbev/mss075 22367748 [OpenAIRE] [PubMed] [DOI]

Ebersbach J.Muellner-Riehl A. N.Michalak I.Tkach N.Hoffmann M. H.Röser M. (2016). In and out of the Qinghai-Tibet Plateau: divergence time estimation and historical biogeography of the large arctic-alpine genus Saxifraga L. J. Biogeogr. 44, 900–910. 10.1111/jbi.12899 [OpenAIRE] [DOI]

Elvander P. E. (1984). The taxonomy of Saxifraga (Saxifragaceae), section Boraphila, subsection Integrifoliae in western North America. Syst. Bot. Mono. 3, 1–44. 10.2307/25027593 [OpenAIRE] [DOI]

Emms D. M.Kelly S. (2015). OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy. Genome Biol. 16, 1–14. 10.1186/s13059-015-0721-2 25583448 [OpenAIRE] [PubMed] [DOI]

Folk R. A.Mandel J. R.Freudenstein J. V. (2015). A protocol for targeted enrichment of intron-containing sequence markers for recent radiations: a phylogenomic example from Heuchera (Saxifragaceae). Appl. Plant Sci. 3, 1500039. 10.3732/apps.1500039 [OpenAIRE] [DOI]

72 references, page 1 of 5
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