Phylogenomic structure and speciation in an emerging model: the Sphagnum magellanicum complex (Bryophyta)

A. Jonathan Shaw; Bryan Piatkowski; Aaron M. Duffy; Blanka Aguero; Karn Imwattana; Marta Nieto-Lugilde; Adam Healey; David J. Weston; Megan N. Patel; Jeremy Schmutz; Jane Grimwood; Joseph B. Yavitt; Kristian Hassel; Hans K. Stenøien; Kjell Ivar Flatberg; Christopher P. Bickford; Karen A. Hicks

doi:10.1111/nph.18429

Phylogenomic structure and speciation in an emerging model: the Sphagnum magellanicum complex (Bryophyta)

A. Jonathan Shaw, Bryan Piatkowski, Aaron M. Duffy, Blanka Aguero, Karn Imwattana, Marta Nieto-Lugilde, Adam Healey, David J. Weston, Megan N. Patel, Jeremy Schmutz, Jane Grimwood, Joseph B. Yavitt, Kristian Hassel, Hans K. Stenøien, Kjell Ivar Flatberg, Christopher P. Bickford, Karen A. Hicks

Plant Systems Biology

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

12 Scopus citations

Abstract

Sphagnum magellanicum is one of two Sphagnum species for which a reference-quality genome exists to facilitate research in ecological genomics. Phylogenetic and comparative genomic analyses were conducted based on resequencing data from 48 samples and RADseq analyses based on 187 samples. We report herein that there are four clades/species within the S. magellanicum complex in eastern North America and that the reference genome belongs to Sphagnum divinum. The species exhibit tens of thousands (RADseq) to millions (resequencing) of fixed nucleotide differences. Two species, however, referred to informally as S. diabolicum and S. magni because they have not been formally described, are differentiated by only 100 (RADseq) to 1000 (resequencing) of differences. Introgression among species in the complex is demonstrated using D-statistics and f₄ ratios. One ecologically important functional trait, tissue decomposability, which underlies peat (carbon) accumulation, does not differ between segregates in the S. magellanicum complex, although previous research showed that many closely related Sphagnum species have evolved differences in decomposability/carbon sequestration. Phylogenetic resolution and more accurate species delimitation in the S. magellanicum complex substantially increase the value of this group for studying the early evolutionary stages of climate adaptation and ecological evolution more broadly.

Original language	English
Pages (from-to)	1497-1511
Number of pages	15
Journal	New Phytologist
Volume	236
Issue number	4
DOIs	https://doi.org/10.1111/nph.18429
State	Published - Nov 2022

Funding

This research was supported by NSF grants DEB-1737899 and DEB-1928514 (principal investigator AJS). The research was also supported by a grant from the Tom and Bruce Shinn Fund from the North Carolina Native Plant Society. The work (proposal: 10.46936/10.25585/60001030) conducted by the US Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, is supported by the Office of Science of the US Department of Energy under contract no. DE-AC02-05CH11231. Collection of starting Sphagnum was made possible through the SPRUCE project, which is supported by Office of Science; Biological and Environmental Research (BER); US Department of Energy (DOE), grant/award no. DE-AC05–00OR22725. Experimental work and analyses were supported by the DOE BER Early Career Research Program. Oak Ridge National Laboratory is managed by UT-Battelle, LLC, for the US DOE under contract no. DE-AC05–00OR22725. Additional support for diversity collections and analysis by NSF DEB-1737899, 1928514. The work conducted by the US Department of Energy Joint Genome Institute is supported by the Office of Science of the US Department of Energy under contract no. DE-AC02-05CH11231. We thank Min Kim of HudsonAlpha for generating chloroplast contigs for phylogenetic analyses. This research was supported by NSF grants DEB‐1737899 and DEB‐1928514 (principal investigator AJS). The research was also supported by a grant from the Tom and Bruce Shinn Fund from the North Carolina Native Plant Society. The work (proposal: 10.46936/10.25585/60001030) conducted by the US Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, is supported by the Office of Science of the US Department of Energy under contract no. DE‐AC02‐05CH11231. Collection of starting was made possible through the SPRUCE project, which is supported by Office of Science; Biological and Environmental Research (BER); US Department of Energy (DOE), grant/award no. DE‐AC05–00OR22725. Experimental work and analyses were supported by the DOE BER Early Career Research Program. Oak Ridge National Laboratory is managed by UT‐Battelle, LLC, for the US DOE under contract no. DE‐AC05–00OR22725. Additional support for diversity collections and analysis by NSF DEB‐1737899, 1928514. The work conducted by the US Department of Energy Joint Genome Institute is supported by the Office of Science of the US Department of Energy under contract no. DE‐AC02‐05CH11231. We thank Min Kim of HudsonAlpha for generating chloroplast contigs for phylogenetic analyses. Sphagnum

Funders	Funder number
DOE BER
North Carolina Native Plant Society
Tom and Bruce Shinn Fund
US Department of Energy Joint Genome Institute
National Science Foundation	DEB‐1928514, DEB‐1737899
U.S. Department of Energy	DE‐AC02‐05CH11231, 1928514, DE‐AC05–00OR22725
Office of Science
Biological and Environmental Research
Oak Ridge National Laboratory

Keywords

Sphagnum
bryophytes
ecological genomics
introgression
peat mosses
peatlands
speciation

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10.1111/nph.18429

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Shaw, A. J., Piatkowski, B., Duffy, A. M., Aguero, B., Imwattana, K., Nieto-Lugilde, M., Healey, A., Weston, D. J., Patel, M. N., Schmutz, J., Grimwood, J., Yavitt, J. B., Hassel, K., Stenøien, H. K., Flatberg, K. I., Bickford, C. P., & Hicks, K. A. (2022). Phylogenomic structure and speciation in an emerging model: the Sphagnum magellanicum complex (Bryophyta). New Phytologist, 236(4), 1497-1511. https://doi.org/10.1111/nph.18429

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title = "Phylogenomic structure and speciation in an emerging model: the Sphagnum magellanicum complex (Bryophyta)",

abstract = "Sphagnum magellanicum is one of two Sphagnum species for which a reference-quality genome exists to facilitate research in ecological genomics. Phylogenetic and comparative genomic analyses were conducted based on resequencing data from 48 samples and RADseq analyses based on 187 samples. We report herein that there are four clades/species within the S. magellanicum complex in eastern North America and that the reference genome belongs to Sphagnum divinum. The species exhibit tens of thousands (RADseq) to millions (resequencing) of fixed nucleotide differences. Two species, however, referred to informally as S. diabolicum and S. magni because they have not been formally described, are differentiated by only 100 (RADseq) to 1000 (resequencing) of differences. Introgression among species in the complex is demonstrated using D-statistics and f4 ratios. One ecologically important functional trait, tissue decomposability, which underlies peat (carbon) accumulation, does not differ between segregates in the S. magellanicum complex, although previous research showed that many closely related Sphagnum species have evolved differences in decomposability/carbon sequestration. Phylogenetic resolution and more accurate species delimitation in the S. magellanicum complex substantially increase the value of this group for studying the early evolutionary stages of climate adaptation and ecological evolution more broadly.",

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author = "Shaw, {A. Jonathan} and Bryan Piatkowski and Duffy, {Aaron M.} and Blanka Aguero and Karn Imwattana and Marta Nieto-Lugilde and Adam Healey and Weston, {David J.} and Patel, {Megan N.} and Jeremy Schmutz and Jane Grimwood and Yavitt, {Joseph B.} and Kristian Hassel and Sten{\o}ien, {Hans K.} and Flatberg, {Kjell Ivar} and Bickford, {Christopher P.} and Hicks, {Karen A.}",

note = "Publisher Copyright: {\textcopyright} 2022 The Authors. New Phytologist {\textcopyright} 2022 New Phytologist Foundation.",

year = "2022",

month = nov,

doi = "10.1111/nph.18429",

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volume = "236",

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Shaw, AJ, Piatkowski, B, Duffy, AM, Aguero, B, Imwattana, K, Nieto-Lugilde, M, Healey, A, Weston, DJ, Patel, MN, Schmutz, J, Grimwood, J, Yavitt, JB, Hassel, K, Stenøien, HK, Flatberg, KI, Bickford, CP & Hicks, KA 2022, 'Phylogenomic structure and speciation in an emerging model: the Sphagnum magellanicum complex (Bryophyta)', New Phytologist, vol. 236, no. 4, pp. 1497-1511. https://doi.org/10.1111/nph.18429

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AU - Shaw, A. Jonathan

AU - Piatkowski, Bryan

AU - Duffy, Aaron M.

AU - Aguero, Blanka

AU - Imwattana, Karn

AU - Nieto-Lugilde, Marta

AU - Healey, Adam

AU - Weston, David J.

AU - Patel, Megan N.

AU - Schmutz, Jeremy

AU - Grimwood, Jane

AU - Yavitt, Joseph B.

AU - Hassel, Kristian

AU - Stenøien, Hans K.

AU - Flatberg, Kjell Ivar

AU - Bickford, Christopher P.

AU - Hicks, Karen A.

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N2 - Sphagnum magellanicum is one of two Sphagnum species for which a reference-quality genome exists to facilitate research in ecological genomics. Phylogenetic and comparative genomic analyses were conducted based on resequencing data from 48 samples and RADseq analyses based on 187 samples. We report herein that there are four clades/species within the S. magellanicum complex in eastern North America and that the reference genome belongs to Sphagnum divinum. The species exhibit tens of thousands (RADseq) to millions (resequencing) of fixed nucleotide differences. Two species, however, referred to informally as S. diabolicum and S. magni because they have not been formally described, are differentiated by only 100 (RADseq) to 1000 (resequencing) of differences. Introgression among species in the complex is demonstrated using D-statistics and f4 ratios. One ecologically important functional trait, tissue decomposability, which underlies peat (carbon) accumulation, does not differ between segregates in the S. magellanicum complex, although previous research showed that many closely related Sphagnum species have evolved differences in decomposability/carbon sequestration. Phylogenetic resolution and more accurate species delimitation in the S. magellanicum complex substantially increase the value of this group for studying the early evolutionary stages of climate adaptation and ecological evolution more broadly.

AB - Sphagnum magellanicum is one of two Sphagnum species for which a reference-quality genome exists to facilitate research in ecological genomics. Phylogenetic and comparative genomic analyses were conducted based on resequencing data from 48 samples and RADseq analyses based on 187 samples. We report herein that there are four clades/species within the S. magellanicum complex in eastern North America and that the reference genome belongs to Sphagnum divinum. The species exhibit tens of thousands (RADseq) to millions (resequencing) of fixed nucleotide differences. Two species, however, referred to informally as S. diabolicum and S. magni because they have not been formally described, are differentiated by only 100 (RADseq) to 1000 (resequencing) of differences. Introgression among species in the complex is demonstrated using D-statistics and f4 ratios. One ecologically important functional trait, tissue decomposability, which underlies peat (carbon) accumulation, does not differ between segregates in the S. magellanicum complex, although previous research showed that many closely related Sphagnum species have evolved differences in decomposability/carbon sequestration. Phylogenetic resolution and more accurate species delimitation in the S. magellanicum complex substantially increase the value of this group for studying the early evolutionary stages of climate adaptation and ecological evolution more broadly.

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KW - ecological genomics

KW - introgression

KW - peat mosses

KW - peatlands

KW - speciation

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JF - New Phytologist

IS - 4

ER -

Phylogenomic structure and speciation in an emerging model: the Sphagnum magellanicum complex (Bryophyta)

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