Phylogenomic structure and speciation in an emerging model: the Sphagnum magellanicum complex (Bryophyta).
Sphagnum
bryophytes
ecological genomics
introgression
peat mosses
peatlands
speciation
Journal
The New phytologist
ISSN: 1469-8137
Titre abrégé: New Phytol
Pays: England
ID NLM: 9882884
Informations de publication
Date de publication:
Nov 2022
Nov 2022
Historique:
received:
19
03
2022
accepted:
03
08
2022
pubmed:
17
8
2022
medline:
22
10
2022
entrez:
16
8
2022
Statut:
ppublish
Résumé
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 f
Substances chimiques
Soil
0
Carbon
7440-44-0
Nucleotides
0
Banques de données
RefSeq
['KU726621']
Dryad
['10.5061/dryad.1c59zw3xc']
Types de publication
Journal Article
Research Support, U.S. Gov't, Non-P.H.S.
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
1497-1511Informations de copyright
© 2022 The Authors. New Phytologist © 2022 New Phytologist Foundation.
Références
Andrews S. 2010. FastQC: a quality control tool for high throughput sequence data. v.011.9 [WWW document] URL https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ [accessed 16 November 2021].
Beike AK, von Stackelberg M, Schallenberg-Rüdinger MT, ST H, Follo M, Quandt D, SF MD, Reski R, Tan BC, Rensing SA. 2014. Molecular evidence for convergent evolution and allopolyploid speciation within the Physcomitrium-Physcomitrella species complex. BMC Evolutionary Biology 14: 158.
Beilstein MA, Nagalingum NS, Clements MD, Manchester SR, Mathews S. 2010. Dated molecular phylogenies indicate a Miocene origin for Arabidopsis thaliana. Proceedings of the National Academy of Science, USA 107: 18724-18728.
Bengtsson F, Granath G, Rydin H. 2016. Photosynthesis, growth, and decay traits in Sphagnum-a multispecies comparison. Ecology and Evolution 6: 3325-3341.
Bengtsson F, Rydin H, Hájek T. 2018. Biochemical determinants of litter quality in 15 species of Sphagnum. Plant and Soil 425: 161-176.
Bhatia G, Patterson N, Sankararaman S, Price AL. 2013. Estimating and interpreting FST: the impact of rare variants. Genome Research 23: 1514-1521.
Brukhin V, Osadtchiy JV JV, Florez-Rueda AM, Smetanin D, Bakin E, Nobre MS, Grossniklaus U. 2019. The Boechera genus as a resource for apomixis research. Frontiers in Plant Science 10: 1-19.
Canty A, Ripley B. 2021. boot: bootstrap R (S-Plus) functions. R package v.1.3-28. [WWW document] URL https://cran.r-project.org/web/packages/boot/index.html [accessed 4 December 2021].
Chang CC, Chow CC, Tellier LCAM, Vattikuti S, Purcell SM, Lee JJ. 2015. Second-generation Plink: rising to the challenge of larger and richer datasets. GigaScience 4: 7.
Chifman J, Kubatko L. 2014. Quartet inference from SNP data under the coalescent model. Bioinformatics 30: 3317-3324.
Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, Handsaker RE, Lunter G, Marth GT, Sherry ST et al. 2011. The variant call format and Vcftools. Bioinformatics 27: 2156-2158.
Danecek P, Bonfield JK, Liddle J, Marshall J, Ohan V, Pollard MO, Whitwham A, Keane T, McCarhty SA, Davies RM et al. 2021. Twelve years of samtools and bcftools. GigaScience 10: 1-4.
Dierckxsens N, Mardulyn P, Smits G. 2017. NOVOPlasty: de novo assembly of organelle genomes from whole genome data. Nucleic Acids Research 45: e18.
Duffy A, Aguero B, Stenøien H, Flatberg KI, Ignatov MS, Hassel K, Shaw AJ. 2020. Phylogenetic structure in the Sphagnum recurvum complex (Bryophyta: Sphagnaceae) relative to taxonomy and geography. American Journal of Botany 107: 1283-1295.
Earl DA, vonHoldt BM. 2012. StructureHarvester: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conservation Genetics Resources 4: 359-361.
Eaton DAR. 2014. PyRAD: assembly of de novo RADseq loci for phylogenetic analyses. Bioinformatics 30: 1844-1849.
Evanno G, Regnaut S, Gaudet J. 2005. Detecting the number of clusters of individuals using the software Structure: a simulation study. Molecular Ecology 14: 611-2620.
Georganas E, Buluç A, Chapman JA, Hofmeyr SA, Aluru C, Egan R, Oliker L, Rokhsar DS, Yelick KA. 2015. HipMer: an extreme-scale de novo genome assembler. Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis 14: 1-11.
Hassel K, Kyrkjeeide MO, Yousefi N, Prestø T, Stenøien H, Shaw AJ, Flatberg KI. 2018. Sphagnum divinum (sp. nov.) and S. medium Limpr. and their relationship to S. magellanicum Brid. Journal of Bryology 3: 197-222.
Hoang DT, Chernomor O, von Haeseler A, Minh BQ, Vinh LS. 2018. UFBoot2: improving the ultrafast bootstrap approximation. Molecular Biology and Evolution 35: 518-522.
Hudson RR, Slatkin M, Maddison WP. 1992. Estimation of levels of gene flow from DNA sequence data. Genetics 132: 583-589.
Huson DH, Bryant D. 2006. Application of phylogenetic networks in evolutionary studies. Molecular Biology and Evolution 23: 254-267.
Jakobsson M, Rosenberg NA. 2007. Clumpp: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics 23: 1801-1806.
Jombart T, Ahmed I. 2011. Adegenet 1.3-1: new tools for the analysis of genome-wide SNP data. Bioinformatics 27: 3070-3071.
Kalyaanamoorthy S, Minh BQ, Wong TKF, von Haeseler A, Jermiin LS. 2017. ModelFinder: fast model selection for accurate phylogenetic estimates. Nature Methods 14: 587-589.
Katoh K, Standley DM. 2013. Mafft multiple sequence alignment software version 7: improvements in performance and usability. Molecular Biology and Evolution 30: 772-780.
Koch MA. 2019. The plant model system Arabidopsis set in an evolutionary, systematic, and spatio-temporal context. Journal of Experimental Botany 70: 55-67.
Korunes KL, Samuk K. 2021. Pixy: unbiased estimation of nucleotide diversity and divergence in the presence of missing data. Molecular Ecology Resources 21: 1359-1368.
Lewis PO. 2001. A likelihood approach to estimating phylogeny from discrete morphological character data. Systematic Biology 50: 913-925.
Li H, Durbin R. 2009. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25: 1754-1760.
Linde A-M. 2019. Rates and patterns of Bryophyte molecular evolution. PhD dissertation, Uppsala Universitet, Stockholm, Sweden.
Malinsky M, Matschiner M, Svardal H. 2021. Dsuite - Fast D-statistics and related admixture evidence from VCF files. Molecular Ecology Resources 21: 584-595.
Malinsky M, Svardal H, Tyers AM, Miska EA, Genner MJ, Turner GF, Durbin R. 2018. Whole-genome sequences of Malawi cichlids reveal multiple radiations interconnected by gene flow. Nature Ecology & Evolution 2: 1940-1955.
McDaniel SF, von Stackelberg M, Richardt S, Quatrano RS, Reski R, Rensing SA. 2009. The speciation history of the Physcomitrium-Physcomitrella species. Evolution 64: 217-231.
Medina R, Johnson MG, Liu Y, Wickett NJ, Shaw AJ, Goffinet B. 2019. Phylogenomic delineation of Physcomitrium (Bryophyta: Funariaceae) based on targeted sequencing of nuclear exons and their flanking regions rejects the retention of Physcomitrella, Physcomitridium and Aphanorrhegma. Journal of Systematics and Evolution 57: 404-417.
Minh BQ, Hahn MW, Lanfear R. 2020b. New methods to calculate concordance factors for phylogenomic datasets. Molecular Biology and Evolution 37: 2727-2733.
Minh BQ, Schmidt HA, Chernomor O, Schrempf D, Woodhams MD, von Haeseler A, Lanfear R. 2020a. IQ-Tree2: new models and efficient methods for phylogenetic inference in the genomic era. Molecular Biology and Evolution 37: 1530-1534.
Nieto-Lugilde M, Werner O, McDaniel SF, Ros RM. 2018. Environmental variation obscures species diversity in southern European populations of the moss genus Ceratodon. Taxon 67: 673-692.
Nikolov LA, Shushkov P, Nevado B, Gan X, Al-Shehbaz IA, Filatov D, Bailey CD, Tsiantis M. 2019. Resolving the backbone of the Brassicaceae phylogeny for investigating trait diversity. New Phytologist 222: 1638-1651.
Olson JS. 1963. Energy storage and the balance of producers and decomposers in ecological systems. Ecology 44: 322-331.
Parchman TL, Gompert Z, Mudge J, Schilkey FD, Benkman CW, Buerkle CA. 2012. Genome-wide association genetics of an adaptive trait in lodgepole pine. Molecular Ecology 21: 2991-3005.
Piatkowski BT, Shaw AJ. 2019. Functional trait evolution in Sphagnum peat mosses and its relationship to niche construction. New Phytologist 223: 939-949.
Piatkowski BT, Yavitt JB, Turetsky MR, Shaw AJ. 2021. Natural selection on a carbon cycling trait drives ecosystem engineering by Sphagnum (peat moss). Proceedings of the Royal Society B: Biological Sciences 288: 20210609.
Pritchard JK, Stephens M, Donnelly P. 2000. Inference of population structure using multilocus genotype data. Genetics 155: 945-959.
R Core Team. 2021. R: a language and environment for statistical computing. Vienna, Austria: R Foundation for Statistical Computing. v.4.1.1. [WWW document] URL https://www.R-project.org/ [accessed 5 January 2022].
Rensing SA, Goffinet B, Meyberg R, Wu S-Z, Bezanillac M. 2020. The moss Physcomitrium (Physcomitrella) patens: a model organism for non-seed plants. Plant Cell 32: 1361-1376.
Revell LJ. 2012. Phytools: an R package for phylogenetic comparative biology (and other things). Methods in Ecology and Evolution 3: 217-223.
Rice P, Longden I, Bleasby A. 2000. Emboss: the European molecular biology open software suite. Trends in Genetics 16: 276-277.
Rydin H, Jeglum J. 2013. The Biology of Peatlands, 2nd edn. New York, NY, USA: Oxford University Press.
Shaw AJ, Cox CJ, Boles SB. 2003. Polarity of peatmoss (Sphagnum) evolution: who says bryophytes have no roots? American Journal of Botany 90: 1777-1787.
Shimodaira H. 2002. An approximately unbiased test of phylogenetic tree selection. Systematic Biology 51: 492-508.
Turetsky MR, Crow SE, Evans RJ, Vitt DH, Wieder RK. 2008. Trade-offs in resource allocation among moss species control decomposition in boreal peatlands. Journal of Ecology 96: 1297-1305.
Van de Auwera GA, O'Connor BD. 2020. Genomics in the cloud: using Docker, GATK, and WDL in Terra, 1st edn. Sebastopol, CA, USA: O'Reilly Media.
Vitt DH, Slack NG. 1984. Niche diversification of Sphagnum relative to environmental factors in northern Minnesota peatlands. Canadian Journal of Botany 62: 1409-1430.
Weston DJ, Turetsky MR, Johnson MG, Granath G, Lindo Z, Belyea LR, Rice SK, Hanson DT, Engelhardt KAM, Schmutz J et al. 2018. The Sphagnome Project: enabling ecological and evolutionary insights through a genus-level sequencing project. New Phytologist 217: 16-25.
Yousefi N, Hassel K, Flatberg KI, Kemppainen P, Trucchi E, Shaw AJ, Kyrkjeeide MO, Szövényi P, Stenøien HK. 2017. Divergent evolution and niche differentiation within the common peatmoss Sphagnum magellanicum. American Journal of Botany 104: 1060-1072.
Yu ZC. 2012. Northern peatland carbon stocks and dynamics: a review. Biogeosciences 9: 4071-4085.
Zhang C, Rabiee M, Sayyari E, Mirarab S. 2018. Astral-III: polynomial time species tree reconstruction from partially resolved gene trees. BMC Bioinformatics 19: 153.