A 250 plastome phylogeny of the grass family (Poaceae): topological support under different data partitions
The systematics of grasses has advanced through applications of plastome phylogenomics, although studies have been largely limited to subfamilies or other subgroups of Poaceae. Here we present a plastome phylogenomic analysis of 250 complete plastomes (179 genera) sampled from 44 of the 52 tribes of...
| Main Authors: | , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
PeerJ Inc.
2018-02-01
|
| Series: | PeerJ |
| Subjects: | |
| Online Access: | https://peerj.com/articles/4299.pdf |
| _version_ | 1797420016735354880 |
|---|---|
| author | Jeffery M. Saarela Sean V. Burke William P. Wysocki Matthew D. Barrett Lynn G. Clark Joseph M. Craine Paul M. Peterson Robert J. Soreng Maria S. Vorontsova Melvin R. Duvall |
| author_facet | Jeffery M. Saarela Sean V. Burke William P. Wysocki Matthew D. Barrett Lynn G. Clark Joseph M. Craine Paul M. Peterson Robert J. Soreng Maria S. Vorontsova Melvin R. Duvall |
| author_sort | Jeffery M. Saarela |
| collection | DOAJ |
| description | The systematics of grasses has advanced through applications of plastome phylogenomics, although studies have been largely limited to subfamilies or other subgroups of Poaceae. Here we present a plastome phylogenomic analysis of 250 complete plastomes (179 genera) sampled from 44 of the 52 tribes of Poaceae. Plastome sequences were determined from high throughput sequencing libraries and the assemblies represent over 28.7 Mbases of sequence data. Phylogenetic signal was characterized in 14 partitions, including (1) complete plastomes; (2) protein coding regions; (3) noncoding regions; and (4) three loci commonly used in single and multi-gene studies of grasses. Each of the four main partitions was further refined, alternatively including or excluding positively selected codons and also the gaps introduced by the alignment. All 76 protein coding plastome loci were found to be predominantly under purifying selection, but specific codons were found to be under positive selection in 65 loci. The loci that have been widely used in multi-gene phylogenetic studies had among the highest proportions of positively selected codons, suggesting caution in the interpretation of these earlier results. Plastome phylogenomic analyses confirmed the backbone topology for Poaceae with maximum bootstrap support (BP). Among the 14 analyses, 82 clades out of 309 resolved were maximally supported in all trees. Analyses of newly sequenced plastomes were in agreement with current classifications. Five of seven partitions in which alignment gaps were removed retrieved Panicoideae as sister to the remaining PACMAD subfamilies. Alternative topologies were recovered in trees from partitions that included alignment gaps. This suggests that ambiguities in aligning these uncertain regions might introduce a false signal. Resolution of these and other critical branch points in the phylogeny of Poaceae will help to better understand the selective forces that drove the radiation of the BOP and PACMAD clades comprising more than 99.9% of grass diversity. |
| first_indexed | 2024-03-09T06:55:33Z |
| format | Article |
| id | doaj.art-ce4cf8bdc1994f828fc1fff749b00391 |
| institution | Directory Open Access Journal |
| issn | 2167-8359 |
| language | English |
| last_indexed | 2024-03-09T06:55:33Z |
| publishDate | 2018-02-01 |
| publisher | PeerJ Inc. |
| record_format | Article |
| series | PeerJ |
| spelling | doaj.art-ce4cf8bdc1994f828fc1fff749b003912023-12-03T10:04:09ZengPeerJ Inc.PeerJ2167-83592018-02-016e429910.7717/peerj.4299A 250 plastome phylogeny of the grass family (Poaceae): topological support under different data partitionsJeffery M. Saarela0Sean V. Burke1William P. Wysocki2Matthew D. Barrett3Lynn G. Clark4Joseph M. Craine5Paul M. Peterson6Robert J. Soreng7Maria S. Vorontsova8Melvin R. Duvall9Beaty Centre for Species Discovery and Botany Section, Canadian Museum of Nature, Ottawa, ON, CanadaPlant Molecular and Bioinformatics Center, Biological Sciences, Northern Illinois University, DeKalb, IL, USACenter for Data Intensive Sciences, University of Chicago, Chicago, IL, USABotanic Gardens and Parks Authority, Kings Park and Botanic Garden, West Perth, WA, AustraliaDepartment of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA, USAJonah Ventures, Manhattan, KS, USADepartment of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, USADepartment of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, USAComparative Plant & Fungal Biology, Royal Botanic Gardens, Kew, Richmond, Surrey, UKPlant Molecular and Bioinformatics Center, Biological Sciences, Northern Illinois University, DeKalb, IL, USAThe systematics of grasses has advanced through applications of plastome phylogenomics, although studies have been largely limited to subfamilies or other subgroups of Poaceae. Here we present a plastome phylogenomic analysis of 250 complete plastomes (179 genera) sampled from 44 of the 52 tribes of Poaceae. Plastome sequences were determined from high throughput sequencing libraries and the assemblies represent over 28.7 Mbases of sequence data. Phylogenetic signal was characterized in 14 partitions, including (1) complete plastomes; (2) protein coding regions; (3) noncoding regions; and (4) three loci commonly used in single and multi-gene studies of grasses. Each of the four main partitions was further refined, alternatively including or excluding positively selected codons and also the gaps introduced by the alignment. All 76 protein coding plastome loci were found to be predominantly under purifying selection, but specific codons were found to be under positive selection in 65 loci. The loci that have been widely used in multi-gene phylogenetic studies had among the highest proportions of positively selected codons, suggesting caution in the interpretation of these earlier results. Plastome phylogenomic analyses confirmed the backbone topology for Poaceae with maximum bootstrap support (BP). Among the 14 analyses, 82 clades out of 309 resolved were maximally supported in all trees. Analyses of newly sequenced plastomes were in agreement with current classifications. Five of seven partitions in which alignment gaps were removed retrieved Panicoideae as sister to the remaining PACMAD subfamilies. Alternative topologies were recovered in trees from partitions that included alignment gaps. This suggests that ambiguities in aligning these uncertain regions might introduce a false signal. Resolution of these and other critical branch points in the phylogeny of Poaceae will help to better understand the selective forces that drove the radiation of the BOP and PACMAD clades comprising more than 99.9% of grass diversity.https://peerj.com/articles/4299.pdfGrassesPhylogenomicsPlastomeClassificationSystematicsIncongruence |
| spellingShingle | Jeffery M. Saarela Sean V. Burke William P. Wysocki Matthew D. Barrett Lynn G. Clark Joseph M. Craine Paul M. Peterson Robert J. Soreng Maria S. Vorontsova Melvin R. Duvall A 250 plastome phylogeny of the grass family (Poaceae): topological support under different data partitions PeerJ Grasses Phylogenomics Plastome Classification Systematics Incongruence |
| title | A 250 plastome phylogeny of the grass family (Poaceae): topological support under different data partitions |
| title_full | A 250 plastome phylogeny of the grass family (Poaceae): topological support under different data partitions |
| title_fullStr | A 250 plastome phylogeny of the grass family (Poaceae): topological support under different data partitions |
| title_full_unstemmed | A 250 plastome phylogeny of the grass family (Poaceae): topological support under different data partitions |
| title_short | A 250 plastome phylogeny of the grass family (Poaceae): topological support under different data partitions |
| title_sort | 250 plastome phylogeny of the grass family poaceae topological support under different data partitions |
| topic | Grasses Phylogenomics Plastome Classification Systematics Incongruence |
| url | https://peerj.com/articles/4299.pdf |
| work_keys_str_mv | AT jefferymsaarela a250plastomephylogenyofthegrassfamilypoaceaetopologicalsupportunderdifferentdatapartitions AT seanvburke a250plastomephylogenyofthegrassfamilypoaceaetopologicalsupportunderdifferentdatapartitions AT williampwysocki a250plastomephylogenyofthegrassfamilypoaceaetopologicalsupportunderdifferentdatapartitions AT matthewdbarrett a250plastomephylogenyofthegrassfamilypoaceaetopologicalsupportunderdifferentdatapartitions AT lynngclark a250plastomephylogenyofthegrassfamilypoaceaetopologicalsupportunderdifferentdatapartitions AT josephmcraine a250plastomephylogenyofthegrassfamilypoaceaetopologicalsupportunderdifferentdatapartitions AT paulmpeterson a250plastomephylogenyofthegrassfamilypoaceaetopologicalsupportunderdifferentdatapartitions AT robertjsoreng a250plastomephylogenyofthegrassfamilypoaceaetopologicalsupportunderdifferentdatapartitions AT mariasvorontsova a250plastomephylogenyofthegrassfamilypoaceaetopologicalsupportunderdifferentdatapartitions AT melvinrduvall a250plastomephylogenyofthegrassfamilypoaceaetopologicalsupportunderdifferentdatapartitions AT jefferymsaarela 250plastomephylogenyofthegrassfamilypoaceaetopologicalsupportunderdifferentdatapartitions AT seanvburke 250plastomephylogenyofthegrassfamilypoaceaetopologicalsupportunderdifferentdatapartitions AT williampwysocki 250plastomephylogenyofthegrassfamilypoaceaetopologicalsupportunderdifferentdatapartitions AT matthewdbarrett 250plastomephylogenyofthegrassfamilypoaceaetopologicalsupportunderdifferentdatapartitions AT lynngclark 250plastomephylogenyofthegrassfamilypoaceaetopologicalsupportunderdifferentdatapartitions AT josephmcraine 250plastomephylogenyofthegrassfamilypoaceaetopologicalsupportunderdifferentdatapartitions AT paulmpeterson 250plastomephylogenyofthegrassfamilypoaceaetopologicalsupportunderdifferentdatapartitions AT robertjsoreng 250plastomephylogenyofthegrassfamilypoaceaetopologicalsupportunderdifferentdatapartitions AT mariasvorontsova 250plastomephylogenyofthegrassfamilypoaceaetopologicalsupportunderdifferentdatapartitions AT melvinrduvall 250plastomephylogenyofthegrassfamilypoaceaetopologicalsupportunderdifferentdatapartitions |