Angiosperm phylogeny based on matK sequence information

K.W. Hilu, T. Borsch, K. Müller, D.E. Soltis, V. Savolainen, M.W. Chase, M. Powell, L.A. Alice, R. Evans, H. Sauquet, C. Neinhuis, T.A.B. Slotta, J.G. Rohwer, C. Campbell, L.W. Chatrou

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Abstract

Plastid matK gene sequences for 374 genera representing all angiosperm orders and 12 genera of gymnosperms were analyzed using parsimony (MP) and Bayesian inference (BI) approaches. Traditionally, slowly evolving genomic regions have been preferred for deep-level phylogenetic inference in angiosperms. The matK gene evolves approximately three times faster than the widely used plastid genes rbcL and atpB. The MP and BI trees are highly congruent. The robustness of the strict consensus tree supercedes all individual gene analyses and is comparable only to multigene-based phylogenies. Of the 385 nodes resolved, 79% are supported by high jackknife values, averaging 88%. Amborella is sister to the remaining angiosperms, followed by a grade of Nymphaeaceae and Austrobaileyales. Bayesian inference resolves Amborella + Nymphaeaceae as sister to the rest, but with weak (0.42) posterior probability. The MP analysis shows a trichotomy sister to the Austrobaileyales representing eumagnoliids, monocots + Chloranthales, and Ceratophyllum + eudicots. The matK gene produces the highest internal support yet for basal eudicots and, within core eudicots, resolves a crown group comprising Berberidopsidaceae/Aextoxicaceae, Santalales, and Caryophyllales + asterids. Moreover, matK sequences provide good resolution within many angiosperm orders. Combined analyses of matK and other rapidly evolving DNA regions with available multigene data sets have strong potential to enhance resolution and internal support in deep level angiosperm phylogenetics and provide additional insights into angiosperm evolution
Original languageEnglish
Pages (from-to)1758-1776
JournalAmerican Journal of Botany
Volume90
Issue number12
DOIs
Publication statusPublished - 2003

Fingerprint

Angiosperms
Phylogeny
angiosperm
Angiospermae
phylogeny
Nymphaeaceae
Austrobaileyales
Amborella
gene
Plastids
Genes
plastid
Chloranthales
Berberidopsidaceae
Aextoxicaceae
plastids
Santalales
genes
Ceratophyllum
Gymnosperms

Keywords

  • noncoding chloroplast dna
  • 3 genomic compartments
  • molecular-data sets
  • plastid gene rbcl
  • basal angiosperms
  • flowering plants
  • 18s rdna
  • nucleotide-sequences
  • bayesian-inference
  • parsimony analysis

Cite this

Hilu, K. W., Borsch, T., Müller, K., Soltis, D. E., Savolainen, V., Chase, M. W., ... Chatrou, L. W. (2003). Angiosperm phylogeny based on matK sequence information. American Journal of Botany, 90(12), 1758-1776. https://doi.org/10.3732/ajb.90.12.1758
Hilu, K.W. ; Borsch, T. ; Müller, K. ; Soltis, D.E. ; Savolainen, V. ; Chase, M.W. ; Powell, M. ; Alice, L.A. ; Evans, R. ; Sauquet, H. ; Neinhuis, C. ; Slotta, T.A.B. ; Rohwer, J.G. ; Campbell, C. ; Chatrou, L.W. / Angiosperm phylogeny based on matK sequence information. In: American Journal of Botany. 2003 ; Vol. 90, No. 12. pp. 1758-1776.
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title = "Angiosperm phylogeny based on matK sequence information",
abstract = "Plastid matK gene sequences for 374 genera representing all angiosperm orders and 12 genera of gymnosperms were analyzed using parsimony (MP) and Bayesian inference (BI) approaches. Traditionally, slowly evolving genomic regions have been preferred for deep-level phylogenetic inference in angiosperms. The matK gene evolves approximately three times faster than the widely used plastid genes rbcL and atpB. The MP and BI trees are highly congruent. The robustness of the strict consensus tree supercedes all individual gene analyses and is comparable only to multigene-based phylogenies. Of the 385 nodes resolved, 79{\%} are supported by high jackknife values, averaging 88{\%}. Amborella is sister to the remaining angiosperms, followed by a grade of Nymphaeaceae and Austrobaileyales. Bayesian inference resolves Amborella + Nymphaeaceae as sister to the rest, but with weak (0.42) posterior probability. The MP analysis shows a trichotomy sister to the Austrobaileyales representing eumagnoliids, monocots + Chloranthales, and Ceratophyllum + eudicots. The matK gene produces the highest internal support yet for basal eudicots and, within core eudicots, resolves a crown group comprising Berberidopsidaceae/Aextoxicaceae, Santalales, and Caryophyllales + asterids. Moreover, matK sequences provide good resolution within many angiosperm orders. Combined analyses of matK and other rapidly evolving DNA regions with available multigene data sets have strong potential to enhance resolution and internal support in deep level angiosperm phylogenetics and provide additional insights into angiosperm evolution",
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author = "K.W. Hilu and T. Borsch and K. M{\"u}ller and D.E. Soltis and V. Savolainen and M.W. Chase and M. Powell and L.A. Alice and R. Evans and H. Sauquet and C. Neinhuis and T.A.B. Slotta and J.G. Rohwer and C. Campbell and L.W. Chatrou",
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Hilu, KW, Borsch, T, Müller, K, Soltis, DE, Savolainen, V, Chase, MW, Powell, M, Alice, LA, Evans, R, Sauquet, H, Neinhuis, C, Slotta, TAB, Rohwer, JG, Campbell, C & Chatrou, LW 2003, 'Angiosperm phylogeny based on matK sequence information', American Journal of Botany, vol. 90, no. 12, pp. 1758-1776. https://doi.org/10.3732/ajb.90.12.1758

Angiosperm phylogeny based on matK sequence information. / Hilu, K.W.; Borsch, T.; Müller, K.; Soltis, D.E.; Savolainen, V.; Chase, M.W.; Powell, M.; Alice, L.A.; Evans, R.; Sauquet, H.; Neinhuis, C.; Slotta, T.A.B.; Rohwer, J.G.; Campbell, C.; Chatrou, L.W.

In: American Journal of Botany, Vol. 90, No. 12, 2003, p. 1758-1776.

Research output: Contribution to journalArticleAcademicpeer-review

TY - JOUR

T1 - Angiosperm phylogeny based on matK sequence information

AU - Hilu, K.W.

AU - Borsch, T.

AU - Müller, K.

AU - Soltis, D.E.

AU - Savolainen, V.

AU - Chase, M.W.

AU - Powell, M.

AU - Alice, L.A.

AU - Evans, R.

AU - Sauquet, H.

AU - Neinhuis, C.

AU - Slotta, T.A.B.

AU - Rohwer, J.G.

AU - Campbell, C.

AU - Chatrou, L.W.

PY - 2003

Y1 - 2003

N2 - Plastid matK gene sequences for 374 genera representing all angiosperm orders and 12 genera of gymnosperms were analyzed using parsimony (MP) and Bayesian inference (BI) approaches. Traditionally, slowly evolving genomic regions have been preferred for deep-level phylogenetic inference in angiosperms. The matK gene evolves approximately three times faster than the widely used plastid genes rbcL and atpB. The MP and BI trees are highly congruent. The robustness of the strict consensus tree supercedes all individual gene analyses and is comparable only to multigene-based phylogenies. Of the 385 nodes resolved, 79% are supported by high jackknife values, averaging 88%. Amborella is sister to the remaining angiosperms, followed by a grade of Nymphaeaceae and Austrobaileyales. Bayesian inference resolves Amborella + Nymphaeaceae as sister to the rest, but with weak (0.42) posterior probability. The MP analysis shows a trichotomy sister to the Austrobaileyales representing eumagnoliids, monocots + Chloranthales, and Ceratophyllum + eudicots. The matK gene produces the highest internal support yet for basal eudicots and, within core eudicots, resolves a crown group comprising Berberidopsidaceae/Aextoxicaceae, Santalales, and Caryophyllales + asterids. Moreover, matK sequences provide good resolution within many angiosperm orders. Combined analyses of matK and other rapidly evolving DNA regions with available multigene data sets have strong potential to enhance resolution and internal support in deep level angiosperm phylogenetics and provide additional insights into angiosperm evolution

AB - Plastid matK gene sequences for 374 genera representing all angiosperm orders and 12 genera of gymnosperms were analyzed using parsimony (MP) and Bayesian inference (BI) approaches. Traditionally, slowly evolving genomic regions have been preferred for deep-level phylogenetic inference in angiosperms. The matK gene evolves approximately three times faster than the widely used plastid genes rbcL and atpB. The MP and BI trees are highly congruent. The robustness of the strict consensus tree supercedes all individual gene analyses and is comparable only to multigene-based phylogenies. Of the 385 nodes resolved, 79% are supported by high jackknife values, averaging 88%. Amborella is sister to the remaining angiosperms, followed by a grade of Nymphaeaceae and Austrobaileyales. Bayesian inference resolves Amborella + Nymphaeaceae as sister to the rest, but with weak (0.42) posterior probability. The MP analysis shows a trichotomy sister to the Austrobaileyales representing eumagnoliids, monocots + Chloranthales, and Ceratophyllum + eudicots. The matK gene produces the highest internal support yet for basal eudicots and, within core eudicots, resolves a crown group comprising Berberidopsidaceae/Aextoxicaceae, Santalales, and Caryophyllales + asterids. Moreover, matK sequences provide good resolution within many angiosperm orders. Combined analyses of matK and other rapidly evolving DNA regions with available multigene data sets have strong potential to enhance resolution and internal support in deep level angiosperm phylogenetics and provide additional insights into angiosperm evolution

KW - noncoding chloroplast dna

KW - 3 genomic compartments

KW - molecular-data sets

KW - plastid gene rbcl

KW - basal angiosperms

KW - flowering plants

KW - 18s rdna

KW - nucleotide-sequences

KW - bayesian-inference

KW - parsimony analysis

U2 - 10.3732/ajb.90.12.1758

DO - 10.3732/ajb.90.12.1758

M3 - Article

VL - 90

SP - 1758

EP - 1776

JO - American Journal of Botany

JF - American Journal of Botany

SN - 0002-9122

IS - 12

ER -

Hilu KW, Borsch T, Müller K, Soltis DE, Savolainen V, Chase MW et al. Angiosperm phylogeny based on matK sequence information. American Journal of Botany. 2003;90(12):1758-1776. https://doi.org/10.3732/ajb.90.12.1758