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Peer-reviewedCC BY-NC-ND 4.0American Journal of Botany

Placing very long branch taxa in the plant tree of life: A case study with Dioscoreales mycoheterotrophs

  • Marybel Soto Gomez1,2,3
  • Qianshi Lin1,2,4
  • Nathaniel J. Klimpert1,2
  • Vivienne K. Y. Lam1,2
  • Juan Viruel3,5,6
  • Vincent S. F. T. Merckx7,8
  • Paula J. Rudall3
  • Sean W. Graham1,2
8 affiliations
  1. 1Department of Botany University of British Columbia 6270 University Boulevard Vancouver V6T 1Z4 BC Canada
  2. 2Biodiversity Research Centre University of British Columbia 2212 Main Mall Vancouver V6T 1Z4 BC Canada
  3. 3Jodrell Laboratory Royal Botanic Gardens Kew TW9 3DS Richmond UK
  4. 4Department of Biology Lakehead University 955 Oliver Rd Thunder Bay P7B 5E1 ON Canada
  5. 5Technological College University of Zaragoza Crta Cuarte sn Huesca 22071 Spain
  6. 6Institute for Biocomputation and Physics of Complex Systems (BIFI) Zaragoza 50018 Spain
  7. 7Naturalis Biodiversity Center Leiden 2332 AA the Netherlands
  8. 8Department of Evolutionary and Population Biology, Institute for Biodiversity and Ecosystem Dynamics University of Amsterdam Amsterdam 1098 XH the Netherlands
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Abstract

Premise: The inclusion of heterotrophic plants in broader systematic studies is challenging due to substantial morphological modification, gene loss, and accelerated substitution rates following photosynthesis loss. In particular, inclusion of very long branch (VLB) taxa with highly elevated rates may lead to phylogenomic misinference.

Methods: We explored how rapidly evolving plastomes behave in model‐based phylogenetic inferences in the yam order Dioscoreales, which experienced convergent photosynthesis losses. Our taxon sampling included mycoheterotrophic lineages displaying a broad range of substitution rates and all photosynthetic genera.

Results: When only moderately rapidly evolving heterotrophs are included, relationships within Dioscoreales are congruent with recent mitochondrial analysis, and generally strongly supported. Photosynthetic Stenomeris (represented by only three genes) is moderately supported as sister to Dioscoreaceae. Notably, Burmanniaceae and Thismiaceae, two mycoheterotrophic families including highly reduced plastomes, are strongly supported as distantly related within Dioscoreales. Constrained analysis rejects combining Thismiaceae with Burmanniaceae, conflicting with current angiosperm classification. Including a subset of VLB mycoheterotrophs in phylogenetic inference results in localized or broad reduction in branch support—substantially so for Afrothismiaceae, a family placing in disparate locations in Dioscoreales (and beyond) in variant analyses, with no ability to differentiate among its alternative placements.

Conclusions: Inclusion of highly rate‐elevated taxa in analyses of Dioscoreales phylogeny can depress branch support. Inferred relationships in the order are otherwise congruent with studies based on mitochondrial data; the family‐level classification needs updating. The extraordinarily rapidly evolving family Afrothismiaceae places inconsistently in diverse plastid analyses, pointing to probable analytical limits for plastid‐based phylogenomic analyses of VLB heterotrophs.

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Cite

BibTeXRIS
BibTeX
@article{gomez2026placing,
  title = {{Placing very long branch taxa in the plant tree of life: A case study with Dioscoreales mycoheterotrophs}},
  author = {Marybel Soto Gomez and Qianshi Lin and Nathaniel J. Klimpert and Vivienne K. Y. Lam and Juan Viruel and Vincent S. F. T. Merckx and Paula J. Rudall and Sean W. Graham},
  journal = {American Journal of Botany},
  year = {2026},
  month = oct,
  doi = {10.1002/ajb2.70267},
  url = {https://doi.org/10.1002/ajb2.70267},
  note = {CC BY-NC-ND 4.0},
}
RIS
TY  - JOUR
TI  - Placing very long branch taxa in the plant tree of life: A case study with Dioscoreales mycoheterotrophs
AU  - Marybel Soto Gomez
AU  - Qianshi Lin
AU  - Nathaniel J. Klimpert
AU  - Vivienne K. Y. Lam
AU  - Juan Viruel
AU  - Vincent S. F. T. Merckx
AU  - Paula J. Rudall
AU  - Sean W. Graham
PY  - 2026
DA  - 2026/10/01
JO  - American Journal of Botany
DO  - 10.1002/ajb2.70267
UR  - https://doi.org/10.1002/ajb2.70267
AB  - Premise: The inclusion of heterotrophic plants in broader systematic studies is challenging due to substantial morphological modification, gene loss, and accelerated substitution rates following photosynthesis loss. In particular, inclusion of very long branch (VLB) taxa with highly elevated rates may lead to phylogenomic misinference.  Methods: We explored how rapidly evolving plastomes behave in model‐based phylogenetic inferences in the yam order Dioscoreales, which experienced convergent photosynthesis losses. Our taxon sampling included mycoheterotrophic lineages displaying a broad range of substitution rates and all photosynthetic genera.  Results: When only moderately rapidly evolving heterotrophs are included, relationships within Dioscoreales are congruent with recent mitochondrial analysis, and generally strongly supported. Photosynthetic Stenomeris (represented by only three genes) is moderately supported as sister to Dioscoreaceae. Notably, Burmanniaceae and Thismiaceae, two mycoheterotrophic families including highly reduced plastomes, are strongly supported as distantly related within Dioscoreales. Constrained analysis rejects combining Thismiaceae with Burmanniaceae, conflicting with current angiosperm classification. Including a subset of VLB mycoheterotrophs in phylogenetic inference results in localized or broad reduction in branch support—substantially so for Afrothismiaceae, a family placing in disparate locations in Dioscoreales (and beyond) in variant analyses, with no ability to differentiate among its alternative placements.  Conclusions: Inclusion of highly rate‐elevated taxa in analyses of Dioscoreales phylogeny can depress branch support. Inferred relationships in the order are otherwise congruent with studies based on mitochondrial data; the family‐level classification needs updating. The extraordinarily rapidly evolving family Afrothismiaceae places inconsistently in diverse plastid analyses, pointing to probable analytical limits for plastid‐based phylogenomic analyses of VLB heterotrophs.
SN  - 0002-9122
SN  - 1537-2197
ER  -