Back to Search
Start Over
Phylogenomic inferencein extremis: A case study with mycoheterotroph plastomes
- Source :
- American Journal of Botany. 105:480-494
- Publication Year :
- 2018
- Publisher :
- Wiley, 2018.
-
Abstract
- Premise of the study Phylogenomic studies employing large numbers of genes, including those based on plastid genomes (plastomes), are becoming common. Nonphotosynthetic plants such as mycoheterotrophs (which rely on root-associated fungi for essential nutrients, including carbon) tend to have highly elevated rates of plastome evolution, substantial genome reduction, or both. Mycoheterotroph plastomes therefore provide excellent test cases for investigating how extreme conditions impact phylogenomic inference. Methods We used parsimony and likelihood analysis of protein-coding gene sets from published and newly completed plastomes to infer the phylogenetic placement of taxa from the 10 angiosperm families in which mycoheterotrophy evolved. Key results Despite multiple very long branches that reflect elevated substitution rates, and frequently patchy gene recovery due to genome reduction, inferred phylogenetic placements of most mycoheterotrophic lineages in DNA-based likelihood analyses are both well supported and congruent with other studies. Amino-acid-based likelihood placements are broadly consistent with DNA-based inferences, but extremely rate-elevated taxa can have unexpected placements-albeit with weak support. In contrast, parsimony analysis is strongly misled by long-branch attraction among many distantly related mycoheterotrophic monocots. Conclusions Mycoheterotrophic plastomes provide challenging cases for phylogenomic inference, as substitutional rates can be elevated and genome reduction can lead to sparse gene recovery. Nonetheless, diverse likelihood frameworks provide generally well-supported and mutually concordant phylogenetic placements of mycoheterotrophs, consistent with recent phylogenetic studies and angiosperm-wide classifications. Previous predictions of parallel photosynthesis loss within families are supported for Burmanniaceae, Ericaceae, Gentianaceae, and Orchidaceae. Burmanniaceae and Thismiaceae should not be combined as a single family in Dioscoreales.
- Subjects :
- 0106 biological sciences
0301 basic medicine
Burmanniaceae
DNA, Plant
Genome, Plastid
Plant Science
Biology
Genes, Plant
010603 evolutionary biology
01 natural sciences
Genome
Evolution, Molecular
Magnoliopsida
03 medical and health sciences
Dioscoreales
Genetics
Amino Acids
Photosynthesis
Orchidaceae
Phylogeny
Ecology, Evolution, Behavior and Systematics
Plant Proteins
2. Zero hunger
Long branch attraction
Models, Genetic
Phylogenetic tree
Corsiaceae
Fungi
Heterotrophic Processes
Genomics
Gentianaceae
15. Life on land
Thismiaceae
biology.organism_classification
Biological Evolution
Petrosaviaceae
030104 developmental biology
Evolutionary biology
Ericaceae
Genome, Plant
Subjects
Details
- ISSN :
- 00029122
- Volume :
- 105
- Database :
- OpenAIRE
- Journal :
- American Journal of Botany
- Accession number :
- edsair.doi.dedup.....0ba250a5614f07989d59efc484dea3f4