Phylogenomic inference in extremis: A case study with mycoheterotroph plastomes

Abstract

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.

Oxygyne: An extraordinarily elusive flower

“…This relationship is most dramatic in achlorophyllous mycoheterotrophic plants, such as Oxygyne, which often have a ghostly appearance (Bolin, Tennakoon, Majid, & Cameron, ) and grow in deep shade, in contrast with most photosynthetic plants (Bidartondo, Burghardt, Gebauer, Bruns, & Read, ). Mycoheterotrophy has evolved independently multiple times (Merckx, Bakkerb, Huysmansa, & Smets, ) and is prominent in monocot families, especially orchids (Orchidaceae) (Lam et al, ). However, elucidating the evolutionary origins of these “ghostly,” morphologically reduced plants across the plant kingdom has proved challenging (Lam et al, ; Merckx et al, ).…”

“…Mycoheterotrophy has evolved independently multiple times (Merckx, Bakkerb, Huysmansa, & Smets, ) and is prominent in monocot families, especially orchids (Orchidaceae) (Lam et al, ). However, elucidating the evolutionary origins of these “ghostly,” morphologically reduced plants across the plant kingdom has proved challenging (Lam et al, ; Merckx et al, ). This is because many have lost traits shared with their photosynthetic ancestors (such as functional leaves), and because plastid genes used in DNA sequencing are either highly divergent or absent (Lam et al, ; Lam, Merckx, & Graham, ; Leake, ; Schelkunov, Penin, & Logacheva, ).…”

“…However, elucidating the evolutionary origins of these “ghostly,” morphologically reduced plants across the plant kingdom has proved challenging (Lam et al, ; Merckx et al, ). This is because many have lost traits shared with their photosynthetic ancestors (such as functional leaves), and because plastid genes used in DNA sequencing are either highly divergent or absent (Lam et al, ; Lam, Merckx, & Graham, ; Leake, ; Schelkunov, Penin, & Logacheva, ). Furthermore, mycoheterotrophs show a strong evolutionary convergence of adaptations to their life history, making the identification of their photosynthetic ancestors challenging (Leake, ).…”

“…Because of its scarcity, Oxygyne is poorly represented in phylogenetic analyses. Broadly sampled phylogenetic trees of mycoheterotrophs, including scarce taxa such as Oxygyne , will be crucial for testing hypotheses relating to the evolutionary origins of mycoheterotrophy in flowering plants (Lam et al, ).…”

Rhizanthella: Orchids unseen

“…Mycoheterotrophy has evolved multiple times independently among flowering plants (Merckx, Bakkerb, Huysmansa, & Smets, ) and is particularly prominent among orchids (family Orchidaceae; Lam et al, ). Like other mycoheterotrophic orchids, Rhizanthella is parasitic, acquiring nutrients from a specific mycorrhizal fungus that forages for soil nutrients (i.e., Nitrogen) and at the same time, dependent on an autotrophic host for a continuous supply of carbon (Bougoure, Brundrett, & Grierson, ; Warcup, ).…”