Genetic consequences of plant edaphic specialisation to solfatara fields; phylogenetic and population genetic analysis of Carex angustisquama (Cyperaceae)

Edaphic specialisation is one of the main drivers of plant diversification
and has multifaceted effects on population dynamics. Carex angustisquama
is a sedge plant growing only on heavily acidified soil in solfatara
fields, where only extremophytes can survive. Because of the lack of
closely related species in similar habitats and its disjunct distribution,
the species offers ideal settings to investigate the effects of adaptation
to solfatara fields and historical biogeography on genetic consequences of
plant edaphic specialisation to solfatara fields. Here, genome-wide
single-nucleotide polymorphisms were used to reveal the phylogenetic
origin of C. angustisquama, and 16 expressed sequence tag–simple sequence
repeat markers were employed to infer population demography of C.
angustisquama. Molecular phylogenetic analysis strongly indicated that C.
angustisquama formed a monophyletic clade with C. doenitzii, a species
growing on non-acidified soil in sympatric sub-alpine zone. The result of
population genetic analysis showed that C. angustisquama possesses much
lower genetic diversity than the sister species, and notably, all 16 loci
were completely homozygous in most individuals of C. angustisquama.
Approximate Bayesian computation analysis supported the model that assumed
hierarchical declines of population size through its evolutionary
sequence. We propose that the edaphic specialist in solfatara fields has
newly attained the adaptation to solfatara fields in the process of
speciation. Furthermore, we found evidence of a drastic reduction in
genetic diversity in C. angustisquama, suggesting that the repeated
founder effects associated with edaphic specialisation and subsequent
population demography bring the loss of genetic diversity to the
extremophyte in solfatara fields.