Conservation genetics, phylogenetics, and photosynthetic pathway evolution in the Cirrhopetalum alliance (Bulbophyllum, orchidaceae) : testing hypotheses of loss of sex and slowdown of diversification

Abstract

Orchids offer rich opportunities for exploring evolutionary questions given their immense diversity and unique life history traits. In this thesis, I use species of the Cirrhopetalum alliance (Bulbophyllum, Orchidaceae) as a model system for understanding the processes and genetic mechanisms underlying the dynamics of orchid evolution at different scales, from within populations to among species. Using an endangered epiphytic orchid, Bulbophyllum bicolor, as a model, I integrated an examination of population genetics with 12 microsatellite loci, taking into account a complex set of its life history traits (long-distance dispersal, self-incompatibility, pollinator-dependent sexual reproduction and clonal growth) to test for the hypothesis of ‘loss of sex’. My results identified just 22 multilocus genotypes among all 15 extant natural populations, with 12 of the populations found to be monoclonal and all three multiclonal ones exhibited a distinct phalanx clonal architecture. All populations were suggested to depend overwhelmingly on clonal growth for persistence, with a concomitant loss of sex due to an absence of pollinators and a lack of mating opportunities at virtually all sites, which are further entrenched by habitat fragmentation. Such cryptic life history impacts, potentially contributing to extinction debt, could be widespread among similarly fragmented, outcrossing tropical epiphytes, demanding urgent conservation attention. A molecular phylogeny of the Cirrhopetalum alliance was reconstructed based on four DNA markers and a broad taxon sampling in tropical Asia, providing sufficient information for the recognition of the Cirrhopetalum alliance clade (CAC) as a well-supported monophyletic group, characterized by clear synapomorphies, following the exclusion of five putative Cirrhopetalum-allied sections, and the inclusion of sect. Desmosanthes. Most sections within the Cirrhopetalum alliance are demonstrated to be polyphyletic or paraphyletic, necessitating a new sectional classification. The inclusion of sect. Desmosanthes revolutionizes our understanding of the alliance, highlighting several significant evolutionary transitions in floral characters that are likely to represent adaptations to different pollination systems. The functional importance of the lateral sepals and labellum is revealed, with contrasting evolutionary patterns linked to different degrees of reproductive fitness: floral specialization (and thus speciation) might be driven through the costs of male fitness associated with the evolution of lateral sepals. The dated phylogeny of CAC based on secondary calibration methods was applied to elucidate the impact of a controversial putative key innovation, Crassulacean acid metabolism (CAM) on the diversification of CAC. My results revealed that species diversification of CAC is positively correlated with the drop in atmospheric CO2 concentration (pCO2) in the late Miocene and a progressive slowdown of diversification afterwards. The evolution of CAM photosynthesis mirrors this pattern, with its origin coinciding with aridification and sharply decreased pCO2 in the late Miocene. CAM was revealed to be correlated with a ten-fold increase in extinction rate compared to C3 photosynthesis; strong asymmetrical transition between CAM and C3 was detected, both of which suggest CAM might represent an “evolutionary dead-end”, reflecting a failure to keep pace with the dynamics of pCO2 and contributing to the slowdown of diversification in CAC.