Molecular and Genome Evolution in the Malesian Slipper Orchids (Paphiopedilum section Barbata).

Abstract

Paphiopedilum section Barbata (Cypripedioideae: Orchidaceae) is an evolutionarily young and charismatic group of terrestrial orchids native to the Himalayas, Indochina and Malesia. It contains several interesting species complexes, variable chromosome numbers (2n=28-42) and genome sizes (2C=55-70 pg) with hybrid speciation suspected on the basis of morphological data. In Chapter 1, I introduce Paphiopedilum and review existing literature on the group. In Chapter 2, I ask: what are the evolutionary relationships within section Barbata? I answer this by sequencing four plastid (ycf1, matK, psa-ycf3ex3 and trnF(GAA)-ndhJ) and two low copy nuclear gene (Xdh and CHS) regions. Analysing the phylogenetic signals revealed patterns of gene tree incongruence and geographical groupings that suggest historical and on-going hybridisation. In Chapter 3, I ask: what biogeographical processes are driving diversification of section Barbata? To answer this I estimate the age of section Barbata from a dated BEAST phylogeny of cloned Xdh sequences and analyse it in relation to the geographical history of Southeast Asia. This revealed that section Barbata arose c. 6.3 Mya (95% HPD range=4.0-8.8 Mya) and that diversification is primarily driven by hybridisation, vicariance and dispersal facilitated by glacial-interglacial cycles of sea-level fluctuations in SE Asia, and possibly chromosomal changes. In Chapter 4, I ask: what genomic changes are occurring in section Barbata? I approach this by characterising repetitive DNA sequences in representative taxa and analyse them against new genome size estimates and published chromosome numbers. The results show that Paphiopedilum genomes are comprised of 61.1-71.5% repetitive DNA, and 28.9-39.5% single or low-copy DNA that is possibly derived from ancient repetitive elements. These findings suggest that a low-rate of repetitive DNA removal, rather than proliferation of any particular family of repetitive element, is driving genome evolution in the group. Finally in Chapter 5, I present my hypotheses on speciation processes in Paphiopedilum and outline avenues for future work.