The influence of space and time on the genetic architecture of rail species (Aves: Rallidae) : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Evolutionary Ecology at Massey University, Palmerston North, New Zealand

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The main subject of this PhD research is the study of the underlying processes of evolutionary changes that lead to biological diversity. Such processes include those operating within and between populations (population divergence), as well as those operating among species (speciation), above the species level (e.g. genera and families) and the mechanisms that promote these divisions. Fundamental to these processes are the effects of genetic, demographic, geographical, ecological, behavioural and environmental factors on diversification. Rails (Aves: Rallidae) are used as an example to address central questions related to how these biological entities originated, when was that biological diversity generated, and why this biodiversity is distributed as it is. This thesis has been divided into four main chapters/papers for convenience to achieve this aim. In the first chapter, complete mitochondrial genomes and fossil data are used to provide a likely estimated time of rail ecology. I estimated that the origin and diversification of crown group Rallidae was during the Eocene about 40.5 (49–33) Mya with evidence of intrafamiliar diversification from Late Eocene to Miocene time. This time is much older than currently available fossils assigned to Rallidae, but more direct evidence of fossils with reasonable taxonomy are likely to emerge. This estimated time implies that rail diversity originated deep in the avian tree supporting an inference of deep ancestry of terrestrial/walking habits among Neoaves. In addition, in the second chapter I used neutral molecular data (nuclear and mitochondrial gene fragments) to reveal the degree of historical biogeographic signal and net diversification in the current lineage distribution using the most complete species-level hypothesis for ralloids. This comprehensive intrafamiliar molecular phylogeny allowed to infer spatial and ecological diversification in Rallidae associated with morphological innovation (frontal shield, body size and flightlessness) and the global retention of diversity in several lineages caused by dispersal, adaptation and exploitation of ecological opportunities. In the third and fourth chapters I explored historical patterns of diversification in a biogeographic context (in spatial and temporal scales) within a clade (Porphyrio but focused on the type species Porphyrio porphyrio) and a highly polymorphic species (Gallirallus philippensis). In the third chapter, a dated phylogeny and the tools of population genetics were used to gain insights into the congeneric relationships, diversification, and the history of expansion of one of the most peculiar clades within Rallidae. I found that the Porphyrio clade arose during the Mid-Miocene, apparently in Africa, with a single Long-Distance Dispersal (LDD) event occurring into the Americas and several other LDD events to the North-East around 10 Mya. Porphyrio porphyrio was not found to be a natural group with P. melanotus appearing in Australasia during the Pleistocene (600 kya). Dispersal, isolation, adaptation and selective pressure accounted for most of the variation found within this clade. On a finer scale, the fourth chapter explored genetic changes within populations of the supertramp and great speciator Gallirallus philippensis using a mitochondrial DNA marker to recognise the genetic changes caused by founder events and provide important insights into the microevolutionary processes that drove the early stages of diversification. This study found that abrupt genetic changes of founder events are related to dispersal, colonisation, range expansion, gene flow, isolation and strong selection forces. The consequences of such processes for speciation and how they affected the population demography and evolutionary history of Gallirallus philippensis in the south western Pacific are discussed. These independent but linked studies within this thesis yield important clues to the evolutionary history that has shaped the diversity of rails. This research contributes to our understanding of Tertiary vertebrate evolution and establishes a bridge between macro– and micro–evolution. Key words: Aves, biogeography, colonisation, dispersal, diversification, DNA, ecology, evolution, extinction, gene flow, isolation, phylogenetics, population genetics, Rallidae, speciation.
Rails (Birds), Genetics, Research Subject Categories::NATURAL SCIENCES::Biology::Other biology