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    Convergent evolution of flightlessness in rails (Aves: Rallidae) : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Evolutionary Ecology at Massey University, Manawatū, New Zealand
    (Massey University, 2022) Gaspar, Julien
    Different species can independently evolve similar phenotypic traits in response to the same environmental challenges. The resulting convergence of traits shows how environmental circumstances that apply selective pressure on the genomes of different lineages can result in analogous adaptations. A remarkable example of this evolutionary process is the secondary loss of flight in birds which repeatedly occurs in avian diversification. Flightlessness in bird species have been encountered on many oceanic islands and is interpreted as an effect of the insular condition that often provides a habitat with few or no predators, reduced competition for resources, and the opportunity to forage without flying. The rails or Rallidae are an exceptional avian family to study the evolution of flightlessness as among the 130 extant species, 30 have independently lost the ability to fly. In this research, genomic and morphological data were integrated to compare traits of volant and flightless species in a phylogenetic context and to investigate the evolutionary processes involved in the loss of flight. First, morphological and phylogenetic data were used to compare species with and without the ability to fly in order to determine whether major phenotypic effects of the transition from volant to flightless are shared among lineages. Second, genome assemblies were generated for representatives of four rails: two volant and two flightless species. Then, a genome-wide comparison of coding regions from volant and flightless rails was performed to detect genetic regions associated with the flightless trait. The newly assembled and annotated genomes showed differences in heterozygosity between flightless and volant species with lower heterozygosity in flightless species that probably reflects their relatively small populations. I found statistical support for similar morphological responses among unrelated flightless lineages, characterised by a shift in energy allocation from the forelimbs to the hindlimbs. Flightless birds exhibited smaller sterna and wings than volant taxa in the same family along with wider pelves and more robust femora. Phylogenetic signal tests showed that those differences were independent of phylogeny and instead demonstrated convergent morphological adaptation associated with a walking ecology. Evidence of different selective pressures between species with and without the ability to fly was detected in hundreds of genes. This included relaxed, intensified, and positive selection in flightless species as well as evolutionary rate differences of genes in volant and flightless taxa and proteins carrying function-altering amino acid changes in the flightless rails. Genes associated with flightlessness were enriched in biological functions that aligned well with the ability to fly such as muscle, bone, limb, and heart development. However, other enriched functions were not directly linked to flying and may result from the ecological consequences of flightlessness; these included the immune system, renal functions, lipid metabolic system, cognition, and the sensory system. Finally, many genes under selective pressures in flightless species were involved in gene regulation and post-translational modification. This suggests that genetic adaptations to flightlessness are not only found in important developmental genes but also in patterns of gene expression and protein modifications. This study presents reliable methods to generate genomic data and to use it to assess the selective pressures involved in a convergent phenotype.
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    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
    (Massey University, 2014) Garcia Ramirez, Juan Carlos
    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.