Au, Yu Ching Eugene. / "December 2011." / Thesis (M.Phil.)--Chinese University of Hong Kong, 2012. / Includes bibliographical references (leaves 143-158). / Abstracts in English and Chinese. / Abstract --- p.i / Abstract (Chinese) --- p.iii / Acknowledgments --- p.v / Contents --- p.vi / List of tables --- p.ix / List of figures --- p.xi / Chapter Chapter 1 --- General Introduction --- p.1 / Chapter Chapter 2 --- Literature Review --- p.5 / Chapter 2.1 --- Brachyuran systematics --- p.5 / Chapter 2.1.1 --- General brachyuran classification --- p.5 / Chapter 2.1.2 --- Podotremata phylogeny --- p.8 / Chapter 2.1.2.1 --- Dromiacea --- p.8 / Chapter 2.1.2.2 --- Raninoida and Cyclodorippoida --- p.12 / Chapter 2.1.3 --- Relationships of the thoracotreme crabs --- p.16 / Chapter 2.1.4 --- Systematics of Varunidae --- p.19 / Chapter 2.2 --- Use of molecular data in decapod and brachyuran phylogenies --- p.23 / Chapter 2.2.1 --- Use of mitochondrial markers and nuclear ribosomal RNA markers --- p.24 / Chapter 2.2.2 --- Employment of nuclear protein-coding genes --- p.25 / Chapter Chapter 3 --- Molecular Phylogeny of Podotremata sensu Guinot (Decapoda: Brachyura) --- p.35 / Chapter 3.1 --- Introduction --- p.35 / Chapter 3.2 --- Materials and Methods --- p.37 / Chapter 3.2.1 --- Sample collection --- p.37 / Chapter 3.2.2 --- "DNA extraction, amplification and sequencing" --- p.38 / Chapter 3.2.3 --- Data analysis --- p.39 / Chapter 3.3 --- Results --- p.40 / Chapter 3.3.1 --- Dataset of individual markers: Histone 3 --- p.40 / Chapter 3.3.2 --- Dataset of individual markers: Enolase --- p.41 / Chapter 3.3.3 --- Dataset of individual markers: PEPCK --- p.43 / Chapter 3.3.4 --- Dataset of individual markers: 12S rRNA --- p.44 / Chapter 3.3.5 --- Dataset of individual markers: 16S rRNA --- p.45 / Chapter 3.3.6 --- Results from concatenatd dataset --- p.46 / Chapter 3.4 --- Discussion --- p.48 / Chapter 3.4.1 --- Use of markers --- p.48 / Chapter 3.4.2 --- The status of Podotremata sensu Guinot --- p.49 / Chapter 3.4.3 --- Dromiacea --- p.50 / Chapter 3.4.4 --- Dromioidea --- p.50 / Chapter 3.4.5 --- Homoloidea --- p.52 / Chapter 3.4.6 --- Raninoidea --- p.54 / Chapter 3.4.7 --- Cyclodorippoidea --- p.55 / Chapter 3.5 --- Conclusion --- p.56 / Chapter Chapter 4 --- Molecular Phyogeny of Family Varunidae (Decapoda: Brachyura) --- p.86 / Chapter 4.1 --- Introduction --- p.86 / Chapter 4.2 --- Materials and Methods --- p.87 / Chapter 4.2.1 --- Sample collection --- p.87 / Chapter 4.2.2 --- "DNA extraction, amplification and sequencing" --- p.88 / Chapter 4.2.3 --- Data analysis --- p.90 / Chapter 4.3 --- Results --- p.91 / Chapter 4.3.1 --- Dataset of individual markers: Histone 3 --- p.91 / Chapter 4.3.2 --- Dataset of individual markers: Enolase --- p.91 / Chapter 4.3.3 --- Dataset of individual markers: GAPDH --- p.92 / Chapter 4.3.4 --- Dataset of individual markers: NaK --- p.93 / Chapter 4.3.5 --- Dataset of individual markers: AK --- p.94 / Chapter 4.3.6 --- Dataset of individual markers: 12S rRNA --- p.95 / Chapter 4.3.7 --- Dataset of individual markers: 16S rRNA --- p.96 / Chapter 4.3.8 --- Results of the concatenated dataset --- p.97 / Chapter 4.4 --- Discussion --- p.98 / Chapter 4.4.1 --- On the dataset: Use of markers and taxon coverage --- p.98 / Chapter 4.4.2 --- Position of Varunidae in Thoracotremata --- p.99 / Chapter 4.4.3 --- Intra-varunid relationships --- p.99 / Chapter 4.4.4 --- Geographical and morphological hypotheses of groupings --- p.102 / Chapter 4.5 --- Conclusion --- p.104 / Chapter Chapter 5 --- General conclusion --- p.140 / References --- p.142 / Appendix: Sequences used in the two studies --- p.159

Thesis (PhD)--Stellenbosch University, 2014. / ENGLISH ABSTRACT: Freshwater organisms, such as crabs (Crustacea: Decapoda: Brachyura), are useful in studies examining inland historical biogeographic patterns and speciation because they are isolated to specific drainage systems, which often serve as barriers to gene flow. The Afrotropical freshwater crab fauna (Potamonautidae) present ideal organisms for investigating hypothesis relating to evolutionary histories because they occur on continental Africa (sub-Sahara) and islands. However, there is a great deal of undiscovered freshwater crab diversity, especially with the prevalence of undiscovered cryptic lineages, which are poorly studied among freshwater crabs, leading to uncertain regional diversity. In this research, multiple genetic (mt- and nuDNA) markers were used to infer the phylogenetic relationships and the biogeographical histories of the Afrotropical freshwater crab superfamily, Potamonautidae. Divergence time estimations were used to infer biogeographic histories, to ascertain whether speciation could be linked to past geologic and / or climatic events. Two widely distributed Potamonautes species complexes were targeted for the investigation of regional cryptic species diversity. In Chapter 2, the intraspecific phylogenetic variability within Potamonautes perlatus sensu lato occurring on the Cape Fold Mountain range (South Africa) was examined, with sampling localities occurring in western- and southern flowing drainages. Previous research suggested possible cryptic speciation within this species complex; however, no tangible inferences could be made because of analytical constraints. Two major clades were recovered: one corresponding to western flowing drainages and another to southern flowing drainages. Moreover, three cryptic lineages were recovered: P. perlatus sensu stricto, restricted to western flowing drainages, and two geographically discrete novel cryptic lineages from the southern flowing drainages, described as P. barbarai sp. nov and P. barnardi sp. nov., with divergence (±2.61 Mya) linked to Pleistocene climatic events. Subsequent to the recovery of the two novel lineages from the Cape Fold Mountain range, the Pleistocene climatic events. Subsequent to the recovery of the two novel lineages from the Cape Fold Mountain range, the revision of the P. clarus / P. depressus species complex from the Tugela and uMkomazi drainages (Drakensberg Mountain range, South Africa) was conducted. This species complex was previously found to comprise at least five cryptic lineages (Chapter 3). A coalescent multilocus (three mt- and three nuDNA) Bayesian species delimitation method was used, and an additional three cryptic lineages were recovered, bringing the total to eight species (two already described as P. clarus and P. depressus), with divergence having occurred approximately 10.3 Mya. Following the recent discovery of novel freshwater crab lineages in the mountainous areas of Mozambique and Malawi, a sampling trip to the Zimbabwean Highlands was undertaken, where a novel freshwater crab species was discovered and described as P. mutareensis, highlighting the need to sample high-lying regions (Chapter 4). Furthermore, two additional novel lineages from Mozambique (P. bellarussus sp. nov.) and the Mpumalanga Province in South Africa (P. flavusjo sp. nov) were described (Chapter 5). In Chapter 6, increased taxon sampling, with additional specimens acquired from various museums and personal collections was used to obtain a better resolution of the phylogeny of the Afrotropical Potamonautidae and to infer the ancestral affinities of the two sub-families, Deckeniinae and Potamonautinae. The Potamonautidae were found to have speciated eastward from West Africa, with a late Cretaceous divergence (±107 – 96.04 Mya). The Potamonautinae originated in West Africa (three genera), while the paraphyletic Potamonautes and Platythelphusa had East African affinities. Potamonautes was not monophyletic, comprising several fragmented geographic clades, which may suggest that this genus requires revision. Nevertheless, the overall speciation within the Potamonautidae reflects past geological and climatic events, such as rifting and uplift episodes and the contraction of forests, which occurred from the Tertiary onwards.