Note: Cover -- Biotic Evolution and Environmental Change in Southeast Asia -- The Systematics Association Special Volume Series -- Title -- Copyright -- Contents -- Contributors -- Foreword -- Preface -- 1: Introduction -- 1.1 Introduction -- 1.2 Overview -- 1.3 Overall contribution -- References -- 2: Wallace, Darwin and Southeast Asia: the real field site of evolution -- 2.1 Darwin in the Galápagos -- 2.2 Wallace in Southeast Asia -- 2.3 Facts, fairness and conspiracies -- References -- 3: Sundaland and Wallacea: geology, plate tectonics and palaeogeography -- 3.1 Introduction -- 3.2 Background -- 3.3 Triassic to Cretaceous: assembly of Sundaland -- 3.4 Mid Cretaceous: collision and termination of subduction -- 3.5 Eocene to Miocene: resumption of subduction -- 3.5.1 Sundaland palaeogeography -- 3.5.2 Sundaland margins -- 3.6 Miocene to Recent: Australia collision in Wallacea -- 3.6.1 Banda: Early Miocene collision -- 3.6.2 Banda: Miocene extension -- 3.6.3 Banda: Pliocene collision -- 3.6.4 Sulawesi -- 3.7 Miocene to Recent: Pacific arcs and northern Australia -- 3.7.1 North Moluccas -- 3.7.2 New Guinea -- 3.7.3 Bird's Head -- 3.8 Miocene to Recent: Sundaland collision, uplift and subsidence -- 3.8.1 Borneo collision -- 3.8.2 Southern Borneo -- 3.8.3 Northern Borneo -- 3.8.4 Dangerous Grounds -- 3.8.5 Sumatra and Java -- 3.9 Pleistocene change -- 3.10 Conclusions -- Acknowledgements -- References -- 4: A review of the Cenozoic palaeoclimate history of Southeast Asia -- 4.1 Introduction -- 4.2 Paleocene -- 4.3 Eocene -- 4.4 Oligocene -- 4.4.1 Oligocene climate history of South China Sea pull-apart basins -- 4.4.2 Oligocene climate records from the Java Sea -- 4.4.3 Summary of Oligocene climate trends -- 4.5 Early and Middle Miocene -- 4.5.1 Malay Basin and West Natuna climate history -- 4.6 Late Miocene and Pliocene. , 4.7 Late Pliocene and Pleistocene -- 4.8 Controls on climate change -- 4.9 Summary and conclusions -- Acknowledgements -- References -- 5: Quaternary dynamics of Sundaland forests -- 5.1 Introduction -- 5.2 Old wine in new bottles: palaeoforests of Sundaland in the present archipelago -- 5.2.1 Historical distribution of Sundaland rainforest -- Significant questions about historical distribution -- How quickly did marine sediments evolve into terrestrial soils on the exposed shelf? -- Do current population sizes correlate with past population sizes? -- How do refugia form naturally? What are the community assembly processes of contraction? -- Did a large inland lake exist on Sundaland, in the position of the Bay of Thailand? -- How did the El Niño-Southern Oscillation (ENSO) cycle differ during the glacial period? Does general or supra-annual mast fruiting require a special hypothesis? -- Was the Sunda Shelf covered by vast peat swamps? -- 5.2.2 Variance in historical biogeography among forest types is predictable -- Mangrove forests -- Lowland forests -- Upland forests -- Outstanding questions about specific forest types -- Do different biogeographic histories lead to predictable differences in the dominant phenotypic traits and seed dispersal characteristics -- Testable hypotheses about historical population size can be generated -- 5.3 Macro-evolutionary dynamics of tropical trees -- 5.3.1 Life history and phenotypic plasticity -- 5.4 The natural historical record: going, going, gone? -- References -- 6: The Malesian floristic interchange: plant migration patterns across Wallace's Line -- 6.1 Introduction -- 6.2 Modern vegetation -- 6.2.1 Phytogeography and biogeographic divisions -- 6.2.2 Wallace's Line for plants -- 6.3 Floristic dispersal tracks and barriers -- 6.3.1 Malesian mountain tracks -- 6.3.2 Monsoon/savannah corridor. , 6.4 Palaeobotanical contributions -- 6.5 Dated phylogenetic trees and historical biogeography -- 6.6 Reassessing plant migration patterns across Wallace's Line -- 6.6.1 Prevailing oceanic or wind currents -- 6.6.2 Area effects and geological history -- 6.6.3 Habitat compatibility -- 6.7 Summary -- Acknowledgements -- References -- 7: Biogeography and distribution patterns of Southeast Asian palms -- 7.1 Introduction -- 7.2 Phylogenetic composition of the Malesian palm flora -- 7.3 Distributions to the west of Wallace's Line -- 7.4 Distributions to the east of Wallace's Line -- 7.5 Bimodal distributions across Wallace's Line -- 7.6 Disjunct distributions -- 7.7 Widespread distributions -- 7.8 Discussion -- Acknowledgements -- References -- 8: Historical biogeography inference in Malesia -- 8.1 Introduction -- 8.1.1 Incorporating landscape history into historical biogeography inference -- LAGRANGE -- SHIBA -- 8.2 An example: Rhododendron section Vireya in Malesia -- 8.2.1 The taxa -- 8.2.2 The landscape -- 8.2.3 LAGRANGE analysis -- Rationale and methods -- Results -- 8.2.4 SHIBA analysis -- Simulation details -- Results -- 8.2.5 DIVA analysis -- 8.3 Discussion -- 8.3.1 Vireya example -- 8.3.2 Methodological approaches and future directions -- Acknowledgements -- References -- Appendix A: Input data for Lagrange -- Appendix B: Input data for SHIBA -- 9: Biodiversity hotspots, evolution and coral reef biogeography: a review -- 9.1 Introduction -- 9.2 Characterising the IAA hotspot: patterns of species richness -- 9.3 Hypotheses that explain the hotspot -- 9.3.1 Centre of Origin hypothesis (CoOr) -- The CoOr as a 'fountain' of new species (a spreading dye model) -- The CoOr as a source of superior competitors -- 9.3.2 Centre of Overlap hypothesis (CoOl) -- CoOl: vicariance -- CoOl: peripheral oceanic islands. , 9.3.3 Centre of Accumulation hypothesis (CoAc) -- CoAc by individuals -- CoAc by faunas -- 9.3.4 Centre of Survival hypothesis (CoS) -- 9.3.5 The Mid Domain Effect (MDE) and null models -- 9.4 Inferred mechanisms of species origination and accumulation -- 9.4.1 Tests of hypotheses: ecological correlates -- 9.4.2 Tests of hypotheses: endemics -- 9.4.3 Tests of hypotheses: phylogenies and fossils -- 9.5 Consequences of the biodiversity hotspot -- 9.6 Conclusion -- Acknowledgements -- References -- 10: Tsunami impacts in the marine environment: review and results from studies in Thailand -- 10.1 Introduction -- 10.2 Review of tsunami environmental impacts -- 10.2.1 Historical record -- 10.2.2 The 2004 Asian Tsunami -- Coral reefs -- Mangroves -- Sediment systems -- Rocky shores -- Littoral terrestrial habitats -- 10.3 Impacts of 2004 tsunami in Ranong and Phang Nga Provinces, Thailand -- 10.3.1 Intertidal sediment systems -- Polychaete abundance -- Polychaete family richness -- Discussion -- 10.3.2 Offshore assessment of the tsunami in Thailand: the Similan Islands -- Introduction -- Survey methodology -- Results: fish surveys -- Results: invertebrate belt transects -- Results: transects and point data -- Discussion -- 10.4 Discussion -- 10.5 Conclusions -- Acknowledgements -- References -- 11: Coalescent-based analysis of demography: applications to biogeography on Sulawesi -- 11.1 Introduction -- 11.1.1 Biogeographical patterns on Sulawesi -- 11.1.2 Coalescence, divergence population genetics and isolation-migration models -- 11.1.3 Violations of models used in divergence population genetics -- 11.2 Methods -- 11.3 Results -- 11.3.1 No violations of the isolation model -- 11.3.2 Asymmetric population structure: a violation of the isolation model -- 11.4 Discussion -- 11.4.1 Future directions -- Acknowledgements -- References. , 12: Aquatic biodiversity hotspots in Wallacea: the species flocks in the ancient lakes of Sulawesi, Indonesia -- 12.1 Introduction -- 12.1.1 The ancient lakes of Sulawesi -- Hydrology, geology and limnology -- Exploration, fauna and species flocks -- 12.2 The species flocks in the ancient lakes of Sulawesi -- 12.2.1 Snails -- Species diversity and distribution -- Lake colonisation, adaptive radiation and introgression -- Adaptive radiation through trophic specialisation -- Coevolution with crabs -- 12.2.2 Crabs -- Ecology and morphology -- Phylogeny and radiation -- 12.2.3 Shrimps -- Lake colonisation, hybridisation and cryptic species -- Ecological diversification -- The evolution of colour patterns -- 12.2.4 Fishes -- The Telmatherina species flock of ancient graben-lake Lake Matano -- Sympatric speciation in Lake Matano's roundfin Telmatherina -- Adaptive radiation in Lake Matano's sharpfins -- No evidence of speciation by sexual selection: colour polymorphic sailfin silversides -- 12.3 Evolution of the Sulawesi lake species flocks -- 12.4 Threats and conservation -- Acknowledgements -- References -- 13: Molecular biogeography and phylogeography of the freshwater fauna of the Indo-Australian Archipelago -- 13.1 Introduction -- 13.1.1 The Indo-Australian Archipelago and its freshwater fauna -- 13.1.2 Molecular biogeography and the origins and purview of phylogeography -- 13.2 Earth and climatic history of the Indo-Australian Archipelago -- 13.2.1 Earth history of the Indo-Australian Archipelago -- 13.2.2 Pleistocene and earlier eustasy and the IAA -- 13.3 The freshwater fauna of the Indo-Australian Archipelago as model biogeographic taxa -- 13.3.1 Phylogenetic biogeography of the freshwater fauna of the Indo-Australian Archipelago -- Invertebrates -- Vertebrates. , 13.3.2 Phylogeography and population structure of the freshwater fauna of the Indo-Australian Archipelago.