SE Asia comprises a collage of continental terranes derived directly or indirectly from the India–Australian margin of eastern Gondwana. The Late Palaeozoic and Mesozoic evolution of the region involved the rifting and separation of three elongate continental slivers from eastern Gondwana and the successive opening and closure of three ocean basins, the Palaeo-Tethys, Meso-Tethys and Ceno-Tethys. The Sukhothai Island Arc System, including the Linchang, Sukhothai and Chanthaburi terranes, is identified between the Sibumasu and Indochina–East Malaya terranes in SE Asia and was formed by back-arc spreading in the Permian. The Jinghong, Nan–Uttaradit and Sra Kaeo sutures represent the closed back-arc basin. The Palaeo-Tethys is represented to the west by the Changning–Menglian, Chiang Mai/Inthanon and Bentong–Raub suture zones. The West Sumatra and West Burma blocks rifted and separated from Gondwana, along with Indochina and East Malaya in the Devonian, and together with South China formed a composite terrane 'Cathaysialand' in the Permian. They were translated westwards to their positions outboard of the Sibumasu Terrane by strike-slip tectonics in the Late Permian–Early Triassic at the zone of convergence between the Meso-Tethys and Palaeo-Pacific plates. SW Borneo is tentatively identified as possibly being the missing 'Argoland' that separated from NW Australia in the Jurassic. Palaeogeographical reconstructions for the Late Palaeozoic and Mesozoic illustrating the tectonic and palaeogeographical evolution of SE Asia are presented.

A new Middle Permian locality in northern Johore, Peninsular Malaysia, yields a small-sized, but compositionally unique, brachiopod fauna consisting of eight species: 'Pseudoleptodus' sp., 'Caricula' cf. 'salebrosa' Grant, 'Neochonetes' ('Nongtaia') aff. 'arabicus' (Hudson & Sudbury), 'Karavankina' sp., 'Transennatia' cf. 'insculpta' (Grant), 'Hustedia' sp., 'Orthothetina' sp., and martiniid indet. The first four genera are new records for Malaysia; in particular, the rare taxa 'Pseudoleptodus' and 'Caricula' characterize the fauna. The brachiopods occur together with the ammonoid 'Agathiceras' sp., the nautiloid 'Foordiceras'? sp., bivalves, and crinoid stems. The locality belongs to the East Malaya terrane of the Cathaysian biotic region, but some affinities to species of the Sibumasu province are recognized. The Malaysian forms of 'Pseudoleptodus', 'Caricula' and 'Transennatia' are similar to those of the Ratburi Limestone (southern Thailand). A Roadian–early Wordian age is interpreted for the Johore fauna. The similarity of brachiopods reported here with those from the Ratburi Limestone suggests that there was species interchange or one-way migration between shallow waters of East Malaya and Sibumasu across the main Palaeo-Tethys. The Tethyan seaway between the two terranes must have been narrower than previously interpreted by some authors to allow such faunal traffic during the Roadian–Wordian time period.

A Permo-Triassic volcanic arc system, the Sukhothai Arc, is recognised between the Indochina and Sibumasu continental blocks. The Chanthaburi terrane is here interpreted as a fault-detached, highly disrupted southern segment of the Sukhothai Arc, occupying part of southeastern Thailand and extending into Cambodia. The Klaeng tectonic line is defined as the boundary between the Chanthaburi terrane and Sibumasu block. The stratigraphy of the Chanthaburi terrane is compared with that of the Sukhothai terrane in Northern Thailand. The Late Palaeozoic-Mesozoic sequences of these two volcanic arc terranes in the Sukhothai Zone share important similarities, but show marked contrasts to those of the Sibumasu and Indochina blocks, where the Late Permian-Triassic is largely absent due to the Indosinian I unconformity (western Indochina) or is dominantly carbonates with little terrigenous clastic input (Sibumasu). There is no clear evidence of pre-Carboniferous sedimentary rocks for either the Sukhothai or Chanthaburi terranes. Late Permian lyttoniid brachiopod shale near Klaeng in the Chanthaburi terrane was revisited. The brachiopod, previously reported as 'Leptodus', is re-identified to 'Oldhamina', the genus previously known, elsewhere in Southeast Asia, only in the Huai Tak Formation of the Sukhothai terrane. 'Oldhamina' in Thailand is confined to the Sukhothai Arc. The marine stratigraphy of the Sukhothai Arc is represented by a Permian-Triassic lithological succession of mixed carbonates and siliciclastics, with common volcanic material. The Late Permian and Triassic litho- and biostratigraphy of the Chanthaburi terrane are comparable with the upper Ngao and Lampang groups of the Sukhothai terrane; in particular, they share similar successions from 'Oldhamina' brachiopod bearing shale to 'Palaeofusulina-Colaniella' foraminifer bearing limestone in the latest Permian. Marine depositional conditions were terminated on the Sukhothai Arc by end-Triassic times, later than on the Indochina block (Late Permian) but earlier than on the Sibumasu block (Jurassic/Cretaceous).

The Early Triassic Induan-Olenekian Stage boundary (Dienerian-Smithian sub-stage boundary) has been identified at a depth of 2719.25 m in the petroleum exploration well Senecio-1 located in the northern Perth Basin, Western Australia. Conodont faunas represent three conodont zones in ascending order, the 'Neospathodus dieneri' Zone, the 'Neospathodus waageni eowaageni' Zone and the 'Neospathodus waageni waageni' Zone. The Induan-Olenekian (Dienerian-Smithian) boundary is placed at the base of the 'Neospathodus waageni eowaageni' Zone equivalent to the first appearance of 'Neospathodus ex. gr. waageni' utilised elsewhere and adopted by the IUGS ICS Triassic Subcommission to define the base of the Olenekian. Bulk kerogen δ13C carbon isotopes define a positive peak of c. 4 per mille that essentially coincides with the Induan-Olenekian boundary as seen in proposed Global Stratotype Sections and Points (GSSPs) in South China and Spiti, India demonstrating the global utility of this level for correlation. An anoxic zone is recognised in the lower part of the Senecio-1 core and the upper limit of this zone is dated as late Induan (late Dienerian). Temporal and spatial mapping of marine anoxia and dysoxia globally demonstrates that pulses of dysoxia/anoxia affected shallow-marine zones at different times in different locations. Dysoxia/anoxia in the shallow-marine environment appeared in the latest Permian at the extinction level, later than in the deep-marine environment, and appears to be largely restricted to the Induan (Griesbachian and Dienerian) and early Olenekian (Smithian). Temporally and geographically restricted upwelling of an oxygen minimum zone into the ocean surface layer due to environmental perturbations including extreme global warming, increased terrestrial chemical weathering intensity and continental erosion, sea level rise, and changes in marine nutrient inventories and productivity rates, is interpreted as a likely cause of observed variation in shallow-marine dysoxia/anoxia in the Early Triassic.

The end-Permian mass extinction is now robustly dated at 252.6 ± 0.2 Ma (U–Pb) and the Permian–Triassic (P–T) GSSP level is dated by interpolation at 252.5 Ma. An isotopic geochronological timescale for the Late Permian–Early Triassic, based on recent accurate high-precision U–Pb single zircon dating of volcanic ashes, together with calibrated conodont zonation schemes, is presented. The duration of the Early Triassic (Induan + Olenekian stages) is estimated at only 5.5 million years. The duration of the Induan Stage (Griesbachian + Dienerian sub-stages) is estimated at ca. one million years and the early Olenekian (Smithian sub-stage) at 0.7 million years duration. Considering this timescale, the "delayed" recovery following the end-Permian mass extinction may not in fact have been particularly protracted, in the light of the severity of the extinction. Conodonts evolved rapidly in the first 1 million years following the mass extinction leading to recognition of high-resolution conodont zones. Continued episodic global environmental and climatic stress following the extinction is recognized by multiple carbon isotope excursions, further faunal turnover and peculiar sedimentary and biotic facies (e.g. microbialites). The end-Permian mass extinction is interpreted to be synchronous globally and between marine and non-marine environments. The nature of the double-phased Late Permian extinction (at the Guadalupian–Lopingian boundary and the P–T boundary), linked to large igneous provinces, suggests a primary role for superplume activity that involved geomagnetic polarity change and massive volcanism.

Late Permian conodonts are for the first time reported from Vietnam. Pa, Sa, Sb, Sc and M elements of the Changhsingian conodont species 'Hindeodus julfensis' (Sweet) are reported from a 40 cm thick limestone in the middle part of the Yenduyet Formation near Son La, NW Vietnam. The occurrence of 'H. julfensis' indicates a Changhsingian age that is consistent with an interpreted early Changhsingian age for a brachiopod fauna slightly higher in the sampled section. The Son La section is located in the Song Da Rift Zone and overlies basaltic volcanics considered equivalent to the Emeishan large igneous province basalts that are plume related. The Permian-Triassic boundary in Vietnam is yet to be precisely located biostratigraphically but proxy chemostratigraphic data indicate its likely position in sections at Nhi Tao and Lung Cam, N. Vietnam and correlation with the Global Stratotype Section and Point at Meishan, South China. The recovered conodonts have a Conodont Colour Alteration Index of 5 and have been heated to c. 600°C but they do not show any evidence of textural alteration due to regional metamorphism such as micro-folding or stretching that would indicate any direct effects of the compressional Indosinian Orogeny.

Colour alteration indices (CAIs) of conodonts in Peninsular Malaysia range in value from 1.5 to 8. The lowestvalues are found in Triassic Limestones in northwest Peninsular Malaysia and the highest values occur in Palaeozoicstrata within or close to zones of deformation or to intrusives. Palaeozoic conodonts from the SibumasuBlock (Western Belt of Peninsular Malaysia) show how a background value of CAI 5; all conodonts of Ordovicianto Middle Permian age have CAIs of at least 5 and locally up to 8. Palaeozoic conodonts of Sibumasu exhibittextural alteration interpreted as the result of regional metamorphism, whereas Triassic conodonts exhibit littletextural alteration. The disparity between CAIs and textural alteration of Palaeozoic vs Triassic conodonts ofSibumasu suggests regional metamorphism of these rocks around the Palaozoic-Mesozoic boundary, whichis consistent with the previously suggested time for the initial collision between the Sibumasu and Indochinablocks. Upper Palaeozoic conodonts from the Indochina Block (Central and Eastern Belts), however, are morevariable. Upper Lower Carboniferous (Namurian) conodonts from the Panching Limestone in the Eastern Beltexhibit a CAI of 3 and appear to have escaped the effects of the regional metamorphism that affected the coevalrocks on the Sibumasu Block. Permian conodonts from limestones along the western margin of the Central Belthave an anomalously high CAI of 5, probably caused by the healing effect of the Main Range granitoids.

New Carboniferous faunas from the Taungnyo Group, Loikaw area are reported. These include two new Late Tournaisian/early Visean (Lower Carboniferous/Mississippian) trilobite species, 'Liobole loikawensis', 'Crassibole karenniensis' and conodont faunas representative of the late Tournaisian 'Scaliognathous anchoralis' and 'Gnathodus typicus-Protognathodus' cordiformis conodonts zone. The age of the Taungnyo Group, Loikaw area is confirmed as Lower Carboniferous (Mississippian) for the sampled part of this stratigraphic unit. The presence of Carboniferous in the Shan Plateau Region of Myanmar is confirmed. The trilobites are most closely related to species from deep water facies of late Tournaisian and Visean age from central and Western Europe. Biogeographic links between upper Tournaisian and early Visean conodonts on the Sibumasu Terrane and Laurentia and Eastern Australian Gondwana support a NW Australian Gondwana margin position for Sibumasu in the Late Paleozoic.

Coiled nautiloid Shells referred to 'Sibyllonautilus bamaensis' Sone sp. nov. are reported from the top of the Gua Bama limestone hill in Pahang, Peninsular Malaysia. This is the first record of the genus in Southeast Asia; a pre-Ladinian, Triassic age is indicated for the occurrence. Based on the presence of 'Sibyllonautilus' and previously reported Late Permian (Lopingian) foraminifers and algae, the Gua Bama limestones are interpreted to range from the Late Permian to the Triassic. It further seems plausible that some parts of Gua Bama are stratigraphically correlated to those of the nearby Gua Sei limestone hill, which has yielded basal Triassic conodonts, and that either or both the Gua Bama and Gua Sei hills may contain yet unconfirmed successions of the Permian-Triassic boundary.

Tropical Southeast (SE) Asia harbors extraordinary species richness and in its entirety comprises four of the Earth's 34 biodiversity hotspots. Here, we examine the assembly of the SE Asian biota through time and space. We conduct meta-analyses of geological, climatic, and biological (including 61 phylogenetic) data sets to test which areas have been the sources of long-term biological diversity in SE Asia, particularly in the pre-Miocene, Miocene, and Plio Pleistocene, and whether the respective biota have been dominated by 'in situ' diversification, immigration and/or emigration, or equilibrium dynamics. We identify Borneo and Indochina, in particular, as major "evolutionary hotspots" for a diverse range of fauna and flora. Although most of the region's biodiversity is a result of both the accumulation of immigrants and in situ diversification, within-area diversification and subsequent emigration have been the predominant signals characterizing Indochina and Borneo's biota since at least the early Miocene. In contrast, colonization events are comparatively rare from younger volcanically active emergent islands such as Java, which show increased levels of immigration events. Few dispersal events were observed across the major biogeographic barrier of Wallace's Line. Accelerated efforts to conserve Borneo's flora and fauna in particular, currently housing the highest levels of SE Asian plant and mammal species richness, are critically required.