The present-day global maximum for marine biodiversity has been located in Southeast Asia since at least the earliest Miocene. The history of biota in the region has been inferred from the present-day biogeography and phylogeny of extant organisms, but these analyses do not provide adequate tests of the various hypotheses proposed for the origins of the diversity hotspot. The papers in this special issue present the results of an interdisciplinary research project designed to reconstruct the history of shallow marine biota and habitats within the hotspot and help understand the ecological context responsible for the maintenance of the diverse regional biota. A series of remarkably complete and fresh exposures were studied from the Kutai Basin (East Kalimantan, Indonesia) that included thick lower to upper Miocene sections of deltaic and marine sediments including abundant and extremely well preserved fossils. New stratigraphic and environmental frameworks allowed comparison of biota from habitats ranging from shelf-edge reefs to nearshore shallow seagrass meadows and coral carpets. Diversity was overall high throughout the interval, especially when compared to diversity in similar modern turbid mixed carbonate-siliciclastic settings. This points to the previously unrecognized importance of these mesophotic habitats for the development of the diverse reef-associated communities in the modern-day hotspot.

Borneo's geologic and paleontological history remains poorly understood because of the lack of outcrops and difficulties with dating. Urban development around the city of Samarinda has produced over four kilometers of well-exposed stratigraphy depicting the progradation of the ancient Mahakam river delta across the Samarinda area, which includes slope, shelf, and deltaic deposits (clastic and carbonate). Previous studies have preliminarily dated the succession as middle Miocene, but reworking and the scarcity of diagnostic fossils make dating difficult. In this paper, an integrated stratigraphic age model has been constructed for the middle Miocene of the Samarinda region with a combination of magnetostratigraphy, sequence stratigraphy, and biostratigraphy (nannofossil, planktonic foraminifera, and larger benthic foraminifera). This age model provides improved temporal constraints for part of the Mahakam Delta succession. It also helps to place the pattern of biodiversity changes seen in Indonesian reef communities into a better time perspective, and permits more accurate sedimentation rates to be determined. It may also serve as a reference point to compare other Neogene sections in Southeast Asia. The two reef complexes at Samarinda, the Batu Putih and the Stadion section, are magnetostratigraphically dated at ∼ 15 Ma and 11.6 Ma, respectively. The new chronology for the Samarinda succession shows that the Mahakam Delta went through a major phase of buildout and progradation during the middle and earliest late Miocene, during which time progradation across the former shelf break took place in the Samarinda area.

We discuss the ages of twelve (clusters of) localities along the northeastern margin of the Kutai Basin (East Kalimantan, Indonesia). These localities form the basis for a large-scale study to improve our documentation of the fossil record of shallow marine environments in the center of maximum biodiversity. We integrated the results of investigations of occurrences of calcareous nannoplankton, (rare) planktonic foraminifera, larger benthic foraminifera, strontium isotope stratigraphy, and magnetostratigraphy. In addition to previously well-documented middle Miocene carbonates, new surface outcrops of early Tortonian- and Messinian-age carbonates are reported.

Larger benthic foraminifera (LBF) show great tolerance to environmental conditions and occur in shallow, tropical marine habitats and depositional settings, including mixed carbonate–siliciclastic (MCS) systems; the latter are characterized by deposition of carbonate producers under the influence of a terrigenous input. In this study, MCS system deposits near Samarinda and Bontang in East Kalimantan (Indonesia) are investigated. These include 10 sections divided into three groups based on their geological age and geographical position: Bontang sections (Burdigalian age), Batu Putih sections (Langhian age), and Stadion sections (Serravallian/Tortonian boundary). Recent studies propose different depositional environments for the studied MCS systems and initiated a need for discrimination among such conflicting interpretations. We apply cluster analysis, detrended correspondence analysis, and analysis of similarity to the LBF assemblage data matrix and interpret the results with predictions from the trophic resource continuum model. The significant differences in LBF diversity and assemblage composition confirm that MCS systems of East Kalimantan developed in differentiated environments. The Batu Putih sections were interpreted to develop in the widest range of depositional environments, from delta front to shelf edge reefs. The Bontang sections were deposited in a narrower range of depositional environments compared to the Batu Putih sections, while the Stadion sections developed in the most restricted environment, under highest terrigenous input in delta front settings.

Seagrass meadows are important shallow-water ecosystems that provide habitat for numerous associated organisms and play a crucial role in nutrient cycling, but their detection in the fossil record is problematic. Indirect indicators are often needed to discriminate seagrass beds from other shallow marine paleohabitats. Here, the stable isotope signatures of mollusk shells are examined to determine if they might provide such an indicator in addition to the faunal composition of mollusk assemblages. Aragonitic shells of 167 gastropods and bivalves from Burdigalian and Tortonian deposits in Java and East Kalimantan (Indonesia) are analyzed for their δ¹⁸O and δ¹³C ratios. The faunas represent fully marine to brackish water environments and include seagrass meadows (with dispersed corals), mixed seagrass-coral, and coral-dominated habitats (with dispersed seagrass). We assess processes and settings that shape inorganic isotope signals in the Miocene ambient waters and fractionation processes occurring at the time of shell deposition. Depleted δ¹⁸O and δ¹³C ratios are shown in brackish water samples. Furthermore, chemosymbiotic species show depleted δ¹³C ratios. A significant difference is found between the carbon isotopic signatures of coral- and seagrass-dominated environments within a stratigraphic interval. Seagrass communities consistently yield comparatively enriched δ¹³C ratios. Hence, stable isotope ratios may provide additional evidence for distinguishing paleoenvironments and are helpful in identifying ecological processes and settings within these environments.

Two late Miocene Tridacna (giant clam) shells from East Kalimantan (Indonesia) were investigated in order to evaluate their potential as subannually resolved paleoenvironmental archives. Via a combination of X-ray diffraction (XRD), laser ablation–inductively coupled plasma–mass spectrometry (LA-ICPMS) trace element analysis, scanning electron microscopy (SEM) and cathodoluminescence (CL) imaging, pristine versus diagenetically altered domains within the shells were identified. LA-ICPMS transects targeting altered aragonite and calcite zones reveal distinct compositional differences in elemental ratios (B/Ca, Mg/Ca, Sr/Ca/ Ba/Ca, Mn/Ca, Al/Ca, La/Ca, Ce/Ca) relative to primary shell aragonite. Pristine shell domains are characterized by an intact banding pattern of alternating dark and light growth bands, with which spatially resolved LA-ICPMS element/Ca and micromilled δ¹⁸O records were aligned. Light δ¹⁸O values correspond to dark growth bands, indicating growth during warm seasons. The Mg/Ca and/or Sr/Ca ratios covary with oscillating stable oxygen isotope profiles. Progressive increase in Mg/Ca with age demonstrates that besides temperature, growth kinetics exert control over Mg incorporation. If interpreted as temperature controlled only, δ¹⁸O from both shells represents average seasonal sea-surface temperature (SST) variability of 2.7 ± 2.1 and 4.6 ± 1.7 °C, respectively. Using published temperature equations and assuming δ¹⁸O_sw  =  −0.88‰, corresponding mean annual paleo–sea-surface temperatures of 27.8 ± 0.2 and 28.5 ± 0.2 °C are estimated. Although the fossil Tridacna shells were noticeably affected by alteration on their external surfaces, their internal aragonitic structure is, to a large extent, well preserved. These corresponding paleoproxy records provide detailed insight into tropical SST variability of the Indo-Pacific region during the late Miocene.

Miocene crustose coralline algae (CCA) from Southeast Asia are poorly known, although the Miocene is the epoch of the onset of the biodiversity hotspot in the region and CCA are crucial to understanding the evolutionary history of reef building. To fill this knowledge gap, CCA from early and middle Miocene reefs and related carbonates in the Kutai Basin in East Kalimantan (Borneo, Indonesia) have been studied. The Kutai Basin was dominated by siliciclastic sediments of the proto-Mahakam Delta. Locally, carbonate buildups occur lateral to, or within, the deltaic succession. CCA in the Kutai Basin occur in carbonate beds that were deposited in a low-energy shallow-water platform setting and in association with coral reefs, encrusting the corals or bioclasts. Two main CCA assemblages are recognized herein: (1) a shallow-water assemblage (S-assemblage), dominated by Neogoniolithon spp., thick crusts of Spongites spp., and Hydrolithon spp.; and (2) the D-assemblage, which consists mainly of thin crusts of Lithothamnion spp., Mesophyllum spp., and Sporolithon spp., and is interpreted to have developed in darker waters. Light reduction in reefs in the proto-Mahakam Delta is interpreted to reflect either increased water depth or higher turbidity resulting from higher siliciclastic input. Assemblages with intermediate composition (I-assemblages) also occur. Common CCA with large cell fusions and groups of heterocysts, typical features of modern reef CCA, in the S-assemblages in the middle Miocene of East Kalimantan reflect the initiation of the reef-building CCA flora in the Indo-Pacific region. The occurrence of this kind of CCA confirms the biogeographic differentiation of a tropical reef flora.

Study of the extinct and extant biota of the Coral Triangle region has not yet provided answers to questions about mechanisms controlling the origins and maintenance of this marine biodiversity hotspot. We present an updated stratigraphy and revise the taxonomic determinations for important historical collections from Indonesia that have been the basis of our knowledge of the history of the region for the past 150 years. Revision of the stratigraphy increases the resolution of ages assigned to most of the collections, and shifts a significant number of coral occurrences from the Pliocene to the late Miocene revealing a new Pliocene sampling gap. The previously recognized Paleogene sampling gap remains open. Analysis of taxonomic turnover with unrevised and revised data show similar overall patterns, with an early Miocene increase in richness followed by a plateau of relatively high richness. Overall, the observed pattern of taxonomic turnover is highly correlated with sample size, suggesting that uneven sampling may be a more important control on the data pattern than processes of speciation and extinction. Highly correlated turnover patterns of zooxanthellate and azooxanthellate taxa are also consistent with this interpretation. The paucity of Paleogene data in the historical collections means that the prevailing paradigm of Neogene origins of high richness in the modern Coral Triangle remains a tautological default hypothesis. New collections are required to adequately estimate rates of taxonomic turnover in the region, and to reconstruct the structure and functioning of ancient ecosystems during the origins of the Coral Triangle biodiversity hotspot.

Miocene bryozoans from the Indonesian Archipelago have seldom been investigated in the past. Several factors combine to explain their poor fossil record, including rare exposures in a lushly vegetated terrane, dominance of inconspicuous encrusting species, and the adverse effects of diagenesis on fossil preservation. A large collection of samples from the Kutai Basin (East Kalimantan) has allowed new insights into the diversity of Miocene bryozoans in this region. The bryozoan assemblage as a whole consists of 123 species; a remarkable increase in known diversity. Substrate availability appears to be the main factor controlling bryozoan distribution. The majority of encrusting species are associated with plate-like scleractinian corals. Collecting curves allow sampled sites to be divided into three groups characterized by high, medium, and low species richness. The site of highest diversity is a mesophotic reef slope, an environment influenced by high input of terrigenous sediment. Ordination plots show no clear patterns of distribution among sites, with putatively endemic species accounting for most of the discrimination. A similar level of endemism and habitat heterogeneity characterizes modern, tropical bryozoan faunas. However, many more intermediate sites need to be sampled to achieve a fuller understanding of the true pattern of bryozoan species distribution in the Miocene of the Kutai Basin.

This study is a preliminary assessment of an extremely diverse Tortonian (late Miocene) mollusk assemblage from a coral carpet environment preserved at Bontang (East Kalimantan, Indonesia). Even though coral-associated aragonitic faunas are rarely well preserved, the composition of the assemblage described here can be used to address the following questions: (1) How do the mollusk assemblages in coral habitats differ from other habitats, and (2) What is the effect of sampling on estimates of taxon richness? The mollusk assemblage is dominated by predatory snails and includes typical modern coral-associated taxa such as the gastropod Coralliophila and the bivalve Tridacna. Our investigation implies that adequate documentation of Cenozoic mollusk diversity in the Indo-Pacific is even more challenging than previously expected as very large samples are required to capture species richness. Further assessments of fossil faunas from coral-dominated habitats will be required to provide insight to development of Indo-Pacific biodiversity through time.

The Kutai Basin (East Kalimantan, Indonesia) contains a rich and well-preserved Miocene fossil record of small patch reefs that developed under the influence of high siliciclastic input associated with the progradation of the Mahakam Delta. In this study, we reconstruct the biodiversity and paleoenvironments on one of these delta-front, mixed carbonate-siliciclastic systems that developed at the Serravallian–Tortonian boundary near the city of Samarinda. In two newly exposed sections, we analyzed the sedimentology and distribution of the main fossil biota including corals, foraminifers, coralline algae, and bryozoans. Seven facies are herein defined, including two dominated by platy corals and two by larger benthic foraminifera. Facies distributions were driven by changes in depth and variations in terrigenous input within a range of delta-front habitats. Despite the turbid conditions, fossil assemblages are highly diverse, including 69 coral species and 28 bryozoan species that occur in coral-dominated facies. Crustose coralline algae were mainly associated with the coral-dominated facies. Larger benthic foraminifera showed broader ecological tolerance within the range represented in the studied sections and thus are common in most facies. These diverse patch reef ecosystems were able to cope with high siliciclastic input during the early development of the Miocene coral reef biota.

A holistic approach is adopted here to evaluate basin-wide trends in carbonate systems, their subenvironments and the potential marine biodiversity partitioning between different habitats within the Coral Triangle biodiversity hotspot in central Southeast Asia. The Central Indonesian Kutai Basin is typical of many Cenozoic Southeast Asian basins in having extensive and varied carbonate systems, and is one of the few regions in the Coral Triangle with detailed systematic multitaxon evaluation of Oligo-Miocene deposits. The Kutai Basin may therefore provide data, when compared with other modern and global datasets, to better understand marine biodiversity development within the global diversity foci. Carbonate systems in the Kutai Basin included small-scale ephemeral features, such as delta-associated patch reefs, mixed carbonate-clastic shelves, and large-scale (> 10 km) land-attached and isolated carbonate platforms affected by varied energy regimes. Twenty-five–plus subenvironments or habitats are spread across the different carbonate systems, with the large-scale platforms hosting over 12–15 different habitats. These subenvironments include clastic-influenced mesophotic coral reefs/carpets, nonclastic- and clastic-influenced sea-grass beds, downslope reworked coral rubble, and shallow low-energy inner platform areas, to name a few. Perhaps paradoxically, the systems that two decades ago were almost unstudied, the clastic-influenced coral reefs/carpets, are now the only ones in the region to have been systematically studied for their marine biota. Detailed biotic studies have therefore only investigated < 4 of the 25-plus potentially habitable carbonate subenvironments within the basin. This variability of carbonate systems and their subenvironments, but paucity of detailed biotic data is typical of many basins within equatorial Southeast Asia. It is recognized that detailed multitaxon biotic studies are in their infancy for Southeast Asia, and that there are challenges of taxonomic bias and/or preservation for many groups within the fossil record. Currently, however, we cannot evaluate marine biodiversity partitioning across the varied habitat mosaics of Southeast Asian carbonate systems with possible pathways discussed for furthering this field of research. It is likely that we are (?grossly) underestimating biodiversity on a basin-wide and probably a system-wide scale. It is hoped that studies of this type will contribute towards better understanding of equatorial marine carbonate systems, their biological inhabitants and producers, and the spatio-temporal development of global biodiversity hotspots.