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Additional file 4 : Supplementary Fig. S1. Heatmap of relative abundance of ASVs grouped by phylum for each species collected from different sites. Scale was log-10 transformed. Supplementary Fig. S2. Two-dimensional plots of Principal Coordinates Analysis utilising Bray Curtis distance matrix showing differences in algal symbiont community in A. lobifera collected from different sites. Supplementary Fig. S3. Two-dimensional plots of Principal Coordinates Analysis utilising Bray Curtis distance matrix showing differences in algal symbiont community in A. lessonii collected from different sites. Supplementary Fig. S4. Two-dimensional plots of Principal Coordinates Analysis utilising Bray Curtis distance matrix showing differences in algal symbiont community in A. radiata collected from different sites.

Accurate assessment of location and timing of speciation of species is needed to discriminate between macroevolutionary models explaining large scale biodiversity patterns. In this paper I evaluate fossil evidence of variation in geographical ranges through time, as well as spatio-temporal variation in morphological parameters to examine geographical aspects of speciation and range variation. Specifically I test for geographical morphological stability within time slices and for temporal modes of morphological change within lineages. Past distribution ranges of all species of the large benthic foraminifera Cycloclypeus have been documented on paleogeographic maps. From those samples with sufficiently well preserved specimens internal morphological data were measured and analysed. Within a small sample of six species in a single genus of reef associated large benthic foraminifera evidence for heterogeneity in geographic speciation modes, including vicariance, peripheral speciation, and sympatric speciation in the centre of the range has been found. Morphological evolution was found to be either homogeneous over large geographic ranges or spatially restricted. In time two gradually evolving lineages were found. Furthermore, an evolutionary transition of two species that previously was regarded as gradual, is shown to be punctuated with intermediate populations occurring restricted in both time and space. I demonstrate the marked heterogeneity of evolutionary processes and the difficulty to make assumptions regarding tempo and mode of evolution. Furthermore, I introduce the concept of geographically undersampled punctuations. This example exposes some of the pitfalls when conclusions regarding the mode and location of speciation are based on the combination of phylogeny and extant distribution alone.

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.