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Growing concern about biodiversity loss underscores the need to quantify and understand temporal change. Here, we review the opportunities presented by biodiversity time series, and address three related issues: (i) recognizing the characteristics of temporal data; (ii) selecting appropriate statistical procedures for analysing temporal data; and (iii) inferring and forecasting biodiversity change. With regard to the first issue, we draw attention to defining characteristics of biodiversity time series—lack of physical boundaries, uni-dimensionality, autocorrelation and directionality—that inform the choice of analytic methods. Second, we explore methods of quantifying change in biodiversity at different timescales, noting that autocorrelation can be viewed as a feature that sheds light on the underlying structure of temporal change. Finally, we address the transition from inferring to forecasting biodiversity change, highlighting potential pitfalls associated with phase-shifts and novel conditions.

The analysis of macroecological patterns has necessitated the use of large, composite datasets recording local‐scale species occurrences distributed across the globe. These datasets, however, have various spatial and temporal biases, including taxonomic under sampling, range gaps for many species, and geographic uncertainty. They have rarely been compared to data collected in the field across large spatial gradients. In this paper we use two datasets built from online repositories plus standardised field collections of death assemblages to reconstruct macroecological patterns for marine bivalves along the eastern coastline of Australia – spanning over 20° of latitude and the transition between tropical and temperate regions. We test the strength of the latitudinal diversity gradient using four diversity measures and identify a biogeographical boundary. The field collection demonstrates a strong latitudinal gradient, but results from the composite datasets were varied. Adding observation‐based records to the composite dataset obscured the latitudinal gradient. The location of the biogeographic boundary was the same in all datasets, and the location mirrored two previously published bioregionalisations. Although broad patterns seen in the field can be uncovered from composite macroecological datasets, care both in dataset construction and choice of methods is needed to ensure robust results.

Ecological interactions, such as predation and bioturbation, are thought to be fundamental determinants of macroevolutionary trends. A data set containing global occurrences of Phanerozoic fossils of benthic marine invertebrates shows escalatory trends in the relative frequency of ecological groups, such as carnivores and noncarnivorous infaunal or mobile organisms. Associations between these trends are either statistically insignificant or interpretable as preservational effects. Thus, there is no evidence that escalation drives macroecological trends at global and million-year time scales. We also find that taxonomic richness and occurrence data are cross-correlated, which justifies the traditional use of one as a proxy of the other.

Likelihood analyses of 1176 fossil assemblages of marine organisms from Phanerozoic (i.e., Cambrian to Recent) assemblages indicate a shift in typical relative-abundance distributions after the Paleozoic. Ecological theory associated with these abundance distributions implies that complex ecosystems are far more common among Meso-Cenozoic assemblages than among the Paleozoic assemblages that preceded them. This transition coincides not with any major change in the way fossils are preserved or collected but with a shift from communities dominated by sessile epifaunal suspension feeders to communities with elevated diversities of mobile and infaunal taxa. This suggests that the end-Permian extinction permanently altered prevailing marine ecosystem structure and precipitated high levels of ecological complexity and alpha diversity in the Meso-Cenozoic.

We present an in-depth characterisation of shells from two bivalve species with crossed lamellar microstructure, namely Tridacna gigas and Fulvia tenuicostata. High-resolution scanning electron microscopy and confocal microscopy imaging reveal a fine structure of nanogranular particles that are inorganic–bioorganic nanocomposites for both shells. In F. tenuicostata, inorganic–organic components are arranged in a polycrystalline fibre-like fabric. T. gigas consists of up to four hierarchical lamellar structural orders and the second-order lamellae consist of elongated nanometre-sized laths. The inorganic matrix is intimately intergrown with the total amount of organic matter (1.8 and 1.5 wt%), and the composition of the shell macromolecules is variable between the two calcareous biominerals. This work shows for the first time the presence of polysaccharide-based compounds that could be essential for the construction of bio-organics as well as many prominent protein bands, glycoproteins and/or glycosaminoglycans of unknown sizes far above 260 kDa in bivalve shells with crossed lamellar microstructure. Chitosan (deacetylated chitin) with apparent molecular weights from 18 to 110 kDa for T. gigas and from 12 kDa till above 110 kDa for F. tenuicostata are detected in gel electrophoresis after Calcofluor staining. In each of the shell extracts, the infrared spectroscopy shows polysaccharides, proteins and lipids. Our findings from two crossed lamellar shells representing two genera of Mollusca: Cardiidae indicate that chitin–protein complexes and lipid–lipoproteins are not restricted only to bivalves with nacroprismatic shells.

It has previously been thought that there was a steep Cretaceous and Cenozoic radiation of marine invertebrates. This pattern can be replicated with a new data set of fossil occurrences representing 3.5 million specimens, but only when older analytical protocols are used. Moreover, analyses that employ sampling standardization and more robust counting methods show a modest rise in diversity with no clear trend after the mid-Cretaceous. Globally, locally, and at both high and low latitudes, diversity was less than twice as high in the Neogene as in the mid-Paleozoic. The ratio of global to local richness has changed little, and a latitudinal diversity gradient was present in the early Paleozoic.

Fossil assemblages are expected to be time-averaged as a result of biological and physical processes that mix skeletal remains. Our quantitative understanding of time-averaging derives primarily from actualistic studies, in which direct numerical dating of individual specimens is used to assess the scale and structure of age mixing in death assemblages (incipient fossil assemblages). Here we examine the age, and the time-averaging of Mactra shells (Bivalvia: Mollusca) gathered from surface mixed siliciclastic-bioclastic sands at three sites on a passive-margin subtropical shelf (the Southern Brazilian Shelf; ∼ 33°S). Sixty Mactra specimens were individually dated using amino acid racemization (AAR) calibrated using radiocarbon ages (n = 15). The time-averaging and the total age variability was based on a Bayesian approach that integrates the estimation errors and uncertainties derived from the posterior distribution associated with the AAR calibration average model. The 14C-calibrated AAR ages, pooled across all three sites, are strongly right-skewed with 97% of the individual mollusk shell age estimates ranging from 0 to 6 cal kyr BP. The magnitude of time-averaging varied inversely with the water depth, from < 15 yr at the deepest site (21 m) up to 1020–1250 yr at the shallowest site (7 m). The substantial variation in the temporal resolution across nearby sites, which are located in a seemingly homogenous depositional setting, indicates the presence of notable (if cryptic) spatial heterogeneities in local sedimentation, production, and exhumation, all increasing with water depth.

We have investigated the possibility of direct accelerator mass spectrometry radiocarbon (AMS 14C) measurement of carbonate samples at ANSTO using the STAR 2 MV tandem accelerator. Each carbonate sample was powdered, mixed with metal powder and pressed into an aluminum cathode for direct carbonate measurement by AMS 14C. Of the three high-purity metal powders (Fe, Nb, and Ag) used in our investigation, Nb was found to be the best metal, which delivered higher carbon beam currents and lower background. Beam currents for targets containing the optimal carbonate mass of 1.5–2.0 mg were ∼8% of those obtained from graphite targets of standard size (>0.5 mg C). Typical measured blank for Carrara marble (IAEA-C1) of ∼40 ka was obtained. Background-corrected 14C values of carbonate targets agreed well with their associated values obtained from high-precision analysis of graphite targets within 2σ uncertainties. Typical precision of this rapid AMS analysis was ∼1% for samples <8 ka. Despite lower precision for carbonate target ages (compared to standard graphite target ages), these ages are useful for palaeobiological applications where a large number of dates are required, such as time-averaging studies.

Time-averaging has evolved from an unrecognized variable in paleoecological analyses to a key concept in understanding the dynamics of sedimentary systems and the formation of fossil deposits. Here we used radiocarbon-calibrated amino acid racemization ages from 173 Fulvia tenuicostata shells collected from Sydney Harbour (NSW, Australia) to quantify time-averaging in surficial and excavated death assemblages. A novel approach to estimating the total age-estimate variability of a collection of specimens is presented that integrates the age-estimation error associated with the AAR calibration model and the effect of time-averaging variability on the age distribution. Fulvia collected from a single 1.6-m deep excavation were used to quantify changes in time-averaging with burial depth. Fulvia collected from surficial death assemblages at six sites were used to quantify spatial variation in time-averaging. The median shell age increased from ∼ 150 yr to ∼ 4230 yr and time-averaging from ∼ 40 yr to ∼ 960 yr with increased burial depth. While four sites contained surface shell assemblages with median ages of ∼ 150 yr and time-averaging of ∼ 40 yr, two sites had death assemblages with older median ages and time-averaging > 1900 yr. A decline in the abundance of Fulvia in the post-colonial period is likely responsible for the rarity of very young shells in the surface death assemblages, while local factors such as dredging and other human activities are likely responsible for the total age-estimate variability in the two highly time-averaged surface collections. These analyses provide a geochronological context for assessing ecological changes in the harbor's benthic communities since colonization and offer an important perspective on the formation of Holocene fossil deposits.

Trait-based approaches advance ecological and evolutionary research because traits provide a strong link to an organism’s function and fitness. Trait-based research might lead to a deeper understanding of the functions of, and services provided by, ecosystems, thereby improving management, which is vital in the current era of rapid environmental change. Coral reef scientists have long collected trait data for corals; however, these are difficult to access and often under-utilized in addressing large-scale questions. We present the Coral Trait Database initiative that aims to bring together physiological, morphological, ecological, phylogenetic and biogeographic trait information into a single repository. The database houses species- and individual-level data from published field and experimental studies alongside contextual data that provide important framing for analyses. In this data descriptor, we release data for 56 traits for 1547 species, and present a collaborative platform on which other trait data are being actively federated. Our overall goal is for the Coral Trait Database to become an open-source, community-led data clearinghouse that accelerates coral reef research. Design Type(s) data integration objective • species comparison design • digital curation • observation design Measurement Type(s) ecological observations Technology Type(s) data item extraction from journal article Factor Type(s) Trait Sample Characteristic(s) Scleractinia • marine coral reef biome Machine-accessible metadata file describing the reported data (ISA-Tab format)