The effects of taxonomic standardization on sampling-standardized estimates of historical diversity

Occurrence-based databases such as the Palaeobiology database (PBDB) provide means of accommodating the heterogeneities of the fossil record when evaluating historical diversity patterns. Although palaeontologists have given ample attention to the effects of taxonomic practice on diversity patterns derived from synoptic databases (those using first and last appearances of taxa), workers have not examined the effects of taxonomic error on occurrence-based diversity studies. Here, we contrast diversity patterns and diversity dynamics between raw data and taxonomically vetted data in the PBDB to evaluate the effects of taxonomic errors. We examine three groups: Palaeozoic gastropods, Jurassic bivalves and Cenozoic bivalves. We contrast genus-level diversity patterns based on: (i) all occurrences assigned to a genus (i.e. both species records and records identifying only the genus), (ii) only occurrences for which a species is identified, and (iii) only occurrences for which a species is identified, but after vetting the genus to which the species is assigned.Extensive generic reassignments elevate origination and extinction rates within Palaeozoic gastropods and origination rates within Cenozoic bivalves. However, vetting increases generic richness markedly only for Cenozoic bivalves, and even then the increase is less than 10%. Moreover, the patterns of standing generic richness are highly similar under all three data treatments. Unless our results are unusual, taxonomic standardization can elevate diversity dynamics in some cases, but it will not greatly change inferred richness over time.     

The Relation of Energy Metabolism and Body Weight in Bivalves (Mollusca: Bivalvia)

On the basis of experimental and published data, the interspecific and intraspecific (ontogenetic) dependence of energy metabolism on body weight in bivalves was calculated. Changes in the parameters of intraspecific allometric dependence under the effect of environmental factors were analyzed. The rate of comparable standard metabolism (coefficient a at k = 0.76) was shown to vary in different taxonomic and zoogeographic groups of bivalves.     

Evolution of the taxonomic diversity of Mongolian Ordovician-Silurian corals

Changes in the taxonomic diversity of Mongolian Ordovician-Silurian corals (Tabulatoidea, Heliolitoidea, Cyrtophyllida, Rugosa) are analyzed. Evolution of the taxonomic diversity is analyzed in two aspects: quantitative and qualitative changes. Changes in the diversity of Mongolian corals are caused by (1) evolutional developmental stage of the group and its adaptational possibilities (internal reason) and (2) changes in the environmental parameters, which reproduce regional and general global events (external reason).     

Biogeography of the Late Triassic wallowaconchid megalodontoid bivalves

Discoveries of Late Triassic alatoform bivalves (family Wallowaconchidae) in Alaska and in south Asia and Arabia reveal a broad distribution for these tropical bivalves, overturning the concept of these bivalves being endemics of offshore island arc terranes in eastern Panthalassa. They occupied an area extending from central Tethys to the eastern Pacific margin of Panthalassa. The Tethyan wallowaconchids occur in nearshore environments on the north margin of Gondwana, indicating an environmental tolerance for continental shelf settings in addition to their primary occurrence on isolated oceanic islands. The new sites reveal a taxonomic diversity among wallowaconchids. Wallowaconchids present in India are conspecific with Wallowaconcha raylenea, the type species of Wallowaconcha, whereas wallowaconchids in Arabia are an undescribed taxon and wallowaconchids in south-central Alaska are small in size and a different undescribed taxon. All known wallowaconchids are of Norian age and they appear to be a wide-ranging component of Late Triassic tropical biotas.     

Genus age,provincial area and the taxonomic structure of marine faunas

Species are unevenly distributed among genera within clades and regions, with most genera species-poor and few species-rich. At regional scales, this structure to taxonomic diversity is generated via speciation, extinction and geographical range dynamics. Here, we use a global database of extant marine bivalves to characterize the taxonomic structure of climate zones and provinces. Our analyses reveal a general, Zipf–Mandelbrot form to the distribution of species among genera, with faunas from similar climate zones exhibiting similar taxonomic structure. Provinces that contain older taxa and/or encompass larger areas are expected to be more species-rich. Although both median genus age and provincial area correlate with measures of taxonomic structure, these relationships are interdependent, nonlinear and driven primarily by contrasts between tropical and extra-tropical faunas. Provincial area and taxonomic structure are largely decoupled within climate zones. Counter to the expectation that genus age and species richness should positively covary, diverse and highly structured provincial faunas are dominated by young genera. The marked differences between tropical and temperate faunas suggest strong spatial variation in evolutionary rates and invasion frequencies. Such variation contradicts biogeographic models that scale taxonomic diversity to geographical area.     

Metabolic dominance of bivalves predates brachiopod diversity decline by more than 150 million years

Brachiopods and bivalves feed in similar ways and have occupied the same environments through geological time, but brachiopods were far more diverse and abundant in the Palaeozoic whereas bivalves dominate the post-Palaeozoic, suggesting a transition in ecological dominance 250 Ma. However, diversity and abundance data alone may not adequately describe key changes in ecosystem function, such as metabolic activity. Here, we use newly compiled body size data for 6066 genera of bivalves and brachiopods to calculate metabolic rates and revisit this question from the perspective of energy use, finding that bivalves already accounted for a larger share of metabolic activity in Palaeozoic oceans. We also find that the metabolic activity of bivalves has increased by more than two orders of magnitude over this interval, whereas brachiopod metabolic activity has declined by more than 50%. Consequently, the increase in bivalve energy metabolism must have occurred via the acquisition of new food resources rather than through the displacement of brachiopods. The canonical view of a mid-Phanerozoic transition from brachiopod to bivalve dominance results from a focus on taxonomic diversity and numerical abundance as measures of ecological importance. From a metabolic perspective, the oceans have always belonged to the clams.     

Detecting the effects of physical disturbance on benthic assemblages in a subtropical estuary: A Beyond BACI approach

The effects of dredging on the benthic communities in the Noosa River, a subtropical estuary in SE Queensland, Australia, were examined using a ‘Beyond BACI’ experimental design. Changes in the numbers and types of animals and characteristics of the sediments in response to dredging in the coarse sandy sediments near the mouth of the estuary were compared with those occurring naturally in two control regions. Samples were collected twice before and twice after the dredging operations, at multiple spatial scales, ranging from metres to kilometres. Significant effects from the dredging were detected on the abundance of some polychaetes and bivalves and two measures of diversity (numbers of polychaete families and total taxonomic richness). In addition, the dredging caused a significant increase in the diversity of sediment particle sizes found in the dredged region compared with elsewhere. Community composition in the dredged region was more similar to that in the control regions after dredging than before. Changes in the characteristics of the sedimentary environment as a result of the dredging appeared to lead to the benthic communities of the dredged region becoming more similar to those elsewhere in the estuary, so dredging in this system may have led to the loss or reduction in area of a specific type of habitat in the estuary with implications for overall patterns of biodiversity and ecosystem function.     

Biogeographic evolution of Permian ammonoids

The distribution of Permian ammonoids within the five major biogeographic provinces (Arctic, Uralian, American, Tethyan, and Australian) is discussed. Changes in the taxonomic and biogeographic structure of assemblages according to stages in the evolution of Permian ammonoids are considered for each region. It is shown that the geographical distributions and taxonomic diversity of ammonoids changed continuously throughout the Late Permian.     

Impact of Polluted Bottom Deposits on the Species Structure and Abundance of Bivalves in Peter the Great Bay,Sea of Japan

Data from long-term (1979–1988) studies of bivalve fauna and of the content of priority pollutants in the bottom deposits of Peter the Great Bay have been analyzed. It was established that the biomass, population density, number of species, and the species diversity indexes of Shannon-Weiner and of the Pielou evenness of bivalves negatively correlated with the total pollution factor, TPF, of bottom sediments. Changes in the ecological parameters of bivalves with an increase in pollution occurred in spurts within the 3.4–3.6 interval of TPF values. The area of such values covered not only the coastal zone of Vladivostok, but also a considerable part of Amursky Bay.     

Dissecting latitudinal diversity gradients: functional groups and clades of marine bivalves

The latitudinal diversity gradient, with maximum taxonomic richness in the tropics, is widely accepted as being pervasive on land, but the existence of this pattern in the sea has been surprisingly controversial. This is partly due to Thorson's influential claim that the normal latitudinal diversity gradient occurs in marine epifauna (taxa living on the surface of the substratum) but not in infauna (burrowing or boring into the substratum), a contrast he attributed to the greater spatial and temporal environmental homogeneity of infaunal habitats. In an analysis of 930 species of north-eastern Pacific marine shelf bivalves, we found that bivalves as a whole, and both infauna and epifauna separately, show a strong latitudinal diversity gradient (measured as number of species per degree latitude) that is closely related to mean sea surface temperature (SST), even in analyses of residuals and first differences. This agrees with results for marine gastropods, but contradicts Thorson's environmental homogeneity hypothesis. The relationship between SST and diversity is consistent with a species-energy hypothesis, but the linkages from SST to diversity remain unclear. Most bivalve clades within broad functional groups conform to the general latitudinal trend, except for the deposit-feeding protobranchs. This group's non-directional pattern may be related to its mode of development, because a similar effect is seen in several other groups locked into this low-fecundity, non-feeding larval mode.     

Increasing variation in taxonomic distinctness reveals clusters of specialists in the deep sea

Changes in biodiversity with latitude or along a given environmental gradient have been described in many studies, including for marine ecosystems. Currently there is no scientific consensus, however, regarding macroecological patterns of diversity vs depth. Here, we describe variation in the biodiversity of fishes along a depth gradient from 0 to 2000 m in the region of the Norfolk Ridge and Lord Howe Rise (Western Pacific), using data obtained during the NORFANZ voyage. We modelled α diversity (richness), β diversity (using Jaccard's coefficient), evenness, taxonomic distinctness and taxonomic resemblances among fish communities. Although α diversity did not change appreciably with depth, β diversity decreased significantly in deeper strata. Both taxonomic resemblances and Jaccard similarities diminished with depth, indicating convergence in community structure. In addition, average taxonomic distinctness showed no clear pattern with depth, but taxonomic trees constructed among species within deeper samples had more variable path‐lengths than those in shallower samples. The presence of taxonomically distinct clusters of highly related species at depth indicates specialised niches that have developed in a relatively extreme (dark, pressurized) yet stable environment. We propose that reduced β diversity and increased variation in taxonomic distinctness might serve as indicators of ecological communities living in harsh environments – a hypothesis that should be tested in other systems, such as deserts, high altitudes or latitudes.     

Functional Diversity as a New Framework for Understanding the Ecology of an Emerging Generalist Pathogen

Emerging infectious disease outbreaks are increasingly suspected to be a consequence of human pressures exerted on natural ecosystems. Previously, host taxonomic communities have been used as indicators of infectious disease emergence, and the loss of their diversity has been implicated as a driver of increased presence. The mechanistic details in how such pathogen–host systems function, however, may not always be explained by taxonomic variation or loss. Here we used machine learning and methods based on Gower’s dissimilarity to quantify metrics of invertebrate functional diversity, in addition to functional groups and their taxonomic diversity at sites endemic and non-endemic for the model generalist pathogen Mycobacterium ulcerans, the causative agent of Buruli ulcer. Changes in these metrics allowed the rapid categorisation of the ecological niche of the mycobacterium’s hosts and the ability to relate specific host traits to its presence in aquatic ecosystems. We found that taxonomic diversity of hosts and overall functional diversity loss and evenness had no bearing on the mycobacterium’s presence, or whether the site was in an endemic area. These findings, however, provide strong evidence that generalist environmentally persistent bacteria such as M. ulcerans can be associated with specific functional traits rather than taxonomic groups of organisms, increasing our understanding of emerging disease ecology and origin.     

Invasive bivalves increase benthic communities complexity in neotropical reservoirs

Invasive bivalves often act as ecosystem engineers, generally causing physical alterations in the ecosystems in which they establish themselves. However, the effects of these physical alterations over benthic macroinvertebrate communities’ structure are less clear. The objective of this study was to characterize the ecological effects of the invasive bivalves Corbicula fluminea and Limnoperna fortunei on the structure of benthic macroinvertebrate communities in neo-tropical reservoirs. Three hypotheses were tested: (1) invasive bivalves act as facilitator species to other benthic macroinvertebrates, resulting in communities with higher number of species, abundance and diversity; (2) invasive bivalves change the taxonomic composition of benthic macroinvertebrate communities; (3) invasive bivalves increase the complexity of benthic macroinvertebrate communities. For that it was used data from 160 sampling sites from four reservoirs. We sampled sites once in each area, during the dry season from 2009 to 2012. The first hypothesis was rejected, as the presence of invasive bivalves significantly decreased the host benthic communities’ number of species and abundance. The second hypothesis was corroborated, as the composition of other benthic macroinvertebrates was shown to be significantly different between sites with and without invasive bivalves. We observed a shift from communities dominated by common soft substrate taxa, such as Chironomidae and Oligochaeta, to communities dominated by the invasive Gastropoda Melanoides tuberculata. The biomass data corroborated that, showing significantly higher biomass of M. tuberculata in sites with invasive bivalves, but significantly lower biomass of native species. Benthic macroinvertebrate communities presenting invasive bivalves showed significantly higher eco-exergy and specific eco-exergy, which corroborate the third hypothesis. These results suggest that while the presence of invasive bivalves limits the abundance of soft bottom taxa such as Chironomidae and Oligochaeta, it enhances benthic communities’ complexity and provide new energetic pathways to benthic communities in reservoirs. This study also suggests a scenario of invasion meltdown, as M. tuberculata was facilitated by the invasive bivalves.     

Molecular phylogeny of Pholadoidea Lamarck, 1809 supports a single origin for xylotrophy (wood feeding) and xylotrophic bacterial endosymbiosis in Bivalvia

The ability to consume wood as food (xylotrophy) is unusual among animals. In terrestrial environments, termites and other xylotrophic insects are the principle wood consumers while in marine environments wood-boring bivalves fulfill this role. However, the evolutionary origin of wood feeding in bivalves has remained largely unexplored. Here we provide data indicating that xylotrophy has arisen just once in Bivalvia in a single wood-feeding bivalve lineage that subsequently diversified into distinct shallow- and deep-water branches, both of which have been broadly successful in colonizing the world’s oceans. These data also suggest that the appearance of this remarkable life habit was approximately coincident with the acquisition of bacterial endosymbionts. Here we generate a robust phylogeny for xylotrophic bivalves and related species based on sequences of small and large subunit nuclear rRNA genes. We then trace the distribution among the modern taxa of morphological characters and character states associated with xylotrophy and xylotrepesis (wood-boring) and use a parsimony-based method to infer their ancestral states. Based on these ancestral state reconstructions we propose a set of plausible hypotheses describing the evolution of symbiotic xylotrophy in Bivalvia. Within this context, we reinterpret one of the most remarkable progressions in bivalve evolution, the transformation of the “typical” myoid body plan to create a unique lineage of worm-like, tube-forming, wood-feeding clams. The well-supported phylogeny presented here is inconsistent with most taxonomic treatments for xylotrophic bivalves, indicating that the bivalve family Pholadidae and the subfamilies Teredininae and Bankiinae of the family Teredinidae are non-monophyletic, and that the principle traits used for their taxonomic diagnosis are phylogenetically misleading.     

Recovery of benthic marine communities from the end‐Permian mass extinction at the low latitudes of eastern Panthalassa

Based on the quantitative community analysis using species‐level identifications, we track the restoration of benthic ecosystems after the end‐Permian mass extinction throughout the Lower Triassic of the western USA. New data on the palaeoecology of the Thaynes Group and Sinbad Formation are provided, which fill a gap between the recently studied palaeoecology of the Griesbachian–Dienerian Dinwoody Formation and the Spathian Virgin Formation. In the Sinbad Formation and Thaynes Group, 17 species (12 genera) of bivalves, 7 species and genera of gastropods and 2 species and genera of brachiopods are recognized. The new bivalve genus Confusionella (Pteriidae) is described. A comprehensive review of the whole Lower Triassic succession of benthic ecosystems of the western USA indicates that mid‐ and inner shelf environments show incipient recovery signals around the Griesbachian–Dienerian transition, during the Smithian and, most profound, during the early Spathian. Ecological data from youngest strata of the Dinwoody Formation as well as stratigraphic ranges of species suggest that the late Dienerian was likely a time interval of environmental stress for benthic ecosystems. Despite some evidence for short‐term environmental disturbances (e.g. shift of dominant taxa, transient drop in alpha‐diversity) during the Smithian–Spathian transition, benthic ecosystems did not show any notable taxonomic turnover at that time, in contrast to the major crisis that affected ammonoids and conodonts. Whereas alpha‐diversity of benthic communities generally increased throughout the Early Triassic, beta‐diversity remained low, which reflects a persistently wide environmental range of benthic species. This observation is in accordance with a recently proposed model that predicts a time lag between increasing within‐habitat diversity (alpha‐diversity) and the onset of taxonomic differentiation between habitats (beta‐diversity) during biotic recoveries from mass extinction events. The observation that beta‐diversity had not significantly increased during the Early Triassic might also provide an explanation for the comparably sluggish increase in benthic diversity during that time, which has previously been attributed to persistent environmental stress.     

On the controversial questions of the taxonomy of Bivalvia (Mollusca): Too many species or too few characters?

Problems emerging in the course of taxonomic studies and species diagnostics of freshwater bivalves are discussed by the example of one of the bivalve groups (the family Unionidae). It is shown that one of the causes of the current, diametrically opposing views on specific and generic systematics of Bivalvia is the fact that researchers revising taxonomic groups ignore complex analysis of several independent characters (conchological, anatomical, biochemical, genetic, etc.).     

Discovery of the Late Changhsingian Bivalve Complex and Two Fauna Extinction Episodes in Northeastern Asia at the End of the Permian

A late Changhsingian bivalve complex including species from the genera Palaeonucula, Dacryomya, Malletia ?, Sarepta ?, Myalina, Pteria, Maitaia, and Unionites is discovered in northeastern Asia for the first time. The transition from the Permian to the Triassic in high-boreal basins has been shown to include two extinction episodes similar to those observed in the low-boreal basins and apparently evoked by trap volcanism activation in Siberia. Changes in benthic foraminifera diversity and vertical distribution of ammonoidea of the genus Otoceras in transitional Permian–Triassic deposits also are considered. Images of bivalves from the most typical taxa are presented.     

An information-theoretical measure of taxonomic diversity

Traditional diversity indices are computed from the abundances of species present and are insensitive to taxonomic differences between species. However, a community in which most species belong to the same genus is intuitively less diverse than another community with a similar number of species distributed more evenly between genera. In this paper, we propose an information-theoretical measure of taxonomic diversity that reflects both the abundances and taxonomic distinctness of the species. Unlike previous measures of taxonomic diversity, such as Rao's quadratic entropy, in this new measure the analyzed taxonomic properties are associated with the single species instead of species pairs.     

Molluscan biological and chemical diversity: secondary metabolites and medicinal resources produced by marine molluscs

The phylum Mollusca represents an enormous diversity of species with eight distinct classes. This review provides a taxonomic breakdown of the published research on marine molluscan natural products and the medicinal products currently derived from molluscs, in order to identify priority targets and strategies for future research. Some marine gastropods and bivalves have been of great interest to natural products chemists, yielding a diversity of chemical classes and several drug leads currently in clinical trials. Molluscs also feature prominently in a broad range of traditional natural medicines, although the active ingredients in the taxa involved are typically unknown. Overall secondary metabolites have only been investigated from a tiny proportion (<1%) of molluscan species. At the class level, the number of species subject to chemical studies mirrors species richness and our relative knowledge of the biology of different taxa. The majority of molluscan natural products research is focused within one of the major groups of gastropods, the opisthobranchs (a subgroup of Heterobranchia), which are primarily comprised of soft‐bodied marine molluscs. Conversely, most molluscan medicines are derived from shelled gastropods and bivalves. The complete disregard for several minor classes of molluscs is unjustified based on their evolutionary history and unique life styles, which may have led to novel pathways for secondary metabolism. The Polyplacophora, in particular, have been identified as worthy of future investigation given their use in traditional South African medicines and their abundance in littoral ecosystems. As bioactive compounds are not always constitutively expressed in molluscs, future research should be targeted towards biosynthetic organs and inducible defence reactions for specific medicinal applications. Given the lack of an acquired immune system, the use of bioactive secondary metabolites is likely to be ubiquitous throughout the Mollusca and broadening the search field may uncover interesting novel chemistry.     

Bivalve ecology in a Silurian shelf environment

The Ludlow Series of the Welsh Borderland represents a gradient from quiet. deep shelf muds to shallow, storm-deposited silts. A fauna of 44 bivalve species shows a pattern of overlapping environmental ranges which span the full extent of the shelf gradient. Bivalve abundance is highest at the extremes of this gradient, where endobyssate forms are common in storm-deposited silts, and nuculoids locally dominate the fauna of the deep shelf muds. Species diversity of bivalves, however, is highest in low-stress. mid-shelf environments, where bivalves of small population sizes comprise a minimal proportion of the benthic fauna. Niche sizes, species diversity. and total environmental range of the bivalves is comparable to that of Ludlow brachiopods, even though the latter group is far more abundant as individuals.