Beyond Functional Diversity: The Importance of Trophic Position to Understanding Functional Processes in Community Evolution

Ecosystem structure—that is the species present, the functions they represent, and how those functions interact—is an important determinant of community stability. This in turn aects how ecosystems respond to natural and anthropogenic crises, and whether species or the ecological functions that they represent are able to persist. Here we use fossil data from museum collections, literature, and the Paleobiology Database to reconstruct trophic networks of Tethyan paleocommunities fromthe Anisian and Carnian (Triassic), Bathonian (Jurassic), and Aptian (Cretaceous) stages, and compare these to a previously reconstructed trophic network from a modern Jamaican reef community. We generated model food webs consistent with functional structure and taxon richnesses of communities, and compared distributions of guild level parameters among communities, to assess the eect of the Mesozoic Marine Revolution on ecosystem dynamics. We found that the trophic space of communities expanded from the Anisian to the Aptian, but this pattern was notmonotonic.We also found that trophic position for a given guild was subject to variation depending on what other guilds were present in that stage. The Bathonian showed the lowest degree of trophic omnivory by top consumers among all Mesozoic networks, and was dominated by longer food chains. In contrast, the Aptian network displayed a greater degree of short food chains and trophic omnivory that we attribute to the presence of large predatory guilds, such as sharks and bony fish. Interestingly, the modern Jamaican community appeared to have a higher proportion of long chains, as was the case in the Bathonian. Overall, results indicate that trophic structure is highly dependent on the taxa and ecological functions present, primary production experienced by the community, and activity of top consumers. Results from this study point to a need to better understand trophic position when planning restoration activities because a community may be so altered by human activity that restoring a species or its interactions may no longer be possible, and alternatives must be considered to restore an important function. Further work may also focus on elucidating the precise roles of top consumers in moderating network structure and community stability

Structure and distribution of chalky deposits in the Pacific oyster using x-ray computed tomography (CT)

Oysters are unusual among bivalves in that they possess chambers, often filled with soft, chalky calcite, that are irregularly scattered throughout the shell. Because the function of these so-called chalky deposits is still unclear, evaluating the growth and distribution of chalk is important for elucidating the ecological function of this unique shell trait. Specimens of the Pacific oyster Magallana gigas, an oyster well known for chalk expression, were grown in Bodega Harbor, Bodega Bay, CA. At the end of an 11 month growing period, specimens were culled and selected animals were submitted for x-ray computed-tomography imaging. Three-dimensional reconstructions of oyster shells were used to assess the overall distribution of chalk, and also to better understand the relationship between chalk and other structures within the shell. Results indicate that chalky deposits underly sculptural features on the shell exterior, such as external ridges and changes in growth direction, and also that there is a relationship between chalk formation and oyster processes of cementation. Overall, chalk is useful for a cementing lifestyle because it enables morphological plasticity needed to conform to irregular substrates, but also acts as a cheap building material to facilitate rapid growth

Sodium molybdate does not inhibit sulfate-reducing bacteria but increases shell growth in the Pacific oyster Magallana gigas.

Recent work on microbe-host interactions has revealed an important nexus between the environment, microbiome, and host fitness. Marine invertebrates that build carbonate skeletons are of particular interest in this regard because of predicted effects of ocean acidification on calcified organisms, and the potential of microbes to buffer these impacts. Here we investigate the role of sulfate-reducing bacteria, a group well known to affect carbonate chemistry, in Pacific oyster (Magallana gigas) shell formation. We reared oyster larvae to 51 days post fertilization and exposed organisms to control and sodium molybdate conditions, the latter of which is thought to inhibit bacterial sulfate reduction. Contrary to expectations, we found that sodium molybdate did not uniformly inhibit sulfate-reducing bacteria in oysters, and oysters exposed to molybdate grew larger shells over the experimental period. Additionally, we show that microbiome composition, host gene expression, and shell size were distinct between treatments earlier in ontogeny, but became more similar by the end of the experiment. Although additional testing is required to fully elucidate the mechanisms, our work provides preliminary evidence that M. gigas is capable of regulating microbiome dysbiosis caused by environmental perturbations, which is reflected in shell development

A database of Holocene nearshore marine mollusc shell geochemistry from the Northeast Pacific

We compiled a database of previously published oxygen and carbon isotope data from archeological, archival, and modern marine molluscs from the Northeast Pacific (32°N to 55°N). Data are from various bivalves and gastropod species. This dataset includes oxygen and carbon isotope data from 598 modern, archaeological, and sub-fossil shells from 8880 BP to the present, from which there are 4,917 total δ13C and 7,366 total δ18O measurements. Database includes the following parameters: paper of original publication, publication year, unique shell identification, unique subsample identification, sample number (given by original authors), subsample number (given by original author), number of subsamples per shell (added here), age in years before present, species, source (midden or modern), latitude, longitude, calculated sea surface temperature (only if published by original authors), tidal height, life mode, habitat, archaeological trinomial (when applicable), oxygen isotope value, and carbon isotope value

A database of Holocene nearshore marine mollusc shell geochemistry from the Northeast Pacific

We compiled a database of previously published oxygen and carbon isotope data from archaeological, archival, and modern marine molluscs from the North American coast of the Northeast Pacific (32oN to 50oN). This database includes oxygen and carbon isotope data from over 550 modern, archaeological, and sub-fossil shells from 8880 years before present (BP) to the present, from which there are 4,845 total δ¹³C and 5,071 total δ¹⁸O measurements. Database includes the following parameters: paper of original publication, publication year, unique shell identification, unique subsample identification, sample number (given by original authors), subsample number (given by original author), number of subsamples per shell (added here), age in years before present, species, source (midden or modern), latitude, longitude, calculated sea surface temperature (only if published by original authors), tidal height, life mode, habitat, archaeological trinomial (when applicable), oxygen isotope value, and carbon isotope value. Shell dating and sampling strategies vary among studies (1-118 samples per shell) and vary significantly by journal discipline. Data are from various bivalves and gastropod species, with Mytilus spp. being the most commonly analyzed taxon. This novel database can be used to investigate changes in nearshore sea surface conditions including warm-cool oscillations, heat waves, and upwelling intensity, and provides nearshore calcite δ¹³C and δ¹⁸O values that can be compared to the vast collections of offshore foraminifera calcite δ¹³C and δ¹⁸O data from marine sediment cores. By utilizing previously published geochemical data from midden and museum shells rather than sampling new specimens, future scientific research can reduce or omit the alteration or destruction of culturally valued specimens and sites

\u3ci\u3eDrosophila\u3c/i\u3e Muller F Elements Maintain a Distinct Set of Genomic Properties Over 40 Million Years of Evolution

The Muller F element (4.2 Mb, ~80 protein-coding genes) is an unusual autosome of Drosophila melanogaster; it is mostly heterochromatic with a low recombination rate. To investigate how these properties impact the evolution of repeats and genes, we manually improved the sequence and annotated the genes on the D. erecta, D. mojavensis, and D. grimshawi F elements and euchromatic domains from the Muller D element. We find that F elements have greater transposon density (25–50%) than euchromatic reference regions (3–11%). Among the F elements, D. grimshawi has the lowest transposon density (particularly DINE-1: 2% vs. 11–27%). F element genes have larger coding spans, more coding exons, larger introns, and lower codon bias. Comparison of the Effective Number of Codons with the Codon Adaptation Index shows that, in contrast to the other species, codon bias in D. grimshawi F element genes can be attributed primarily to selection instead of mutational biases, suggesting that density and types of transposons affect the degree of local heterochromatin formation. F element genes have lower estimated DNA melting temperatures than D element genes, potentially facilitating transcription through heterochromatin. Most F element genes (~90%) have remained on that element, but the F element has smaller syntenic blocks than genome averages (3.4–3.6 vs. 8.4–8.8 genes per block), indicating greater rates of inversion despite lower rates of recombination. Overall, the F element has maintained characteristics that are distinct from other autosomes in the Drosophila lineage, illuminating the constraints imposed by a heterochromatic milieu