Rare coral under the genomic microscope: timing and relationships among Hawaiian Montipora

Background Evolutionary patterns of scleractinian (stony) corals are difficult to infer given the existence of few diagnostic characters and pervasive phenotypic plasticity. A previous study of Hawaiian Montipora (Scleractinia: Acroporidae) based on five partial mitochondrial and two nuclear genes revealed the existence of a species complex, grouping one of the rarest known species (M. dilatata, which is listed as Endangered by the International Union for Conservation of Nature - IUCN) with widespread corals of very different colony growth forms (M. flabellata and M. cf. turgescens). These previous results could result from a lack of resolution due to a limited number of markers, compositional heterogeneity or reflect biological processes such as incomplete lineage sorting (ILS) or introgression. Results All 13 mitochondrial protein-coding genes from 55 scleractinians (14 lineages from this study) were used to evaluate if a recent origin of the M. dilatata species complex or rate heterogeneity could be compromising phylogenetic inference. Rate heterogeneity detected in the mitochondrial data set seems to have no significant impacts on the phylogenies but clearly affects age estimates. Dating analyses show different estimations for the speciation of M. dilatata species complex depending on whether taking compositional heterogeneity into account (0.8 [0.05–2.6] Myr) or assuming rate homogeneity (0.4 [0.14–0.75] Myr). Genomic data also provided evidence of introgression among all analysed samples of the complex. RADseq data indicated that M. capitata colour morphs may have a genetic basis. Conclusions Despite the volume of data (over 60,000 SNPs), phylogenetic relationships within the M. dilatata species complex remain unresolved most likely due to a recent origin and ongoing introgression. Species delimitation with genomic data is not concordant with the current taxonomy, which does not reflect the true diversity of this group. Nominal species within the complex are either undergoing a speciation process or represent ecomorphs exhibiting phenotypic polymorphisms.info:eu-repo/semantics/publishedVersio

The Ecology of Sponges at Palmyra Atoll: Variability, Introduced Species and their Potential Direct and Indirect Impacts

Anthropogenic pressures, direct and indirect, have left no coral reef untouched. Those that remain in a near-pristine condition are remote islands and atolls removed from the majority of direct impacts, but even these are still subjected to the pressures of global climate change to which they are demonstrating a higher resilience than those which are already severely compromised. These near-pristine systems should be protected, managed and studied to better understand how they function and hopefully ensure the future of coral reefs. Unfortunately a number of the remote atolls and islands in the Pacific were modified or used by the US military during WWII, which altered these systems in unknown ways and threatened their surrounding reefs. Palmyra Atoll in the Central Pacific for example had its lagoons dredged and blocked to create more landmass for building, along with the creation of a channel through the reef to allow boat access into the lagoons making them susceptible to introduced species. Fortunately the surrounding reefs at Palmyra are still in a near-pristine condition with high densities of scleractinian corals, however the lagoon fauna is now predominantly sponges. Sponges in high enough densities can have considerable impacts on semi-enclosed bodies of water through their high filtering capabilities and could even threaten native species through competition if they were to extend onto non-lagoon reefs. Therefore, the broad aim of this thesis was to understand the ecology of the sponges in the lagoons at Palmyra and determine their potential impacts on the atoll directly and indirectly. To answer these questions I collected sponge assemblage data across the lagoons at both shallow and deep depths and sampled those species found on the reefs, which were surprisingly entirely different from the lagoon species. I then modelled a suite of environmental predictors to ascertain whether environmental conditions might be maintaining the sponges in the lagoon. To further examine whether the sponges were capable of extending onto the reef I also looked at larval recruitment patterns and assessed the temporal stability with semi-permanent quadrats. The initial surveys revealed the presence of at least two introduced species: Haliclona caerulea (Hechtel 1965) and Gelliodes fibrosa (Wilson 1925). Molecular tools were then employed to confirm the identification and attempt to ascertain the introduction pathway of H. caerulea. Finally, to assess the potential impact of the sponges on the water column I calculated the filtration rates of all the morphologies in the lagoon and extrapolated to the time required to clear all the available water in the lagoon as well as the removal rates of dissolved organic carbon and oxygen. Overall the lagoons appear to have undergone a phase-shift from a coral to sponge dominated system. However, the direct threat of the sponges extending onto the adjacent near-pristine reef currently seems negligible as they appear to be relatively “stable” (sponge mortality and recruitment are in equilibrium) and maintained in the lagoons by the environmental conditions, despite larval production. Sponge diversity changed over depths but the total number of species was consistent with other atoll systems despite the military modifications, with the most prominent sponge being a Hawaiian endemic species: Iotrochota protea (de Laubenfels 1950). The introduction of H. caerulea, a Caribbean sponge is thought to have occurred to Palmyra via Hawaiʻi; however, the molecular data also revealed further cryptic speciation at both the species and order levels, suggesting greater species diversity at Palmyra than previously believed. Finally, the indirect impacts of the sponges on the water column also appear to be small and with limited future risks to the reef organisms, as recruitment and mortality are currently in equilibrium and therefore unlikely to increase dramatically in percentage cover. Globally sponges can play important functional roles in semi-enclosed bodies of water and in summary, despite the sponges being the most dominant fauna on the hard substrate in the lagoons, they appear to pose little threat to the atoll and the adjacent reefs either directly or indirectly despite the confirmed introduction of non-endemic species. However, it must be noted that the time since the modification (70 years) is not that long in an evolutionary sense, so the sponges may still have the potential to extend onto the reef, particularly if there are any dramatic changes to the environmental conditions on the outer reefs. Therefore, to detect whether the sponges are extending onto the reef I propose, as a future management tool, the use of I. protea as an indicator species. The use of multidisciplinary approaches to answer important ecological questions with respect to the potential for sponges to have negative impacts on the nonlagoon reefs proved to be essential in understanding whether the modifications to the lagoons and the subsequent dominance of sponges could be threatening one of the last few remaining near-pristine reef systems in the world

The complete mitochondrial genome of Achatinella mustelina (Gastropoda: Pulmonata: Stylommatophora)

In this study, we report the complete mitochondrial genome sequence of Achatinella mustelina, an endangered Hawaiian tree snail. The mitogenome is 16 323 bp in length and has a base composition of A (34.7%), T (42.6%), C (12.7%) and G (10.0%). Similar to other Pulmonates, it contains 13 protein-coding genes, 2 rRNA genes and 22 tRNA genes. To our knowledge, this is the first mitochondrial genome sequenced within the Achatinelloidea superfamily, which contains a high number of endangered species. As such, this mitogenome will be useful in conservation genetics studies

Shared genomic outliers across two divergent population clusters of a highly threatened seagrass

The seagrass, Zostera capensis, occurs across a broad stretch of coastline and wide environmental gradients in estuaries and sheltered bays in southern and eastern Africa. Throughout its distribution, habitats are highly threatened and poorly protected, increasing the urgency of assessing the genomic variability of this keystone species. A pooled genomic approach was employed to obtain SNP data and examine neutral genomic variation and to identify potential outlier loci to assess differentiation across 12 populations across the ∼9,600 km distribution of Z. capensis. Results indicate high clonality and low genomic diversity within meadows, which combined with poor protection throughout its range, increases the vulnerability of this seagrass to further declines or local extinction. Shared variation at outlier loci potentially indicates local adaptation to temperature and precipitation gradients, with Isolation-by-Environment significantly contributing towards shaping spatial variation in Z. capensis. Our results indicate the presence of two population clusters, broadly corresponding to populations on the west and east coasts, with the two lineages shaped only by frequency differences of outlier loci. Notably, ensemble modelling of suitable seagrass habitat provides evidence that the clusters are linked to historical climate refugia around the Last Glacial Maxi-mum. Our work suggests a complex evolutionary history of Z. capensis in southern and eastern Africa that will require more effective protection in order to safeguard this important ecosystem engineer into the future

Divergence times in demosponges (Porifera): first insights from new mitogenomes and the inclusion of fossils in a birth-death clock model

Background: Approximately 80% of all described extant sponge species belong to the class Demospongiae. Yet, despite their diversity and importance, accurate divergence times are still unknown for most demosponge clades. The estimation of demosponge divergence time is key to answering fundamental questions on the origin of Demospongiae, their diversification and historical biogeography. Molecular sequence data alone is not informative on an absolute time scale, and therefore needs to be "calibrated" with additional data such as fossils. Here, we calibrate the molecular data with the fossilized birth-death model, which compared to strict node dating, allows for the inclusion of young and old fossils in the analysis of divergence time. We use desma-bearing sponges, a diverse group of demosponges that form rigid skeletons and have a rich and continuous fossil record dating back to the Cambrian (similar to 500 Ma), to date the demosponge radiation and constrain the timing of key evolutionary events, like the transition from marine to freshwater habitats. To infer a dated phylogeny of Demospongiae we assembled the mitochondrial genomes of six desma-bearing demosponges from reduced-representation genomic libraries. The total dataset included 33 complete demosponge mitochondrial genomes and 30 fossils. Results: Our study supports a Neoproterozoic origin of Demospongiae. Novel age estimates for the split of freshwater and marine sponges dating back to the Carboniferous and the previously assumed recent (similar to 18 Ma) diversification of freshwater sponges is supported. Moreover, we provide detailed age estimates for a possible diversification of Tetractinellidae (similar to 315 Ma), the Astrophorina (similar to 240 Ma), the Spirophorina (similar to 120 Ma) and the family Corallistidae (similar to 88 Ma) all of which are considered as key groups for dating the Demospongiae due to their extraordinary rich and continuous fossil history. Conclusion: This study provides novel insights into the evolution of Demospongiae. Observed discrepancies of our dated phylogeny with their putative first fossil appearance dates are discussed for selected sponge groups. For instance, a Carboniferous origin of the order Tetractinellida seems to be too late, compared to their first appearance in the fossil record in the Middle Cambrian. This would imply that Paleozoic spicule forms are not homologous to post-Paleozoic forms

Application of COMPOCHIP Microarray to Investigate the Bacterial Communities of Different Composts

A microarray spotted with 369 different 16S rRNA gene probes specific to microorganisms involved in the degradation process of organic waste during composting was developed. The microarray was tested with pure cultures, and of the 30,258 individual probe-target hybridization reactions performed, there were only 188 false positive (0.62%) and 22 false negative signals (0.07%). Labeled target DNA was prepared by polymerase chain reaction amplification of 16S rRNA genes using a Cy5-labeled universal bacterial forward primer and a universal reverse primer. The COMPOCHIP microarray was applied to three different compost types (green compost, manure mix compost, and anaerobic digestate compost) of different maturity (2, 8, and 16 weeks), and differences in the microorganisms in the three compost types and maturity stages were observed. Multivariate analysis showed that the bacterial composition of the three composts was different at the beginning of the composting process and became more similar upon maturation. Certain probes (targeting Sphingobacterium, Actinomyces, Xylella/Xanthomonas/ Stenotrophomonas, Microbacterium, Verrucomicrobia, Planctomycetes, Low G + C and Alphaproteobacteria) were more influential in discriminating between different composts. Results from denaturing gradient gel electrophoresis supported those of microarray analysis. This study showed that the COMPOCHIP array is a suitable tool to study bacterial communities in composts

From polyps to pixels: understanding coral reef resilience to local and global change across scales

Abstract Context Coral reef resilience is the product of multiple interacting processes that occur across various interacting scales. This complexity presents challenges for identifying solutions to the ongoing worldwide decline of coral reef ecosystems that are threatened by both local and global human stressors. Objectives We highlight how coral reef resilience is studied at spatial, temporal, and functional scales, and explore emerging technologies that are bringing new insights to our understanding of reef resilience. We then provide a framework for integrating insights across scales by using new and existing technological and analytical tools. We also discuss the implications of scale on both the ecological processes that lead to declines of reefs, and how we study those mechanisms. Methods To illustrate, we present a case study from Kāneʻohe Bay, Hawaiʻi, USA, linking remotely sensed hyperspectral imagery to within-colony symbiont communities that show differential responses to stress. Results In doing so, we transform the scale at which we can study coral resilience from a few individuals to entire ecosystems. Conclusions Together, these perspectives guide best practices for designing management solutions that scale from individuals to ecosystems by integrating multiple levels of biological organization from cellular processes to global patterns of coral degradation and resilience

Long-term ecological research on Colorado Shortgrass Steppe

The SGS-LTER research site was established in 1980 by researchers at Colorado State University as part of a network of long-term research sites within the US LTER Network, supported by the National Science Foundation. Scientists within the Natural Resource Ecology Lab, Department of Forest and Rangeland Stewardship, Department of Soil and Crop Sciences, and Biology Department at CSU, California State Fullerton, USDA Agricultural Research Service, University of Northern Colorado, and the University of Wyoming, among others, have contributed to our understanding of the structure and functions of the shortgrass steppe and other diverse ecosystems across the network while maintaining a common mission and sharing expertise, data and infrastructure.Poster presented at the LTER All Scientists Meeting held in Estes Park, CO on September 10-13, 2012