High-Throughput Sequencing for Life-History Sorting and for Bridging Reference Sequences in Marine Gerromorpha (Insecta: Heteroptera)

Accurate identification and association of larval specimens with adults is a major challenge in insect taxonomy. Fortunately, it is now possible for nonexperts to sort collections of bulk samples with DNA barcodes rapidly and cost-effectively. We demonstrate this process using nanopore barcoding of 757 marine insects (Insecta: Gerromorpha), of which 81% were nymphs and many samples did not have co-occurring adult males for specific identification. We successfully associated 738 specimens (97%) to nine gerromorphan species, which would have been impossible to identify using morphological characters alone. This improved ability to incorporate information from all life-history stages has led to greater precision of species distributional ranges—knowledge that will be crucial for a more complete understanding of marine insects. We also highlighted two distinct, nonoverlapping Gerromorpha COI sequence databases on GenBank—a consequence of using two different primer sets to amplify different regions of COI. This issue inevitably hinders species identification with DNA-based methods, particularly for poorly represented groups such as marine insects. We bridged these databases by analyzing full-length COI sequences. We believe this will inspire future studies to incorporate DNA-based methods for more adult–larval association studies and for enhancing existing genetic resources, especially in understudied groups.

Early exposure to UV radiation causes telomere shortening and poorer condition later in life

Determining the contribution of elevated ultraviolet–B radiation (UVBR; 280 — 315 nm) to amphibian population declines is being hindered by a lack of knowledge about how different acute UVBR exposure regimes during early life history stages might affect post–metamorphic stages via long–term carryover effects. We acutely exposed tadpoles of the Australian green tree frog (Litoria caerulea) to a combination of different UVBR irradiances and doses in a multi–factorial experiment, and then reared them to metamorphosis in the absence of UVBR to assess carryover effects in subsequent juvenile frogs. Dose and irradiance of acute UVBR exposure influenced carryover effects into metamorphosis in somewhat opposing manners. Higher doses of UVBR exposure in larvae yielded improved rates of metamorphosis. However, exposure at a high irradiance resulted in frogs metamorphosing smaller in size and in poorer condition than frogs exposed to low and medium irradiance UVBR as larvae. We also demonstrate some of the first empirical evidence of UVBR-induced telomere shortening in vivo, which is one possible mechanism for life–history trade–offs impacting condition post-metamorphosis. These findings contribute to our understanding of how acute UVBR exposure regimes in early life affect later life–history stages, which has implications for how this stressor may shape population dynamics.

Niche Shifts From Trees to Fecundity to Recruitment That Determine Species Response to Climate Change

Anticipating the next generation of forests requires understanding of recruitment responses to habitat change. Tree distribution and abundance depend not only on climate, but also on habitat variables, such as soils and drainage, and on competition beneath a shaded canopy. Recent analyses show that North American tree species are migrating in response to climate change, which is exposing each population to novel climate-habitat interactions (CHI). Because CHI have not been estimated for either adult trees or regeneration (recruits per year per adult basal area), we cannot evaluate migration potential into the future. Using the Masting Inference and Forecasting (MASTIF) network of tree fecundity and new continent-wide observations of tree recruitment, we quantify impacts for redistribution across life stages from adults to fecundity to recruitment. We jointly modeled response of adult abundance and recruitment rate to climate/habitat conditions, combined with fecundity sensitivity, to evaluate if shifting CHI explain community reorganization. To compare climate effects with tree fecundity, which is estimated from trees and thus is "conditional" on tree presence, we demonstrate how to quantify this conditional status for regeneration. We found that fecundity was regulated by temperature to a greater degree than other stages, yet exhibited limited responses to moisture deficit. Recruitment rate expressed strong sensitivities to CHI, more like adults than fecundity, but still with substantial differences. Communities reorganized from adults to fecundity, but there was a re-coalescence of groups as seedling recruitment partially reverted to community structure similar to that of adults. Results provide the first estimates of continent-wide community sensitivity and their implications for reorganization across three life-history stages under climate change.

Juveniles and larvae of eleven fish species collected from three countries of the Arabian Gulf and the Arabian Sea

The finding of larval and juvenile specimens from the Omani coast of the Arabian Sea and the Arabian Gulf waters of Saudi Arabia and Iraq is reported for the first time. Based on available information, one larva was a leptocephalus, Conger sp. (family Congridae) and one larva of an acronurus stage belonging to the genus Acanthurus (family Acanthuridae). Also juveniles of the following families are included in the present study: Clupeidae – Tenualosa ilisha (Hamilton, 1822) and Nematalosa sp.; Dactylopteridae – Dactyloptena orientalis (Cuvier, 1829); Gobiidae – Acentrogobius sp.; Bothidae – Arnoglossus aspilos (Bleeker, 1851); Scatophagidae – Scatophagus argus (Linnaeus, 1766); Sparidae – Acanthopagrus arabicus Iwatsuki, 2013 and Sparidentex hasta (Valenciennes, 1830); Tetraodontidae – Lagocephalus sp. The discovery of the barred rather than spotted juveniles of S. argus collected from pure freshwater environment of the Shatt al-Arab River, Basrah, Iraq was remarkable; it raises questions whether there is more than one species within the nominal S. argus. For both larvae and juveniles of bothid flounders, the olfactory organ is a useful character for the examination of the developmental stage of the metamorphosing specimens. The occurrence of the different early life history stages of fishes from the three Arabian countries shows the needs them to be studied further so that inferences about the areas and periods of spawning and development of these fishes can be made more accurately.

Direct and latent effects of ocean acidification on the transition of a sea urchin from planktonic larva to benthic juvenile

Ongoing ocean acidification (OA) is expected to affect marine organisms and ecosystems. While sea urchins can survive a wide range of pH, this comes at a high energetic cost, and early life stages are particularly vulnerable. Information on how OA affects transitions between life-history stages is scarce. We evaluated the direct and indirect effects of pH (pHT 8.0, 7.6 and 7.2) on the development and transition between life-history stages of the sea urchin Strongylocentrotus droebachiensis, from fertilization to early juvenile. Continuous exposure to low pH negatively affected larval mortality and growth. At pH 7.2, formation of the rudiment (the primordial juvenile) was delayed by two days. Larvae raised at pH 8.0 and transferred to 7.2 after competency had mortality rates five to six times lower than those kept at 8.0, indicating that pH also has a direct effect on older, competent larvae. Latent effects were visible on the larvae raised at pH 7.6: they were more successful in settling (45%) and metamorphosing (30%) than larvae raised at 8.0 (17 and 1% respectively). These direct and indirect effects of OA on settlement and metamorphosis have important implications for population survival.

A Mechanistic Framework for Understanding the Effects of Climate Change on the Link Between Flowering and Fruiting Phenology

Phenological shifts are a widely studied consequence of climate change. Little is known, however, about certain critical phenological events, nor about mechanistic links between shifts in different life-history stages of the same organism. Among angiosperms, flowering times have been observed to advance with climate change, but, whether fruiting times shift as a direct consequence of shifting flowering times, or respond differently or not at all to climate change, is poorly understood. Yet, shifts in fruiting could alter species interactions, including by disrupting seed dispersal mutualisms. In the absence of long-term data on fruiting phenology, but given extensive data on flowering, we argue that an understanding of whether flowering and fruiting are tightly linked or respond independently to environmental change can significantly advance our understanding of how fruiting phenologies will respond to warming climates. Through a case study of biotically and abiotically dispersed plants, we present evidence for a potential functional link between the timing of flowering and fruiting. We then propose general mechanisms for how flowering and fruiting life history stages could be functionally linked or independently driven by external factors, and we use our case study species and phenological responses to distinguish among proposed mechanisms in a real-world framework. Finally, we identify research directions that could elucidate which of these mechanisms drive the timing between subsequent life stages. Understanding how fruiting phenology is altered by climate change is essential for all plant species but is particularly critical to sustaining the large numbers of plant species that rely on animal-mediated dispersal, as well as the animals that rely on fruit for sustenance.

The Evolution of Hox Genes in Spiralia

The decoding of genomes of a larger number of animal species have provided further insights into the genomic Hox gene organization and with this indicated the evolutionary changes during the radiation of several clades. The expansion of gene expression studies during development and life history stages of more species, complete the picture of the relationship between cluster organisation and temporal and spatial correlation of the Hox activity. Now these results open the opportunity to look deeper into the regulatory pathways that form these patterns and identify what exact changes caused the evolution of the application of this iconical gene set for the evolution of new larval forms and new structures. Here we review recent progress of Hox gene related research in the large clade Spiralia, that comprises Annelida, Mollusca, Lophophorata, Platyhelminthes, Nemertea and others. Albeit their relationship to each other is not resolved yet, there are emerging patterns that indicate that Hox genes are mainly used for patterning late, adult body parts and that Hox genes are often not expressed on the larval stages. Hox genes seem also often recruited for the formation of morphological novelties. Together with the emerging genomic information Hox genes show a much more dynamic evolutionary history than previously assumed.

Habitat Use Throughout a Chondrichthyan's Life

<p>Over the last few decades, much effort has been devoted towards evaluating and reducing bycatch in marine fisheries. There has been a particular focus on quantifying the risk to chondrichthyans, primarily because of their relatively high vulnerability to overfishing. A key part of risk assessment is evaluating the distributional overlap of the fish with the fisheries, where fish distribution is influenced by habitat use. I synthesised published observations of habitat use for different life history stages of chondrichthyans and hypothesised the associated catch composition in terms of fish sex, size, and maturity. I then searched for these catch compositions, and thereby locations, using New Zealand research vessel catch data. Results show that some life history stages and habitats for certain species can be identified, whereas others could not. Pupping ground criteria were met for Callorhynchus milii (ELE), Hydrolagus novaezealandiae (GSH), and Hydrolagus bemisi (GSP); nursery ground criteria were met for Callorhynchus milii (ELE), mating ground criteria were met for Callorhynchus milii (ELE), Hydrolagus novaezealandiae (GSH), Hydrolagus bemisi (GSP), and Harriotta raleighana (LCH); lek-like mating criteria were met for Hydrolagus novaezealandiae (GSH). For those life-history stage habitats not found, this may be because these are outside of the coverage of the data set (and likely also commercial fisheries), or because they do not actually exist for some chondrichthyans. On the basis of results, I propose to change the order of species in the New Zealand qualitative (Level 1) risk assessment, and rise the relative risk for Hydrolagus bemisi (GSP), given the species vulnerability of pupping grounds.</p>

Habitat Use Throughout a Chondrichthyan's Life

<p>Over the last few decades, much effort has been devoted towards evaluating and reducing bycatch in marine fisheries. There has been a particular focus on quantifying the risk to chondrichthyans, primarily because of their relatively high vulnerability to overfishing. A key part of risk assessment is evaluating the distributional overlap of the fish with the fisheries, where fish distribution is influenced by habitat use. I synthesised published observations of habitat use for different life history stages of chondrichthyans and hypothesised the associated catch composition in terms of fish sex, size, and maturity. I then searched for these catch compositions, and thereby locations, using New Zealand research vessel catch data. Results show that some life history stages and habitats for certain species can be identified, whereas others could not. Pupping ground criteria were met for Callorhynchus milii (ELE), Hydrolagus novaezealandiae (GSH), and Hydrolagus bemisi (GSP); nursery ground criteria were met for Callorhynchus milii (ELE), mating ground criteria were met for Callorhynchus milii (ELE), Hydrolagus novaezealandiae (GSH), Hydrolagus bemisi (GSP), and Harriotta raleighana (LCH); lek-like mating criteria were met for Hydrolagus novaezealandiae (GSH). For those life-history stage habitats not found, this may be because these are outside of the coverage of the data set (and likely also commercial fisheries), or because they do not actually exist for some chondrichthyans. On the basis of results, I propose to change the order of species in the New Zealand qualitative (Level 1) risk assessment, and rise the relative risk for Hydrolagus bemisi (GSP), given the species vulnerability of pupping grounds.</p>

Impact of the local environmental variability on the patterns of coral recruitment on Indo-Pacific reefs

<p>Coral reefs are threatened by a range of human activities at both local and global scales. The result of these impacts has resulted in a worldwide decline in the coral reef ecosystems. Corals are the principle reef builders and the maintenance of their populations is fundamental for healthy reef ecosystems. Local environmental factors are critically important in shaping coral populations, particularly at the post-settlement phase, when young coral colonies are most vulnerable to disturbances. In this context, understanding the environmental factors that drive coral recruitment and affect coral survivorship in the early life history stages is vital to effectively manage coral reefs. In this thesis I began by investigating the effect of abiotic and biological factors on coral recruitment and juvenile coral life history stages using settlement panels deployed in the Wakatobi Marine National Park (SE Sulawesi, Indonesia). My objectives were to assess the spatio-temporal variability in coral recruitment rates and juvenile abundance. I used a modelling approach to identify the environmental factors that affected the distribution and abundance patterns of corals. Then, I focused on the main environmental factors, identified from previously published research, affecting coral recruitment. I conducted a caging experiment to assess the impact of fish predation on coral juveniles. Finally, I analysed the development of the benthic community and the interactions between corals and benthic organisms in the first two years of colonisation of artificial bare surfaces. I found high spatial and temporal variability in recruitment rates over seven years of data, values were lower than on other Indo-Pacific reefs and ranged from 9.6 (±8.21 SE) to 317.19 (±12.76 SE) rec. m⁻²; while juvenile abundance ranged from 4.2 (±1.49 SE) to 33 (±6.36 SE) juv. m⁻². The local characteristics of the sites, such as coral cover, influenced the distribution of coral colonies in early life history stages; furthermore differences in coral density between the two life history stages (juvenile and recruits) were consistent over time. However, no single or combination of factors adequately explained abundance patterns for either recruits or juveniles. Fish predation did not appear to be the main cause of coral post-settlement mortality in the Wakatobi and it affected only 10.8% of the coral juveniles in the experiment. In contrast, 58.51% of the coral juveniles were found to be overgrown by algae and other invertebrates, however only turf and green encrusting algae affected coral survivorship. Coral colony abundance and the number of interactions with other benthic organisms, especially crustose coralline algae (CCA) and sponges, increased over time on panels and they were different between the front and back side of the panels, which was attributed to differences in light and predation regimes. Coral recruitment was higher on older benthic communities, although none of the known coral recruitment promoters, such as CCA, or competitors, such as turf algae, were correlated with coral abundance. My results show that changes in coral populations between the recruit and juvenile stages are likely driven by small-scale processes. The site characteristics determine the final patterns, which vary over time following temporal fluctuations in environmental factors. The effect of the interactions between algae and sponges with coral recruits and their influence on juvenile survivorship suggests these organisms having a role in coral recruitment success and highlight their importance as a focus for reef management. Furthermore, the use of long term studies allowed a better understanding of the high variability present in coral recruitment and the trends of the recruitment process, which are useful information for conservative purposes.</p>