Using integrative taxonomy to distinguish cryptic halfbeak species and interpret distribution patterns, fisheries landings, and speciation

Context. Species classification disputes can be resolved using integrative taxonomy, which involves the use of both phenotypic and genetic information to determine species boundaries. Aims. Our aim was to clarify species boundaries of two commercially important cryptic species of halfbeak (Hemiramphidae), whose distributions overlap in south-eastern Australia, and assist fisheries management. Methods. We applied an integrative taxonomic approach to clarify species boundaries and assist fisheries management. Key results. Mitochondrial DNA and morphological data exhibited significant differences between the two species. The low level of mitochondrial DNA divergence, coupled with the lack of difference in the nuclear DNA, suggests that these species diverged relatively recently (c. 500 000 years ago) when compared with other species within the Hyporhamphus genus (>2.4 million years ago). Genetic differences between the species were accompanied by differences in modal gill raker counts, mean upper- jaw and preorbital length, and otolith shape. Conclusions. On the basis of these genetic and morphological differences, as well as the lack of morphological intergradation between species along the overlapping boundaries of their geographical distributions, we propose that Hyporhamphus australis and Hyporhamphus melanochir remain valid species. Implications. This study has illustrated the need for an integrative taxonomic approach when assessing species boundaries and has provided a methodological framework for studying other cryptic fish species in a management context

Anthropogenic disturbance and evolutionary parameters: a lemon shark population experiencing habitat loss

The level of genetic variation in natural populations influences evolutionary potential, and may therefore influence responses to selection in the face of future environmental changes. By combining long-term monitoring of marked individuals with genetic pedigree reconstruction, we assessed whether habitat loss influenced genetic variation in a lemon shark (Negaprion brevirostris) population at an isolated nursery lagoon (Bimini, Bahamas). We also tracked changes in the strength and direction of natural selection. Contrary to initial expectations, we found that after the habitat loss neutral genetic variation increased, as did additive genetic variance for juvenile morphological traits (body length and mass). We hypothesize that these effects might result from philopatric behavior in females coupled with a possible influx of male genotypes from other nursery sites. We also found changes in the strength of selection on morphological traits, which weakened considerably after the disturbance; habitat loss therefore changed the phenotypes favored by natural selection. Because such human-induced shifts in the adaptive landscape may be common, we suggest that conservation biologists should not simply focus on neutral genetic variation per se, but also on assessing and preserving evolutionary parameters, such as additive genetic variation and selection

Demographic histories shape population genomics of the common coral grouper (Plectropomus leopardus)

Many coral reef fishes display remarkable genetic and phenotypic variation across their geographic ranges. Understanding how historical and contemporary processes have shaped these patterns remains a focal question in evolutionary biology since they reveal how diversity is generated and how it may respond to future environmental change. Here, we compare the population genomics and demographic histories of a commercially and ecologically important coral reef fish, the common coral grouper (Plectropomus leopardus [Lacepede 1802]), across two adjoining regions (the Great Barrier Reef; GBR, and the Coral Sea, Australia) spanning approximately 14 degrees of latitude and 9 degrees of longitude. We analysed 4548 single nucleotide polymorphism (SNP) markers across 11 sites and show that genetic connectivity between regions is low, despite their relative proximity (similar to 100km) and an absence of any obvious geographic barrier. Inferred demographic histories using 10,479 markers suggest that the Coral Sea population was founded by a small number of GBR individuals and that divergence occurred similar to 190 kya under a model of isolation with asymmetric migration. We detected population expansions in both regions, but estimates of contemporary effective population sizes were approximately 50% smaller in Coral Sea sites, which also had lower genetic diversity. Our results suggest that P. leopardus in the Coral Sea have experienced a long period of isolation that precedes the recent glacial period (similar to 10-120 kya) and may be vulnerable to localized disturbances due to their relative reliance on local larval replenishment. While it is difficult to determine the underlying events that led to the divergence of the Coral Sea and GBR lineages, we show that even geographically proximate populations of a widely dispersed coral reef fish can have vastly different evolutionary histories

Gut content metabarcoding of specialized feeders is not a replacement for environmental DNA assays of seawater in reef environments

In tropical marine ecosystems, the coral-based diet of benthic-feeding reef fishes provides a window into the composition and health of coral reefs. In this study, for the first time, we compare multi-assay metabarcoding sequences of environmental DNA (eDNA) isolated from seawater and partially digested gut items from an obligate corallivore butterflyfish (Chaetodon lunulatus) resident to coral reef sites in the South China Sea. We specifically tested the proportional and statistical overlap of the different approaches (seawater vs gut content metabarcoding) in characterizing eukaryotic community composition on coral reefs. Based on 18S and ITS2 sequence data, which differed in their taxonomic sensitivity, we found that gut content detections were only partially representative of the eukaryotic communities detected in the seawater based on low levels of taxonomic overlap (3 to 21%) and significant differences between the sampling approaches. Overall, our results indicate that dietary metabarcoding of specialized feeders can be complimentary to, but is no replacement for, more comprehensive environmental DNA assays of reef environments that might include the processing of different substrates (seawater, sediment, plankton) or traditional observational surveys. These molecular assays, in tandem, might be best suited to highly productive but cryptic oceanic environments (kelp forests, seagrass meadows) that contain an abundance of organisms that are often small, epiphytic, symbiotic, or cryptic.</p

Gut microbial communities of hybridising pygmy angelfishes reflect species boundaries

Hybridisation and introgression of eukaryotic genomes can generate new species or subsume existing ones, with direct and indirect consequences for biodiversity. An understudied component of these evolutionary forces is their potentially rapid effect on host gut microbiomes, and whether these pliable microcosms may serve as early biological indicators of speciation. We address this hypothesis in a field study of angelfishes (genus Centropyge), which have one of the highest prevalence of hybridisation within coral reef fish. In our study region of the Eastern Indian Ocean, the parent fish species and their hybrids cohabit and display no differences in their diet, behaviour, and reproduction, often interbreeding in mixed harems. Despite this ecological overlap, we show that microbiomes of the parent species are significantly different from each other in form and function based on total community composition, supporting the division of parents into distinct species, despite the confounding effects of introgression acting to homogenize parent species identity at other molecular markers. The microbiome of hybrid individuals, on the other hand, are not significantly different to each of the parents, instead harbouring an intermediate community composition. These findings suggest that shifts in gut microbiomes may be an early indicator of speciation in hybridising species

The microbiome of the gastrointestinal tract of a range-shifting marine herbivorous fish

Globally, marine species\u27 distributions are being modified due to rising ocean temperatures. Increasing evidence suggests a circum-global pattern of poleward extensions in the distributions of many tropical herbivorous species, including the ecologically important rabbitfis

Cancellation of vorticity in steady-state non-isentropic flows of complex fluids

In steady-state non-isentropic flows of perfect fluids there is always thermodynamic generation of vorticity when the difference between the product of the temperature with the gradient of the entropy and the gradient of total enthalpy is different from zero. We note that this property does not hold in general for complex fluids for which the prominent influence of the material substructure on the gross motion may cancel the thermodynamic vorticity. We indicate the explicit condition for this cancellation (topological transition from vortex sheet to shear flow) for general complex fluids described by coarse-grained order parameters and extended forms of Ginzburg-Landau energies. As a prominent sample case we treat first Korteweg's fluid, used commonly as a model of capillary motion or phase transitions characterized by diffused interfaces. Then we discuss general complex fluids. We show also that, when the entropy and the total enthalpy are constant throughout the flow, vorticity may be generated by the inhomogeneous character of the distribution of material substructures, and indicate the explicit condition for such a generation. We discuss also some aspects of unsteady motion and show that in two-dimensional flows of incompressible perfect complex fluids the vorticity is in general not conserved, due to a mechanism of transfer of energy between different levels.Comment: 12 page

Digging for DNA at depth: rapid universal metabarcoding surveys (RUMS) as a tool to detect coral reef biodiversity across a depth gradient

Background Effective biodiversity monitoring is fundamental in tracking changes in ecosystems as it relates to commercial, recreational, and conservation interests. Current approaches to survey coral reef ecosystems center on the use of indicator species and repeat surveying at specific sites. However, such approaches are often limited by the narrow snapshot of total marine biodiversity that they describe and are thus hindered in their ability to contribute to holistic ecosystem-based monitoring. In tandem, environmental DNA (eDNA) and next-generation sequencing metabarcoding methods provide a new opportunity to rapidly assess the presence of a broad spectrum of eukaryotic organisms within our oceans, ranging from microbes to macrofauna. Methods We here investigate the potential for rapid universal metabarcoding surveys (RUMS) of eDNA in sediment samples to provide snapshots of eukaryotic subtropical biodiversity along a depth gradient at two coral reefs in Okinawa, Japan based on 18S rRNA. Results Using 18S rRNA metabarcoding, we found that there were significant separations in eukaryotic community assemblages (at the family level) detected in sediments when compared across different depths ranging from 10 to 40 m (p = 0.001). Significant depth zonation was observed across operational taxonomic units assigned to the class Demospongiae (sponges), the most diverse class (contributing 81% of species) within the phylum Porifera; the oldest metazoan phylum on the planet. However, zonation was not observed across the class Anthozoa (i.e., anemones, stony corals, soft corals, and octocorals), suggesting that the former may serve as a better source of indicator species based on sampling over fine spatial scales and using this universal assay. Furthermore, despite their abundance on the examined coral reefs, we did not detect any octocoral DNA, which may be due to low cellular shedding rates, assay sensitivities, or primer biases. Discussion Overall, our pilot study demonstrates the importance of exploring depth effects in eDNA and suggest that RUMS may be applied to provide a baseline of information on eukaryotic marine taxa at coastal sites of economic and conservation importance