Genetic population structure of the blue sea star (<i>Linckia laevigata</i>) and the boring giant clam (<i>Tridacna crocea</i>) across Malaysia

Various studies on population genetics in the Indo-Pacific that include the Coral Triangle region have revealed phylogeographic patterns in marine species populations. However, little is known about the population structure and connectivity pattern among the coral reefs in four seas surrounding Malaysia: the Strait of Malacca (Andaman Sea), the South China Sea, the Sulu Sea, and the Sulawesi Sea. In view of this, we examined the genetic population structure of two invertebrate species: the blue sea star (Linckia laevigata) and the boring clam (Tridacna crocea) from seven localities across Malaysia, including Pulau Layang-Layang in the Spratly Islands. Additional samples of L. laevigata were obtained from the Davao Gulf, the Philippines. The analyses were based on partial mitochondrial cytochrome oxidase I sequences of L. laevigata and T. crocea. Populations of L. laevigata and T. crocea showed departure from neutrality, indicating selection or population expansion. However, a mismatch analysis suggested population expansion. Lack of genetic population structure in L. laevigata (ΦST = − 0.001, P = 0.399) implies high connectivity among the sampled reef sites. There was subtle genetic structuring in populations of T. crocea (ΦST = 0.032, P = 0.009), but AMOVA did not detect any structure in the a priori groupings. The genetic population structure and scale in connectivity are most likely attributed to the life history traits of the sea star and giant clam species, and also to the geological history and seasonal current patterns of the region

Ecological health of coral reefs in Zanzibar

Coral reefs are important ecosystems in terms of their biodiversity and ecosystem functions. Particularly at local scales, coral reefs are vulnerable to natural and anthropogenic disturbances, leading to the degradation of reef health. Here, we employed two different methods to monitor reef health. First, we conducted line transect surveys to record the benthic community structure to infer ecological reef health. Secondly, trace metal concentrations in sediment samples and a bioindicator sponge species, Haliclona fascigera, were compared among sites to detect cryptic degradation and unknown sources of pollution. The study area comprised six reefs situated along the coast of Zanzibar’s main agglomeration, Stone Town, and subject to different types of disturbances and conservation management schemes. Overall, coral reef health was found to decrease with increasing proximity to Stone Town, with living hard coral cover being particularly low on reefs closest to Stone Town, which coincided with greater fishing, tourism, and pollution pressures. Reef assessments based on trace metal analyses differed from the community structure surveys. All sites showed high levels of arsenic and cadmium contamination, with some samples revealing concerning levels of chromium, copper and zinc. The reefs differed significantly between each other in terms of trace metal concentration for both sediments (p = 0.031, PERMANOVA) and sponge samples (p = 0.001, PERMANOVA). Trace metal concentrations were not correlated with distance to Stone Town, highlighting the downstream effects of industrial and urban sewage on even remote reefs. Coral reef health assessment was found to be dependent on the survey method employed, which is why we recommend the combination of complementary methods

Baseline concentrations, spatial distribution and origin of trace elements in marine surface sediments of the northern Antarctic Peninsula

Increased human activity in the Antarctic Peninsula combined with accelerated melting of its glaciers highlights the importance of monitoring trace element concentrations. Surface sediment samples were collected around King George Island, Hope Bay and in the Bransfield Strait in February 2020 and were analysed by X-ray fluorescence spectroscopy and inductively coupled plasma mass spectrometry. The methods display a good correlation. Our results show clear distinctions between these regions for selected elements with high local heterogeneities. Hope Bay exhibited lower concentrations of Fe, Mn, Co, V, Zn while most stations in the Bransfield Strait and around King George Island showed moderate to significant enrichment in Cu, As and Cd. Twelve stations presented a moderate ecological risk. The consistency of our values supports a natural rather than anthropogenic origin, possibly related to volcanism and the geology of the area. However, our results suggest an increase in Cr that should be further investigated

The Molecular Biogeography of the Indo-Pacific: Testing Hypotheses With Multispecies Genetic Patterns

Aim: To test hypothesized biogeographic partitions of the tropical Indo-Pacific Ocean with phylogeographic data from 56 taxa, and to evaluate the strength and nature of barriers emerging from this test. \u3eLocation: The Indo-Pacific Ocean. Time Period: Pliocene through the Holocene. Major Taxa Studied: Fifty-six marine species. Methods: We tested eight biogeographic hypotheses for partitioning of the Indo-Pacific using a novel modification to analysis of molecular variance. Putative barriers to gene flow emerging from this analysis were evaluated for pairwise ΦST, and these ΦST distributions were compared to distributions from randomized datasets and simple coalescent simulations of vicariance arising from the Last Glacial Maximum. We then weighed the relative contribution of distance versus environmental or geographic barriers to pairwise ΦST with a distance-based redundancy analysis (dbRDA). Results: We observed a diversity of outcomes, although the majority of species fit a few broad biogeographic regions. Repeated coalescent simulation of a simple vicariance model yielded a wide distribution of pairwise ΦST that was very similar to empirical distributions observed across five putative barriers to gene flow. Three of these barriers had median ΦST that were significantly larger than random expectation. Only 21 of 52 species analysed with dbRDA rejected the null model. Among these, 15 had overwater distance as a significant predictor of pairwise ΦST, while 11 were significant for geographic or environmental barriers other than distance. Main Conclusions: Although there is support for three previously described barriers, phylogeographic discordance in the Indo-Pacific Ocean indicates incongruity between processes shaping the distributions of diversity at the species and population levels. Among the many possible causes of this incongruity, genetic drift provides the most compelling explanation: given massive effective population sizes of Indo-Pacific species, even hard vicariance for tens of thousands of years can yield ΦST values that range from 0 to nearly 0.5

Identifying Fishes through DNA Barcodes and Microarrays

Background: International fish trade reached an import value of 62.8 billion Euro in 2006, of which 44.6% are covered by the European Union. Species identification is a key problem throughout the life cycle of fishes: from eggs and larvae to adults in fisheries research and control, as well as processed fish products in consumer protection. Methodology/Principal Findings: This study aims to evaluate the applicability of the three mitochondrial genes 16S rRNA (16S), cytochrome b (cyt b), and cytochrome oxidase subunit I (COI) for the identification of 50 European marine fish species by combining techniques of ‘‘DNA barcoding’’ and microarrays. In a DNA barcoding approach, neighbour Joining (NJ) phylogenetic trees of 369 16S, 212 cyt b, and 447 COI sequences indicated that cyt b and COI are suitable for unambiguous identification, whereas 16S failed to discriminate closely related flatfish and gurnard species. In course of probe design for DNA microarray development, each of the markers yielded a high number of potentially species-specific probes in silico, although many of them were rejected based on microarray hybridisation experiments. None of the markers provided probes to discriminate the sibling flatfish and gurnard species. However, since 16S-probes were less negatively influenced by the ‘‘position of label’’ effect and showed the lowest rejection rate and the highest mean signal intensity, 16S is more suitable for DNA microarray probe design than cty b and COI. The large portion of rejected COI-probes after hybridisation experiments (.90%) renders the DNA barcoding marker as rather unsuitable for this high-throughput technology. Conclusions/Significance: Based on these data, a DNA microarray containing 64 functional oligonucleotide probes for the identification of 30 out of the 50 fish species investigated was developed. It represents the next step towards an automated and easy-to-handle method to identify fish, ichthyoplankton, and fish products

The molecular biogeography of the Indo‐Pacific: Testing hypotheses with multispecies genetic patterns

Aim: To test hypothesized biogeographic partitions of the tropical Indo‐Pacific Ocean with phylogeographic data from 56 taxa, and to evaluate the strength and nature of barriers emerging from this test. Location: The Indo‐Pacific Ocean. Time period: Pliocene through the Holocene. Major taxa studied: Fifty‐six marine species. Methods: We tested eight biogeographic hypotheses for partitioning of the Indo‐ Pacific using a novel modification to analysis of molecular variance. Putative barriers to gene flow emerging from this analysis were evaluated for pairwise ΦST, and these ΦST distributions were compared to distributions from randomized datasets and simple coalescent simulations of vicariance arising from the Last Glacial Maximum. We then weighed the relative contribution of distance versus environmental or geographic barriers to pairwise ΦST with a distance‐based redundancy analysis (dbRDA). Results: We observed a diversity of outcomes, although the majority of species fit a few broad biogeographic regions. Repeated coalescent simulation of a simple vicariance model yielded a wide distribution of pairwise ΦST that was very similar to empirical distributions observed across five putative barriers to gene flow. Three of these barriers had median ΦST that were significantly larger than random expectation. Only 21 of 52 species analysed with dbRDA rejected the null model. Among these, 15 had overwater distance as a significant predictor of pairwise ΦST, while 11 were significant for geographic or environmental barriers other than distance. Main conclusions: Although there is support for three previously described barriers, phylogeographic discordance in the Indo‐Pacific Ocean indicates incongruity between processes shaping the distributions of diversity at the species and population levels. Among the many possible causes of this incongruity, genetic drift provides the most compelling explanation: given massive effective population sizes of Indo‐Pacific species, even hard vicariance for tens of thousands of years can yield ΦST values that range from 0 to nearly 0.5

Inter-rater reliability of categorical versus continuous scoring of fish vitality: does it affect the utility of the reflex action mortality predictor (RAMP) approach?

Scoring reflex responsiveness and injury of aquatic organisms has gained popularity as predictors of discard survival. Given this method relies upon the individual interpretation of scoring criteria, an evaluation of its robustness is done here to test whether protocol-instructed, multiple raters with diverse backgrounds (research scientist, technician, and student) are able to produce similar or the same reflex and injury score for one of the same flatfish (European plaice, Pleuronectes platessa) after experiencing commercial fishing stressors. Inter-rater reliability for three raters was assessed by using a 3-point categorical scale (‘absent’, ‘weak’, ‘strong’) and a tagged visual analogue continuous scale (tVAS, a 10 cm bar split in three labelled sections: 0 for ‘absent’, ‘weak’, ‘moderate’, and ‘strong’) for six reflex responses, and a 4-point scale for four injury types. Plaice (n = 304) were sampled from 17 research beam-trawl deployments during four trips. Fleiss kappa (categorical scores) and intra-class correlation coefficients (ICC, continuous scores) indicated variable inter-rater agreement by reflex type (ranging between 0.55 and 0.88, and 67% and 91% for Fleiss kappa and ICC, respectively), with least agreement among raters on extent of injury (Fleiss kappa between 0.08 and 0.27). Despite differences among raters, which did not significantly influence the relationship between impairment and predicted survival, combining categorical reflex and injury scores always produced a close relationship of such vitality indices and observed delayed mortality. The use of the continuous scale did not improve fit of these models compared with using the reflex impairment index based on categorical scores. Given these findings, we recommend using a 3-point categorical over a continuous scale. We also determined that training rather than experience of raters minimised inter-rater differences. Our results suggest that cost-efficient reflex impairment and injury scoring may be considered a robust technique to evaluate lethal stress and damage of this flatfish species on-board commercial beam-trawl vessels

Ökologie, genetische Populationsstruktur und molekulare Phylogenie von Fischen der Korallenriffe im Golf von Aqaba und nördlichen Roten Meer

Aim of this thesis is the study of biogeography and ecology, genetic population structure, and molecular phylogeny of fishes on coral reefs in the Gulf of Aqaba and northern Red Sea. Ecological and genetic pattern are compared on different spatial scales and molecular markers add a temporal scale to study of evolutionary processes.Biogeographic analysis supported the differentiation of the Arabian sub-province from the Indian Ocean, but the affiliation of the Arabian Gulf is not clear.The analysis of the genetic population structure based on the mtDNA control region revealed homogenity between populations of Pterois miles in the Gulf of Aqaba and northern Red Sea and indicate high levels of gene flow.Investigations on interrupted gene flow in the evolutionary history of lionfishes (Scorpaenidae) revealed a differentiation between the Indian Ocean and Western Pacific. Phylogenetic analysis of cyt b and 16S rDNA sequences of the siblings P. miles and P. volitans suggest a divergence time of 2.4-8.3 million years. This coincide with tectonic events and sea level changes in Southeast Asia during the glacial maxima. Additionally, this genetic study gave indications for taxonomic revision of the genera Pterois and Dendrochirus.Ecological studies on the shore fishes off the Jordanian coast showed that fish species richness was positively correlated with hard substrate cover and benthic diversity. Abundance of corallivores was positively linked to live coral cover. The multivariate analysis of the fish community has revealed several associations of fishes in different habitats, such as deep and shallow reef slope.The northern tip of the Gulf of Aqaba and its western shores are particularly subject to human disturbances. Fish abundance at an industrial site was 50% lower than on an undisturbed reef and the trophic community structure was different

Ecology, genetic population structure, and molecular phylogeny of fishes on coral reefs in the Gulf of Aqaba and northern Red Sea

Aim of this thesis is the study of biogeography and ecology, genetic population structure, and molecular phylogeny of fishes on coral reefs in the Gulf of Aqaba and northern Red Sea. Ecological and genetic pattern are compared on different spatial scales and molecular markers add a temporal scale to study of evolutionary processes.Biogeographic analysis supported the differentiation of the Arabian sub-province from the Indian Ocean, but the affiliation of the Arabian Gulf is not clear.The analysis of the genetic population structure based on the mtDNA control region revealed homogenity between populations of Pterois miles in the Gulf of Aqaba and northern Red Sea and indicate high levels of gene flow.Investigations on interrupted gene flow in the evolutionary history of lionfishes (Scorpaenidae) revealed a differentiation between the Indian Ocean and Western Pacific. Phylogenetic analysis of cyt b and 16S rDNA sequences of the siblings P. miles and P. volitans suggest a divergence time of 2.4-8.3 million years. This coincide with tectonic events and sea level changes in Southeast Asia during the glacial maxima. Additionally, this genetic study gave indications for taxonomic revision of the genera Pterois and Dendrochirus.Ecological studies on the shore fishes off the Jordanian coast showed that fish species richness was positively correlated with hard substrate cover and benthic diversity. Abundance of corallivores was positively linked to live coral cover. The multivariate analysis of the fish community has revealed several associations of fishes in different habitats, such as deep and shallow reef slope.The northern tip of the Gulf of Aqaba and its western shores are particularly subject to human disturbances. Fish abundance at an industrial site was 50% lower than on an undisturbed reef and the trophic community structure was different