Observation of a coral-dwelling gall crab (Cryptochiridae) in a dead coral host highlights their vulnerability to reef degradation

Coral-associated fauna contributes greatly to coral reef biodiversity. Many species are obligately associated with their hosts on which they depend for food and/or refuge from predators. Their close relationship with their hosts makes them vulnerable to coral mortality. Here I report a coral-dwelling gall crab (Cryptochiridae) inhabiting a partially dead Echinopora Lamarck, 1816 coral, at Magoodhoo Island, Faafu Atoll, Maldives. Cryptochirids are thought to feed off the mucus provided by their coral host, although some questions about their feeding biology remain. This observation highlights that these crabs remain associated with a dead host, even if it can no longer provide nutrients. The strong host association makes gall crabs vulnerable to widespread habitat degradation

<i>Lithoscaptus aquarius</i> sp. nov. (Decapoda: Cryptochiridae) described from a <i>Catalaphyllia jardinei</i> (Scleractinia) out of the aquarium trade

A new species of gall crab collected from elegance coral, Catalaphyllia jardinei, is described in this paper. The male holotype was collected from a reef tank in Germany in 2016, and it is described here using integrative taxonomy. This species, named Lithoscaptus aquarius sp. nov., is the thirteenth assigned to the genus. It is morphologically and phylogenetically closest to Lithoscaptus semperi, a cryptochirid associated with Trachyphyllia geoffroyi. Like L. semperi, it has a large, broad W-shaped depression on the anterior half of the carapace, but the carapace surface of L. aquarius sp. nov. is smooth overall, lacking spines or tubercles. This new species is so named because it was found in a reef tank after searching in vain for material during fieldwork campaigns over the course of several years

Phylomitogenomics elucidates the evolution of symbiosis in Thoracotremata (Decapoda: Cryptochiridae, Pinnotheridae, Varunidae)

BackgroundThoracotremata belong to the large group of “true” crabs (infraorder Brachyura), and they exhibit a wide range of physiological and morphological adaptations to living in terrestrial, freshwater and marine habitats. Moreover, the clade comprises various symbiotic taxa (Aphanodactylidae, Cryptochiridae, Pinnotheridae, some Varunidae) that are specialised in living with invertebrate hosts, but the evolutionary history of these symbiotic crabs is still partially unresolved.MethodsHere we assembled and characterised the complete mitochondrial genomes (hereafter mitogenomes) of three gall crab species (Cryptochiridae): Kroppcarcinus siderastreicola, Opecarcinus hypostegus and Troglocarcinus corallicola. A phylogenetic tree of the Thoracotremata was reconstructed using 13 protein-coding genes and two ribosomal RNA genes retrieved from three new gall crab mitogenomes and a further 72 available thoracotreme mitogenomes. Furthermore, we applied a comparative analysis to characterise mitochondrial gene order arrangement, and performed a selection analysis to test for selective pressure of the protein-coding genes in symbiotic Cryptochiridae, Pinnotheridae, and Varunidae (Asthenognathus inaequipes and Tritodynamia horvathi).ResultsThe results of the phylogenetic reconstruction confirm the monophyly of Cryptochiridae, which clustered separately from the Pinnotheridae. The latter clustered at the base of the tree with robust branch values. The symbiotic varunids A. inaequipes and T. horvathi clustered together in a clade with free-living Varunidae species, highlighting that symbiosis in the Thoracotremata evolved independently on multiple occasions. Different gene orders were detected in symbionts and free-living species when compared with the ancestral brachyuran gene order. Lastly, the selective pressure analysis detected two positively selected sites in the nad6 gene of Cryptochiridae, but the evidence for positive selection in Pinnotheridae and A. inaequipes and T. horvathi was weak. Adaptive evolution of mitochondrial protein-coding genes is perhaps related to the presumably higher energetic demands of a symbiotic lifestyle.<br/

Conservation of Coral-Associated Fauna

Coral reefs are some of the most biodiverse ecosystems harboring thousands of species, many of them symbionts that play important roles in the survival of their hosts. These associated taxa, mostly invertebrates, remain largely unstudied and the conservation status of the majority of these species is not assessed. With coral reefs under severe global and local threats, effective conservation measures based on a whole ecosystem approach are needed. The IUCN Red List is the most up to date inventory of species’ conservation status, yet does not include symbiont fauna of important host organisms. Here we suggest including associated taxa in future endangerment assessments, especially those living in obligate symbiosis

DNA barcoding, dwelling morphology, and fecundity of the gall-forming shrimp <i>Paratypton siebenrocki</i> Balss, 1914 (Caridea: Palaemonidae)

Tropical coral reefs offer a wide variety of habitats to countless invertebrate species. Sessile host organisms especially are inhabited by small taxa, of which decapod crustaceans form one of the most diverse communities. Symbiotic palaemonid shrimp species associ-ate with marine invertebrate hosts from multiple phyla, including cnidarians such as stony corals (Scleractinia). The intriguing gall- forming shrimp Paratypton siebenrocki, a symbiont of Acropora corals in the Indo-Pacific, was collected in the Saudi Arabian Red Sea, Kenya, and the Maldives. Based on morphology P. siebenrocki has been considered to be most closely related to the genera Anapontonia and Metapontonia; however, no clear clustering with either palaemonid genus was observed in a phylogenetic recon-struction based on 16S and COI mtDNA. Here we photo-document the dwellings of P. siebenrocki in Acropora spp. for the first time, and furthermore we report on the reproductive output of this species. The number of eggs ranged from 345 to 909 (n = 6), and embryo volume differed strongly between early- and late-stage embryos. The carapace length ranged from 2.58 to 4.55 mm for the females and 1.51 to 2.5 mm for the males (n = 5). The number and size of the embryos, combined with their specialised, secluded lifestyle, sug-gest that P. siebenrocki allocates highe

Genomic survey sequencing and complete mitochondrial genome of the elkhorn coral crab Domecia acanthophora (Desbonne in Desbonne &amp; Schramm, 1867) (Decapoda: Brachyura: Domeciidae)

The elkhorn coral crab Domecia acanthophora inhabits shallow-water coral reefs in the Western Atlantic. The species has a wide distribution and, although primarily associated with endangered Acropora corals, has been recorded from a myriad of hosts. Here we conducted the first genomic survey and complete mitochondrial assemblage and characterisation of any species of Domeciidae, as well as the first species within Trapezioidea. The estimated size of the nuclear genome ranged from 0.64 Gbp to 1.76 Gbp, revealing a small genome. Repetitive elements of the genome were estimated here at 66.4% and 74%, respectively, with the majority of the repetitive elements consisting of LINE, LTR, and satellite DNA. The assembled A-T rich mitochondrial genome consisted of 15,568 bp in length, with 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes and two ribosomal RNA (rRNA) genes. A 619 bp long non-coding region was identified as the supposed D-loop/control region, containing eight microsatellites. The 22 tRNA genes, ranging from 65 to 71 bp in length, displayed a typical “cloverleaf” secondary structure, with the exception of tRNA-Ser1 which lacked part of the DHU arm and tRNA-Asp displayed a deletion of the TΨC loop but not the arm. Two transposition events of two tRNA genes were also found when comparing the gene order of D. acanthophora to that of the brachyuran basic gene order, which had not been reported before. Despite belonging to a widely distributed, well-known superfamily of coral-associated crabs, the Trapezioidea, very little was known about this species from a genetics perspective, which is remedied here by providing a new genomic resource for D. acanthophora

Diversification and distribution of gall crabs (Brachyura: Cryptochiridae: <i>Opecarcinus</i>) associated with Agariciidae corals

Coral reefs are home to the greatest diversity of marine life, and many species on reefs live in symbiotic associations. Studying the historical biogeography of symbiotic species is key to unravelling (potential) coevolutionary processes and explaining species richness patterns. Coral-dwelling gall crabs (Cryptochiridae) live in obligate symbiosis with a scleractinian host, and are ideally suited to study the evolutionary history between heterogeneous taxa involved in a symbiotic relationship. The genus Opecarcinus Kropp and Manning, 1987, like its host coral family Agariciidae, occurs in both Indo-Pacific and Caribbean seas, and is the only cryptochirid genus with a circumtropical distribution. Here, we use mitochondrial and nuclear DNA gene fragments of Opecarcinus specimens sampled from 21 Indo-Pacific localities and one Atlantic (Caribbean) locality. We applied several species delimitation tests to characterise species diversity, inferred a Bayesian molecular-clock time-calibrated phylogeny to estimate divergence times and performed an ancestral area reconstruction. Time to the most recent common ancestor (tMRCA) of Opecarcinus is estimated at 15−6 Mya (middle Miocene—late Miocene). The genus harbours ~ 15 undescribed species as well as several potential species complexes. There are indications of strict host-specificity patterns in certain Opecarcinus species in the Indo-Pacific and Atlantic, however, a robust phylogeny reconstruction of Agariciidae corals—needed to test this further—is currently lacking. The Indo-West Pacific was inferred to be the most probable ancestral area, from where the Opecarcinus lineage colonised the Western Atlantic and subsequently speciated into O. hypostegus. Opecarcinus likely invaded from the Indo-West Pacific across the East Pacific Barrier to the Atlantic, before the full closure of the Isthmus of Panama. The subsequent speciation of O. hypostegus, is possibly associated with newly available niches in the Caribbean, in combination with genetic isolation following the closure of the Panama Isthmus

Host use of the elkhorn coral crab <i>Domecia acanthophora</i> (Brachyura : Domeciidae), with a phylogeny of the genus

Coral-dwelling crabs form a diverse community on coral reefs, and various families independently colonised scleractinian corals. Species of Domecia have a circumtropical distribution, with two known species in the Indo-Pacific, one in the West Atlantic and one in the East Atlantic. New host records for the West Atlantic species D. acanthophora are recorded from Guadeloupe, as well as the first dwellings in Acropora prolifera from Curaçao. Here we provide an overview of all known hosts of Domecia species and, based on COI mtDNA, the first phylogeny of the genus. The coral Orbicella faveolata and the sponge Callyspongia sp. are recorded as new hosts for D. acanthophora. Host records for this species now include eight scleractinian hosts, Millepora fire corals and records on sponges. Our phylogenetic reconstruction shows that D. acanthophora is closest to the wide-ranging Indo-Pacific species D. hispida, and more distantly related to D. glabra. Domecia acanthophora appears to be less host specific than its congeners D. hispida and D. glabra that predominantly associate with Pocillopora and Acropora corals, respectively. Differences in host-specificity between Indo-Pacific and Atlantic species are briefly discussed in the light of similar observations on other coral-dwelling crab species

Integrating a UAV-derived DEM in object-based image analysis increases habitat classification accuracy on coral reefs

Very shallow coral reefs (<5 m deep) are naturally exposed to strong sea surface temperature variations, UV radiation and other stressors exacerbated by climate change, raising great concern over their future. As such, accurate and ecologically informative coral reef maps are fundamental for their management and conservation. Since traditional mapping and monitoring methods fall short in very shallow habitats, shallow reefs are increasingly mapped with Unmanned Aerial Vehicles (UAVs). UAV imagery is commonly processed with Structure-from-Motion (SfM) to create orthomosaics and Digital Elevation Models (DEMs) spanning several hundred metres. Techniques to convert these SfM products into ecologically relevant habitat maps are still relatively underdeveloped. Here, we demonstrate that incorporating geomorphometric variables (derived from the DEM) in addition to spectral information (derived from the orthomosaic) can greatly enhance the accuracy of automatic habitat classification. Therefore, we mapped three very shallow reef areas off KAUST on the Saudi Arabian Red Sea coast with an RTK-ready UAV. Imagery was processed with SfM and classified through object-based image analysis (OBIA). Within our OBIA workflow, we observed overall accuracy increases of up to 11% when training a Random Forest classifier on both spectral and geomorphometric variables as opposed to traditional methods that only use spectral information. Our work highlights the potential of incorporating a UAV’s DEM in OBIA for benthic habitat mapping, a promising but still scarcely exploited asset