Mangrove prop roots support diverse epibiont communities, but they are generally regarded as inhospitable for corals. However, recent reports have documented corals thriving on mangrove roots in the U.S. Virgin Islands and Cuba, and it has been proposed that mangroves may provide a refuge from environmental conditions that trigger coral mortality on nearby reefs. It also raises interesting questions about the potential evolutionary significance of coral populations in mangrove forest. We investigated diverse mangrove habitats for the presence of corals at Calabash Caye, Belize, part of a recently designated marine reserve on Turneffe Atoll. Here we present data on the distribution, size and morphology of 127 colonies of branching Porites found in a survey of 1858 meters of mangrove prop roots fringing three qualitatively distinct bodies of water: a high-flow channel, a moderate-flow creek, and a low-flow mangrove pond. The distribution of Porites was highly clumped, with 108 colonies occurring in a 178-meter stretch of shoreline along the high flow channel. Colony morphology varied widely, from bushy colonies with more than 40 branch tips per 1000 cm3 of ecological volume, to spindly colonies with fewer than 10 branch tips per 1000 cm3, to new recruits that have not yet developed distinct branches. Comparisons of the same coral-bearing roots in 2013 and 2014 revealed that colonies can experience substantial growth in a year’s time. We also document a much more diverse coral fauna living in the mangroves at Crooked Creek, a high flow environment on the western edge of Turneffe Atoll. The data described here contribute to an emerging picture of mangroves as potentially important habitat for corals, while suggesting that different types of mangrove habitat vary in their suitability for different species of coral. Future studies are needed to identify the critical environmental features of mangrove habitats that support coral, to further characterize those corals that can utilize mangrove habitat, and to investigate potential connectivity between coral populations in mangroves and nearby reef habitats.

Exon capture across species has been one of the most broadly applied approaches to acquire multi-locus data in phylogenomic studies of non-model organisms. Methods for assembling loci from short-read sequences (eg, Illumina platforms) that rely on mapping reads to a reference genome may not be suitable for studies comprising species across a wide phylogenetic spectrum; thus, de novo assembling methods are more generally applied. Current approaches for assembling targeted exons from short reads are not particularly optimized as they cannot (1) assemble loci with low read depth, (2) handle large files efficiently, and (3) reliably address issues with paralogs. Thus, we present Assexon: a streamlined pipeline that de novo assembles targeted exons and their flanking sequences from raw reads. We tested our method using reads from Lepisosteus osseus (4.37 Gb) and Boleophthalmus pectinirostris (2.43 Gb), which are captured using baits that were designed based on genome sequence of Lepisosteus oculatus and Oreochromis niloticus, respectively. We compared performance of Assexon to PHYLUCE and HybPiper, which are commonly used pipelines to assemble ultra-conserved element (UCE) and Hyb-seq data. A custom exon capture analysis pipeline (CP) developed by Yuan et al was compared as well. Assexon accurately assembled more than 3400 to 3800 (20%-28%) loci than PHYLUCE and more than 1900 to 2300 (8%-14%) loci than HybPiper across different levels of phylogenetic divergence. Assexon ran at least twice as fast as PHYLUCE and HybPiper. Number of loci assembled using CP was comparable with Assexon in both tests, while Assexon ran at least 7 times faster than CP. In addition, some steps of CP require the user’s interaction and are not fully automated, and this user time was not counted in our calculation. Both Assexon and CP retrieved no paralogs in the testing runs, but PHYLUCE and Hybpiper did. In conclusion, Assexon is a tool for accurate and efficient assembling of large read sets from exon capture experiments. Furthermore, Assexon includes scripts to filter poorly aligned coding regions and flanking regions, calculate summary statistics of loci, and select loci with reliable phylogenetic signal. Assexon is available at https://github.com/yhadevol/Assexon .

Mangrove prop roots support diverse epibiont communities, but they are generally regarded as inhospitable for corals. However, recent reports have documented corals thriving on mangrove roots in the U.S. Virgin Islands and Cuba, and it has been proposed that mangroves may provide a refuge from environmental conditions that trigger coral mortality on nearby reefs. It also raises interesting questions about the potential evolutionary significance of coral populations in mangrove forest. We investigated diverse

Al Wajh Bank in the northern Red Sea contains an extensive coral reef system that potentially supports a novel fish community. The large (1500km2) and shallow (< 40m depth) lagoon experiences greater temperature and salinity fluctuations, as well as higher turbidity, than most other Red Sea reefs. Since these conditions often influence coral community structure and introduce physiological challenges to its resident organisms, changes in reef-associated fishes are expected. We present critical baseline data on fish biodiversity and benthic composition for the Al Wajh Bank. Underwater visual census of conspicuous fishes and standardized collections of cryptobenthic fishes were combined to provide a comprehensive assessment of these fish communities. We documented 153 fish species and operational taxonomic units, including undescribed species, within 24 families on reefs largely dominated by hard coral and soft sediment (39% and 32% respectively). The families Pomacentridae and Gobiidae contributed the most towards fish diversity and abundance. Bray-Curtis dissimilarity distances among sampled sites suggest a distinctive fish community within the lagoon, and coefficients of variation for each species show high variation in their distribution across the lagoon. Species accumulation curves predict that additional sampling would document many more species throughout Al Wajh. Our findings provide the most extensive biodiversity survey of fishes from this region to date and record the condition of the reef prior to major coastal development planned to occur in the near future.