Tropical ectotherms are hypothesized to be vulnerable to environmental changes, but cascading effects of organismal tolerances on the assembly and functioning of reef fish communities are largely ...unknown. Here, we examine differences in organismal traits, assemblage structure, and productivity of cryptobenthic reef fishes between the world's hottest, most extreme coral reefs in the southern Arabian Gulf and the nearby, but more environmentally benign, Gulf of Oman. We show that assemblages in the Arabian Gulf are half as diverse and less than 25% as abundant as in the Gulf of Oman, despite comparable benthic composition and live coral cover. This pattern appears to be driven by energetic deficiencies caused by responses to environmental extremes and distinct prey resource availability rather than absolute thermal tolerances. As a consequence, production, transfer, and replenishment of biomass through cryptobenthic fish assemblages is greatly reduced on Earth's hottest coral reefs. Extreme environmental conditions, as predicted for the end of the 21st century, could thus disrupt the community structure and productivity of a critical functional group, independent of live coral loss.
The wave of new global conservation targets, the conclusion of the High Seas Treaty negotiations, and the expansion of extractive use into the deep sea call for a paradigm shift in ocean ...conservation. The current reductionist 2D representation of the ocean to set targets and measure impacts will fail at achieving effective biodiversity conservation. Here, we develop a framework that overlays depth realms onto marine ecoregions to conduct the first three-dimensional spatial analysis of global marine conservation achievements and fisheries footprint. Our novel approach reveals conservation gaps of mesophotic, rariphotic, and abyssal depths and an underrepresentation of high protection levels across all depths. In contrast, the 3D footprint of fisheries covers all depths, with benthic fishing occurring down to the lower bathyal and mesopelagic fishing peaking in areas overlying abyssal depths. Additionally, conservation efforts are biased towards areas where the lowest fishing pressures occur, compromising the effectiveness of the marine conservation network. These spatial mismatches emphasize the need to shift towards 3D thinking to achieve ocean sustainability.
How coral reefs survive as oases of life in low-productivity oceans has puzzled scientists for centuries. The answer may lie in internal nutrient cycling and/or input from the pelagic zone. ...Integrating meta-analysis, field data, and population modeling, we show that the ocean's smallest vertebrates, cryptobenthic reef fishes, promote internal reef fish biomass production through extensive larval supply from the pelagic environment. Specifically, cryptobenthics account for two-thirds of reef fish larvae in the near-reef pelagic zone despite limited adult reproductive outputs. This overwhelming abundance of cryptobenthic larvae fuels reef trophodynamics via rapid growth and extreme mortality, producing almost 60% of consumed reef fish biomass. Although cryptobenthics are often overlooked, their distinctive demographic dynamics may make them a cornerstone of ecosystem functioning on modern coral reefs.
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•Dwarfgobies are a diverse group of cryptobenthic reef fishes diversifying within the Coral Triangle.•We study the pattern and timing of speciation in two clades of dwarfgobies using ...time-calibrated phylogenies.•Rapid speciation occurred at small geographic scales within the CT during the Pleistocene.•Speciation occurred in allopatry and sympatry, in some cases associated with niche partitioning and assortative mating.•The number of endemic species and the overall species-richness in the Coral Triangle is likely severely underestimated.
The Coral Triangle is widely regarded as the richest marine biodiversity hot-spot in the world. One factor that has been proposed to explain elevated species-richness within the Coral Triangle is a high rate of in situ speciation within the region itself. Dwarfgobies (Gobiidae: Eviota) are a diverse genus of diminutive cryptobenthic reef fishes with limited dispersal ability, and life histories and ecologies that increase potential for speciation. We use molecular phylogenetic and biogeographic data from two clades of Eviota species to examine patterns, processes and timing associated with species origination within the Coral Triangle. Sequence data from mitochondrial and nuclear DNA were used to generate molecular phylogenies and median-joining haplotype networks for the genus Eviota, with emphasis on the E. nigriventris and E. bifasciata complexes – two species groups with distributions centered in the Coral Triangle. The E. nigriventris and E. bifasciata complexes both contain multiple genetically distinct, geographically restricted color morphs indicative of recently-diverged species originating within the Coral Triangle. Relaxed molecular-clock dating estimates indicate that most speciation events occurred within the Pleistocene, and the geographic pattern of genetic breaks between species corresponds well with similar breaks in other marine fishes and sessile invertebrates. Regional isolation due to sea-level fluctuations may explain some speciation events in these species groups, yet other species formed with no evidence of physical isolation. The timing of diversification events and present day distributions of Eviota species within the Coral Triangle suggest that both allopatric speciation (driven by ephemeral and/or ‘soft’ physical barriers to gene flow) and sympatric speciation (driven by niche partitioning and assortative mating) may be driving diversification at local scales within the Coral Triangle. The presence of multiple young, highly-endemic cryptic species of Eviota within the Coral Triangle suggests that (i) the Coral Triangle is indeed a “cradle” of reef fish biodiversity and that (ii) our current approximations of reef fish diversity in the region may be significantly underestimated.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK
A new species of deep-reef fish in the goby genus Palatogobius is described from recent submersible collections off Curaçao and Dominica. Video footage of schools of this species reveal predation by ...the invasive Indo-Pacific lionfish (Pterois spp.), the first record of undescribed fauna potentially being eaten by lionfish outside of its native range. We present molecular phylogenetic data for all valid species of Palatogobius and related genera, as well as a taxonomic key to the species of Palatogobius and a generic key to Palatogobius and related genera in the western Atlantic. Lastly, we discuss ecological and behavioral aspects of some deep-reef fishes in light of potential threats from invasive lionfish.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Cryptobenthic reef fishes (CRF) are an important component of coral reef communities that are often overlooked, as their cryptic nature and very small size make them difficult to assess using visual ...methods. The prevailing method for quantifying communities of CRF is to use enclosures and anesthetics to collect fishes from within the reef. Environmental DNA (eDNA) sampling of water around reefs may be an alternative or supplemental way to quantify CRF communities. Here, we compare the ability to characterize CRF communities using eDNA sequences from water samples collected from within the interstices of the reef, with corresponding anesthetic stations from the same microhabitat. A total of 676 CRF from 33 species were collected from anesthetic stations, whereas only four species of CRF were detected from the eDNA samples taken at the same locations. Main factors contributing to these results may have been: (1) low standing biomass of CRF, thus low abundance of detectable DNA in the eDNA water samples; (2) large number of non-targeted metazoan reads that “drowned” the detections of specific CRF sequences; and (3) lack of sequences available in public databases that represent the high level of endemism present in CRF and a need for more complete taxonomic inventory.
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EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
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.
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IZUM, KILJ, NUK, PILJ, PNG, SAZU, UL, UM, UPUK
For decades, age‐structured stock assessments have been a key component to managing fishery resources worldwide. Fisheries management systems have been under increasing demand to generate a greater ...volume and quality of age estimates. Traditional aging techniques, which require physical preparation followed by microscopic examination of fish otoliths, are labor‐intensive, expensive, and inherently subjective among individual analysts, making repeatability and precision a challenge. Here we investigated an innovative approach to aging fish from their otoliths using Fourier‐transformed near‐infrared spectroscopy and partial least squares regression models. Models were fit to and validated on spectra and used to microscopically estimate ages of Pacific cod from three years of fishery‐independent otolith data out of the Bering sea. Calibrated and validated models for each year, as well as on an ensemble of the three years, yielded high precision for the multiyear model (R2 = 0.869, RMSE = 0.614, PA = 63%, CV = 7.412), and independent year models (R2 = 0.844–0.891, RMSE = 0.555–0.615, PA = 65%, CV = 6.313–6.775). These metrics of model performance were highly comparable to precision from the traditional microscopic aging approach (R2 = 0.763–0.869, RMSE = 0.639–0.737, PA = 63%–70%, CV = 5.671–6.698). In all cases, a two‐sided Kolmogorov–Smirnov test showed no significant difference between reference and model estimated age distributions. Our results illustrate how Fourier‐transformed near‐infrared spectroscopy can be utilized on otoliths to predict age estimates with substantially greater efficiency, good precision, high repeatability, and no loss in data integrity compared to the traditional microscopic method for aging Pacific cod.
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FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SAZU, SBCE, SBMB, UL, UM, UPUK
The
Eviota zebrina
complex includes eight species of closely-related dwarfgobies, four of which are herein described as new. The complex is named for
Eviota zebrina
Lachner & Karnella, 1978, an ...Indian Ocean species with the holotype from the Seychelles Islands and also known from the Maldives, which was once thought to range into the Gulf of Aqaba and the Red Sea eastward to the Great Barrier Reef of Australia. Our analysis supports the recognition of four genetically distinct, geographically non-overlapping, species within what was previously called
E. zebrina
, with
E. zebrina
being restricted to the Indian Ocean,
E. marerubrum
sp. nov.
described from the Red Sea,
E. longirostris
sp. nov.
described from western New Guinea, and
E. pseudozebrina
sp. nov.
described from Fiji. The caudal fin of all four of these species is crossed by oblique black bars in preservative, but these black bars are absent from the four other species included in the complex. Two of the other species within the complex,
E. tetha
and
E. gunawanae
are morphologically similar to each other in having the AITO cephalic-sensory pore positioned far forward and opening anteriorly.
Eviota tetha
is known from lagoonal environments in Cenderawasih Bay and Raja Ampat, West Papua, and
E. gunawanae
is known only from deeper reefs (35–60 m) from Fakfak Regency, West Papua. The final two species are
E. cometa
which is known from Fiji and Tonga and possesses red bars crossing the caudal fin (but lost in preservative) and a 9/8 dorsal/anal-fin formula, and
E. oculineata
sp. nov.
, which is described as new from New Guinea and the Solomon Islands, and possesses an 8/7 dorsal/anal-fin formula and lacks red caudal bars.
Eviota oculineata
has been confused with
E. cometa
in the past.
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IZUM, KILJ, NUK, PILJ, PNG, SAZU, UL, UM, UPUK
Understanding the diversity and ecology of deep-reef fishes is challenging. Due to intensive and widely dispersed sampling, the Greater Caribbean (GC) fauna of species found on shallow reefs is much ...better characterized than the fauna of deep-reef species restricted to mesophotic (40–130 m) and rariphotic (130–300 m) depths. Our knowledge about deep-reef fishes is based on ship-board sampling and the recent use of rebreather diving, remotely operated vehicles (ROVs), baited remote underwater videos, and crewed submersibles. Submersible research on GC deep-reef fishes began in the 1960s and has flourished over the last decade through research by the Smithsonian Institution’s Deep Reef Observation Project (DROP). Here we quantify the contribution of submersible research, particularly the surge by DROP, to our understanding of the diversity of the deep-reef fish fauna of the GC. We compared shallow- and deep-reef fish faunas of three GC sites subjected to DROP research to faunas of three sites without such research. DROP increased the size of the deep faunas at three islands ∼9-fold, and they have deep-reef faunas ∼2–4 times the size of those of the other three sites. Those deep-reef faunas have high proportions of small cryptobenthic fishes, which also represent a major component of shallow faunas. That research increased the rate of discovery (collection) of new species of deep-reef fishes ∼6-fold and accounts for 31% of the deep-reef species first discovered within the GC. Substantial numbers of new species at each of the three DROP islands were not found at the other two. This indicates that other parts of the GC likely harbor many undetected deep-reef fishes, and that the size of the deep-reef fauna of the GC is significantly underestimated. These results show that small research submersibles are versatile, highly productive tools for deep-reef studies. They allow long-duration dives at any depth, while offering unparalleled views of their surroundings to study the ecology of deep-reef fishes (e.g., DROP’s definition of the rariphotic assemblage from fish depth distributions). Submersibles can efficiently collect reef fishes of a broad range of taxa, ecotypes and sizes, leading to a more comprehensive understanding of the regional GC deep-reef fish fauna.
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