Two new species of Varicus from Caribbean deep reefs, with comments on the related genus Pinnichthys (Teleostei, Gobiidae, Gobiosomatini, Nes subgroup).

Tropical deep reefs (~40-300 m) are diverse ecosystems that serve as habitats for diverse communities of reef-associated fishes. Deep-reef fish communities are taxonomically and ecologically distinct from those on shallow reefs, but like those on shallow reefs, they are home to a species-rich assemblage of small, cryptobenthic reef fishes, including many species from the family Gobiidae (gobies). Here we describe two new species of deep-reef gobies, Varicusprometheussp. nov. and V.roatanensissp. nov., that were collected using the submersible Idabel from rariphotic reefs off the island of Roatan (Honduras) in the Caribbean. The new species are the 11th and 12th species of the genus Varicus, and their placement in the genus is supported by morphological data and molecular phylogenetic analyses. Additionally, we also collected new specimens of the closely-related genus and species Pinnichthysaimoriensis during submersible collections off the islands of Bonaire and St. Eustatius (Netherland Antilles) and included them in this study to expand the current description of that species and document its range extension from Brazil into the Caribbean. Collectively, the two new species of Varicus and new records of P.aimoriensis add to our growing knowledge of cryptobenthic fish diversity on deep reefs of the Caribbean.

Historic trophic decline in New England's coastal marine ecosystem.

Overfishing is a worldwide occurrence that simplifies marine food webs, changes trophic patterns, and alters community structure, affecting not only the density of harvested species but also their trophic function. The northwestern Atlantic has a history of heavy fishing, and over the past century has also experienced destructive bottom fishing and harmful mobile fishing gear. After confirming that preservation solvent did not alter the nitrogen stable isotopes of preserved samples, we used museum specimens and modern samples to analyze nitrogen stable isotopes in tissues of two common demersal fishes pre-1950 (1850 to 1950) compared to 2021 to assess changes in trophic positions of coastal New England consumers over this time period. Both the mesopredator Centropristis striata (black sea bass) and the benthivore Stenotomus chrysops (scup) experienced significant declines in trophic position during this time. C. striata declined almost a full trophic level, S. chrysops declined half a trophic level, and these species are now occupying almost the same trophic position. Heavy fishing activities potentially shorten food chains, simplify trophic complexity, lessen the separation of trophic niches, and generally flatten food webs. The consequences of these within-species shifts are poorly investigated but could generate underappreciated cascading impacts on community structure and function. Archived natural-history collections are an invaluable resource for investigating ecological changes in natural communities through time. The evaluation of changing trophic positions via stable isotope analysis may allow fisheries managers to quantify large-scale effects of fishing on ecosystems and food webs over time.

Generic reassignment of Centropristis fuscula Poey, 1861 (Teleostei: Serranidae), with re-description of the species and comments on its geographical range and sexual system.

Centropristes fusculus Poey, 1861 historically has variously and somewhat perplexingly been assigned to Centropristis Cuvier, 1829, Prionodes Jenyns, 1840, and Serranus Cuvier, 1816. Here, we provide evidence from comparisons of morphology, ecology, and sexual systems for its inclusion in Serranus and redescribe the species based on the holotype and 60 specimens from Brazil, the Caribbean, the United States, and Uruguay. Serranus fusculus is a simultaneous hermaphrodite, a sexual system that is relevant to its generic placement. The inclusion of Serranus fusculus in the genus Serranus increases to 33 the number of currently valid Serranus species, of which two are found in the Western Indian Ocean, six in the eastern Pacific and 25 in the Atlantic Ocean (15 restricted to the western Atlantic and 10 to the eastern and Central Atlantic). An identification key to western Atlantic species of the genus is provided.

The impact of paleoclimatic changes on body size evolution in marine fishes.

Body size is an important species trait, correlating with life span, fecundity, and other ecological factors. Over Earth's geological history, climate shifts have occurred, potentially shaping body size evolution in many clades. General rules attempting to summarize body size evolution include Bergmann's rule, which states that species reach larger sizes in cooler environments and smaller sizes in warmer environments, and Cope's rule, which poses that lineages tend to increase in size over evolutionary time. Tetraodontiform fishes (including pufferfishes, boxfishes, and ocean sunfishes) provide an extraordinary clade to test these rules in ectotherms owing to their exemplary fossil record and the great disparity in body size observed among extant and fossil species. We examined Bergmann's and Cope's rules in this group by combining phylogenomic data (1,103 exon loci from 185 extant species) with 210 anatomical characters coded from both fossil and extant species. We aggregated data layers on paleoclimate and body size from the species examined, and inferred a set of time-calibrated phylogenies using tip-dating approaches for downstream comparative analyses of body size evolution by implementing models that incorporate paleoclimatic information. We found strong support for a temperature-driven model in which increasing body size over time is correlated with decreasing oceanic temperatures. On average, extant tetraodontiforms are two to three times larger than their fossil counterparts, which otherwise evolved during periods of warmer ocean temperatures. These results provide strong support for both Bergmann's and Cope's rules, trends that are less studied in marine fishes compared to terrestrial vertebrates and marine invertebrates.

Molecular phylogeny of the threadfin fishes (Polynemidae) using ultraconserved elements.

Threadfins (Teleostei: Polynemidae) are a group of fishes named for their elongated and threadlike pectoral-fin rays. These fishes are commonly found in the world's tropical and subtropical waters, and are an economically important group for people living in these regions, with more than 100,000 t harvested in recent years. However, we do not have a detailed understanding of polynemid evolutionary history such that these fishes can be monitored, managed and conserved as an important tropical food source. Recent studies hypothesize at least one genus of threadfins is polyphyletic, and no studies have focused on generating a hypothesis of relationship for the Polynemidae using DNA sequences. In this study, we analyse a genomic dataset of ultraconserved-element and mitochondrial loci to construct a phylogeny of the Polynemidae. We recover the threadfins as a clade sister to flatfishes, with the most taxonomically rich genus, Polydactylus, being resolved as polyphyletic. When comparing our dataset to data from previous studies, we find that a few recent broad-scale phylogenies of fishes have incorporated mislabelled, misidentified or chimeric terminals into their analyses, impacting the relationships of threadfins they recover. We highlight these problematic sequences, providing revised identifications based on the data sequenced in this study. We then discuss the intrarelationships of threadfins, highlighting morphological or ecological characters that support the clades we recover.

The critical role of natural history museums in advancing eDNA for biodiversity studies: a case study with Amazonian fishes.

Ichthyological surveys have traditionally been conducted using whole-specimen, capture-based sampling with varied but conventional fishing gear. Recently, environmental DNA (eDNA) metabarcoding has emerged as a complementary, and possible alternative, approach to whole-specimen methodologies. In the tropics, where much of the diversity remains undescribed, vast reaches continue unexplored, and anthropogenic activities are constant threats; there have been few eDNA attempts for ichthyological inventories. We tested the discriminatory power of eDNA using MiFish primers with existing public reference libraries and compared this with capture-based methods in two distinct ecosystems in the megadiverse Amazon basin. In our study, eDNA provided an accurate snapshot of the fishes at higher taxonomic levels and corroborated its effectiveness to detect specialized fish assemblages. Some flaws in fish metabarcoding studies are routine issues addressed in natural history museums. Thus, by expanding their archives and adopting a series of initiatives linking collection-based research, training and outreach, natural history museums can enable the effective use of eDNA to survey Earth's hotspots of biodiversity before taxa go extinct. Our project surveying poorly explored rivers and using DNA vouchered archives to build metabarcoding libraries for Neotropical fishes can serve as a model of this protocol.

Corrigenda: A new species of Chromis damselfish from the tropical western Atlantic (Teleostei, Pomacentridae). ZooKeys 1008: 107-138. https://zookeys.pensoft.net/article/58805/.

[This corrects the article DOI: 10.3897/zookeys.1008.58805.].

Phylogenomics and Historical Biogeography of Seahorses, Dragonets, Goatfishes, and Allies (Teleostei: Syngnatharia): Assessing Factors Driving Uncertainty in Biogeographic Inferences.

The charismatic trumpetfishes, goatfishes, dragonets, flying gurnards, seahorses, and pipefishes encompass a recently defined yet extraordinarily diverse clade of percomorph fishes-the series Syngnatharia. This group is widely distributed in tropical and warm-temperate regions, with a great proportion of its extant diversity occurring in the Indo-Pacific. Because most syngnatharians feature long-range dispersal capabilities, tracing their biogeographic origins is challenging. Here, we applied an integrative phylogenomic approach to elucidate the evolutionary biogeography of syngnatharians. We built upon a recently published phylogenomic study that examined ultraconserved elements by adding 62 species (total 169 species) and one family (Draconettidae), to cover ca. 25% of the species diversity and all 10 families in the group. We inferred a set of time-calibrated trees and conducted ancestral range estimations. We also examined the sensitivity of these analyses to phylogenetic uncertainty (estimated from multiple genomic subsets), area delimitation, and biogeographic models that include or exclude the jump-dispersal parameter ($j)$. Of the three factors examined, we found that the $j$ parameter has the strongest effect in ancestral range estimates, followed by number of areas defined, and tree topology and divergence times. After accounting for these uncertainties, our results reveal that syngnatharians originated in the ancient Tethys Sea ca. 87 Ma (84-94 Ma; Late Cretaceous) and subsequently occupied the Indo-Pacific. Throughout syngnatharian history, multiple independent lineages colonized the eastern Pacific (6-8 times) and the Atlantic (6-14 times) from their center of origin, with most events taking place following an east-to-west route prior to the closure of the Tethys Seaway ca. 12-18 Ma. Ultimately, our study highlights the importance of accounting for different factors generating uncertainty in macroevolutionary and biogeographic inferences.[Historical biogeography; jump-dispersal parameter; macroevolutionary uncertainty; marine fishes; syngnathiformes; ultraconserved elements].

Testing the Utility of Alternative Metrics of Branch Support to Address the Ancient Evolutionary Radiation of Tunas, Stromateoids, and Allies (Teleostei: Pelagiaria).

The use of high-throughput sequencing technologies to produce genome-scale data sets was expected to settle some long-standing controversies across the Tree of Life, particularly in areas where short branches occur at deep timescales. Instead, these data sets have often yielded many well-supported but conflicting topologies, and highly variable gene-tree distributions. A variety of branch-support metrics beyond the nonparametric bootstrap are now available to assess how robust a phylogenetic hypothesis may be, as well as new methods to quantify gene-tree discordance. We applied multiple branch-support metrics to a study of an ancient group of marine fishes (Teleostei: Pelagiaria) whose interfamilial relationships have proven difficult to resolve due to a rapid accumulation of lineages very early in its history. We analyzed hundreds of loci including published ultraconserved elements and newly generated exonic data along with their flanking regions to represent all 16 extant families for more than 150 out of 284 valid species in the group. Branch support was typically lower at inter- than intra-familial relationships regardless of the type of marker used. Several nodes that were highly supported with bootstrap had a very low site and gene-tree concordance, revealing underlying conflict. Despite this conflict, we were able to identify four consistent interfamilial clades, each comprised of two or three families. Combining exons with their flanking regions also produced increased branch lengths at the deep branches of the pelagiarian tree. Our results demonstrate the limitations of employing current metrics of branch support and species-tree estimation when assessing the confidence of ancient evolutionary radiations and emphasize the necessity to embrace alternative measurements to explore phylogenetic uncertainty and discordance in phylogenomic data sets.[Concatenation; exons; introns; phylogenomics; species-tree methods; target capture.].

Exon probe sets and bioinformatics pipelines for all levels of fish phylogenomics.

Exon markers have a long history of use in phylogenetics of ray-finned fishes, the most diverse clade of vertebrates with more than 35,000 species. As the number of published genomes increases, it has become easier to test exons and other genetic markers for signals of ancient duplication events and filter out paralogues that can mislead phylogenetic analysis. We present seven new probe sets for current target-capture phylogenomic protocols that capture 1,104 exons explicitly filtered for paralogues using gene trees. These seven probe sets span the diversity of teleost fishes, including four sets that target five hyperdiverse percomorph clades which together comprise ca. 17,000 species (Carangaria, Ovalentaria, Eupercaria, and Syngnatharia + Pelagiaria combined). We additionally included probes to capture legacy nuclear exons and mitochondrial markers that have been commonly used in fish phylogenetics (despite some exons being flagged for paralogues) to facilitate integration of old and new molecular phylogenetic matrices. We tested these probes experimentally for 56 fish species (eight species per probe set) and merged new exon-capture sequence data into an existing data matrix of 1,104 exons and 300 ray-finned fish species. We provide an optimized bioinformatics pipeline to assemble exon capture data from raw reads to alignments for downstream analysis. We show that legacy loci with known paralogues are at risk of assembling duplicated sequences with target-capture, but we also assembled many useful orthologous sequences that can be integrated with many PCR-generated matrices. These probe sets are a valuable resource for advancing fish phylogenomics because targeted exons can easily be extracted from increasingly available whole genome and transcriptome data sets, and also may be integrated with existing PCR-based exon and mitochondrial data.

Confronting Sources of Systematic Error to Resolve Historically Contentious Relationships: A Case Study Using Gadiform Fishes (Teleostei, Paracanthopterygii, Gadiformes).

Reliable estimation of phylogeny is central to avoid inaccuracy in downstream macroevolutionary inferences. However, limitations exist in the implementation of concatenated and summary coalescent approaches, and Bayesian and full coalescent inference methods may not yet be feasible for computation of phylogeny using complicated models and large data sets. Here, we explored methodological (e.g., optimality criteria, character sampling, model selection) and biological (e.g., heterotachy, branch length heterogeneity) sources of systematic error that can result in biased or incorrect parameter estimates when reconstructing phylogeny by using the gadiform fishes as a model clade. Gadiformes include some of the most economically important fishes in the world (e.g., Cods, Hakes, and Rattails). Despite many attempts, a robust higher-level phylogenetic framework was lacking due to limited character and taxonomic sampling, particularly from several species-poor families that have been recalcitrant to phylogenetic placement. We compiled the first phylogenomic data set, including 14,208 loci ($>$2.8 M bp) from 58 species representing all recognized gadiform families, to infer a time-calibrated phylogeny for the group. Data were generated with a gene-capture approach targeting coding DNA sequences from single-copy protein-coding genes. Species-tree and concatenated maximum-likelihood (ML) analyses resolved all family-level relationships within Gadiformes. While there were a few differences between topologies produced by the DNA and the amino acid data sets, most of the historically unresolved relationships among gadiform lineages were consistently well resolved with high support in our analyses regardless of the methodological and biological approaches used. However, at deeper levels, we observed inconsistency in branch support estimates between bootstrap and gene and site coefficient factors (gCF, sCF). Despite numerous short internodes, all relationships received unequivocal bootstrap support while gCF and sCF had very little support, reflecting hidden conflict across loci. Most of the gene-tree and species-tree discordance in our study is a result of short divergence times, and consequent lack of informative characters at deep levels, rather than incomplete lineage sorting. We use this phylogeny to establish a new higher-level classification of Gadiformes as a way of clarifying the evolutionary diversification of the order. We recognize 17 families in five suborders: Bregmacerotoidei, Gadoidei, Ranicipitoidei, Merluccioidei, and Macrouroidei (including two subclades). A time-calibrated analysis using 15 fossil taxa suggests that Gadiformes evolved $\sim $79.5 Ma in the late Cretaceous, but that most extant lineages diverged after the Cretaceous-Paleogene (K-Pg) mass extinction (66 Ma). Our results reiterate the importance of examining phylogenomic analyses for evidence of systematic error that can emerge as a result of unsuitable modeling of biological factors and/or methodological issues, even when data sets are large and yield high support for phylogenetic relationships. [Branch length heterogeneity; Codfishes; commercial fish species; Cretaceous-Paleogene (K-Pg); heterotachy; systematic error; target enrichment.].

Evolutionary determinism and convergence associated with water-column transitions in marine fishes.

Repeatable, convergent outcomes are prima facie evidence for determinism in evolutionary processes. Among fishes, well-known examples include microevolutionary habitat transitions into the water column, where freshwater populations (e.g., sticklebacks, cichlids, and whitefishes) recurrently diverge toward slender-bodied pelagic forms and deep-bodied benthic forms. However, the consequences of such processes at deeper macroevolutionary scales in the marine environment are less clear. We applied a phylogenomics-based integrative, comparative approach to test hypotheses about the scope and strength of convergence in a marine fish clade with a worldwide distribution (snappers and fusiliers, family Lutjanidae) featuring multiple water-column transitions over the past 45 million years. We collected genome-wide exon data for 110 (∼80%) species in the group and aggregated data layers for body shape, habitat occupancy, geographic distribution, and paleontological and geological information. We also implemented approaches using genomic subsets to account for phylogenetic uncertainty in comparative analyses. Our results show independent incursions into the water column by ancestral benthic lineages in all major oceanic basins. These evolutionary transitions are persistently associated with convergent phenotypes, where deep-bodied benthic forms with truncate caudal fins repeatedly evolve into slender midwater species with furcate caudal fins. Lineage diversification and transition dynamics vary asymmetrically between habitats, with benthic lineages diversifying faster and colonizing midwater habitats more often than the reverse. Convergent ecological and functional phenotypes along the benthic-pelagic axis are pervasive among different lineages and across vastly different evolutionary scales, achieving predictable high-fitness solutions for similar environmental challenges, ultimately demonstrating strong determinism in fish body-shape evolution.

Misidentification of Bellator gymnostethus (Gilbert, 1892) as Prionotus ruscarius Gilbert amp; Starks, 1904 (Scorpaeniformes: Triglidae).

The checklist by Robertson et al. (2017) of fishes from the tropical eastern Pacific included information on three members of the family Triglidae: Bellator loxias (Jordan, 1897), Prionotus ruscarius and P. stephanophrys Lockington, 1881. Unfortunately, the identification of four specimens as P. ruscarius is incorrect, as they are Bellator gymnostethus. We thank Benjamin Victor for bringing these misidentifications to our notice through his work with mtDNA sequence data from the Barcode of Life Database (BOLD: http://www.boldsystems.org). The photographs of the four specimens on the BOLD website clearly depict a Bellator species rather than a Prionotus. However, the photograph in the 2017 paper (Figure 75, page 78), is correctly identified and labelled as P. ruscarius, and this species was collected on the cruise of the Miguel Oliver discussed in Robertson et al. (2017), see Benavides Moreno et al. (2019). This correction brings the number of triglids collected on that cruise to four species.

Asymmetrical gene flow in five co-distributed syngnathids explained by ocean currents and rafting propensity.

Ocean circulation driving macro-algal rafting is believed to serve as an important mode of dispersal for many marine organisms, leading to predictions on population-level genetic connectivity and the directionality of effective dispersal. Here, we use genome-wide single nucleotide polymorphism data to investigate whether gene flow directionality in two seahorses (Hippocampus) and three pipefishes (Syngnathus) follows the predominant ocean circulation patterns in the Gulf of Mexico and northwestern Atlantic. In addition, we explore whether gene flow magnitudes are predicted by traits related to active dispersal ability and habitat preference. We inferred demographic histories of these co-distributed syngnathid species, and coalescent model-based estimates indicate that gene flow directionality is in agreement with ocean circulation data that predicts eastward and northward macro-algal transport. However, the magnitude to which ocean currents influence this pattern appears strongly dependent on the species-specific traits related to rafting propensity and habitat preferences. Higher levels of gene flow and stronger directionality are observed in Hippocampus erectus, Syngnathus floridae and Syngnathus louisianae, which closely associated with the pelagic macro-algae Sargassum spp., compared to Hippocampus zosterae and the Syngnathus scovelli/Syngnathus fuscus sister-species pair, which prefer near shore habitats and are weakly associated with pelagic Sargassum. This study highlights how the combination of population genomic inference together with ocean circulation data can help explain patterns of population structure and diversity in marine ecosystems.

The marine fishes of St Eustatius Island, northeastern Caribbean: an annotated, photographic catalog.

Sint Eustatius (Statia) is a 21 km2 island situated in the northeastern Caribbean Sea. The most recent published sources of information on that island's marine fish fauna is in two non-governmental organization reports from 2015-17 related to the formation of a marine reserve. The species-list in the 2017 report was based on field research in 2013-15 using SCUBA diving surveys, shallow "baited underwater video surveys" (BRUVs), and data from fishery surveys and scientific collections over the preceding century. That checklist comprised 304 species of shallow (mostly) and deep-water fishes. In 2017 the Smithsonian Deep Reef Observation Project surveyed deep-reef fishes at Statia using the crewed submersible Curasub. That effort recorded 120 species, including 59 new occurrences records. In March-May 2020, two experienced citizen scientists completed 62 SCUBA dives there and recorded 244 shallow species, 40 of them new records for Statia. The 2017-2020 research effort increased the number of species known from the island by 33.6% to 406. Here we present an updated catalog of that marine fish fauna, including voucher photographs of 280 species recorded there in 2017 and 2020. The Statia reef-fish fauna likely is incompletely documented as it has few small, shallow, cryptobenthic species, which are a major component of the regional fauna. A lack of targeted sampling is probably the major factor explaining that deficit, although a limited range of benthic marine habitats may also be contributing.

A new species of Chromis damselfish from the tropical western Atlantic (Teleostei, Pomacentridae).

Initially described in 1882, Chromis enchrysurus, the Yellowtail Reeffish, was redescribed in 1982 to account for an observed color morph that possesses a white tail instead of a yellow one, but morphological and geographic boundaries between the two color morphs were not well understood. Taking advantage of newly collected material from submersible studies of deep reefs and photographs from rebreather dives, this study sought to determine whether the white-tailed Chromis is actually a color morph of Chromis enchrysurus or a distinct species. Phylogenetic analyses of mitochondrial genes cytochrome b and cytochrome c oxidase subunit I separated Chromis enchrysurus and the white-tailed Chromis into two reciprocally monophyletic clades. A principal component analysis based on 27 morphological characters separated the two groups into clusters that correspond with caudal-fin coloration, which was either known or presumed based on the specimen's collection site according to biogeographic data on species boundaries in the Greater Caribbean. Genetic, morphological, and biogeographic data all indicate that the white-tailed Chromis is a distinct species, herein described as Chromis vanbebberae sp. nov. The discovery of a new species within a conspicuous group such as damselfishes in a well-studied region of the world highlights the importance of deep-reef exploration in documenting undiscovered biodiversity.

Response to Comment on "Demographic dynamics of the smallest marine vertebrates fuel coral reef ecosystem functioning".

Allgeier and Cline suggest that our model overestimates the contributions of cryptobenthic fishes to coral reef functioning. However, their 20-year model ignores the basic biological limits of population growth. If incorporated, cryptobenthic contributions to consumed fish biomass remain high (20 to 70%). Disturbance cycles and uncertainties surrounding the fate of large fishes on decadal scales further demonstrate the important role of cryptobenthic fishes.

Psilotris vantasselli, a new species of goby from the tropical western Atlantic (Teleostei: Gobiidae: Gobiosomatini: Nes subgroup).

A new species of goby is described from submersible and scuba collections off Bonaire and New Providence Island, Bahamas. A molecular phylogenetic analysis of mitochondrial and nuclear genes confirms the placement of the new species within the genus Psilotris of the Nes subgroup of the Gobiosomatini. The new species is easily distinguished from congeners and morphologically similar species of Varicus by its unique coloration, which includes eight narrow, bright yellow bars on the trunk, each with a small orange spot centered on the lateral midline. In addition, the combination of the absence of scales on the head and body and the presence of modified ctenoid scales on the base of the caudal fin, branched pelvic-fin rays, and 15-16 pectoral-fin rays further differentiates the new species from other species of Psilotris and Varicus.

Demographic dynamics of the smallest marine vertebrates fuel coral reef ecosystem functioning.

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.

The evolution of microendemism in a reef fish (Hypoplectrus maya).

Marine species tend to have extensive distributions, which are commonly attributed to the dispersal potential provided by planktonic larvae and the rarity of absolute barriers to dispersal in the ocean. Under this paradigm, the occurrence of marine microendemism without geographic isolation in species with planktonic larvae poses a dilemma. The recently described Maya hamlet (Hypoplectrus maya, Serranidae) is exactly such a case, being endemic to a 50-km segment of the Mesoamerican Barrier Reef System (MBRS). We use whole-genome analysis to infer the demographic history of the Maya hamlet and contrast it with the sympatric and pan-Caribbean black (H. nigricans), barred (H. puella) and butter (H. unicolor) hamlets, as well as the allopatric but phenotypically similar blue hamlet (H. gemma). We show that H. maya is indeed a distinct evolutionary lineage, with genomic signatures of inbreeding and a unique demographic history of continuous decrease in effective population size since it diverged from congeners just ~3,000 generations ago. We suggest that this case of microendemism may be driven by the combination of a narrow ecological niche and restrictive oceanographic conditions in the southern MBRS, which is consistent with the occurrence of an unusually high number of marine microendemics in this region. The restricted distribution of the Maya hamlet, its decline in both census and effective population sizes, and the degradation of its habitat place it at risk of extinction. We conclude that the evolution of marine microendemism can be a fast and dynamic process, with extinction possibly occurring before speciation is complete.