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, Varicus prometheus sp. nov. and V. roatanensis sp. 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 Pinnichthys aimoriensis 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

Extreme environmental conditions reduce coral reef fish biodiversity and productivity

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

Photography-based taxonomy is inadequate, unnecessary, and potentially harmful for biological sciences

The question whether taxonomic descriptions naming new animal species without type specimen(s) deposited in collections should be accepted for publication by scientific journals and allowed by the Code has already been discussed in Zootaxa (Dubois & Nemésio 2007; Donegan 2008, 2009; Nemésio 2009a–b; Dubois 2009; Gentile & Snell 2009; Minelli 2009; Cianferoni & Bartolozzi 2016; Amorim et al. 2016). This question was again raised in a letter supported by 35 signatories published in the journal Nature (Pape et al. 2016) on 15 September 2016. On 25 September 2016, the following rebuttal (strictly limited to 300 words as per the editorial rules of Nature) was submitted to Nature, which on 18 October 2016 refused to publish it. As we think this problem is a very important one for zoological taxonomy, this text is published here exactly as submitted to Nature, followed by the list of the 493 taxonomists and collection-based researchers who signed it in the short time span from 20 September to 6 October 2016

Patterns of evolution in gobies (Teleostei: Gobiidae): a multi-scale phylogenetic investigation

A dissertation submitted in Partial Fulfillment of the Requirements for the Degree of DOCTOR OF PHILOSOPHY in MARINE BIOLOGY from Texas A&M University-Corpus Christi in Corpus Christi, Texas.The family of fishes commonly known as gobies (Teleostei: Gobiidae) is one of the most diverse lineages of vertebrates in the world. With more than 1700 species of gobies spread among more than 200 genera, gobies are the most species-rich family of marine fishes. Gobies can be found in nearly every aquatic habitat on earth, and are often the most diverse and numerically abundant fishes in tropical and subtropical habitats, especially coral reefs. Their remarkable taxonomic, morphological and ecological diversity make them an ideal model group for studying the processes driving taxonomic and phenotypic diversification in aquatic vertebrates. Unfortunately the phylogenetic relationships of many groups of gobies are poorly resolved, obscuring our understanding of the evolution of their ecological diversity. This dissertation is a multi-scale phylogenetic study that aims to clarify phylogenetic relationships across the Gobiidae and demonstrate the utility of this family for studies of macroevolution and speciation at multiple evolutionary timescales. In the first chapter, I present a DNA sequence matrix derived from two nuclear genes to help resolve intergeneric level phylogenetic relationships with the Gobiidae. My study is the first to use data from conserved nuclear loci to infer relationships across the Gobioidei, and the results provide strong support for the monophyly of, and interrelationships between, several ecologically divergent clades. Specifically, I show that gobies are asymmetrically divided into two clades, one of which contains primarily marine species and the other comprises mostly estuarine or freshwater taxa. In the second chapter, I focus on the evolution of microhabitat association and morphology in one of the most diverse lineages of gobies, the reef-associated genus Eviota. Eviota species have invaded novel microhabitats multiple times throughout their evolutionary history, often occurring independently of diagnostic morphological changes in pectoral-fin ray branching and arrangement of sensory cephalic lateralis pores. The combination of historical ecological flexibility coupled with resilience to local extinction events may explain the elevated extant biodiversity in Eviota. Lastly, in my third chapter, I use Eviota as a model for studying fine-scale speciation in the Coral Triangle, a marine biodiversity hotspot in the Western Pacific Ocean. A phylogeographic analysis of two species complexes that have diverged within the Coral Triangle provides strong support for the hypothesis that the Coral Triangle serves as a `center of origin' or cradle of new species. Specifically, I demonstrate that a combination of biotic and abiotic factors may be contributing to rapid speciation both in allopatry and sympatry within the last 1.5 million years. The presence of recently diverged cryptic species in the Coral Triangle implies that our current estimates of biodiversity in this marine hotspot are severely underestimated. Ultimately, this dissertation demonstrates that gobies and other ecologically diverse clades of fishes serve as excellent model groups for studying the processes driving taxonomic and phenotypic diversification in marine species at a variety of spatial and temporal scales. This project will serve as a foundation for future studies that aim to use more comprehensive genomic datasets to address questions regarding drivers of speciation and ecological diversification in gobiid fishes.Life SciencesCollege of Science and Engineerin

Bathygobius soporator

<i>Bathygobius soporator</i> sublineages <p> Distinct mitochondrial sublineages within <i>B. soporator</i> were observed by Tornabene <i>et al</i>. (2010), as they recognized the presence of two genetic lineages of <i>B. soporator</i> in the western Atlantic. The current study confirms the presence of these sublineages. With the inclusion of West African material in our dataset, there are now three clades of <i>B. soporator</i>. Two of these clades contain individuals from the western Atlantic and the third clade consists of individuals from Guinea. One of the two western Atlantic clades consists of individuals from the Gulf of Mexico and Atlantic coast of Florida (“lineage 3” of Tornabene <i>et al</i>. 2010). The other western Atlantic clade has representatives from throughout the western Atlantic, but not from the Gulf of Mexico (“lineage 2” of Tornabene <i>et al</i>. 2010). The specimens of <i>B. soporator</i> from Guinea in this study are morphologically indistinguishable from specimens of the two western Atlantic clades of <i>B. soporator</i>. The western Atlantic lineages of <i>B. soporator</i> were not described as distinct species by Tornabene <i>et al.</i> (2010) despite their occurrence in sympatry in some locations, due to the possibility of deep coalescence, the lack of diagnostic morphological or pigmentation characters, and the lack of additional independent information from nuclear genes. Although the current study incorporates the nuclear gene RAG1, the level of polymorphism in this gene alone was not high enough to resolve the species that comprise the <i>B. soporator</i> group, much less the three smaller clades within <i>B. soporator</i> itself. Thus, the question of whether or not <i>B. soporator</i> (<i>sensu</i> Tornabene <i>et al</i>. 2010) represents several cryptic species remains unanswered.</p> <p> Because the sublineages have only been observed in mtDNA thus far, the possibility of deep coalescence cannot be ruled out as an explanation for the observed pattern of divergence. On the other hand, the three clades of <i>B. soporator</i> may indeed represent genetically and evolutionarily distinct, reproductively isolated independent species. If we assume that <i>B. andrei</i> and its Atlantic counterpart (whether <i>B. soporator</i>, <i>B. lacertus</i>, or the common ancestor of the two) became separated roughly 2.8-3.1 mya by the closure of the Isthmus of Panama (Lessios 2008), then the diversification between the two western Atlantic clades of <i>B. soporator</i> and the West African clade must have occurred significantly later than the closure of the Isthmus of Panama. Models of vicariance and/or dispersal that would explain this pattern of distribution are difficult to hypothesize because of our poor understanding of the effect of Pliocene glaciations on the trans-Atlantic ocean currents that would be responsible for facilitating or preventing gene flow between amphi-Atlantic populations. Although the finer details of surface currents during and since the Pliocene are not known, the overall surface patterns within the Atlantic may have been stabilized following the closure of the Isthmus of Panama (Maier-Reimer <i>et al</i>. 1990; Haug and Tiedemann 1998), which may have contributed to the formation of semi-permiable barriers to gene flow and subsequent speciation within the Atlantic basin (e.g. Muss <i>et al</i>. 2001).</p> <p> Several genera of tropical and subtropical fish have similar patterns of recent west-to-east Atlantic dispersal and diversification after the closure of the Isthmus of Panama (Floeter <i>et al</i>. 2008: fig 10, scenario “e”). Some examples include seahorses of the <i>Hippocampus erectus</i> -group (Casey <i>et al</i>. 2004), blennies of the genus <i>Ophioblennius</i> (Muss <i>et al.</i> 2001), and wrasses of the genus <i>Clepticus</i> (Heiser <i>et al</i>. 2000). In these three examples the African members are most closely related to members throughout the western Atlantic (<i>Hippocampus erectus</i> - group), South American members (<i>Clepticus</i>), or are separated from Caribbean members by a mid-Atlantic Ridge clade (<i>Ophioblennius</i>). A similar pattern is also seen in the goby <i>Gnatholepis thompsoni</i>, which has recently invaded the eastern Atlantic via a central Atlantic “stepping stone” population (Rocha et al. 2005). Unlike our study however, the aforementioned examples do not exhibit separation between a Gulf of Mexico clade and Caribbean/South American clade. <i>Bathygobius soporator</i> does occur in the Cape Verde Islands in the central Atlantic, but specimens were not available for this study. A population genetic analysis of <i>B. soporator</i> with increased sample sizes from each lineage plus the central Atlantic, as well as a phylogenetic analysis using a more sensitive nuclear gene may further clarify the present biogeographic distribution and increase our understanding of the relationships between the three mitochondrial lineages of <i>B. soporator</i>.</p>Published as part of <i>Tornabene, Luke & Pezold, Frank, 2011, Phylogenetic analysis of Western Atlantic Bathygobius (Teleostei: Gobiidae), pp. 27-36 in Zootaxa 3042</i> on page 32, DOI: <a href="http://zenodo.org/record/200832">10.5281/zenodo.200832</a&gt

Bathygobius antilliensis

<i>Bathygobius antilliensis</i> group <p> This group includes <i>B. ramosus, B. lineatus</i>, <i>B. curacao</i> and <i>B. antilliensis</i>. <i>Bathygobius curacao</i> was recovered as the basal member of this group, followed by the two Eastern Pacific species, and <i>B. antilliensis</i>. The <i>B. antilliensis</i> group is part of a polytomy containing the <i>B. soporator</i> group plus <i>B. geminatus</i>, a clade containing two Indopacific <i>B. fuscus</i> and <i>B. coalitus</i>, and <i>B. mystacium</i>.</p> <p> Miller & Smith’s (1989) most parsimonious Wagner tree (based on 46 morphological characters) placed <i>B. ramosus</i> in a clade with three Indo-Pacific <i>Bathygobius</i> species (<i>B. cyclopterus</i> (Valenciennes, 1837), <i>B. cotticeps</i> (Steindachner, 1879), and <i>B. niger</i> (Smith, 1960), this group being basal to the remaining 11 <i>Bathygobius</i> species on their tree (including <i>B. soporator</i>, <i>B. andrei</i>, <i>B. curacao</i> and <i>B. mystacium</i>). The group consisting of <i>B. ramosus</i> and its Indo-Pacific allies was characterized by having a complex multifurcate branching pattern on the first two free pectoral fin rays, although <i>B. ramosus</i> lacks the head scales and the projection on the tubular anterior naris that are present on the Indo-Pacific species (Miller & Smith 1989; Miller & Stefanni 2001). <i>B. antilliensis</i> also lacks head scales and the projection on the anterior naris, and this species also typically possesses a more extensive pectoral fin ray branching pattern than other western Atlantic congeners, although the branching is not usually as extensive as observed <i>B. ramosus</i> and is somewhat variable within the species. A pattern of multifurcate free pectoral fin rays may be a synapomorphy of the more derived members of the <i>B. antilliensis</i> group (both <i>B. curacao</i> and <i>B. lineatus</i> have a single branching point on upper pectoral rays), and possibly a larger clade that contains the Indo-Pacific <i>B. cyclopterus</i>, <i>B. cotticeps</i>, and <i>B. niger</i>. Alternatively, Miller & Stefanni (2001) questioned the homology of this character, as it has been demonstrated to be homoplasious in the Atlantic-Mediterranean genera <i>Gobius</i> and <i>Mauligobius</i> (Miller 1984, 1986; Brito and Miller 2001). Two hypotheses were suggested to explain the relationship between <i>B. ramosus</i> and its potential Indo-Pacific allies (Miller & Smith 1989; Miller & Stefanni 2001): <i>B. ramosus</i> arose from an invasion across the Eastern Pacific barrier by western Pacific stock; or <i>B. ramosus</i> represents a Pacific survival of circumtropical post-Tethyan stock, whose Atlantic sister-species must have gone extinct. The recent discovery of the Atlantic sister-species (<i>B. antilliensis</i>) supports the latter hypothesis. If <i>B. antilliensis</i> and <i>B. ramosus</i> are sister species isolated by the closure of the Isthmus of Panama, then the speciation events separating <i>B. curacao</i>, <i>B. lineatus</i>, and the common ancestor of <i>B. antilliensis</i> and <i>B. ramosus</i> must have predated this closure.</p> <p> In terms of both morphology and genetics, <i>B. curacao</i> is very divergent from all other species in our analysis including other members of the <i>B. antilliensis</i> group. Miller & Smith (1989) hypothesized that <i>B. curacao’s</i> closest allies are the West African species <i>B. burtoni</i> (O'Shaughnessy 1875) and <i>B. casamancus</i> (Rochebrune 1880), and the Indo-Pacific species <i>B. cocosensis</i> (Bleeker 1854) and <i>B. petrophilus</i> (Bleeker 1853). While <i>B. petrophilus</i>, <i>B. burtoni</i> and <i>B. casamancus</i> were not available for our analysis, our molecular analyses show no evidence of a close relationship between <i>B. curacao</i> and the Indo-Pacific <i>B. cocosensis</i>. A combined molecular and morphological analysis that includes additional old-world <i>Bathygobius</i> species would further clarify the relationship between the <i>B. antilliensis</i> group and potential old-world allies.</p>Published as part of <i>Tornabene, Luke & Pezold, Frank, 2011, Phylogenetic analysis of Western Atlantic Bathygobius (Teleostei: Gobiidae), pp. 27-36 in Zootaxa 3042</i> on page 30, DOI: <a href="http://zenodo.org/record/200832">10.5281/zenodo.200832</a&gt

Bathygobius mystacium

Bathygobius mystacium and B. geminatus Bathygobius mystacium is both morphologically and genetically distinct from most other New World Bathygobius species, although it overlaps with B. geminatus in some meristic counts and morphometric measurements. The neighbor-joining tree of Tornabene et al. (2010) showed these two species as being genetically similar, however the phylogeny from our concatenated dataset failed to resolve the placement of B. mystacium. Bathygobius geminatus was resolved as the sister species to the B. soporator group, however we refrain from including this species in the B. soporator group as the posterior probability value of this relationship was a modest 0.70. The relationships between B. geminatus, B. mystacium and their congeners were variable and were not well-supported across each of the individual gene trees. The Wagner parsimony tree from Miller & Smith (1989) generated from morphological data shows B. mystacium as the basal member of a clade also containing B. soporator and B. andrei. This relationship is not supported by any of our analyses.Published as part of Tornabene, Luke & Pezold, Frank, 2011, Phylogenetic analysis of Western Atlantic Bathygobius (Teleostei: Gobiidae), pp. 27-36 in Zootaxa 3042 on page 32, DOI: 10.5281/zenodo.20083

Data from: A new mesophotic goby, Palatogobius incendius (Teleostei: Gobiidae), and the first record of invasive lionfish preying on undescribed biodiversity

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