Carole C. Baldwin

Using DNA barcoding to assess Caribbean reef fish biodiversity: expanding taxonomic and geographic coverage.

This paper represents a DNA barcode data release for 3,400 specimens representing 521 species of fishes from 6 areas across the Caribbean and western central Atlantic regions (FAO Region 31). Merged with our prior published data, the combined efforts result in 3,964 specimens representing 572 species of marine fishes and constitute one of the most comprehensive DNA barcoding “coverages” for a region reported to date. The barcode data are providing new insights into Caribbean shorefish diversity, allowing for more and more accurate DNA-based identifications of larvae, juveniles, and unknown specimens. Examples are given correcting previous work that was erroneous due to database incompleteness.

GenSeq: An updated nomenclature and ranking for genetic sequences from type and non-type sources

Abstract An improved and expanded nomenclature for genetic sequences is introduced that corresponds with a ranking of the reliability of the taxonomic identification of the source specimens. This nomenclature is an advancement of the “Genetypes” naming system, which some have been reluctant to adopt because of the use of the “type” suffix in the terminology. In the new nomenclature, genetic sequences are labeled “genseq,” followed by a reliability ranking (e.g., 1 if the sequence is from a primary type), followed by the name of the genes from which the sequences were derived (e.g., genseq-1 16S, COI). The numbered suffix provides an indication of the likely reliability of taxonomic identification of the voucher. Included in this ranking system, in descending order of taxonomic reliability, are the following: sequences from primary types – “genseq-1,” secondary types – “genseq-2,” collection-vouchered topotypes – “genseq-3,” collection-vouchered non-types – “genseq-4,” and non-types that lack specimen vouchers but have photo vouchers – “genseq-5.” To demonstrate use of the new nomenclature, we review recently published new-species descriptions in the ichthyological literature that include DNA data and apply the GenSeq nomenclature to sequences referenced in those publications. We encourage authors to adopt the GenSeq nomenclature (note capital “G” and “S” when referring to the nomenclatural program) to provide a searchable tag (e.g., “genseq”; note lowercase “g” and “s” when referring to sequences) for genetic sequences from types and other vouchered specimens. Use of the new nomenclature and ranking system will improve integration of molecular phylogenetics and biological taxonomy and enhance the ability of researchers to assess the reliability of sequence data. We further encourage authors to update sequence information on databases such as GenBank whenever nomenclatural changes are made.

Seven new species within western Atlantic Starksia atlantica, S. lepicoelia, and S. sluiteri (Teleostei, Labrisomidae), with comments on congruence of DNA barcodes and species

Abstract Specimens of Starksia were collected throughout the western Atlantic, and a 650-bp portion of the mitochondrial gene cytochrome oxidase-c subunit I (COl) was sequenced as part of a re-analysis of species diversity of western Central Atlantic shorefishes. A neighbor-joining tree constructed from the sequence data suggests the existence of several cryptic species. Voucher specimens from each genetically distinct lineage and color photographs of vouchers taken prior to dissection and preservation were examined for diagnostic morphological characters. The results suggest that Starksia atlantica, Starksia lepicoelia, and Starksia sluiteri are species complexes, and each comprises three or more species. Seven new species are described. DNA data usually support morphological features, but some incongruence between genetic and morphological data exists. Genetic lineages are only recognized as species if supported by morphology. Genetic lineages within western Atlantic Starksia generally correspond to geography, such that members of each species complex have a very restricted geographical distribution. Increasing geographical coverage of sampling locations will almost certainly increase the number of Starksia species and species complexes recognized in the western Atlantic. Combining molecular and morphological investigations is bringing clarity to the taxonomy of many genera of morphologically similar fishes and increasing the number of currently recognized species. Future phylogenetic studies should help resolve species relationships and shed light on patterns of speciation in western Atlantic Starksia.

Connectivity across the Caribbean Sea: DNA Barcoding and Morphology Unite an Enigmatic Fish Larva from the Florida Straits with a New Species of Sea Bass from Deep Reefs off Curacao

Integrative taxonomy, in which multiple disciplines are combined to address questions related to biological species diversity, is a valuable tool for identifying pelagic marine fish larvae and recognizing the existence of new fish species. Here we combine data from DNA barcoding, comparative morphology, and analysis of color patterns to identify an unusual fish larva from the Florida Straits and demonstrate that it is the pelagic larval phase of a previously undescribed species of Liopropoma sea bass from deep reefs off Curaçao, southern Caribbean. The larva is unique among larvae of the teleost family Serranidae, Tribe Liopropomini, in having seven elongate dorsal-fin spines. Adults of the new species are similar to the golden bass, Liopropoma aberrans, with which they have been confused, but they are distinct genetically and morphologically. The new species differs from all other western Atlantic liopropomins in having IX, 11 dorsal-fin rays and in having a unique color pattern–most notably the predominance of yellow pigment on the dorsal portion of the trunk, a pale to white body ventrally, and yellow spots scattered across both the dorsal and ventral portions of the trunk. Exploration of deep reefs to 300 m using a manned submersible off Curaçao is resulting in the discovery of numerous new fish species, improving our genetic databases, and greatly enhancing our understanding of deep-reef fish diversity in the southern Caribbean. Oh the mother and child reunion is only a moment away. Paul Simon.

Invasive lionfish preying on critically endangered reef fish

Caribbean coral reef ecosystems are at the forefront of a global decline and are now facing a new threat: elimination of vulnerable species by the invasive lionfish (Pterois spp.). In addition to being threatened by habitat destruction and pollution, the critically endangered social wrasse (Halichoeres socialis), endemic to Belize’s inner barrier reef, has a combination of biological traits (small size, schooling, and hovering behavior) that makes it a target for the invasive lionfish. Based on stomach content analyses, this small fish comprises almost half of the lionfish diet at the inner barrier reef in Belize. The combination of lionfish predation, limited range, and ongoing habitat destruction makes the social wrasse the most threatened coral reef fish in the world. Other species with small range and similar traits occur elsewhere in the Caribbean and face similar risks.

DNA barcoding fishes.

This chapter is an overview of the techniques for DNA barcoding of fishes from field collection to DNA sequence analysis. Recommendations for modifications of field protocols and best tissue sampling practices are made. A variety of DNA extraction protocols is provided, including high-throughput robot-assisted methods. A pair of well-tested forward and reverse primers for PCR amplification and sequencing are presented. These primers have been successfully used for DNA barcode on a wide array of marine fish taxa and also work well in most freshwater and cartilaginous fishes. Recipes and cycling protocols for both PCR amplification and sequencing and cleanup methods for the reaction products are provided. A method for the consistent production of high-quality DNA barcodes from DNA sequence data is given and stringent guidelines for judging the quality of raw sequence data are laid out.

A New Species of Soapfish (Teleostei: Serranidae: Rypticus), with Redescription of R. subbifrenatus and Comments on the Use of DNA Barcoding in Systematic Studies

A new species of Rypticus is described from the Bahamas, Bermuda, Florida, and the Caribbean Sea. The species previously has been confused with the spotted soapfish, R. subbifrenatus Gill 1861, with which it shares a similar pattern of dark spotting on the body. The new species differs from R. subbifrenatus in having yellow pigment on the pectoral fin and distal portions of the soft dorsal, caudal, and anal fins in life (pale in preservative); a different configuration of dark spots on the head; usually dark spots on the belly and caudal fin; almost always four dorsal-fin spines; and modally 25 total dorsal-fin elements, 15 pectoral-fin rays, and 23 total caudal-fin rays. The lower jaw typically extends further anteriorly beyond the upper jaw in the new species than in R. subbifrenatus, and the caudal peduncle is usually narrower. The new Rypticus typically inhabits deeper waters than R. subbifrenatus, and is commonly found on vertical slopes and walls vs. shallow, flat areas. The new species likely would have continued to go unnoticed without examination of genetic data, as there was little reason to look further at R. subbifrenatus until DNA barcoding revealed two distinct genetic lineages within the species. The value of DNA barcoding data in systematic studies and the need for increased support of taxonomy are highlighted. A neotype for Rypticus subbifrenatus is designated.

A new Liopropoma sea bass (Serranidae, Epinephelinae, Liopropomini) from deep reefs off Curaçao, southern Caribbean, with comments on depth distributions of western Atlantic liopropomins

Abstract Collecting reef-fish specimens using a manned submersible diving to 300 m off Curaçao, southern Caribbean, is resulting in the discovery of numerous new fish species. The new Liopropoma sea bass described here differs from other western Atlantic members of the genus in having VIII, 13 dorsal-fin rays; a moderately indented dorsal-fin margin; a yellow-orange stripe along the entire upper lip; a series of approximately 13 white, chevron-shaped markings on the ventral portion of the trunk; and a reddish-black blotch on the tip of the lower caudal-fin lobe. The new species, with predominantly yellow body and fins, closely resembles the other two “golden basses” found together with it at Curaçao: L. aberrans and L. olneyi. It also shares morphological features with the other western Atlantic liopropomin genus, Bathyanthias. Preliminary phylogenetic data suggest that western Atlantic liopropomins, including Bathyanthias, are monophyletic with respect to Indo-Pacific Liopropoma, and that Bathyanthias is nested within Liopropoma, indicating a need for further study of the generic limits of Liopropoma. The phylogenetic data also suggest that western Atlantic liopropomins comprise three monophyletic clades that have overlapping depth distributions but different depth maxima (3–135 m, 30–150 m, 133–411 m). The new species has the deepest depth range (182–241 m) of any known western Atlantic Liopropoma species. Both allopatric and depth-mediated ecological speciation may have contributed to the evolution of western Atlantic Liopropomini.

A new Haptoclinus blenny (Teleostei, Labrisomidae) from deep reefs off Curaçao, southern Caribbean, with comments on relationships of the genus

Abstract A second species of the blenniiform genus Haptoclinus is described from deep reefs off Curaçao, southern Caribbean. Haptoclinus dropi sp. n. differs from the northwestern Caribbean Haptoclinus apectolophus Böhlke and Robins, 1974, in having 29 total dorsal-fin elements—III-I-XIII, 12 (vs. 31—III-I-XIV, 13 or III-I-XIII, 14); 19 anal-fin soft rays (vs. 20-21); 12 pectoral-fin rays (vs. 13); 12 precaudal vertebrae (vs. 13); and the first dorsal-fin spine longer than the second (vs. the second longer than the first). It further differs from Haptoclinus apectolophus in lacking scales (vs. three-quarters of body densely scaled), in having a distinctive pattern of spotting on the trunk and fins in preservative (vs. no spotting), and in lacking a fleshy flap on the anterior rim of the posterior nostril (vs. flap present). Color in life is unknown for Haptoclinus apectolophus, and the color description presented for the new species constitutes the first color information for the genus. Familial placement of Haptoclinus remains questionable, but the limited relevant information obtained from morphological examination of the new species provides additional support for a close relationship with the Chaenopsidae. Haptoclinus dropi represents one of numerous new teleost species emerging from sampling to 300 m off Curaçao as part of the Smithsonian Institution’s Deep Reef Observation Project (DROP).

Osteology and relationships ofPseudotrichonotus altivelis (Teleostei: Aulopiformes: Pseudotrichonotidae)

The osteology of the rate Japanese fishPseudotrichonotus altivelis is described based on several specimens collected off the Izu Peninsula. Relationships ofPseudotrichonotus are discussed based on osteological comparisons with other neoteleosts. The placement ofPseudotrichonotus among iniomous fishes has been questioned because of its lower numbers of caudal-fin, pelvic-fin, and branchiostegal rays. Our investigation supports an iniomous affinity forPseudotrichonotus, specifically as a member of the Aulopiformes. Within that group,Pseudotrichonotus belongs in a new suborder diagnosed herein, the Synodontoidei, which also includes the Aulopidae (Aulopus), Synodontidae (Synodus andTrachinocephalus), and Harpadontidae (Harpadon andSaurida). A synodontoid affinity forAulopus has never been suggested, but numerous osteological features support the monophyly of this clade. Synodontoids have a peculiar proximal segmentation of most principal caudal-fin rays, expanded neural and haemal spines on posterior vertebrae, cartilage extending along the ventral margin of the anterior ceratohyal, ventral displacement of the first one to three epineurals, supraneurals with large laminar expansions and six or more branchiostegals on the posterior ceratohyal. They lack median caudal cartilages. Among synodontoids,Pseudotrichonotus is the sister group of the Synodontidae plus Harpadontidae, with which it shares paired peritoneal pigment spots, an abrupt transition between the epipleurals in and beneath the horizontal septum, and absence of the fourth pharyngobranchial toothplate. Our study does not support a previously proposed relationship betweenBathysaurus and synodontids.