DNA Barcoding: Error Rates Based on Comprehensive Sampling

DNA barcoding has attracted attention with promises to aid in species identification and discovery; however, few well-sampled datasets are available to test its performance. We provide the first examination of barcoding performance in a comprehensively sampled, diverse group (cypraeid marine gastropods, or cowries). We utilize previous methods for testing performance and employ a novel phylogenetic approach to calculate intraspecific variation and interspecific divergence. Error rates are estimated for (1) identifying samples against a well-characterized phylogeny, and (2) assisting in species discovery for partially known groups. We find that the lowest overall error for species identification is 4%. In contrast, barcoding performs poorly in incompletely sampled groups. Here, species delineation relies on the use of thresholds, set to differentiate between intraspecific variation and interspecific divergence. Whereas proponents envision a “barcoding gap” between the two, we find substantial overlap, leading to minimal error rates of ~17% in cowries. Moreover, error rates double if only traditionally recognized species are analyzed. Thus, DNA barcoding holds promise for identification in taxonomically well-understood and thoroughly sampled clades. However, the use of thresholds does not bode well for delineating closely related species in taxonomically understudied groups. The promise of barcoding will be realized only if based on solid taxonomic foundations

New records of Tylokepon with the description of a new species (Epicaridea, Bopyridae, Keponinae)

The parasitic isopod genus Tylokepon is recorded for the first time from the Mariana Islands and Australia. Tylokepon marianensis sp. n. is described from the Mariana Islands, infesting Thusaenys irami (Laurie, 1906). The holotype female differs from other known Tylokepon females by the tri-lobed projection on pereomere 6, almost smooth lateral plates and pleopods, shape of oostegite 1, and widely opened brood pouch. The host is first recorded for bearing bopyrids. The new record of T. bonnieri Stebbing, 1904 from Australia on the type host extends the range of this species from China and India. A table of localities and hosts and a key to all species of Tylokepon are provided

Diversification and distribution of gall crabs (Brachyura: Cryptochiridae: <i>Opecarcinus</i>) associated with Agariciidae corals

Coral reefs are home to the greatest diversity of marine life, and many species on reefs live in symbiotic associations. Studying the historical biogeography of symbiotic species is key to unravelling (potential) coevolutionary processes and explaining species richness patterns. Coral-dwelling gall crabs (Cryptochiridae) live in obligate symbiosis with a scleractinian host, and are ideally suited to study the evolutionary history between heterogeneous taxa involved in a symbiotic relationship. The genus Opecarcinus Kropp and Manning, 1987, like its host coral family Agariciidae, occurs in both Indo-Pacific and Caribbean seas, and is the only cryptochirid genus with a circumtropical distribution. Here, we use mitochondrial and nuclear DNA gene fragments of Opecarcinus specimens sampled from 21 Indo-Pacific localities and one Atlantic (Caribbean) locality. We applied several species delimitation tests to characterise species diversity, inferred a Bayesian molecular-clock time-calibrated phylogeny to estimate divergence times and performed an ancestral area reconstruction. Time to the most recent common ancestor (tMRCA) of Opecarcinus is estimated at 15−6 Mya (middle Miocene—late Miocene). The genus harbours ~ 15 undescribed species as well as several potential species complexes. There are indications of strict host-specificity patterns in certain Opecarcinus species in the Indo-Pacific and Atlantic, however, a robust phylogeny reconstruction of Agariciidae corals—needed to test this further—is currently lacking. The Indo-West Pacific was inferred to be the most probable ancestral area, from where the Opecarcinus lineage colonised the Western Atlantic and subsequently speciated into O. hypostegus. Opecarcinus likely invaded from the Indo-West Pacific across the East Pacific Barrier to the Atlantic, before the full closure of the Isthmus of Panama. The subsequent speciation of O. hypostegus, is possibly associated with newly available niches in the Caribbean, in combination with genetic isolation following the closure of the Panama Isthmus

In situ observation of sexual reproduction of Holothuria tubulosa Gmelin 1788 (Echinodermata: Holothuroidea) in the Azores (NE Atlantic)

Copyright © SPC 2010.[...]. In the Azores, H. tubulosa spawning occurs in the summer months (so far observed in July and August) during the afternoon, which may follow the annual pattern, during warm sea temperatures (22–26°C) and being synchronous in both sexes, as stated by Despalotovic et al. (2004) in the Adriatic Sea. [...

Short-Lived Aggregations of Filograna/Salmacina Tube Worms in the Gulf of Oman

Dense aggregations of serpulid worms were encountered in the Daymaniyat Islands (Gulf of Oman) from 10 to 20 m depth, over the period January–March, 2021. The species responsible for these aggregations belongs to the Filograna/Salmacina-complex (Annelida: Serpulidae). This species has been present in the area and observed along the Oman coastline, but high-density aggregates like this have not been reported before. The most probable cause of the aggregations, supported by field observations and Aqua-MODIS satellite data, was natural eutrophication with a subsequent algal bloom linked to the local winter monsoon. This observation emphasises the importance of documenting biodiversity and dynamics of reef communities along the Oman coastline

Aggregations of a Sessile Ctenophore, Coeloplana sp., on Indo-West Pacific Gorgonians

We document the benthic ctenophores Coeloplana sp. and Vallicula multiformis from Oman, extending their geographic range. A new Coeloplana species was found forming aggregations on gorgonians of two octocoral host genera, Melithaea and Euplexaura, representing associations previously unknown to occur in the Indo-West Pacific region. Our findings also illustrate the concurrent presence of the ectocommensal ophiuroid Ophiothela mirabilis, which adversely affects other Coeloplana species in the tropical West Atlantic, where it is considered invasive. This exploration contributes to our understanding of the biogeography, species distribution, and ectosymbiotic associations of these genera, setting the stage for a comprehensive species description and in-depth analysis of host relationships in future studies

DNA barcoding of reef brittle stars (Ophiuroidea, Echinodermata) from the southwestern Indian Ocean evolutionary hot spot of biodiversity

In anticipation of the current biodiversity crisis, it has become critical to rapidly and accurately assess biodiversity. DNA barcoding has proved efficient in facilitating the discovery and description of thousands of species and also provides insight into the dynamics of biodiversity. Here, we sequenced a portion of the mitochondrial cytochrome c oxidase subunit I (COI) gene from all morphospecies of reef brittle stars collected during a large-scale biodiversity survey in the southwestern Indian Ocean (SWIO). Three methods of species delineation (Automatic Barcode Gap Discovery, Generalized Mixed Yule Coalescent model, and Bayesian Poisson Tree Processes) showed concordant results and revealed 51 shallow reef species in the region. Mean intraspecific genetic distances (0.005–0.064) and mean interspecific genetic distances within genera (0.056–0.316) were concordant with previous echinoderm studies. This study revealed that brittle-star biodiversity is underestimated by 20% within SWIO and by >40% when including specimens from the Pacific Ocean. Results are discussed in terms of endemism, diversification processes, and conservation implications for the Indo-West Pacific marine biodiversity. We emphasize the need to further our knowledge on biodiversity of invertebrate groups in peripheral areas.Agence Nationale de la Recherche, Grant/ Award Number: ANR-06-BDIV-002 (BIOTAS); FP7 People: Marie-Curie Actions, Grant/ Award Number: MC-CIG-618480; Grant/ Award Number: ANR-06-BDIV-002http://www.ecolevol.orgam2018Genetic

Envisioning a marine biodiversity observation network

Author Posting. © University of California Press and American Institute of Biological Sciences, 2013. This article is posted here by permission of University of California Press and American Institute of Biological Sciences for personal use, not for redistribution. The definitive version was published in BioScience 63 (2013): 350-361, doi:10.1525/bio.2013.63.5.8.Humans depend on diverse ocean ecosystems for food, jobs, and sustained well-being, yet many stressors threaten marine life. Extensive research has demonstrated that maintaining biodiversity promotes ocean health and service provision; therefore, monitoring the status and trends of marine biodiversity is important for effective ecosystem management. However, there is no systematic sustained program for evaluating ocean biodiversity. Coordinating existing monitoring and building a proactive marine biodiversity observation network will support efficient, economical resource management and conservation and should be a high priority. A synthesis of expert opinions suggests that, to be most effective, a marine biodiversity observation network should integrate biological levels, from genes to habitats; link biodiversity observations to abiotic environmental variables; site projects to incorporate environmental forcing and biogeography; and monitor adaptively to address emerging issues. We summarize examples illustrating how to leverage existing data and infrastructure to meet these goals

The littoral sea cucumbers (Echinodermata: Holothuroidea) of Guam re-assessed – a diversity curve that still does not asymptote

The Micronesian island of Guam has been an important site for the study of littoral tropical holothurian taxonomy for almost 200 years. Despite substantial attention by both expeditions and resident taxonomists, new records are still regularly added to the fauna, demonstrating the challenge of documenting even such large and well-known animals in a small hyper-diverse area. Guam is the type locality of species described by Quoy & Gaimard (1833) and Brandt (1835). A survey of the sea cucumber fauna by Rowe & Doty (1977) led to one of the most used guides for the identification of tropical Pacific sea cucumbers because of the color illustrations of living animals it presented. Focus on echinoderms including holothurians continued with numerous new records added in the following decades. Paulay (2003a) summarized the fauna last, recording 46-47 species. At this stage the fauna was thought to be well documented. A week-long workshop on holothurian systematics sponsored by the National Science Foundation PEET (Partnerships for Enhancing Expertise in Taxonomy) project in 2010 included a substantial field work component, sampling both during the day and night, with snorkeling and SCUBA, across a variety of habitats. This survey yielded 40 species, including numerous new records and even species. Further sampling by Kerr’s lab since the workshop has added additional records. The littoral holothuroid fauna of Guam now comprises 65 species in 17 genera and 7 families. Half of the 19 newly recorded species are the result of unravelling cryptic species in complexes, the other half are based on new collections. Eleven species are known from single specimens, suggesting that much still remains to be learned about the fauna