Allen G. Collins

Allen G. Collins
National Oceanic and Atmospheric Administration | NOAA · Office of Science and Technology

PhD, 1999 University of California Berkeley

About

504
Publications
110,839
Reads
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9,751
Citations
Introduction
Information on these pages has been cobbled together by some automated process. I do not vouch for its accuracy.
Additional affiliations
January 2010 - present
University of São Paulo
January 2007 - December 2011
University of Kansas
Description
  • Adjunct
January 2006 - present

Publications

Publications (504)
Article
Full-text available
DNA barcoding is critical to conservation and biodiversity research, yet public reference databases are incomplete. Existing barcode databases are biased toward cytochrome oxidase subunit I (COI) and frequently lack associated voucher specimens or geospatial metadata, which can hinder reliable species assignments. The emergence of metabarcoding app...
Preprint
Full-text available
Platyhelminthes (flatworms) are a diverse invertebrate phylum that are useful for exploring life history evolution. Within Platyhelminthes, only two clades develop through a larval stage: freeliving polyclads and parasitic neodermatans. Neodermatan larvae are considered evolutionarily derived, whereas polyclad larvae are hypothesized to be retained...
Article
Full-text available
In this work, staurozoans of two distinct morphotypes are reported in Kitsunezaki (Ishinomaki City, Miyagi, Japan) in the years following the Great East Japan Earthquake and Tsunami. Staurozoa specimens were collected from Eisenia and Gelidium macroalgal beds at the Kitsunezaki survey site (October 2019–July 2021). Morphological observations indica...
Article
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Freshwater jellyfish comprising the genus Craspedacusta are thought to have originated in the Yangtze River, China and have since spread to all continents except Antarctica. In this study, jellyfish were collected from Haruta-ike, an artificial pond in Chikuma City, Nagano (Japan). Medusae were identified as Craspedacusta sowerbii using morphologic...
Article
Morphological variability within Cassiopea is well documented and has led to inaccuracies in the establishment of species boundaries in this taxon. Cassiopea medusae specimens from the Western Pacific (Japan and the Philippines) were analysed using multiple lines of complementary evidence, including types of cnidae, macro-morphology and molecular d...
Article
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Discussion around avoidance and mitigation of jellyfish stings has traditionally focused on swimmers and divers being mindful of their behavior relative to swimming medusae (pelagic jellyfish). This framework must be restructured with the inclusion of the oblique risk posed by novel autonomous stinging structures like cassiosomes from Cassiopea (a...
Article
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Cryptic species have been detected across Metazoa, and while no apparent morphological features distinguish them, it should not impede taxonomists from formal descriptions. We accepted this challenge for the jellyfish genus Aurelia, which has a long and confusing taxonomic history. We demonstrate that morphological variability in Aurelia medusae ov...
Article
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Higher-level relationships of the Hydrozoan subclass Hydroidolina, which encompasses the vast majority of medusozoan cnidarian species diversity, have been elusive to confidently infer. The most widely adopted phylogenetic framework for Hydroidolina based on ribosomal RNA data received low support for several higher level relationships. To address...
Article
Full-text available
DNA metabarcoding is an increasingly popular technique to investigate biodiversity; however, many methodological unknowns remain, especially concerning the biases resulting from marker choice. Regions of the cytochrome c oxidase subunit I (COI) and 18S rDNA (18S) genes are commonly employed “universal” markers for eukaryotes, but the extent of taxo...
Article
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To better understand the biodiversity-biogeographic polar connections between southern South America and Antarctica (SSA & A), we used benthic communities of hydroids as a model to investigate marine assemblages by evaluating classic spatial divisions at different geographical resolutions. Using a georeferenced dataset of 249 species and multivaria...
Article
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The performance of DNA metabarcoding approaches for characterizing biodiversity can be influenced by multiple factors. Here, we used morphological assessment of taxa in zooplankton samples to develop a large barcode database and to assess the congruence of taxonomic identification with metabarcoding under different conditions. We analysed taxonomic...
Article
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Biodiversity is the engine of ocean ecosystems and economies. Efficiently characterizing it, rapidly at high resolution, is the frontier for understanding global change and management. The biggest impediment to breaching that frontier is inadequate DNA reference libraries, which can currently identify <25% of animal species in environmental profile...
Article
Full-text available
Many jellyfish species are known to cause a painful sting, but box jellyfish (class Cubozoa) are a well-known danger to humans due to exceptionally potent venoms. Cubozoan toxicity has been attributed to the presence and abundance of cnidarian specific pore-forming toxins called jellyfish toxins (JFTs), which are highly hemolytic and cardiotoxic. H...
Article
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Recent advances in molecular sequencing technology and the increased availability of fieldable laboratory equipment have provided researchers with the opportunity to conduct real-time or near real-time gene-based biodiversity assessments of aquatic ecosystems. In this study, we developed a workflow and portable kit for fieldable environmental DNA s...
Article
Full-text available
Recent advances in molecular sequencing technology and the increased availability of fieldable laboratory equipment have provided researchers with the opportunity to conduct real-time or near real-time gene-based biodiversity assessments of aquatic ecosystems. In this study, we developed a workflow and portable kit for fieldable environmental DNA s...
Article
Full-text available
Astarini IA, Ningsih EY, Simanungkalit D, Ardiana SA, Al Malik MD, Yusmalinda NLA, Sembiring A, Pertiwi NPD, Cahyani NKD, Collins A. 2021. Genetic variation of longtail tuna Thunnus tonggol landed in four fish markets in Indonesia based on mitochondrial DNA. Biodiversitas 22: 1644-1651. Longtail tuna (Thunnus tonggol, Family: Scombridae) is an econ...
Preprint
Full-text available
Higher-level relationships of the Hydrozoan subclass Hydroidolina, which encompasses the vast majority of medusozoan cnidarian species diversity, have been elusive to confidently infer. The most widely adopted phylogenetic framework for Hydriodolina based on ribosomal RNA data received low support for several higher level relationships. To address...
Article
On April 10, 2015, three individuals of an undescribed species of ctenophore were observed moving just above the seafloor in the Arecibo Amphitheater inside the Guajataca Canyon, north-northwest of Puerto Rico at a depth of approximately 3,900 m. The ctenophore is distinctive; having two prominent tentacle arms, a body that is rectangular when obse...
Article
Full-text available
Species delimitation in marine taxa is often problematic given large intraspecific variation. Based on extensive, recently published genetic sampling from specimens of the hydrozoan families Campanulariidae, Clytiidae and Obeliidae, we evaluate morphological variation in this group, correlating morphometric and phylogenetic patterns for species del...
Article
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This article describes or redescribes four hexactinellid sponges, namely Poliopogon amadou, Euplectella sanctipauli sp. nov., Bolosoma perezi sp. nov. and Advhena magnifica gen. et sp. nov. P. amadou, E. sanctipauli sp. nov. and B. perezi sp. nov. represent new findings for the South Atlantic deep-sea fauna, including the first record of Bolosoma f...
Article
Despite growing knowledge on deep‐sea benthic fauna, patterns of changes in species composition combining both bathymetric and latitudinal variation are still poorly known. In the first synthesis on the beta diversity patterns of assemblages of hydroids across an entire ocean basin, our aim was to infer limits and gradients of species distribution...
Article
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Snorkelers in mangrove forest waters inhabited by the upside-down jellyfish Cassiopea xamachana report discomfort due to a sensation known as stinging water, the cause of which is unknown. Using a combination of histology, microscopy, microfluidics, videography, molecular biology, and mass spectrometry-based proteomics, we describe C. xamachana sti...
Article
Traits affect the survival and reproduction of individuals in different habitat conditions, ultimately altering their distributions. In the oceans, changes in environmental conditions with bathymetry may influence the occurrence of specific traits. Therefore, characterizing trait variation with depth can illuminate drivers related to the distributi...
Article
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We provide preliminary insights into the global phylogeographic and evolutionary patterns across species of the hydrozoan superfamily Plumularioidea (Cnidaria: Hydrozoa). We analyzed 1,114 16S sequences of 198 putative species of Plumularioidea collected worldwide. We investigated genetic connections and divergence in relation to present‐day and an...
Article
This study reinforces and extends the findings of previous molecular studies showing that there is a close relationship between species assigned to the sponge genera Halicnemia, Higginsia, Paratimea and Stelligera and that the family Heteroxyidae is polyphyletic. The present study has led to the description of one new species of Halicnemia and six...
Article
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Background Anthozoa, Endocnidozoa, and Medusozoa are the 3 major clades of Cnidaria. Medusozoa is further divided into 4 clades, Hydrozoa, Staurozoa, Cubozoa, and Scyphozoa—the latter 3 lineages make up the clade Acraspeda. Acraspeda encompasses extraordinary diversity in terms of life history, numerous nuisance species, taxa with complex eyes riva...
Conference Paper
Gelatinous macrozooplankton can dominate many oligotrophic systems and are especially conspicuous in deep-sea and pelagic ecosystems. Due to the logistical challenges imposed by sea-ice cover, the gelatinous zooplankton fauna of the Arctic Ocean remains largely unknown, with the notable exception of the data collected during the Hidden Ocean series...
Article
This study reinforces and extends the findings of previous molecular studies showing that there is a close relationship between species assigned to the sponge genera Halicnemia, Higginsia, Paratimea and Stelligera and that the family Heteroxyidae is polyphyletic. The present study has led to the description of one new species of Halicnemia and six...
Article
Full-text available
The presence of dark pigment spots associated with primary tentacles (or structures derived from them, i.e., rhopalioids) in Staurozoa was recently overlooked in a study on the evolution of cnidarian eyes (defined as a “region made of photoreceptor cells adjacent to pigment cells”, irrespective of image formation, i.e., including all photoreceptive...
Preprint
Full-text available
The presence of dark pigment spots associated with primary tentacles (or structures derived from them, i.e., rhopalioids) in Staurozoa was recently overlooked in a study on the evolution of cnidarian eyes (defined as a “region made of photoreceptor cells adjacent to pigment cells”, irrespective of image formation, i.e., including all photoreceptive...
Poster
Full-text available
Cnidarians are a stunning group of animals with diverse ecologies, life histories, and morphologies. Relationships within the cnidarian tree of life have been the subject of controversy for many years and the position of several nodes, especially within the Anthozoa, remain unresolved. This project aims to clarify the relationships among and within...
Article
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Marine hydroids are important benthic components of shallow and deep waters worldwide, but their taxonomy is controversial because diagnostic morphological characters to categorize taxa are limited. Their genetic relationships are also little investigated. We tested taxonomic hypotheses within the highly speciose superfamily Plumularioidea by integ...
Article
In this review, we present the current state of biodiversity knowledge for the class Staurozoa (Cnidaria), including richness estimates, geographical and bathymetric distributions, substrate use, feeding, behavior, life cycle, and conservation. Based on non-parametric, statistical incidence estimators, the global inventory of 50 known and accepted...
Article
Full-text available
Background The phylogeny of Cnidaria has been a source of debate for decades, during which nearly all-possible relationships among the major lineages have been proposed. The ecological success of Cnidaria is predicated on several fascinating organismal innovations including stinging cells, symbiosis, colonial body plans and elaborate life histories...
Preprint
Full-text available
The presence of dark pigment spots associated with primary tentacles (or structures derived from them, i.e., rhopalioids) in Staurozoa was recently overlooked in a study on the evolution of cnidarian eyes (defined as a “region made of photoreceptor cells adjacent to pigment cells”, irrespective of image formation, i.e., including all photoreceptive...
Article
Full-text available
Background A number of shelled and shell-less gastropods are known to use multiple defensive mechanisms, including internally generated or externally obtained biochemically active compounds and structures. Within Nudipleura, nudibranchs within Cladobranchia possess such a special defense: the ability to sequester cnidarian nematocysts – small capsu...
Article
We present phylogenetic analyses (parsimony, maximum likelihood and Bayesian inference) for 69 lineages of anthoathecate hydroids based on 18 morphological characters (12 proposed for the first time) plus mitochondrial (16S and COI) and nuclear (18S and 28S) molecular markers. This study aims to test the monophyly of the present concept of the fami...
Article
Full-text available
The Convention on Biological Diversity (CBD) commits its 196 nation parties to conserve biological diversity, use its components sustainably, and share fairly and equitably the benefits from the utilization of genetic resources. The last of these objectives was further codified in the Convention's Nagoya Protocol (NP), which came into effect in 201...