Allen G. Collins
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View article: Benthoplanidae, a new family of benthic ctenophores (Platyctenida), based on morphological and genetic data
Benthoplanidae, a new family of benthic ctenophores (Platyctenida), based on morphological and genetic data Open
We present a phylogenetic analysis of benthic ctenophores of the order Platyctenida, sampling all but one genus. Using complete mitochondrial genomes and nuclear ribosomal data and a reassessment of anatomy, our integrated analysis uncover…
View article: Taxon‐specific <scp>BLAST</scp> percent identity thresholds for identification of unknown sequences using metabarcoding
Taxon‐specific <span>BLAST</span> percent identity thresholds for identification of unknown sequences using metabarcoding Open
The identification of organisms in environmental samples using metabarcoding relies on factors such as taxonomic assignment methods, genetic markers, reference databases and confidence thresholds for taxonomic assignment. Because lineages …
View article: Anthozoan eDNA primer set characterizes Ctenophora and Medusozoa inhabiting mesophotic and deep waters off the Gulf Coast of the southern USA
Anthozoan eDNA primer set characterizes Ctenophora and Medusozoa inhabiting mesophotic and deep waters off the Gulf Coast of the southern USA Open
While gelatinous zooplankton (GZ) constitute a vital component of the marine food web, understanding their biology and ecology has been hindered because traditional collection methods often destroy their fragile bodies. Environmental DNA (…
View article: DNA barcoding deep-water zooplankton from the Gulf of Alaska, North Pacific Ocean
DNA barcoding deep-water zooplankton from the Gulf of Alaska, North Pacific Ocean Open
DNA barcoding is a method of identifying individual organisms using short DNA fragments matched to a database of reference sequences. For metazoan plankton, a high proportion of species that reside in the deep ocean still lack reliable ref…
View article: Species-specific primer development for identifying the major jellyfish contributors to DNA in the sediments
Species-specific primer development for identifying the major jellyfish contributors to DNA in the sediments Open
Gelatinous zooplankton ("jellies") have been hypothesized to be the missing link in balancing the current carbon budget mismatch in the "biological carbon pump." During and just after jellyfish bloom events, large amounts of carbon are pro…
View article: Phenol-Chloroform environmental DNA (eDNA) Extraction Protocol for Okeanos Explorer Specimens v1
Phenol-Chloroform environmental DNA (eDNA) Extraction Protocol for Okeanos Explorer Specimens v1 Open
This protocol is used to extract environmental DNA (eDNA) from disc filters through which water samples taken by NOAA Ocean Exporation's NOAA Ship Okeanos Explorer have been filtered.
View article: Complete linear mitochondrial genomes for <i>Cephea cephea</i> and <i>Mastigias albipunctata</i> (Scyphozoa: Rhizostomeae), with an analysis of phylogenetic relationships
Complete linear mitochondrial genomes for <i>Cephea cephea</i> and <i>Mastigias albipunctata</i> (Scyphozoa: Rhizostomeae), with an analysis of phylogenetic relationships Open
Jellyfishes of the order Rhizostomeae include ecologically and economically important species predisposed to forming massive aggregations. This study reports the first complete mitochondrial genome of two rhizostomes: Cephea cephea (Forskå…
View article: Copula lucentia sp. nov., a new box jellyfish (Cnidaria: Cubozoa: Carybdeida) from Western Mediterranean Sea
Copula lucentia sp. nov., a new box jellyfish (Cnidaria: Cubozoa: Carybdeida) from Western Mediterranean Sea Open
A new species of box jellyfish, Copula lucentia sp. nov., is described from El Campello, Spain, and compared to the holotype of Copula sivickisi that was successfully recovered after being lost for almost 60 years. So far, the only cubozoa…
View article: Redescription of the deep-sea benthic ctenophore genus Tjalfiella from the North Atlantic (Class Tentaculata, Order Platyctenida, Family Tjalfiellidae)
Redescription of the deep-sea benthic ctenophore genus Tjalfiella from the North Atlantic (Class Tentaculata, Order Platyctenida, Family Tjalfiellidae) Open
Some of the most fascinating and poorly known animals on this planet are comb jellies of the phylum Ctenophora. About one-quarter of ctenophore richness is encompassed by the benthic species of the order Platyctenida, nearly all known from…
View article: A Cnidarian Phylogenomic Tree Fitted With Hundreds of 18S Leaves
A Cnidarian Phylogenomic Tree Fitted With Hundreds of 18S Leaves Open
Cnidarians are critical members of aquatic communities and have been an experimental system for a diversity of research areas ranging from development to biomechanics to global change biology. Yet, we still lack a well-resolved, taxonomica…
View article: Integrating molecular and morphological evidence revives the blubber jellyfish, <i>Catostylus purpurus</i> (Scyphozoa: Rhizostomeae; Catostylidae) of the Indo-Pacific (Philippines)
Integrating molecular and morphological evidence revives the blubber jellyfish, <i>Catostylus purpurus</i> (Scyphozoa: Rhizostomeae; Catostylidae) of the Indo-Pacific (Philippines) Open
Jellyfishes have ecological and societal value, but our understanding of taxonomic identity of many jellyfish species remains limited. Here, an approach integrating morphological and molecular (16S ribosomal RNA and cytochrome oxidase I) d…
View article: Copula lucentia sp. nov., a new box jellyfish (Cnidaria: Cubozoa: Carybdeida) from Western Mediterranean Sea
Copula lucentia sp. nov., a new box jellyfish (Cnidaria: Cubozoa: Carybdeida) from Western Mediterranean Sea Open
A new species of box jellyfish, Copula lucentia sp. nov., is described from El Campello, Alicante, Spain and compared to the holotype of Copula sivickisi that was successfully recovered after being lost for almost 60 years. So far, the onl…
View article: A morphological review of the jellyfish genus Nausithoe Kölliker, 1853 (Nausithoideae, Coronatae, Scyphozoa, Cnidaria)
A morphological review of the jellyfish genus Nausithoe Kölliker, 1853 (Nausithoideae, Coronatae, Scyphozoa, Cnidaria) Open
In this study we address the diversity of the scyphozoan jellyfish genus Nausithoe Kölliker, 1853 (Nausithoidae, Coronatae), questioning the feasibility of using some characters of the medusa stage to identify species and filling in gaps c…
View article: Drivers behind the diversity and distribution of a widespread midwater narcomedusa
Drivers behind the diversity and distribution of a widespread midwater narcomedusa Open
Narcomedusae play a key role as top‐down regulators in the midwater, the largest and most understudied biome on Earth. Here, we used ecological niche modeling in three‐dimensions (3D), ecomorphology, and phylogeny, to answer evolutionary a…
View article: A phylogenomic approach to resolving interrelationships of polyclad flatworms, with implications for life-history evolution
A phylogenomic approach to resolving interrelationships of polyclad flatworms, with implications for life-history evolution Open
Platyhelminthes (flatworms) are a diverse invertebrate phylum useful for exploring life-history evolution. Within Platyhelminthes, only two clades develop through a larval stage: free-living polyclads and parasitic neodermatans. Neodermata…
View article: Heterogeneity in diagnostic characters across ecoregions: A case study with Botrynema (Hydrozoa: Trachylina: Halicreatidae)
Heterogeneity in diagnostic characters across ecoregions: A case study with Botrynema (Hydrozoa: Trachylina: Halicreatidae) Open
Introduction Botrynema, a genus of medusozoans in the trachyline family Halicreatidae, currently contains two species: B. brucei and B. ellinorae , distinguished by the presence or absence, respectively, of an apical knob as a diagnostic c…
View article: Table S2 from A phylogenomic approach to resolving interrelationships of polyclad flatworms, with implications for life-history evolution
Table S2 from A phylogenomic approach to resolving interrelationships of polyclad flatworms, with implications for life-history evolution Open
Transcriptome assembly and orthology assignment statistics for samples included in our polyclad phylogenetic reconstruction (Figure 1).
View article: Table S3 from A phylogenomic approach to resolving interrelationships of polyclad flatworms, with implications for life-history evolution
Table S3 from A phylogenomic approach to resolving interrelationships of polyclad flatworms, with implications for life-history evolution Open
Mode of development for species and genera in this study recorded from the literature and personal observation.
View article: Table S1 from A phylogenomic approach to resolving interrelationships of polyclad flatworms, with implications for life-history evolution
Table S1 from A phylogenomic approach to resolving interrelationships of polyclad flatworms, with implications for life-history evolution Open
Samples included in our polyclad phylogenetic reconstruction (Figure 1). Table includes SRA accession numbers, collecting locality, and method of identification.
View article: A morphological review of the jellyfish genus Nausithoe Kölliker, 1853 (Nausithoideae, Coronatae, Scyphozoa, Cnidaria)
A morphological review of the jellyfish genus Nausithoe Kölliker, 1853 (Nausithoideae, Coronatae, Scyphozoa, Cnidaria) Open
This dataset contains the digitized treatments in Plazi based on the original journal article Molinari, Clarissa G., Collins, Allen G., Morandini, André C. (2023): A morphological review of the jellyfish genus Nausithoe Kölliker, 1853 (Nau…
View article: The time is right for an Antarctic biorepository network
The time is right for an Antarctic biorepository network Open
Antarctica is a central driver of the Earth’s climate and health. The Southern Ocean surrounding Antarctica serves as a major sink for anthropogenic CO2 and heat (1), and the loss of Antarctic ice sheets contributes significantly to sea le…
View article: A cnidarian phylogenomic tree fitted with hundreds of 18S leaves
A cnidarian phylogenomic tree fitted with hundreds of 18S leaves Open
Cnidarians are critical members of aquatic communities and have been an experimental system for a diversity of research areas ranging from development to biomechanics to global change biology. Yet we still lack a well-resolved, taxonomical…
View article: Morphology is not always useful for diagnosis, and that’s ok: Species hypotheses should not be bound to a class of data. Reply to Brown and Gibbons (S Afr J Sci. 2022;118(9/10), Art. #12590)
Morphology is not always useful for diagnosis, and that’s ok: Species hypotheses should not be bound to a class of data. Reply to Brown and Gibbons (S Afr J Sci. 2022;118(9/10), Art. #12590) Open
This paper serves as a reply to the Commentary by Brown and Gibbons (S Afr J Sci. 2022;118(9/10), Art. #12590) on our recently published paper on systematics of the moon jellyfish genus Aurelia (Lawley et al. PeerJ 2021;9, e11954)). We emp…
View article: Skimming for barcodes: rapid production of mitochondrial genome and nuclear ribosomal repeat reference markers through shallow shotgun sequencing
Skimming for barcodes: rapid production of mitochondrial genome and nuclear ribosomal repeat reference markers through shallow shotgun sequencing Open
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 spec…