On September 11, 2022, two megamouth sharks (Megachasma pelagios), estimated at 3.7–4.6 m TL, wer... more On September 11, 2022, two megamouth sharks (Megachasma pelagios), estimated at 3.7–4.6 m TL, were observed swimming together near the surface about 39 km off the coast of San Diego, CA, USA. Megamouth sharks are rarely observed pelagic sharks, and the film from this encounter provided new insight into the social behavior of this species. We attempt to put the behavior of these two individuals into the context of past sightings, known megamouth shark biology, and with analogous behavior observed in other shark and pelagic fish species.
Fish are the most diverse and widely distributed vertebrates, yet little is known about the micro... more Fish are the most diverse and widely distributed vertebrates, yet little is known about the microbial ecology of fishes nor the biological and environmental factors that influence the fish microbiome. The microbiota from 101 species of Southern California marine fishes, spanning 22 orders, 55 families, and 83 genera representing ~25% of local marine fish diversity, was analyzed to identify patterns that explain microbial diversity patterns in a geographical subset of marine fish biodiversity. We compared fish microbiomes (gill, skin, midgut, and hindgut) using alpha, beta, and gamma diversity along with establishing a novel method to estimate microbial biomass (Qiime2 plugin katharoseq). For oceanic fishes from the neritic zone, host size and distance from shore were negatively associated with microbial biomass densities and diversity in the gills. Body site was the strongest driver for beta diversity with strong evidence of phylosymbiosis observed across the gill, skin, and hindgut...
FIGURE 8. Distribution records for selected species of Cirrhilabrus: closed circle, C. cyanogular... more FIGURE 8. Distribution records for selected species of Cirrhilabrus: closed circle, C. cyanogularis; closed square, C. rubripinnis; open circle, C. filamentosus; half circle, C. filamentosus + C. cyanogularis; closed triangle, C. tonozukai; half triangle, C. tonozukai + C. filamentosus; closed star, C. tonozukai + C. cyanogularis.
FIGURE 6. Cirrhilabrus cyanogularis, aquarium specimen from Sulawesi, Indonesia. Specimen not ret... more FIGURE 6. Cirrhilabrus cyanogularis, aquarium specimen from Sulawesi, Indonesia. Specimen not retained. Photo by K. Endoh.
FIGURE 7. Cirrhilabrus sanguineus, freshly euthanized female, ZRC 60168, 41.2 mm SL, from Cannoni... more FIGURE 7. Cirrhilabrus sanguineus, freshly euthanized female, ZRC 60168, 41.2 mm SL, from Cannoniers Point, off the northern coast of Mauritius. DNA sample obtained from right pectoral fin. Photo by K. Lim.
FIGURE 4. Cirrhilabrus sanguineus, x-radiograph of BPBM 24779, 66.5 mm SL, neotype (above), and B... more FIGURE 4. Cirrhilabrus sanguineus, x-radiograph of BPBM 24779, 66.5 mm SL, neotype (above), and BPBM 22542, 48.3 mm SL (below). Radiograph by B.W. Frable.
Conniella apterygia is redescribed from re-examination of the holotype, two paratypes, and six ad... more Conniella apterygia is redescribed from re-examination of the holotype, two paratypes, and six additional specimens. The genus is closely allied to Cirrhilabrus, sharing similarities in general morphological and meristic details, but is separated from Cirrhilabrus and most other labrid fishes in lacking pelvic fins and a pelvic girdle. Recent molecular phylogenetic studies have provided strong evidence for the deep nesting of Conniella within Cirrhilabrus, contradicting its generic validity and suggesting that the loss of pelvic elements is autapomorphic. Consequently, the species is redescribed and assigned to the genus Cirrhilabrus, as Cirrhilabrus apterygia new combination. The pelvic morphologies of related cirrhilabrin labrids are discussed, and a new synapomorphy is identified for Paracheilinus.
This paper is a checklist of the fishes that have been documented, through both published and unp... more This paper is a checklist of the fishes that have been documented, through both published and unpublished sources, in marine and estuarine waters, and out 200 miles, from the United States-Canadian border on the Beaufort Sea to Cabo San Lucas, Mexico. A minimum of 241 families and 1,644 species are known within this range, including both native and nonnative species. For each of these species, we include maximum size, geographic and depth ranges, whether it is native or nonnative, as well as a brief mention of any taxonomic issues.
DNA metabarcoding is an important tool for molecular ecology. However, its effectiveness hinges o... more DNA metabarcoding is an important tool for molecular ecology. However, its effectiveness hinges on the quality of reference sequence databases and classification parameters employed. Here we evaluate the performance of MiFish 12S taxonomic assignments using a case study of California Current Large Marine Ecosystem fishes to determine best practices for metabarcoding. Specifically, we use a taxonomy cross-validation by identity framework to compare classification performance between a global database comprised of all available sequences and a curated database that only includes sequences of fishes from the California Current Large Marine Ecosystem. We demonstrate that the curated, regional database provides higher assignment accuracy than the comprehensive global database. We also document a tradeoff between accuracy and misclassification across a range of taxonomic cutoff scores, highlighting the importance of parameter selection for taxonomic classification. Furthermore, we compare...
Biodiversity Information Science and Standards, 2018
The Scripps Institution of Oceanography (SIO) at the University of California, San Diego maintain... more The Scripps Institution of Oceanography (SIO) at the University of California, San Diego maintains one of the largest combined oceanographic collections in the world comprising four collections: Geological (sediment cores and dredged rocks), Pelagic Invertebrates, Benthic Invertebrates and Marine Vertebrates. After surviving threats of dissolution, the SIO Collections are now securely funded and have been able to make other collections available to the scientific community. Over the last few years, both the Marine Vertebrate (SIO-MVC) and Benthic Invertebrate (SIO-BIC) Collections have received National Science Foundation (NSF) and institutional funding to integrate important at-risk collections from University of California, Los Angeles (UCLA), the Monterey Bay Aquarium Research Institute (MBARI) and the University of Victoria. The UCLA Ichthyological Collection, around 9000 lots, was at risk of disposal due to hazardous material concerns and lack of institutional support. The coll...
Cirrhilabrus cyanogularis, sp. nov., is described on the basis of the holotype and three paratype... more Cirrhilabrus cyanogularis, sp. nov., is described on the basis of the holotype and three paratypes from Banguingui Island, Sulu Archipelago, Philippines, and a paratype from Sulawesi, Indonesia. The new species belongs to a complex consisting of C. filamentosus (Klausewitz), C. rubripinnis Randall & Carpenter, and C. tonozukai Allen & Kuiter. Aside from similar nuptial male coloration, the four species share the following character combination: a single row of cheek scales; dorsal-fin spines taller than dorsal-fin rays (slightly incised between spinuous and soft dorsal fin in C. rubripinnis and C. cyanogularis; last three dorsal-fin spines converging to form a single filament in C. tonozukai and C. filamentosus); relatively long pelvic fins (reaching past anal-fin origin); and isthmus and breast blue. The new species differs from the other members of the complex in lacking a dorsal filament, as well as possessing six predorsal scales, more extensive blue coloration on the isthmus, l...
Pomacentrus vatosoa, new species, is described on the basis of four specimens collected from Nosy... more Pomacentrus vatosoa, new species, is described on the basis of four specimens collected from Nosy Faho, Madagascar. The new species is distinctive in having a pearlescent-white body with a large black spot midlaterally behind the pectoral fin, a black saddle of similar size on the dorsal edge of the caudal peduncle, and a black recurved band from the orbit to origin of dorsal fin. Aside from details in live coloration, the new species is readily diagnosed from congeners in having the following combination of characters: dorsal-fin rays XIV, 13–14; anal-fin rays II, 14; pectoral-fin rays 18–19; tubed lateral scales 19–20; gill rakers 5–6+17–18 = 22–24; infraorbitals naked; teeth on lower jaw partly biserial; no distinct notch between infraorbitals 1 and 2; and a crescent opening of the supraorbital canal above the eye. The new species appears to be most closely related to Pomacentrus atriaxillaris on the basis of meristic data, though comparative molecular sequences for P. atriaxillaris are lacking. Assignment of the new species to the genus Pomacentrus is accompanied with a brief discussion of the systematic contention within the Pomacentridae.
The labrid fish Cirrhilabrus sanguineus Cornic is redescribed on the basis of the neotype, two ma... more The labrid fish Cirrhilabrus sanguineus Cornic is redescribed on the basis of the neotype, two male specimens, and an additional female specimen recently collected from the northern coast of Mauritius. We provide new live and nuptial colouration descriptions, as well as the first documented female specimen for the species. we also include a molecular phylogenetic analysis of related species, with brief comments on phylogenetic interpretation of putative relationships amongst members of the genus Cirrhilabrus.
The data presented herein support the article "Molecular phylogenetics of the Neotropical fi... more The data presented herein support the article "Molecular phylogenetics of the Neotropical fish family Prochilodontidae (Teleostei: Characiformes)" (B.F. Melo, B.L. Sidlauskas, B.W. Frable, K. Hoekzema, R.P. Vari, C. Oliveira, 2016) [1], which inferred phylogenetic relationships of the prochilodontids from an alignment of three mitochondrial and three nuclear loci (5279 bp) for all 21 recognized prochilodontid species and 22 related species. Herein, we provide primer sequences, museum voucher information and GenBank accession numbers. Additionally, we more fully describe the maximum-likelihood and Bayesian phylogenetic analyses of the concatenated dataset, detail the Bayesian species tree analysis, and provide the maximum likelihood topologies congruent with prior morphological hypotheses that were compared with the unconstrained tree using Shimodaira-Hasegawa tests.
Molecular phylogenetics and evolution, Sep 2, 2016
Migratory detritivores of the characiform family Prochilodontidae occur throughout the freshwater... more Migratory detritivores of the characiform family Prochilodontidae occur throughout the freshwaters of much of South America. Prochilodontids often form massive populations and many species achieve substantial body sizes; a combination that makes them one of the most commercially important fish groups on the continent. Their economic significance notwithstanding, prochilodontids have never been the subject of a comprehensive molecular phylogenetic analysis. Using three mitochondrial and three nuclear loci spanning all prochilodontid species, we generated a novel phylogenetic hypothesis for the family. Our results strongly support monophyly of the family and the three included genera. A novel, highly supported placement of Ichthyoelephas sister to the clade containing Prochilodus and Semaprochilodus diverges from a previous morphological hypothesis. Most previously hypothesized interspecific relationships are corroborated and some longstanding polytomies within Prochilodus and Semapro...
On September 11, 2022, two megamouth sharks (Megachasma pelagios), estimated at 3.7–4.6 m TL, wer... more On September 11, 2022, two megamouth sharks (Megachasma pelagios), estimated at 3.7–4.6 m TL, were observed swimming together near the surface about 39 km off the coast of San Diego, CA, USA. Megamouth sharks are rarely observed pelagic sharks, and the film from this encounter provided new insight into the social behavior of this species. We attempt to put the behavior of these two individuals into the context of past sightings, known megamouth shark biology, and with analogous behavior observed in other shark and pelagic fish species.
Fish are the most diverse and widely distributed vertebrates, yet little is known about the micro... more Fish are the most diverse and widely distributed vertebrates, yet little is known about the microbial ecology of fishes nor the biological and environmental factors that influence the fish microbiome. The microbiota from 101 species of Southern California marine fishes, spanning 22 orders, 55 families, and 83 genera representing ~25% of local marine fish diversity, was analyzed to identify patterns that explain microbial diversity patterns in a geographical subset of marine fish biodiversity. We compared fish microbiomes (gill, skin, midgut, and hindgut) using alpha, beta, and gamma diversity along with establishing a novel method to estimate microbial biomass (Qiime2 plugin katharoseq). For oceanic fishes from the neritic zone, host size and distance from shore were negatively associated with microbial biomass densities and diversity in the gills. Body site was the strongest driver for beta diversity with strong evidence of phylosymbiosis observed across the gill, skin, and hindgut...
FIGURE 8. Distribution records for selected species of Cirrhilabrus: closed circle, C. cyanogular... more FIGURE 8. Distribution records for selected species of Cirrhilabrus: closed circle, C. cyanogularis; closed square, C. rubripinnis; open circle, C. filamentosus; half circle, C. filamentosus + C. cyanogularis; closed triangle, C. tonozukai; half triangle, C. tonozukai + C. filamentosus; closed star, C. tonozukai + C. cyanogularis.
FIGURE 6. Cirrhilabrus cyanogularis, aquarium specimen from Sulawesi, Indonesia. Specimen not ret... more FIGURE 6. Cirrhilabrus cyanogularis, aquarium specimen from Sulawesi, Indonesia. Specimen not retained. Photo by K. Endoh.
FIGURE 7. Cirrhilabrus sanguineus, freshly euthanized female, ZRC 60168, 41.2 mm SL, from Cannoni... more FIGURE 7. Cirrhilabrus sanguineus, freshly euthanized female, ZRC 60168, 41.2 mm SL, from Cannoniers Point, off the northern coast of Mauritius. DNA sample obtained from right pectoral fin. Photo by K. Lim.
FIGURE 4. Cirrhilabrus sanguineus, x-radiograph of BPBM 24779, 66.5 mm SL, neotype (above), and B... more FIGURE 4. Cirrhilabrus sanguineus, x-radiograph of BPBM 24779, 66.5 mm SL, neotype (above), and BPBM 22542, 48.3 mm SL (below). Radiograph by B.W. Frable.
Conniella apterygia is redescribed from re-examination of the holotype, two paratypes, and six ad... more Conniella apterygia is redescribed from re-examination of the holotype, two paratypes, and six additional specimens. The genus is closely allied to Cirrhilabrus, sharing similarities in general morphological and meristic details, but is separated from Cirrhilabrus and most other labrid fishes in lacking pelvic fins and a pelvic girdle. Recent molecular phylogenetic studies have provided strong evidence for the deep nesting of Conniella within Cirrhilabrus, contradicting its generic validity and suggesting that the loss of pelvic elements is autapomorphic. Consequently, the species is redescribed and assigned to the genus Cirrhilabrus, as Cirrhilabrus apterygia new combination. The pelvic morphologies of related cirrhilabrin labrids are discussed, and a new synapomorphy is identified for Paracheilinus.
This paper is a checklist of the fishes that have been documented, through both published and unp... more This paper is a checklist of the fishes that have been documented, through both published and unpublished sources, in marine and estuarine waters, and out 200 miles, from the United States-Canadian border on the Beaufort Sea to Cabo San Lucas, Mexico. A minimum of 241 families and 1,644 species are known within this range, including both native and nonnative species. For each of these species, we include maximum size, geographic and depth ranges, whether it is native or nonnative, as well as a brief mention of any taxonomic issues.
DNA metabarcoding is an important tool for molecular ecology. However, its effectiveness hinges o... more DNA metabarcoding is an important tool for molecular ecology. However, its effectiveness hinges on the quality of reference sequence databases and classification parameters employed. Here we evaluate the performance of MiFish 12S taxonomic assignments using a case study of California Current Large Marine Ecosystem fishes to determine best practices for metabarcoding. Specifically, we use a taxonomy cross-validation by identity framework to compare classification performance between a global database comprised of all available sequences and a curated database that only includes sequences of fishes from the California Current Large Marine Ecosystem. We demonstrate that the curated, regional database provides higher assignment accuracy than the comprehensive global database. We also document a tradeoff between accuracy and misclassification across a range of taxonomic cutoff scores, highlighting the importance of parameter selection for taxonomic classification. Furthermore, we compare...
Biodiversity Information Science and Standards, 2018
The Scripps Institution of Oceanography (SIO) at the University of California, San Diego maintain... more The Scripps Institution of Oceanography (SIO) at the University of California, San Diego maintains one of the largest combined oceanographic collections in the world comprising four collections: Geological (sediment cores and dredged rocks), Pelagic Invertebrates, Benthic Invertebrates and Marine Vertebrates. After surviving threats of dissolution, the SIO Collections are now securely funded and have been able to make other collections available to the scientific community. Over the last few years, both the Marine Vertebrate (SIO-MVC) and Benthic Invertebrate (SIO-BIC) Collections have received National Science Foundation (NSF) and institutional funding to integrate important at-risk collections from University of California, Los Angeles (UCLA), the Monterey Bay Aquarium Research Institute (MBARI) and the University of Victoria. The UCLA Ichthyological Collection, around 9000 lots, was at risk of disposal due to hazardous material concerns and lack of institutional support. The coll...
Cirrhilabrus cyanogularis, sp. nov., is described on the basis of the holotype and three paratype... more Cirrhilabrus cyanogularis, sp. nov., is described on the basis of the holotype and three paratypes from Banguingui Island, Sulu Archipelago, Philippines, and a paratype from Sulawesi, Indonesia. The new species belongs to a complex consisting of C. filamentosus (Klausewitz), C. rubripinnis Randall & Carpenter, and C. tonozukai Allen & Kuiter. Aside from similar nuptial male coloration, the four species share the following character combination: a single row of cheek scales; dorsal-fin spines taller than dorsal-fin rays (slightly incised between spinuous and soft dorsal fin in C. rubripinnis and C. cyanogularis; last three dorsal-fin spines converging to form a single filament in C. tonozukai and C. filamentosus); relatively long pelvic fins (reaching past anal-fin origin); and isthmus and breast blue. The new species differs from the other members of the complex in lacking a dorsal filament, as well as possessing six predorsal scales, more extensive blue coloration on the isthmus, l...
Pomacentrus vatosoa, new species, is described on the basis of four specimens collected from Nosy... more Pomacentrus vatosoa, new species, is described on the basis of four specimens collected from Nosy Faho, Madagascar. The new species is distinctive in having a pearlescent-white body with a large black spot midlaterally behind the pectoral fin, a black saddle of similar size on the dorsal edge of the caudal peduncle, and a black recurved band from the orbit to origin of dorsal fin. Aside from details in live coloration, the new species is readily diagnosed from congeners in having the following combination of characters: dorsal-fin rays XIV, 13–14; anal-fin rays II, 14; pectoral-fin rays 18–19; tubed lateral scales 19–20; gill rakers 5–6+17–18 = 22–24; infraorbitals naked; teeth on lower jaw partly biserial; no distinct notch between infraorbitals 1 and 2; and a crescent opening of the supraorbital canal above the eye. The new species appears to be most closely related to Pomacentrus atriaxillaris on the basis of meristic data, though comparative molecular sequences for P. atriaxillaris are lacking. Assignment of the new species to the genus Pomacentrus is accompanied with a brief discussion of the systematic contention within the Pomacentridae.
The labrid fish Cirrhilabrus sanguineus Cornic is redescribed on the basis of the neotype, two ma... more The labrid fish Cirrhilabrus sanguineus Cornic is redescribed on the basis of the neotype, two male specimens, and an additional female specimen recently collected from the northern coast of Mauritius. We provide new live and nuptial colouration descriptions, as well as the first documented female specimen for the species. we also include a molecular phylogenetic analysis of related species, with brief comments on phylogenetic interpretation of putative relationships amongst members of the genus Cirrhilabrus.
The data presented herein support the article "Molecular phylogenetics of the Neotropical fi... more The data presented herein support the article "Molecular phylogenetics of the Neotropical fish family Prochilodontidae (Teleostei: Characiformes)" (B.F. Melo, B.L. Sidlauskas, B.W. Frable, K. Hoekzema, R.P. Vari, C. Oliveira, 2016) [1], which inferred phylogenetic relationships of the prochilodontids from an alignment of three mitochondrial and three nuclear loci (5279 bp) for all 21 recognized prochilodontid species and 22 related species. Herein, we provide primer sequences, museum voucher information and GenBank accession numbers. Additionally, we more fully describe the maximum-likelihood and Bayesian phylogenetic analyses of the concatenated dataset, detail the Bayesian species tree analysis, and provide the maximum likelihood topologies congruent with prior morphological hypotheses that were compared with the unconstrained tree using Shimodaira-Hasegawa tests.
Molecular phylogenetics and evolution, Sep 2, 2016
Migratory detritivores of the characiform family Prochilodontidae occur throughout the freshwater... more Migratory detritivores of the characiform family Prochilodontidae occur throughout the freshwaters of much of South America. Prochilodontids often form massive populations and many species achieve substantial body sizes; a combination that makes them one of the most commercially important fish groups on the continent. Their economic significance notwithstanding, prochilodontids have never been the subject of a comprehensive molecular phylogenetic analysis. Using three mitochondrial and three nuclear loci spanning all prochilodontid species, we generated a novel phylogenetic hypothesis for the family. Our results strongly support monophyly of the family and the three included genera. A novel, highly supported placement of Ichthyoelephas sister to the clade containing Prochilodus and Semaprochilodus diverges from a previous morphological hypothesis. Most previously hypothesized interspecific relationships are corroborated and some longstanding polytomies within Prochilodus and Semapro...
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Papers by Benjamin Frable