FIGURE 1. Three Trachinocephalus specimens collected from Papua New Guinean waters. (A) T. gaugui... more FIGURE 1. Three Trachinocephalus specimens collected from Papua New Guinean waters. (A) T. gauguini, NTUM 11085, SL = 51.3 mm (B) T. gauguini, NTUM 11212, SL = 76.4 mm (C) T. trachinus, NTUM 11201, SL = 40.6 mm. (Photographed by J.-N. Chen).
Imagery has become a key tool for assessing deep-sea megafaunal biodiversity, historically based ... more Imagery has become a key tool for assessing deep-sea megafaunal biodiversity, historically based on physical sampling using fishing gears. Image datasets provide quantitative and repeatable estimates, small-scale spatial patterns and habitat descriptions. However, taxon identification from images is challenging and often relies on morphotypes without considering a taxonomic framework. Taxon identification is particularly challenging in regions where the fauna is poorly known and/or highly diverse. Furthermore, the efficiency of imagery and physical sampling may vary among habitat types. Here, we compared biodiversity metrics (alpha and gamma diversity, composition) based on physical sampling (dredging and trawling) and towed-camera still images (1) along the upper continental slope of Papua New Guinea (sedimented slope with wood-falls, a canyon and cold seeps), and (2) on the outer slopes of the volcanic islands of Mayotte, dominated by hard bottoms. The comparison was done on selec...
In the northern South China Sea (SCS) we explored methane dynamics in the water column during SON... more In the northern South China Sea (SCS) we explored methane dynamics in the water column during SONNE-cruise SO266 in October/November 2018. Two depth zones contained elevated methane concentrations: the upper 400 m (<10 nM) and near gas seeps at the seafloor (up to 2100 nM). Seeps occurred at Four Way Closure Ridge (FWCR) at the active continental margin as well as at Southern Summit Formosa Ridge (SSFR) at the passive continental margin. In the upper ocean, methane dynamics correlated with (1) temperature, (2) water masses, and (3) suspended matter. In the first case, elevated methane concentrations and aerobic methane oxidation rates (MOxs) occurred in water with temperatures > 10°C and > 20°C, respectively. Both 16S rRNA gene and pmoA amplicon analyses revealed distinct microbial and methanotrophic communities in water with temperature of 27°C, ∼10°C, and 3°C. Second, we found elevated methane concentrations in 200–400 m in the FWCR-region whereas increased methane concentrations occurred in the uppermost 100 m above SSFR. The deeper plume above FWCR might be due to an intrusion of the Kuroshio water mass into SCS keeping the methane from being aerobically oxidized in the warm surface water and vented to the atmosphere. Finally, all peak methane concentrations occurred in water depth, with rather low backscatter, i.e., in water depth with less suspended matter. At the seafloor, ocean currents and long-term seepage appeared to control methane dynamics. We derived methane fluxes of 0.08–0.12 mmol m–2 d–1 from a 4.5 km2 area at FWCR and of 3.0–79.9 mmol m–2 d–1 from a 0.01 km2 area at SSFR. Repetitive sampling of the area at SSFR indicated that changing directions of ocean currents possibly affected methane concentrations and thus flux. In contrast to these seepage sites with distinct methane plumes, retrieval of drilling equipment produced no methane plume. Even gas emission triggered by seafloor drilling did not supply measureable methane concentrations after 3 h, but caused an increase in methanotrophic activity as determined by rate measurements and molecular-biological analyses. Apparently, only long-term seepage can generate methane anomalies in the ocean.
FIGURE 2. Distribution records of Trachinocephalus gauguini. Circle, occurrence described in Pola... more FIGURE 2. Distribution records of Trachinocephalus gauguini. Circle, occurrence described in Polanco et al. (2016); triangle, new record from Papua New Guinea (this study).
The Elopomorpha (eels and relatives) is a morphologically diverse group of predominantly marine t... more The Elopomorpha (eels and relatives) is a morphologically diverse group of predominantly marine teleost fishes comprising about 1000 species placed in 25 families. It is one of the three major living teleost lineages along with the Osteoglossomorpha and Clupeocephala. Among a few morphological synapomorphies that have been offered as evidence for the monophyly of the Elopomorpha, the remarkable leptocephalus larvae stand out. Several studies aiming at reconstructing the elopomorph phylogeny using morphological or molecular characters led to inconsistent results. In this study, we have tested previous hypotheses regarding inter-and intra-relationships of the Elopomorpha using a multi-locus dataset composed of three nuclear and three mitochondrial genes. Our analyses were based on likelihood phylogenetic reconstruction methods using different character-weighting data matrices and gene partition schemes to assess reliability of our findings. Our results confirm the respective monophyly of the Elopomorpha, Osteoglossomorpha and Clupeocephala. The majority of our analyses identify the Elopomorpha as the sister group of a clade containing the rest of the Teleostei. Within the Elopomorpha, the Elopiformes is the sister group of the remaining taxa. The Albuliformes sensu Forey et al. (1996) and the Notacanthiformes are never sister-taxa in our phylogenetic trees, in contradiction with the recent mitogenomic hypothesis and current classification. Our results place the Notacanthiformes as the sister group of the Anguilliformes, including Saccopharyngiformes. Among anguilliforms, the families Congridae and Muraenesocidae are not monophyletic. The recently discovered anguilliform ''living fossil'' family Protanguillidae is not the sister group of the remaining Anguilliformes, instead, the sister group of the Synaphobranchidae. Based on the results presented here, we propose a revised classification for the Elopomorpha, comprised of four orders, including a resurrected Notacanthiformes but surrendering the Saccopharyngiformes. Within Anguilliformes, we recognized four monophyletic suborders named Protanguilloidei, Muraenoidei, Anguilloidei, and Congroidei.
The Acanthomorpha is the largest group of teleost fishes with about one third of extant vertebrat... more The Acanthomorpha is the largest group of teleost fishes with about one third of extant vertebrate species. In the course of its evolution this lineage experienced several episodes of radiation, leading to a large number of descendant lineages differing profoundly in morphology, ecology, distribution and behavior. Although Acanthomorpha was recognized decades ago, we are only now beginning to decipher its large-scale, time-calibrated phylogeny, a prerequisite to test various evolutionary hypotheses explaining the tremendous diversity of this group. In this study, we provide new insights into the early evolution of the acanthomorphs and the euteleost allies based on the phylogenetic analysis of a newly developed dataset combining nine nuclear and mitochondrial gene markers. Our inferred tree is time-calibrated using 15 fossils, some of which have not been used before. While our phylogeny strongly supports a monophyletic Neoteleostei, Ctenosquamata (i.e., Acanthomorpha plus Myctophiformes), and Acanthopterygii, we find weak support (bootstrap value < 48%) for the traditionally defined Acanthomorpha, as well as evidence of non-monophyly for the traditional Paracanthopterygii, Beryciformes, and Percomorpha. We corroborate the new Paracanthopterygii sensu including Polymixiiformes, Zeiformes, Gadiformes, Percopsiformes, and likely the enigmatic Stylephorus chordatus. Our timetree largely agrees with other recent studies based on nuclear loci in inferring an Early Cretaceous origin for the acanthomorphs followed by a Late Cretaceous/Early Paleogene radiation of major lineages. This is in contrast to mitogenomic studies mostly inferring Jurassic or even Triassic ages for the origin of the acanthomorphs. We compare our results to those of previous studies, and attempt to address some of the issues that may have led to incongruence between the fossil record and the molecular clock studies, as well as between the different molecular timetrees.
FIGURE 1. Three Trachinocephalus specimens collected from Papua New Guinean waters. (A) T. gaugui... more FIGURE 1. Three Trachinocephalus specimens collected from Papua New Guinean waters. (A) T. gauguini, NTUM 11085, SL = 51.3 mm (B) T. gauguini, NTUM 11212, SL = 76.4 mm (C) T. trachinus, NTUM 11201, SL = 40.6 mm. (Photographed by J.-N. Chen).
Imagery has become a key tool for assessing deep-sea megafaunal biodiversity, historically based ... more Imagery has become a key tool for assessing deep-sea megafaunal biodiversity, historically based on physical sampling using fishing gears. Image datasets provide quantitative and repeatable estimates, small-scale spatial patterns and habitat descriptions. However, taxon identification from images is challenging and often relies on morphotypes without considering a taxonomic framework. Taxon identification is particularly challenging in regions where the fauna is poorly known and/or highly diverse. Furthermore, the efficiency of imagery and physical sampling may vary among habitat types. Here, we compared biodiversity metrics (alpha and gamma diversity, composition) based on physical sampling (dredging and trawling) and towed-camera still images (1) along the upper continental slope of Papua New Guinea (sedimented slope with wood-falls, a canyon and cold seeps), and (2) on the outer slopes of the volcanic islands of Mayotte, dominated by hard bottoms. The comparison was done on selec...
In the northern South China Sea (SCS) we explored methane dynamics in the water column during SON... more In the northern South China Sea (SCS) we explored methane dynamics in the water column during SONNE-cruise SO266 in October/November 2018. Two depth zones contained elevated methane concentrations: the upper 400 m (<10 nM) and near gas seeps at the seafloor (up to 2100 nM). Seeps occurred at Four Way Closure Ridge (FWCR) at the active continental margin as well as at Southern Summit Formosa Ridge (SSFR) at the passive continental margin. In the upper ocean, methane dynamics correlated with (1) temperature, (2) water masses, and (3) suspended matter. In the first case, elevated methane concentrations and aerobic methane oxidation rates (MOxs) occurred in water with temperatures > 10°C and > 20°C, respectively. Both 16S rRNA gene and pmoA amplicon analyses revealed distinct microbial and methanotrophic communities in water with temperature of 27°C, ∼10°C, and 3°C. Second, we found elevated methane concentrations in 200–400 m in the FWCR-region whereas increased methane concentrations occurred in the uppermost 100 m above SSFR. The deeper plume above FWCR might be due to an intrusion of the Kuroshio water mass into SCS keeping the methane from being aerobically oxidized in the warm surface water and vented to the atmosphere. Finally, all peak methane concentrations occurred in water depth, with rather low backscatter, i.e., in water depth with less suspended matter. At the seafloor, ocean currents and long-term seepage appeared to control methane dynamics. We derived methane fluxes of 0.08–0.12 mmol m–2 d–1 from a 4.5 km2 area at FWCR and of 3.0–79.9 mmol m–2 d–1 from a 0.01 km2 area at SSFR. Repetitive sampling of the area at SSFR indicated that changing directions of ocean currents possibly affected methane concentrations and thus flux. In contrast to these seepage sites with distinct methane plumes, retrieval of drilling equipment produced no methane plume. Even gas emission triggered by seafloor drilling did not supply measureable methane concentrations after 3 h, but caused an increase in methanotrophic activity as determined by rate measurements and molecular-biological analyses. Apparently, only long-term seepage can generate methane anomalies in the ocean.
FIGURE 2. Distribution records of Trachinocephalus gauguini. Circle, occurrence described in Pola... more FIGURE 2. Distribution records of Trachinocephalus gauguini. Circle, occurrence described in Polanco et al. (2016); triangle, new record from Papua New Guinea (this study).
The Elopomorpha (eels and relatives) is a morphologically diverse group of predominantly marine t... more The Elopomorpha (eels and relatives) is a morphologically diverse group of predominantly marine teleost fishes comprising about 1000 species placed in 25 families. It is one of the three major living teleost lineages along with the Osteoglossomorpha and Clupeocephala. Among a few morphological synapomorphies that have been offered as evidence for the monophyly of the Elopomorpha, the remarkable leptocephalus larvae stand out. Several studies aiming at reconstructing the elopomorph phylogeny using morphological or molecular characters led to inconsistent results. In this study, we have tested previous hypotheses regarding inter-and intra-relationships of the Elopomorpha using a multi-locus dataset composed of three nuclear and three mitochondrial genes. Our analyses were based on likelihood phylogenetic reconstruction methods using different character-weighting data matrices and gene partition schemes to assess reliability of our findings. Our results confirm the respective monophyly of the Elopomorpha, Osteoglossomorpha and Clupeocephala. The majority of our analyses identify the Elopomorpha as the sister group of a clade containing the rest of the Teleostei. Within the Elopomorpha, the Elopiformes is the sister group of the remaining taxa. The Albuliformes sensu Forey et al. (1996) and the Notacanthiformes are never sister-taxa in our phylogenetic trees, in contradiction with the recent mitogenomic hypothesis and current classification. Our results place the Notacanthiformes as the sister group of the Anguilliformes, including Saccopharyngiformes. Among anguilliforms, the families Congridae and Muraenesocidae are not monophyletic. The recently discovered anguilliform ''living fossil'' family Protanguillidae is not the sister group of the remaining Anguilliformes, instead, the sister group of the Synaphobranchidae. Based on the results presented here, we propose a revised classification for the Elopomorpha, comprised of four orders, including a resurrected Notacanthiformes but surrendering the Saccopharyngiformes. Within Anguilliformes, we recognized four monophyletic suborders named Protanguilloidei, Muraenoidei, Anguilloidei, and Congroidei.
The Acanthomorpha is the largest group of teleost fishes with about one third of extant vertebrat... more The Acanthomorpha is the largest group of teleost fishes with about one third of extant vertebrate species. In the course of its evolution this lineage experienced several episodes of radiation, leading to a large number of descendant lineages differing profoundly in morphology, ecology, distribution and behavior. Although Acanthomorpha was recognized decades ago, we are only now beginning to decipher its large-scale, time-calibrated phylogeny, a prerequisite to test various evolutionary hypotheses explaining the tremendous diversity of this group. In this study, we provide new insights into the early evolution of the acanthomorphs and the euteleost allies based on the phylogenetic analysis of a newly developed dataset combining nine nuclear and mitochondrial gene markers. Our inferred tree is time-calibrated using 15 fossils, some of which have not been used before. While our phylogeny strongly supports a monophyletic Neoteleostei, Ctenosquamata (i.e., Acanthomorpha plus Myctophiformes), and Acanthopterygii, we find weak support (bootstrap value < 48%) for the traditionally defined Acanthomorpha, as well as evidence of non-monophyly for the traditional Paracanthopterygii, Beryciformes, and Percomorpha. We corroborate the new Paracanthopterygii sensu including Polymixiiformes, Zeiformes, Gadiformes, Percopsiformes, and likely the enigmatic Stylephorus chordatus. Our timetree largely agrees with other recent studies based on nuclear loci in inferring an Early Cretaceous origin for the acanthomorphs followed by a Late Cretaceous/Early Paleogene radiation of major lineages. This is in contrast to mitogenomic studies mostly inferring Jurassic or even Triassic ages for the origin of the acanthomorphs. We compare our results to those of previous studies, and attempt to address some of the issues that may have led to incongruence between the fossil record and the molecular clock studies, as well as between the different molecular timetrees.
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Papers by Jhen-Nien Chen