•A high-resolution (1 km) model study of Red Snapper larvae dispersal.•Buoyancy and ontogenetic vertical migration are pivotal behaviors.•Ocean advection can shape larvae dispersal.•Limited ...connectivity between areas west and east of the Mississippi Delta.
Advancements in computing power and improved biophysical dispersal models, have enhanced our ability to realistically simulate distributions and behaviors of fish larvae. In this study, a 1 km high-resolution ocean model capable of capturing the ocean's mesoscale and sub-mesoscale motions is integrated with a biophysical dispersal model that considers a range of larval behaviors. Together they are used to investigate the dispersal and connectivity of Red Snapper (Lutjanus campechanus) larvae, a key species for both commercial and recreational fisheries in the northern Gulf of Mexico (GOM). We quantify how various larval behaviors influence the spatiotemporal dispersal, connectivity and settling of Red Snapper larvae focusing on egg buoyancy, larvae swimming capability, and ontogenetic vertical migration. Alongside habitat preferences, the ocean advection of Red Snapper larvae is crucial in shaping their dispersal patterns. Moreover, our simulations suggest different settling and connectivity characteristics between the eastern and western GOM. These results, indicate the need to divide these regions into distinct entities for stock management, rather than treating them as a unified stock as conventionally done.
Abstract
Reliable estimation of phylogeny is central to avoid inaccuracy in downstream macroevolutionary inferences. However, limitations exist in the implementation of concatenated and summary ...coalescent approaches, and Bayesian and full coalescent inference methods may not yet be feasible for computation of phylogeny using complicated models and large data sets. Here, we explored methodological (e.g., optimality criteria, character sampling, model selection) and biological (e.g., heterotachy, branch length heterogeneity) sources of systematic error that can result in biased or incorrect parameter estimates when reconstructing phylogeny by using the gadiform fishes as a model clade. Gadiformes include some of the most economically important fishes in the world (e.g., Cods, Hakes, and Rattails). Despite many attempts, a robust higher-level phylogenetic framework was lacking due to limited character and taxonomic sampling, particularly from several species-poor families that have been recalcitrant to phylogenetic placement. We compiled the first phylogenomic data set, including 14,208 loci ($>$2.8 M bp) from 58 species representing all recognized gadiform families, to infer a time-calibrated phylogeny for the group. Data were generated with a gene-capture approach targeting coding DNA sequences from single-copy protein-coding genes. Species-tree and concatenated maximum-likelihood (ML) analyses resolved all family-level relationships within Gadiformes. While there were a few differences between topologies produced by the DNA and the amino acid data sets, most of the historically unresolved relationships among gadiform lineages were consistently well resolved with high support in our analyses regardless of the methodological and biological approaches used. However, at deeper levels, we observed inconsistency in branch support estimates between bootstrap and gene and site coefficient factors (gCF, sCF). Despite numerous short internodes, all relationships received unequivocal bootstrap support while gCF and sCF had very little support, reflecting hidden conflict across loci. Most of the gene-tree and species-tree discordance in our study is a result of short divergence times, and consequent lack of informative characters at deep levels, rather than incomplete lineage sorting. We use this phylogeny to establish a new higher-level classification of Gadiformes as a way of clarifying the evolutionary diversification of the order. We recognize 17 families in five suborders: Bregmacerotoidei, Gadoidei, Ranicipitoidei, Merluccioidei, and Macrouroidei (including two subclades). A time-calibrated analysis using 15 fossil taxa suggests that Gadiformes evolved $\sim $79.5 Ma in the late Cretaceous, but that most extant lineages diverged after the Cretaceous–Paleogene (K-Pg) mass extinction (66 Ma). Our results reiterate the importance of examining phylogenomic analyses for evidence of systematic error that can emerge as a result of unsuitable modeling of biological factors and/or methodological issues, even when data sets are large and yield high support for phylogenetic relationships. Branch length heterogeneity; Codfishes; commercial fish species; Cretaceous-Paleogene (K-Pg); heterotachy; systematic error; target enrichment.
Phylogenetic hypotheses among Gadiformes fishes at the suborder, family, and subfamily levels are controversial. To address this problem, we analyze nuclear and mitochondrial DNA (mtDNA) sequences ...for the most extensive taxonomic sampling compiled to date, representing all of the recognized families and subfamilies in the order (except the monotypic family Lyconidae). Our study sampled 117 species from 46 genera, comprising around 20% of the species described for the order (more than 60% of all genera in the order) and produced 2740
bp of DNA sequence data for each species. Our analysis was successful in confirming the monophyly of Gadiformes and most of the proposed families for the order, but alternative hypotheses of sister-group relationships among families were poorly resolved. Our results are consistent with dividing Gadiformes into 12 families in three suborders, Muraenolepidoidei, Macrouroidei, and Gadoidei. Muraenolepidoidei contains the single family Muraenolepididae. The suborder Macrouroidei includes at least three families: Macrouridae, Macruronidae and Steindachneriidae. Macrouridae is deeply divided into two well-supported subfamilies: Macrourinae and Bathygadinae, suggesting that Bathygadinae may be ranked at the family level. The suborder Gadoidei includes the families: Merlucciidae, Melanonidae, Euclichthyidae, Gadidae, Ranicipitidae, and Bregmacerotidae. Additionally, Trachyrincinae could be ranked at family level including two subfamilies: Trachyrincinae and Macrouroidinae within Gadoidei. Further taxonomic sampling and sequencing efforts are needed in order to corroborate these relationships.
Midwater fish faunas over three cold seep habitats >1000m (AC601, GC852, AT340) and over a cold-water coral bank (VK826, <1000m) in the north-central Gulf of Mexico (GOM) are described and compared. ...Day and night discrete-depth sampling was accomplished at each study site, 9–29 August 2007, using an opening–closing Tucker trawl towed at depth for 30min. The 159 Tucker trawl stations yielded 9802 individuals and at least 126 species (30 families) of juvenile and adult midwater fishes. Myctophidae (38 species, 28% of the total catch), Stomiidae (17 species, 1.4%), Gonostomatidae (12 species, 56%), Sternoptychidae (10 species, 6%), and Phosichthyidae (5 species, 6%) dominated catches at all sites. Thirty-one species (8 families) comprised about 90% of the overall abundance of fishes across the four sites. Despite the wide separation of study sites and some differences in physical oceanography, geographic and temporal patterns in mesopelagic fish assemblages were not evident (ANOSIM, Global R=0.20, p=0.1%, pairwise R values <0.3). However, station groupings were related mostly to similarities in sampled depths (SIMPROF, p<1.5%). Upper water-column station groups (<400m) were typified by Lepidophanes guentheri, Diaphus dumerilii, Vinciguerria nimbaria, Vinciguerria poweriae, Valenciennellus tripunctulatus, Argyropelecus aculeatus, Notolychnus valdiviae, Benthosema suborbitale, Gonostoma elongatum, and Hygophum taaningi. Deeper station groups (mean depth=609m) were typified by Cyclothone alba, Cyclothone acclinidens, Cyclothone braueri, Cyclothone obscura, Cyclothone pallida, Cyclothone pseudopallida, V. tripunctulatus, and Hygophum benoiti. Depth, diel, and size distributions were also analyzed for abundant species. For example, Cyclothone spp., abundant at all sites except VK826, usually occurred in deeper waters (>130m), especially during daylight hours (>335m). Most Cyclothone individuals were captured at night at GC852, whereas catches were more evenly distributed across times at AT340 and VK826. Cyclothone spp. individuals occurred in the deeper parts of the sampled depth range at AT340 and VK826 at all times compared with GC852, where they appeared to undergo a diel migration. The two most abundant Cyclothone spp., C. pallida and C. pseudopallida, had the broadest depth ranges (150–1377m) and exhibited a trend for larger specimens to occur deeper at GC852. Most V. tripunctulatus were captured at night and tended to have larger mean sizes in deeper waters. This species did not exhibit strong diel patterns of vertical distribution. Shallower depths were occupied at night by some individuals at all sites, but most individuals remained somewhat deeper at night at VK826 (350–450m at night and 200–350m by day) and AT340 (200–600m at night and 300–500m by day) compared with GC852 (150–450m at night and 750 and 1000m by day). Nearly all Vinciguerria poweriae were caught at night, and no clear trend of size with depth was apparent. This species occupied a wider depth range at night, with most in the upper 200m. Most myctophids, the strongest diel migrators, were captured at night at the offshore stations. The dominant myctophid, N. valdiviae, was most abundant at GC852 (550–1050m by day and 50–750m at night), but diel movement was more distinct at AT340 (<200m at night and 350–500m by day). No size-related trends with depth were apparent at any site for N. valdiviae, and size distributions were similar among sites.
This study and others support the hypothesis that there is a geographically similar mesopelagic fish fauna throughout the GOM. However, the fauna does vary by depth, with some species remaining in deep waters at all times (e.g., Cyclothone spp.) and others occurring at mid-depths and exhibiting varying degrees of diel migration (e.g., many myctophids). Even though faunal composition is similar across the GOM, some species exhibit different movement behaviors at different locations. Such variances could be related to differences in physical or chemical factors, food resources, lunar phase, or bottom depth.
The tree of life of fishes is in a state of flux because we still lack a comprehensive phylogeny that includes all major groups. The situation is most critical for a large clade of spiny-finned ...fishes, traditionally referred to as percomorphs, whose uncertain relationships have plagued ichthyologists for over a century. Most of what we know about the higher-level relationships among fish lineages has been based on morphology, but rapid influx of molecular studies is changing many established systematic concepts. We report a comprehensive molecular phylogeny for bony fishes that includes representatives of all major lineages. DNA sequence data for 21 molecular markers (one mitochondrial and 20 nuclear genes) were collected for 1410 bony fish taxa, plus four tetrapod species and two chondrichthyan outgroups (total 1416 terminals). Bony fish diversity is represented by 1093 genera, 369 families, and all traditionally recognized orders. The maximum likelihood tree provides unprecedented resolution and high bootstrap support for most backbone nodes, defining for the first time a global phylogeny of fishes. The general structure of the tree is in agreement with expectations from previous morphological and molecular studies, but significant new clades arise. Most interestingly, the high degree of uncertainty among percomorphs is now resolved into nine well-supported supraordinal groups. The order Perciformes, considered by many a polyphyletic taxonomic waste basket, is defined for the first time as a monophyletic group in the global phylogeny. A new classification that reflects our phylogenetic hypothesis is proposed to facilitate communication about the newly found structure of the tree of life of fishes. Finally, the molecular phylogeny is calibrated using 60 fossil constraints to produce a comprehensive time tree. The new time-calibrated phylogeny will provide the basis for and stimulate new comparative studies to better understand the evolution of the amazing diversity of fishes.
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•Phylogeny for the genus Coryphaenoides that represents breadth of habitat use and distribution.•Abyssal species form a monophyletic lineage that includes two non-abyssal species.•The ...genus may have originated in Southern/Pacific Ocean where contemporary diversity is highest.•The abyssal lineage likely arose secondarily in the S/P Ocean but diversified in the N. Atlantic.
Here we consider the role of depth as a driver of evolution in a genus of deep-sea fishes. We provide a phylogeny for the genus Coryphaenoides (Gadiformes: Macrouridae) that represents the breadth of habitat use and distributions for these species. In our consensus phylogeny species found at abyssal depths (>4000m) form a well-supported lineage, which interestingly also includes two non-abyssal species, C. striaturus and C. murrayi, diverging from the basal node of that lineage. Biogeographic analyses suggest the genus may have originated in the Southern and Pacific Oceans where contemporary species diversity is highest. The abyssal lineage seems to have arisen secondarily and likely originated in the Southern/Pacific Oceans but diversification of this lineage occurred in the Northern Atlantic Ocean. All abyssal species are found in the North Atlantic with the exception of C. yaquinae in the North Pacific and C. filicauda in the Southern Ocean. Abyssal species tend to have broad depth ranges and wide distributions, indicating that the stability of the deep oceans and the ability to live across wide depths may promote population connectivity and facilitate large ranges. We also confirm that morphologically defined subgenera do not agree with our phylogeny and that the Giant grenadier (formerly Albatrossia pectoralis) belongs to Coryphaenoides, indicating that a taxonomic revision of the genus is needed. We discuss the implications of our findings for understanding the radiation and diversification of this genus, and the likely role of adaptation to the abyss.
In August 2007, October 2008 and September–October 2010, 241 Tucker trawl and plankton net tows were conducted at the surface to depths of 1377 m at six locations in the northern and eastern Gulf of ...Mexico (GOM) to document leptocephalus diversity and determine how assemblage structure, larval size, abundance and isotopic signatures differ across the region and with depth. Overall, 2696 leptocephali representing 59 distinct taxa from 10 families were collected. Five families accounted for 96% of the total catch with Congridae and Ophichthidae being the most abundant. The top four most abundant species composed 59% of the total catch and included: Ariosoma balearicum, Paraconger caudilimbatus, Rhynchoconger flavus and Ophichthus gomesii. Four anguilliform species not previously documented in the GOM as adults or leptocephali were collected in this study, including Monopenchelys acuta, Quassiremus ascensionis, Saurenchelys stylura and one leptocephalus only known from its larval stage, Leptocephalus proboscideus. Leptocephalus catches were significantly greater at night than during the day. Catches at night were concentrated in the upper 200 m of the water column and significantly declined with increasing depth. Leptocephali abundances and assemblages were significantly different between sites on the upper continental slope (c. 500 m depth) and sites on the middle to lower continental slope (c. 1500–2300 m). Sites on the lower continental slope had a mixture of deep‐sea demersal, bathypelagic and coastal species, whereas upper‐slope sites contained several numerically dominant species (e.g., A. balearicum, P. caudilimbatus) that probably spawn over the continental shelf and upper slope of the GOM. Standard lengths of the four dominant species differed between sites and years, indicating heterochronic reproduction and potential larval source pools within and outside of the GOM. Stable‐isotope analyses (δ13C and δ15N) conducted on 185 specimens from six families revealed that leptocephali had a wide range of isotopic values at the family and size‐class levels. Species in the families Muraenidae, Congridae and Ophichthidae had similar δ15N values compared with the broad range of δ15N values seen in the deep‐sea families Nemichthyidae, Nettastomatidae and Synaphobranchidae. Stable‐isotope values were variably related to length, with δ15N values being positively size correlated in ophichthids and δ13C values being negatively size correlated in A. balearicum and P. caudilimbatus. Results suggest that leptocephali feed in various water depths and masses, and on different components of POM, which could lead to niche partitioning. Ecological aspects of these important members of the plankton community provide insight into larval connectivity in the GOM as well as the early life history of Anguilliformes.
Leading deep-sea research expeditions requires a breadth of training and experience, and the opportunities for Early Career Researchers (ECRs) to obtain focused mentorship on expedition leadership ...are scarce. To address the need for leadership training in deep-sea expeditionary science, the Crustal Ocean Biosphere Research Accelerator (COBRA) launched a 14-week virtual Master Class with both synchronous and asynchronous components to empower students with the skills and tools to successfully design, propose, and execute deep-sea oceanographic field research. The Master Class offered customized and distributed training approaches and created an open-access syllabus with resources, including reading material, lectures, and on-line resources freely-available on the Master Class website (cobra.pubpub.org). All students were Early Career Researchers (ECRs, defined here as advanced graduate students, postdoctoral scientists, early career faculty, or individuals with substantial industry, government, or NGO experience) and designated throughout as COBRA Fellows. Fellows engaged in topics related to choosing the appropriate deep-sea research asset for their Capstone “dream cruise” project, learning about funding sources and how to tailor proposals to meet those source requirements, and working through an essential checklist of pre-expedition planning and operations. The Master Class covered leading an expedition at sea, at-sea operations, and ship-board etiquette, and the strengths and challenges of telepresence. It also included post-expedition training on data management strategies and report preparation and outputs. Throughout the Master Class, Fellows also discussed education and outreach, international ocean law and policy, and the importance and challenges of team science. Fellows further learned about how to develop concepts respectfully with regard to geographic and cultural considerations of their intended study sites. An assessment of initial outcomes from the first iteration of the COBRA Master Class reinforces the need for such training and shows great promise with one-quarter of the Fellows having submitted a research proposal to national funding agencies within six months of the end of the class. As deep-sea research continues to accelerate in scope and speed, providing equitable access to expedition training is a top priority to enable the next generation of deep-sea science leadership.
Recent investigations of demersal fish communities in deepwater (>50m) habitats have considerably increased our knowledge of the factors that influence the assemblage structure of fishes across ...mesophotic to deep-sea depths. While different habitat types influence deepwater fish distribution, whether different types of rugged seafloor features provide functionally equivalent habitat for fishes is poorly understood. In the northeastern Caribbean, different types of rugged features (e.g., seamounts, banks, canyons) punctuate insular margins, and thus create a remarkable setting in which to compare demersal fish communities across various features. Concurrently, several water masses are vertically layered in the water column, creating strong stratification layers corresponding to specific abiotic conditions. In this study, we examined differences among fish assemblages across different features (e.g., seamount, canyon, bank/ridge) and water masses at depths ranging from 98 to 4060m in the northeastern Caribbean. We conducted 26 remotely operated vehicle dives across 18 sites, identifying 156 species of which 42% of had not been previously recorded from particular depths or localities in the region. While rarefaction curves indicated fewer species at seamounts than at other features in the NE Caribbean, assemblage structure was similar among the different types of features. Thus, similar to seamount studies in other regions, seamounts in the Anegada Passage do not harbor distinct communities from other types of rugged features. Species assemblages, however, differed among depths, with zonation generally corresponding to water mass boundaries in the region. High species turnover occurred at depths <1200m, and may be driven by changes in water mass characteristics including temperature (4.8–24.4°C) and dissolved oxygen (2.2–9.5mg per l). Our study suggests the importance of water masses in influencing community structure of benthic fauna, while considerably adding to the knowledge of mesophotic and deep-sea fish biogeography.
•Seamounts do not harbor distinct communities from other rugged seafloor features.•Depth zonation of demersal fishes corresponds with water mass stratification.•Strong species turnover at depths shallower than 1200m.•New depth and/or locality information for 42% of demersal fishes.•Increased knowledge of the biogeography of mesophotic and deep-sea fishes.
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