Phylogenetic Systematics of the Prickleback Family Stichaeidae (Cottiformes: Zoarcoidei) using Morphological Data

The prickleback family Stichaeidae, as currently recognized, is a diverse group of small (\u3c30 cm TL) eel- or blenny-like marine fishes distributed in intertidal, subtidal, and continental slope waters of the North Pacific, Arctic, and North Atlantic oceans. Stichaeidae is one of nine families within the Cottiformes suborder Zoarcoidei and includes six subfamilies, 38 genera, and about 80 species. However, there are questions regarding the monophyly of the family and its position within Zoarcoidei, due in part to a lack of fundamental descriptive anatomical data for the family. The first chapter of my dissertation describes the osteology of Xiphister, a genus of Stichaeidae that includes two species, X. atropurpureus and X. mucosus, found in intertidal and subtidal waters from southern Alaska to southern California. I describe and illustrate their skeletal anatomy, clarify aspects of their anatomy discussed by previous researchers, and describe for the first time elements such as the hyoid and gill arches, scales, and the development of their lateral line canals. These data establish a foundation for the further anatomical and systematic studies of Stichaeidae, and Zoarcoidei generally. Some members of Stichaeidae, including both species of Xiphister , have multiple lateral line canals on their trunk, which is a feature found in only 15 families of teleostean fishes. In the second chapter of my dissertation, the structure and ontogeny of lateral line canals of both species of Xiphister were studied using cleared & stained specimens and histology. Both species have seven cephalic canals and three paired canals on the trunk located on the dorsolateral, mediolateral, and ventrolateral body surfaces. The ventrolateral canal also includes a short loop across the ventral surface of the abdomen. The trunk canals and four short branches of the infraorbitals that extend across the cheek are supported by small ossified rings. The trunk canals develop asynchronously and separately from the development of scales, suggesting that the ossified rings that support the canals are not modified scales. Results from histology show that neuromasts, the sensory components of the mechanosensory system, are found only in the cephalic, dorsolateral, and mediolateral canals; the ventrolateral canal and its loop lack neuromasts. The evolution and functional role of multiple trunk lateral line canals is discussed. The third chapter of my dissertation examines the phylogenetic systematics of Stichaeidae using 106 morphological characters and 60 terminal taxa, including 30 genera of Stichaeidae, representatives from all eight other families of Zoarcoidei, and additional outgroup taxa. The suborder Zoarcoidei was recovered as a monophyletic group sister to Cottoidei within the order Cottiformes. Within Zoarcoidei, however, the family Stichaeidae was not recovered as a monophyletic family. Only two of the six subfamilies within Stichaeidae, Lumpeninae and Neozoarcinae, were recovered as monophyletic. The high level of homoplasy in the remaining four stichaeid subfamilies, and the inclusion of zoarcoid families nested within Stichaeidae, suggests that the current classification of Stichaeidae does not accurately reflect the evolutionary history of Zoarcoidei

Spatial and temporal variability in the relative contribution of king mackerel (Scomberomorus cavalla) stocks to winter mixed fisheries off South Florida

King mackerel (Scomberomorus cavalla) are ecologically and economically important scombrids that inhabit U.S. waters of the Gulf of Mexico (GOM) and Atlantic Ocean (Atlantic). Separate migratory groups, or stocks, migrate from eastern GOM and southeastern U.S. Atlantic to south Florida waters where the stocks mix during winter. Currently, all winter landings from a management-defined south Florida mixing zone are attributed to the GOM stock. In this study, the stock composition of winter landings across three south Florida sampling zones was estimated by using stock-specific otolith morphological variables and Fourier harmonics. The mean accuracies of the jackknifed classifications from stepwise linear discriminant function analysis of otolith shape variables ranged from 66−76% for sex-specific models. Estimates of the contribution of the Atlantic stock to winter landings, derived from maximum likelihood stock mixing models, indicated the contribution was highest off southeastern Florida (as high as 82.8% for females in winter 2001−02) and lowest off southwestern Florida (as low as 14.5% for females in winter 2002−03). Overall, results provided evidence that the Atlantic stock contributes a certain, and perhaps a significant (i.e., ≥50%), percentage of landings taken in the management-defined winter mixing zone off south Florida, and the practice of assigning all winter mixing zone landings to the GOM stock shoul

Composition and temporal patterns of larval fish communities in Chesapeake and Delaware Bays, USA

Comparing larval fish assemblages in different estuaries provides insights about the coastal distribution of larval populations, larval transport, and adult spawning locations. We simultaneously compared the larval fish assemblages entering 2 Middle Atlantic Bight (MAB) estuaries(Delaware Bay and Chesapeake Bay, USA) through weekly sampling from 2007 to 2009. In total,43 taxa (32 families) and 36 taxa (24 families) were collected in Delaware and Chesapeake Bays,respectively. Mean taxonomic diversity, mean richness, and evenness were generally lower in Delaware Bay. Communities of both bays were dominated by Anchoaspp., Gobiosomaspp.,Micropogonias undulatus, and Brevoortia tyrannus; Paralichthys spp. was more abundant in Delaware Bay and Microgobius thalassinus was more abundant in Chesapeake Bay. Inter-annual variation in the larval fish communities was low at both sites, with a relatively consistent composition across years, but strong seasonal (intra-annual) variation in species composition occurred in both bays. Two groups were identified in Chesapeake Bay: a ‘winter’ group dominated by shelf-spawned species and a ‘summer’ group comprising obligate estuarine species and coastal species.In Delaware Bay, 4 groups were identified: a ‘summer’ group of mainly obligate estuarine fishes being replaced by a ‘fall’ group; ‘winter’ and ‘spring’ groups were dominated by shelf-spawned and obligate estuarine species, respectively. This study demonstrates that inexpensive and simultaneous sampling in different estuaries provides important insights into the variability in community structure of fish assemblages at large spatial scales

Dimensions of biodiversity in Chesapeake Bay demersal fishes: patterns and drivers through space and time

Biodiversity has typically been described in terms of species richness and composition, but theory and growing empirical evidence indicate that the diversity of functional traits, the breadth of evolutionary relationships, and the equitability with which individuals or biomass are distributed among species better characterize patterns and processes within ecosystems. Yet, the advantages of including such data come at the expense of measuring traits, sequencing genes, and counting or weighing individuals, and it remains unclear whether this greater resolution yields substantial benefits in describing diversity. We summarized a decade of high-resolution trawl data from a bimonthly trawl survey to investigate spatial and seasonal patterns of demersal fish diversity in the Chesapeake Bay, USA, with the goal of identifying areas and times of mismatch between different dimensions of diversity, and their response to environmental forcing. We found moderate to strong positive relationships among all metrics of diversity, and that functional and phylogenetic differences were well-reflected in an index derived from taxonomic (Linnaean) hierarchy. Compared with species richness and species diversity, functional, phylogenetic, and taxonomic indices peaked later in the year, which was a consequence of the distribution of biomass among functionally and evolutionarily divergent species. Generalized additive models revealed that spatial, temporal, and environmental variables explained roughly similar proportions of deviance across all aspects of diversity, suggesting that these three factors do not differentially affect the functional and phylogenetic aspects of community structure. We conclude that an index of diversity derived from taxonomic hierarchy served well as a practical surrogate for functional and phylogenetic diversity of the demersal fish community in this system. We also emphasize the importance of evenness in understanding diversity patterns, especially since most ecological communities in nature are dominated by one or few species

Gene expression signature-based chemical genomic prediction identifies a novel class of HSP90 pathway modulators

SummaryAlthough androgen receptor (AR)-mediated signaling is central to prostate cancer, the ability to modulate AR signaling states is limited. Here we establish a chemical genomic approach for discovery and target prediction of modulators of cancer phenotypes, as exemplified by AR signaling. We first identify AR activation inhibitors, including a group of structurally related compounds comprising celastrol, gedunin, and derivatives. To develop an in silico approach for target pathway identification, we apply a gene expression-based analysis that classifies HSP90 inhibitors as having similar activity to celastrol and gedunin. Validating this prediction, we demonstrate that celastrol and gedunin inhibit HSP90 activity and HSP90 clients, including AR. Broadly, this work identifies new modes of HSP90 modulation through a gene expression-based strategy

Supplement 1. R script containing all data analyses, and functional, phylogenetic, and taxonomic trees in Newick format.

<h2>File List</h2><div> <p><a href="ChesMMAP_Analysis.R">ChesMMAP_Analysis.R</a> (MD5: 76c1bf2a66778c549c104f1f981f3344)</p> <p><a href="Functional_dendrogram.txt">Functional_dendrogram.txt</a> (MD5: 150ae02926a1d4019fbbb62a8389622f)</p> <p><a href="Phylogenetic_tree.txt">Phylogenetic_tree.txt</a> (MD5: 86896bc31f31d11d3fdf77f33b3ddb62)</p> <p><a href="Taxonomic_tree.txt">Taxonomic_tree.txt</a> (MD5: 4dcd4fa2bf8eb6db567b7a1ff7dcb236)</p> </div><h2>Description</h2><div> <p>The code included in ChesMMAP Analysis.R reports all analyses run in the paper, including building functional, phylogenetic, and taxonomic trees, kriging interpolation, and construction of generalized additive models.</p> <p>The three text files include the functional, phylogenetic, and taxonomic trees in Newick format.</p> </div