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Dive into the research topics where Jon A. Moore is active.

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Featured researches published by Jon A. Moore.


Proceedings of the National Academy of Sciences of the United States of America | 2012

Resolution of ray-finned fish phylogeny and timing of diversification

Thomas J. Near; Ron I. Eytan; Alex Dornburg; Kristen L. Kuhn; Jon A. Moore; Matthew P. Davis; Peter C. Wainwright; Matt Friedman; W. Leo Smith

Ray-finned fishes make up half of all living vertebrate species. Nearly all ray-finned fishes are teleosts, which include most commercially important fish species, several model organisms for genomics and developmental biology, and the dominant component of marine and freshwater vertebrate faunas. Despite the economic and scientific importance of ray-finned fishes, the lack of a single comprehensive phylogeny with corresponding divergence-time estimates has limited our understanding of the evolution and diversification of this radiation. Our analyses, which use multiple nuclear gene sequences in conjunction with 36 fossil age constraints, result in a well-supported phylogeny of all major ray-finned fish lineages and molecular age estimates that are generally consistent with the fossil record. This phylogeny informs three long-standing problems: specifically identifying elopomorphs (eels and tarpons) as the sister lineage of all other teleosts, providing a unique hypothesis on the radiation of early euteleosts, and offering a promising strategy for resolution of the “bush at the top of the tree” that includes percomorphs and other spiny-finned teleosts. Contrasting our divergence time estimates with studies using a single nuclear gene or whole mitochondrial genomes, we find that the former underestimates ages of the oldest ray-finned fish divergences, but the latter dramatically overestimates ages for derived teleost lineages. Our time-calibrated phylogeny reveals that much of the diversification leading to extant groups of teleosts occurred between the late Mesozoic and early Cenozoic, identifying this period as the “Second Age of Fishes.”


Proceedings of the National Academy of Sciences of the United States of America | 2013

Phylogeny and tempo of diversification in the superradiation of spiny-rayed fishes

Thomas J. Near; Alex Dornburg; Ron I. Eytan; Benjamin P. Keck; W. Leo Smith; Kristen L. Kuhn; Jon A. Moore; Samantha A. Price; Frank T. Burbrink; Matt Friedman; Peter C. Wainwright

Spiny-rayed fishes, or acanthomorphs, comprise nearly one-third of all living vertebrates. Despite their dominant role in aquatic ecosystems, the evolutionary history and tempo of acanthomorph diversification is poorly understood. We investigate the pattern of lineage diversification in acanthomorphs by using a well-resolved time-calibrated phylogeny inferred from a nuclear gene supermatrix that includes 520 acanthomorph species and 37 fossil age constraints. This phylogeny provides resolution for what has been classically referred to as the “bush at the top” of the teleost tree, and indicates acanthomorphs originated in the Early Cretaceous. Paleontological evidence suggests acanthomorphs exhibit a pulse of morphological diversification following the end Cretaceous mass extinction; however, the role of this event on the accumulation of living acanthomorph diversity remains unclear. Lineage diversification rates through time exhibit no shifts associated with the end Cretaceous mass extinction, but there is a global decrease in lineage diversification rates 50 Ma that occurs during a period when morphological disparity among fossil acanthomorphs increases sharply. Analysis of clade-specific shifts in diversification rates reveal that the hyperdiversity of living acanthomorphs is highlighted by several rapidly radiating lineages including tunas, gobies, blennies, snailfishes, and Afro-American cichlids. These lineages with high diversification rates are not associated with a single habitat type, such as coral reefs, indicating there is no single explanation for the success of acanthomorphs, as exceptional bouts of diversification have occurred across a wide array of marine and freshwater habitats.


Archive | 2005

A habitat classification scheme for seamount landscapes: assessing the functional role of deep-water corals as fish habitat

Peter J. Auster; Jon A. Moore; Kari B. Heinonen; Les Watling

Seamounts are drowned volcanoes rising from abyssal depths. Fishes on seamounts exploit a range of landscape features that likely enhance probabilities of prey capture and reduce predator success. The epifaunal community on seamounts is dominated by suspension-feeders of which deep-water corals are a dominant element. Such taxa are widespread components of seamount landscapes but their functional role in mediating the distribution and abundance of fishes remains unknown. Here we propose a hierarchical habitat classification matrix, which includes deep-water corals, as a foundation for partitioning seamount landscapes in which fishes are observed. This scheme is based on our observations of fish distributions from the New England Seamounts, as well as literature review. Features of an idealized seamount landscape were divided at multiple spatial scales and included features at habitat class, subclass and microhabitat levels. Habitat classes were divided by major sediment types (i.e., basalt, fine grained sediments). Habitat subclasses included pavement, ridges, walls, ledges and tubes for basalt substrates and flat sediment, ripples and waves for fine-grained sediments. Microhabitat features were classified as flow related features, emergent structures (i.e., geologic and biologic including deep-water corals), and other biogenic structures (e.g., coral debris, depressions, burrows). Variations in the distribution of structures at multiple spatial scales can influence boundary flows and the ability of fishes to search for prey (e.g., where active searching by swimming can occur, where pelagic prey delivery is sufficient when station-keeping) and avoid predators (e.g., the ability to efficiently exhibit various avoidance behaviors such as shelter seeking). Placing fish abundance data in such a matrix of habitat types enables a variety of statistical approaches for testing for non-random distributions of fishes on seamounts and quantifying the functional role of corals as fish habitat.


Evolution | 2015

The impact of shifts in marine biodiversity hotspots on patterns of range evolution: Evidence from the Holocentridae (squirrelfishes and soldierfishes)

Alex Dornburg; Jon A. Moore; Jeremy M. Beaulieu; Ron I. Eytan; Thomas J. Near

One of the most striking biodiversity patterns is the uneven distribution of marine species richness, with species diversity in the Indo‐Australian Archipelago (IAA) exceeding all other areas. However, the IAA formed fairly recently, and marine biodiversity hotspots have shifted across nearly half the globe since the Paleogene. Understanding how lineages have responded to shifting biodiversity hotspots represents a necessary historic perspective on the formation and maintenance of global marine biodiversity. Such evolutionary inferences are often challenged by a lack of fossil evidence that provide insights into historic patterns of abundance and diversity. The greatest diversity of squirrelfishes and soldierfishes (Holocentridae) is in the IAA, yet these fishes also represent some of the most numerous fossil taxa in deposits of the former West Tethyan biodiversity hotspot. We reconstruct the pattern of holocentrid range evolution using time‐calibrated phylogenies that include most living species and several fossil lineages, demonstrating the importance of including fossil species as terminal taxa in ancestral area reconstructions. Holocentrids exhibit increased range fragmentation following the West Tethyan hotspot collapse. However, rather than originating within the emerging IAA hotspot, the IAA has acted as a reservoir for holocentrid diversity that originated in adjacent regions over deep evolutionary time scales.


PLOS ONE | 2015

Exploration of the Canyon-Incised Continental Margin of the Northeastern United States Reveals Dynamic Habitats and Diverse Communities

Andrea M. Quattrini; Martha S. Nizinski; Jason D. Chaytor; Amanda W.J. Demopoulos; E. Brendan Roark; Jon A. Moore; Taylor P. Heyl; Peter J. Auster; Brian P. Kinlan; Carolyn D. Ruppel; Kelley Elliott; Brian R.C. Kennedy; Elizabeth Lobecker; Adam Skarke; Timothy M. Shank

The continental margin off the northeastern United States (NEUS) contains numerous, topographically complex features that increase habitat heterogeneity across the region. However, the majority of these rugged features have never been surveyed, particularly using direct observations. During summer 2013, 31 Remotely-Operated Vehicle (ROV) dives were conducted from 494 to 3271 m depth across a variety of seafloor features to document communities and to infer geological processes that produced such features. The ROV surveyed six broad-scale habitat features, consisting of shelf-breaching canyons, slope-sourced canyons, inter-canyon areas, open-slope/landslide-scar areas, hydrocarbon seeps, and Mytilus Seamount. Four previously unknown chemosynthetic communities dominated by Bathymodiolus mussels were documented. Seafloor methane hydrate was observed at two seep sites. Multivariate analyses indicated that depth and broad-scale habitat significantly influenced megafaunal coral (58 taxa), demersal fish (69 taxa), and decapod crustacean (34 taxa) assemblages. Species richness of fishes and crustaceans significantly declined with depth, while there was no relationship between coral richness and depth. Turnover in assemblage structure occurred on the middle to lower slope at the approximate boundaries of water masses found previously in the region. Coral species richness was also an important variable explaining variation in fish and crustacean assemblages. Coral diversity may serve as an indicator of habitat suitability and variation in available niche diversity for these taxonomic groups. Our surveys added 24 putative coral species and three fishes to the known regional fauna, including the black coral Telopathes magna, the octocoral Metallogorgia melanotrichos and the fishes Gaidropsarus argentatus, Guttigadus latifrons, and Lepidion guentheri. Marine litter was observed on 81% of the dives, with at least 12 coral colonies entangled in debris. While initial exploration revealed the NEUS region to be both geologically dynamic and biologically diverse, further research into the abiotic conditions and the biotic interactions that influence species abundance and distribution is needed.


Bulletin of The Peabody Museum of Natural History | 2008

False Boarfish Neocyttus helgae in the Western North Atlantic

Jon A. Moore; Peter J. Auster; Danielle Calini; Kari B. Heinonen; Kimberly Barber; Barbara Hecker

Abstract Direct underwater observations at seamounts across the western North Atlantic basin revealed the presence of the false boarfish, Neocyttus helgae (Oreosomatidae), at depths of 915 to 1829 m. These observations extend the known range of this species across the North Atlantic basin and support the hypothesis that seamounts are stepping stones for dispersal. Fishes were associated with basalt habitats featuring corals and sponges (both nearly horizontal basalt sheets and steep cliffs) as well as depressions in sheets of basalt. These features provided refuge from flow and predators as well as immediate access to zooplankton and pelagic prey delivered by rapid currents. Encounters with fishes were primarily as single individuals or pairs. Territorial behaviors, such as raised dorsal spine and lateral display, occurred when submersible vehicles approached fish, suggesting that territorial defense is a common behavioral attribute.


Molecular Phylogenetics and Evolution | 2012

Molecular phylogenetics of squirrelfishes and soldierfishes (Teleostei: Beryciformes: Holocentridae): Reconciling more than 100 years of taxonomic confusion

Alex Dornburg; Jon A. Moore; Rachel Webster; Dan L. Warren; Matthew C. Brandley; Teresa L. Iglesias; Peter C. Wainwright; Thomas J. Near

Squirrelfishes and soldierfishes (Holocentridae) are among the most conspicuous species in the nocturnal reef fish community. However, there is no clear consensus regarding their evolutionary relationships, which is reflected in a complicated taxonomic history. We collected DNA sequence data from multiple single copy nuclear genes and one mitochondrial gene sampled from over fifty percent of the recognized holocentrid species and infer the first species-level phylogeny of the Holocentridae. Our results strongly support the monophyly of the clades Myripristinae (soldierfishes) and Holocentrinae (squirrelfishes). The molecular phylogenies differ with regard to previous hypotheses of relationships within the Myriprisitinae, resolving a clade of cryptic reef associated and deep water non-reef dwelling lineages (Corniger+Plectrypops+Ostichthys) that is the sister lineage to a monophyletic Myripristis. Within Holocentrinae, Neoniphon and Sargocentron are strongly supported as paraphyletic, while Holocentrus is nested within Sargocentron. Using Bayesian ancestral state reconstruction methods, we demonstrate the taxonomically diagnostic characters for Neoniphon and Sargocentron likely represent character states with a complex evolutionary history that is not reflective of shared common ancestry. We propose a new classification for Holocentrinae, recognizing four lineages that are treated as genera: Sargocentron Fowler, 1904, Holocentrus Scopoli, 1777, Flameo Jordan and Evermann, 1898, and Neoniphon Castelnau, 1875.


Molecular Phylogenetics and Evolution | 2017

New insights on the sister lineage of percomorph fishes with an anchored hybrid enrichment dataset

Alex Dornburg; Jeffrey P. Townsend; Willa Brooks; Elizabeth Spriggs; Ron I. Eytan; Jon A. Moore; Peter C. Wainwright; Alan R. Lemmon; Emily Moriarty Lemmon; Thomas J. Near

Percomorph fishes represent over 17,100 species, including several model organisms and species of economic importance. Despite continuous advances in the resolution of the percomorph Tree of Life, resolution of the sister lineage to Percomorpha remains inconsistent but restricted to a small number of candidate lineages. Here we use an anchored hybrid enrichment (AHE) dataset of 132 loci with over 99,000 base pairs to identify the sister lineage of percomorph fishes. Initial analyses of this dataset failed to recover a strongly supported sister clade to Percomorpha, however, scrutiny of the AHE dataset revealed a bias towards high GC content at fast-evolving codon partitions (GC bias). By combining several existing approaches aimed at mitigating the impacts of convergence in GC bias, including RY coding and analyses of amino acids, we consistently recovered a strongly supported clade comprised of Holocentridae (squirrelfishes), Berycidae (Alfonsinos), Melamphaidae (bigscale fishes), Cetomimidae (flabby whalefishes), and Rondeletiidae (redmouth whalefishes) as the sister lineage to Percomorpha. Additionally, implementing phylogenetic informativeness (PI) based metrics as a filtration method yielded this same topology, suggesting PI based approaches will preferentially filter these fast-evolving regions and act in a manner consistent with other phylogenetic approaches aimed at mitigating GC bias. Our results provide a new perspective on a key issue for studies investigating the evolutionary history of more than one quarter of all living species of vertebrates.


Bulletin of The Peabody Museum of Natural History | 2009

Commensalism Between Juvenile Cusk Eels and Pancake Urchins on Western North Atlantic Seamounts

Jon A. Moore; Peter J. Auster

ABSTRACT We describe a commensal relationship between small (approximately 6 to 9 cm) deep-sea cusk eels, one tentatively identified as Barathrites sp. (Osteichthyes: Ophidiidae), and pancake urchins, both Hygrosoma petersi and Phorosoma placenta (Echinodermata: Echinothuriidae). These interactions were observed in situ using a remotely operated vehicle (ROV), deployed at depths of 1410 to 1775 m on three seamounts in the western North Atlantic (Bear and Rehoboth seamounts in the New England Seamounts and Yakutat Seamount in the Corner Rise Seamounts). Full motion video and still frames documented individual cusk eels associated with urchins in open fine-grained sediment and coral rubble habitats. Cusk eels foraged around the periphery of urchins and took refuge at the base and among the long spines on the aboral surface. We suggest that such associations provide juvenile cusk eels with shelter from predators or flow (or both) and access to prey far from other forms of refugia.


Bulletin of The Peabody Museum of Natural History | 2010

A New Species of the Roughy Genus Hoplostethus (Teleostei: Trachichthyidae) from the Philippines

Jon A. Moore; Kathryn A. Dodd

ABSTRACT A new species of roughy in the genus Hoplostethus is described from a single specimen collected at depths of 648 to 660 m just east of the Calagua Islands off the east coast of Luzon Island, Philippines. It is characterized by extremely thick fin spines (greatest width of dorsal fin spines 17.4% to 23.1% of spine length; width of spines on pelvic fin 12.9% to 14.2% of spine length; width of anal fin spines 24.4% to 34.2% of spine length), lack of black pigment in the spinous portion of the dorsal fin, and a unique combination of counts and morphometric characters (56 digitiform pyloric caeca, 13 enlarged ventral scutes, ventral fin origin to anal fin origin 38.7% of standard length).

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Tracey Sutton

Nova Southeastern University

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Alex Dornburg

North Carolina Museum of Natural Sciences

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April Cook

Nova Southeastern University

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Michael Vecchione

National Museum of Natural History

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Martha S. Nizinski

National Museum of Natural History

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Kevin M. Boswell

Florida International University

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Mahmood S. Shivji

Nova Southeastern University

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Tamara M. Frank

Nova Southeastern University

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Gregory J. Watkins-Colwell

American Museum of Natural History

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