Alison Gould

California Academy of Sciences · Department of Ichthyology

This study presents the assembly and comparative genomic analysis of luminous Photobacterium strains isolated from the light organs of 12 fish species using Oxford Nanopore Technologies (ONT) sequencing. The majority of assemblies achieved chromosome-level continuity, consisting of one large (>3 Mbp) and one small (~1.5 Mbp) contig, with near compl...

The bioluminescent symbiosis involving the urchin cardinalfish, Siphamia tubifer , and Photobacterium mandapamensis , a luminous member of the Vibrionaceae, is highly specific compared to other bioluminescent fish-bacteria associations. Despite this high degree of specificity, patterns of genetic diversity have been observed for the symbionts from...

Several species of luminous bacteria in the genus Photobacterium are the light organ symbionts of teleost fishes. Photobacterium leiognathi and its subspecies, P. mandapamensis , in particular, commonly form bioluminescent symbioses with fish hosts in the Leiognathidae and Acropomatidae families as well as with cardinalfish in the genus Siphamia (A...

The bioluminescent symbiosis involving the sea urchin cardinalfish Siphamia tubifer and the luminous bacterium Photobacterium mandapamensis is an emerging vertebrate model for the study of microbial symbiosis. However, little genetic data is available for the host, limiting the scope of research that can be implemented with this association. We pre...

The bioluminescent symbiosis between the sea urchin cardinalfish Siphamia tubifer (Kurtiformes: Apogonidae) and the luminous bacterium Photobacterium mandapamensis is an emerging vertebrate-bacteria model for the study of microbial symbiosis. However, there is little genetic data available for the host fish, limiting the scope of potential research...

Symbiotic relationships between bioluminescent bacteria and fishes have evolved multiple times across hundreds of fish taxa, but relatively little is known about the specificity of these associations and how stable they are over host generations. This study describes the degree of specificity of a bioluminescent symbiosis between cardinalfishes in...

Symbiotic relationships between bioluminescent bacteria and fishes have evolved multiple times across hundreds of fish taxa, but relatively little is known about the specificity of these associations and how conserved they have been through time. This study describes the degree of specificity of a bioluminescent symbiosis between cardinalfishes in...

All organisms depend on symbiotic associations with bacteria for their success, yet how these interspecific interactions influence the population structure, ecology, and evolution of microbial symbionts is not well understood. Additionally, patterns of genetic variation in interacting species can reveal ecological traits that are important to gene...

All organisms depend on symbiotic associations with bacteria for their success, yet the processes by which specific symbioses are established and persist remain largely undescribed. To examine the ecological mechanisms involved in maintaining symbiont specificity over host generations, we examined the population genomics of a binary symbiosis invol...

This is a collection of articles that reference the PNAS publication "Microbiome interactions shape host fitness", available at https://doi.org/10.1073/pnas.1809349115 Each figure of the paper is here with clickable links in context that link to each of the analyses performed. Each of the computational analyses presented are the actual analysis use...

Gut bacteria can affect key aspects of host fitness, such as development, fecundity, and lifespan, while the host, in turn, shapes the gut microbiome. However, it is unclear to what extent individual species versus community interactions within the microbiome are linked to host fitness. Here, we combinatorially dissect the natural microbiome of Dro...

Gut bacteria can affect key aspects of host fitness, such as development, fecundity, and lifespan, while the host in turn shapes the gut microbiome. Microbiomes co-evolve with their hosts and have been implicated in host speciation. However, it is unclear to what extent individual species versus community interactions within the microbiome are link...

Discrepancies between potential and observed dispersal distances of reef fish indicate the need for a better understanding of the influence of larval behaviour on recruitment and dispersal. Population genetic studies can provide insight on the degree to which populations are connected, and the development of restriction site-associated sequencing (...

Characteristics of the life history of the coral reef-dwelling cardinalfish Siphamia tubifer, from Okinawa, Japan, were defined. A paternal mouthbrooder, S. tubifer, is unusual in forming a bioluminescent symbiosis with Photobacterium mandapamensis. The examined S. tubifer (n = 1273) ranged in size from 9·5 to 43·5 mm standard length (LS ), and the...

The evolution of a symbiosis requires the maintenance of an intimate host-symbiont association over ecological time. My dissertation research investigates the ecological mechanisms that facilitate the maintenance of specificity of a vertebrate-microbe symbiosis involving the coral reef cardinalfish, Siphamia tubifer, and the luminous bacterium, Pho...

The symbiotically luminous, reef-dwelling cardinalfish, Siphamia tubifer (Perciformes: Apogonidae), exhibits daily site fidelity, homing behavior, and a preference for the long-spined urchin, Diadema setosum, as its daytime host. The fish acquires its symbiont during larval development and releases large numbers of the bacteria with its feces daily...

The sea urchin cardinalfish, Siphamia tubifer (Perciformes: Apogonidae), is unusual among coral reef fishes for its use of bioluminescence, produced by symbiotic bacteria, while foraging at night. As a foundation for understanding the relationship between the symbiosis and the ecology of the fish, this study examined the diel behavior, host urchin...

Background/Question/Methods The cardinalfish, Siphamia tubifer (Perciformes: Apogonidae) inhabits coral reefs throughout the Indo-West Pacific, seeking protection among the spines of sea urchins during the day. At our study site in Okinawa, Japan, S. tubifer aggregates in groups among the spines of the long-spined sea urchin, Diadema setosum, and...

We determined reproductive and growth rates of three common copepods in the low-salinity zone of the San Francisco Estuary during spring–summer of 2006 and 2007. Rates were low, particularly during summer. The egg production rate of Eurytemora affinis in spring averaged ∼3 eggs female−1 day−1 or 0.04 day−1, while that of Pseudodiaptomus forbesi in...

Photobacterium mandapamensis is one of three luminous Photobacterium species able to form species-specific bioluminescent symbioses with marine fishes. Here, we present the draft genome sequence of P. mandapamensis strain svers.1.1, the bioluminescent symbiont of the cardinal fish Siphamia versicolor, the first genome of a symbiotic, luminous Photo...

Limnoithona tetraspina is a small cyclopoid copepod that was introduced to the San Francisco Estuary (SFE), USA, in 1993 and became the most abundant copepod species in the low-salinity zone (LSZ). Two previous studies have shown that it feeds only on motile prey, predominantly ciliates. Little is otherwise known of its biology or its role in the e...

We developed Bayesian hierarchical models to estimate life stage durations of copepods from data on life stage frequencies over time in laboratory cohorts. This approach can determine stage duration or development rate, as well as other parameters of the development process, with probability distributions for each parameter. Uncertainty arising fro...