Phylogenetic divergence between the obligate luminous symbionts of flashlight fishes demonstrates specificity of bacteria to host genera

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/107544/1/emi412135.pd

Beijerinck and the bioluminescent bacteria: microbiological experiments in the late 19th and early 20th centuries

Microbiological research in the days before specialized equipment, or even electricity, required a great deal of ingenuity. The revival of 90-year-old bioluminescent bacteria from Beijerinck's laboratory in Delft prompted a review of his work with these microorganisms and revealed their use in simple techniques for the investigation of, among other things, sugar metabolism in yeasts, oxygen generation and uptake and even the survival of microorganisms in liquid hydrogen. He used variant strains of bioluminescent bacteria in an attempt to study heredity and variation in biological systems and described one of the earliest examples of enzyme induction.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/79076/1/j.1574-6941.2010.01004.x.pd

Evolution and diversification of a sexually dimorphic luminescent system in ponyfishes (Teleostei: Leiognathidae), including diagnoses for two new genera

A phylogeny was generated for Leiognathidae, an assemblage of bioluminescent, Indo-Pacific schooling fishes, using 6175 characters derived from seven mitochondrial genes ( 16S , COI , ND4 , ND5 , tRNA-His , tRNA-Ser , tRNA-Leu ), two nuclear genes ( 28S , histone H3 ), and 15 morphological transformations corresponding to features of the fishes' sexually dimorphic light-organ system (LOS; e.g., circumesophageal light organ, lateral lining of the gas bladder, transparent flank and opercular patches). Leiognathidae comprises three genera, Gazza , Leiognathus , and Secutor . Our results demonstrate that Leiognathidae, Gazza , and Secutor are monophyletic, whereas Leiognathus is not. The recovered pattern of relationships reveals that a structurally complex, strongly sexually dimorphic and highly variable species-specific light organ is derived from a comparatively simple non-dimorphic structure, and that evolution of other sexually dimorphic internal and external features of the male LOS are closely linked with these light-organ modifications. Our results demonstrate the utility of LOS features, both for recovering phylogeny and resolving taxonomic issues in a clade whose members otherwise exhibit little morphological variation. We diagnose two new leiognathid genera, Photopectoralis and Photoplagios , on the basis of these apomorphic LOS features and also present derived features of the LOS to diagnose several additional leiognathid clades, including Gazza and Secutor . Furthermore, we show that five distinct and highly specialized morphologies for male-specific lateral luminescence signaling, which exhibit species-specific variation in structure, have evolved in these otherwise outwardly conservative fishes. Leiognathids inhabit turbid coastal waters with poor visibility and are often captured in mixed assemblages of several species. We hypothesize that the species-specific, sexually dimorphic internal and external modifications of the leiognathid LOS provide compelling evidence for an assortative mating scheme in which males use species-specific patterns of lateral luminescence signaling to attract mates, and that this system functions to maintain reproductive isolation in these turbid coastal environments. © The Willi Hennig Society 2005.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/72092/1/j.1096-0031.2005.00067.x.pd

Natural replacement of vertically inherited lux‐rib genes of Photobacterium aquimaris by horizontally acquired homologues

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/92440/1/emi4355_sm_FigS1.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/92440/2/emi4355_sm_TableS1.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/92440/3/emi4355.pd

Historical microbiology: revival and phylogenetic analysis of the luminous bacterial cultures of M . W . B eijerinck

Luminous bacteria isolated by M artinus W . B eijerinck were sealed in glass ampoules in 1924 and 1925 and stored under the names P hotobacterium phosphoreum and ‘ P hotobacterium splendidum ’. To determine if the stored cultures were viable and to assess their evolutionary relationship with currently recognized bacteria, portions of the ampoule contents were inoculated into culture medium. Growth and luminescence were evident after 13 days of incubation, indicating the presence of viable cells after more than 80 years of storage. The B eijerinck strains are apparently the oldest bacterial cultures to be revived from storage. Multi‐locus sequence analysis, based on the 16S rRNA , gapA , gyrB , pyrH , recA , luxA , and luxB genes, revealed that the B eijerinck strains are distant from the type strains of P . phosphoreum , ATCC 11040 T , and V ibrio splendidus , ATCC 33125 T , and instead form an evolutionarily distinct clade of V ibrio . Newly isolated strains from coastal seawater in N orway, F rance, U ruguay, M exico, and J apan grouped with the B eijerinck strains, indicating a global distribution for this new clade, designated as the beijerinckii clade. Strains of the beijerinckii clade exhibited little sequence variation for the seven genes and approximately 6300 nucleotides examined despite the geographic distances and the more than 80 years separating their isolation. Gram‐negative bacteria therefore can survive for many decades in liquid storage, and in nature, they do not necessarily diverge rapidly over time.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/88047/1/fem1177.pd

Essential Role of Correlations in Governing Charge Transport in Disordered Organic Materials

The transport of photoinjected charges in disordered organic films is often interpreted using a formula based on a Gaussian disorder model (GDM) that neglects spatial correlations due to charge-dipole interactions, even though such correlations have recently been shown to explain the universal electric field dependence observed in these systems. Based on extensive computer simulations of a 3D disorder model that includes such correlations, we present a new formula for analyzing experiments that accurately describes transport in these materials

Genome Evolution in the Obligate but Environmentally Active Luminous Symbionts of Flashlight Fish

The luminous bacterial symbionts of anomalopid flashlight fish are thought to be obligately dependent on their hosts for growth and share several aspects of genome evolution with unrelated obligate symbionts, including genome reduction. However, in contrast to most obligate bacteria, anomalopid symbionts have an active environmental phase that may be important for symbiont transmission. Here we investigated patterns of evolution between anomalopid symbionts compared with patterns in free-living relatives and unrelated obligate symbionts to determine if trends common to obligate symbionts are also found in anomalopid symbionts. Two symbionts, ?Candidatus Photodesmus katoptron? and ?Candidatus Photodesmus blepharus,? have genomes that are highly similar in gene content and order, suggesting genome stasis similar to ancient obligate symbionts present in insect lineages. This genome stasis exists in spite of the symbiont?s inferred ability to recombine, which is frequently lacking in obligate symbionts with stable genomes. Additionally, we used genome comparisons and tests of selection to infer which genes may be particularly important for the symbiont?s ecology compared with relatives. In keeping with obligate dependence, substitution patterns suggest that most symbiont genes are experiencing relaxed purifying selection compared with relatives. However, genes involved in motility and carbon storage, which are likely to be used outside the host, appear to be under increased purifying selection. Two chemoreceptor chemotaxis genes are retained by both species and show high conservation with amino acid sensing genes, suggesting that the bacteria may actively seek out hosts using chemotaxis toward amino acids, which the symbionts are not able to synthesize

Phylogenetic analysis of host–symbiont specificity and codivergence in bioluminescent symbioses

Several groups of marine fishes and squids form mutualistic bioluminescent symbioses with luminous bacteria. The dependence of the animal on its symbiont for light production, the animal's specialized anatomical adaptations for harboring bacteria and controlling light emission, and the host family bacterial species specificity characteristic of these associations suggest that bioluminescent symbioses are tightly coupled associations that might involve coevolutionary interactions. Consistent with this possibility, evidence of parallel cladogenesis has been reported for squid–bacterial associations. However, genetic adaptations in the bacteria necessary for and specific to symbiosis have not been identified, and unlike obligate endosymbiotic associations in which the bacteria are transferred vertically, bacterially bioluminescent hosts acquire their light-organ symbionts from the environment with each new host generation. These contrasting observations led us to test the hypotheses of species specificity and codivergence in bioluminescent symbioses, using an extensive sampling of naturally formed associations. Thirty-five species of fish in seven teleost families (Chlorophthalmidae, Macrouridae, Moridae, Trachichthyidae, Monocentridae, Acropomatidae, Leiognathidae) and their light-organ bacteria were examined. Phylogenetic analysis of a taxonomically broad sampling of associations was based on mitochondrial 16S rRNA and cytochrome oxidase I gene sequences for the fish and on recA , gyrB and luxA sequences for bacteria isolated from the light organs of these specimens. In a fine-scale test focused on Leiognathidae, phylogenetic analysis was based also on histone H3 subunit and 28S rRNA gene sequences for the fish and on gyrB , luxA , luxB , luxF and luxE sequences for the bacteria. Deep divergences were revealed among the fishes, and clear resolution was obtained between clades of the bacteria. In several associations, bacterial species identities contradicted strict host family bacterial species specificity. Furthermore, the fish and bacterial phylogenies exhibited no meaningful topological congruence; evolutionary divergence of host fishes was not matched by a similar pattern of diversification in the symbiotic bacteria. Re-analysis of data reported for squids and their luminous bacteria also revealed no convincing evidence of codivergence. These results refute the hypothesis of strict host family bacterial species specificity and the hypothesis of codivergence in bioluminescent symbioses. © The Willi Hennig Society 2007.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/73754/1/j.1096-0031.2007.00157.x.pd

The Leiognathus aureus complex (Perciformes: Leiognathidae) with the description of a new species

Taxonomic analysis of a group of morphologically similar ponyfishes (Perciformes: Leiognathidae) establishes a complex comprising three valid species: Leiognathus aureus Abe and Haneda, 1972, widely distributed in the western Pacific Ocean (Taiwan, Philippines, Thailand, Singapore, Indonesia, and northern Australia); L. hataii Abe and Haneda, 1972, currently known only from Ambon, Indonesia; and L. panayensis sp. nov. Kimura and Dunlap, currently known only from Panay Island, the Philippines. The L. aureus complex can be defined by the following combination of characters: mouth protruding forward, not downward; small but sharp conical teeth uniserially on jaws; a black line between lower margin of eye and lower jaw articulation; and lateral line incomplete, ending below posterior part of dorsal fin base or on anterior caudal peduncle. Leiognathus hataii differs from both L. aureus and L. panayensis in having a large dark blotch below the spinous dorsal fin base and fewer counts of scales (lateral line scales 50–58 vs. 64–85 in the latter two species; scales above lateral line 7–10 vs. 12–18; scales below lateral line 22–26 vs. 30–41). Leiognathus panayensis is distinguished from L. aureus in having a deeper body (41–51% SL vs. 35–45% SL in the latter), long posterior limb of maxilla (21–25% HL vs. 15–23% HL), wholly scaled belly (vs. naked along preanal median keel), and a dark blotch on nape (vs. absent).Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/41594/1/10228_2003_Article_160.pd

The evaluation of linear forms

This presentation deals with the evaluation and transformation of linear forms. Especial emphasis is given to implicit methods in which it is not necessary to find the explicit values, x i . The relation of the Aitken triple product matrix CA −1 B to the result of a linear transformation of linear forms is noted, and the numerical computation of this triple product matrix is indicated with the use of the simple Abbreviated Doolittle solution. Application is also made to the evaluation of A −1 and of A −1 C .Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/45755/1/11336_2005_Article_BF02288592.pd