1
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Lau ES, Goodheart JA, Anderson NT, Liu VL, Mukherjee A, Oakley TH. Similar enzymatic functions in distinct bioluminescence systems: Evolutionary recruitment of sulfotransferases in ostracod light organs. bioRxiv 2024:2023.04.12.536614. [PMID: 37090632 PMCID: PMC10120648 DOI: 10.1101/2023.04.12.536614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Genes from ancient families are sometimes involved in the convergent evolutionary origins of similar traits, even across vast phylogenetic distances. Sulfotransferases are an ancient family of enzymes that transfer sulfate from a donor to a wide variety of substrates, including probable roles in some bioluminescence systems. Here we demonstrate multiple sulfotransferases, highly expressed in light organs of the bioluminescent ostracod Vargula tsujii , transfer sulfate in vivo to the luciferin substrate, vargulin. We find luciferin sulfotransferases of ostracods are not orthologous to known luciferin sulfotransferases of fireflies or sea pansies; animals with distinct and convergently evolved bioluminescence systems compared to ostracods. Therefore, distantly related sulfotransferases were independently recruited at least three times, leading to parallel evolution of luciferin metabolism in three highly diverged organisms. Re-use of homologous genes is surprising in these bioluminescence systems because the other components, including luciferins and luciferases, are completely distinct. Whether convergently evolved traits incorporate ancient genes with similar functions or instead use distinct, often newer, genes may be constrained by how many genetic solutions exist for a particular function. When fewer solutions exist, as in genetic sulfation of small molecules, evolution may be more constrained to use the same genes time and again.
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2
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Varney RM, Speiser DI, Cannon JT, Aguilar MA, Eernisse DJ, Oakley TH. A morphological basis for path-dependent evolution of visual systems. Science 2024; 383:983-987. [PMID: 38422123 DOI: 10.1126/science.adg2689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 01/11/2024] [Indexed: 03/02/2024]
Abstract
Path dependence influences macroevolutionary predictability by constraining potential outcomes after critical evolutionary junctions. Although it has been demonstrated in laboratory experiments, path dependence is difficult to demonstrate in natural systems because of a lack of independent replicates. Here, we show that two types of distributed visual systems recently evolved twice within chitons, demonstrating rapid and path-dependent evolution of a complex trait. The type of visual system that a chiton lineage can evolve is constrained by the number of openings for sensory nerves in its shell plates. Lineages with more openings evolve visual systems with thousands of eyespots, whereas those with fewer openings evolve visual systems with hundreds of shell eyes. These macroevolutionary outcomes shaped by path dependence are both deterministic and stochastic because possibilities are restricted yet not entirely predictable.
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Affiliation(s)
| | | | | | | | | | - Todd H Oakley
- University of California, Santa Barbara, Santa Barbara, CA, USA
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3
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Hensley NM, Rivers TJ, Gerrish GA, Saha R, Oakley TH. Collective synchrony of mating signals modulated by ecological cues and social signals in bioluminescent sea fireflies. Proc Biol Sci 2023; 290:20232311. [PMID: 38018106 PMCID: PMC10685132 DOI: 10.1098/rspb.2023.2311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 11/06/2023] [Indexed: 11/30/2023] Open
Abstract
Individuals often employ simple rules that can emergently synchronize behaviour. Some collective behaviours are intuitively beneficial, but others like mate signalling in leks occur across taxa despite theoretical individual costs. Whether disparate instances of synchronous signalling are similarly organized is unknown, largely due to challenges observing many individuals simultaneously. Recording field collectives and ex situ playback experiments, we describe principles of synchronous bioluminescent signals produced by marine ostracods (Crustacea; Luxorina) that seem behaviorally convergent with terrestrial fireflies, and with whom they last shared a common ancestor over 500 Mya. Like synchronous fireflies, groups of signalling males use visual cues (intensity and duration of light) to decide when to signal. Individual ostracods also modulate their signal based on the distance to nearest neighbours. During peak darkness, luminescent 'waves' of synchronous displays emerge and ripple across the sea floor approximately every 60 s, but such periodicity decays within and between nights after the full moon. Our data reveal these bioluminescent aggregations are sensitive to both ecological and social light sources. Because the function of collective signals is difficult to dissect, evolutionary convergence, like in the synchronous visual displays of diverse arthropods, provides natural replicates to understand the generalities that produce emergent group behaviour.
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Affiliation(s)
- Nicholai M. Hensley
- Department of Ecology, Evolution, and Marine Biology, University of California Santa Barbara, Santa Barbara, CA 93106-9620, USA
| | - Trevor J. Rivers
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66405, USA
| | - Gretchen A. Gerrish
- Center for Limnology, Trout Lake Station, University of Wisconsin, Boulder Junction, Madison, WI 54512, USA
| | - Raj Saha
- Roux Institute, Northeastern University, Portland, ME 04101, USA
| | - Todd H. Oakley
- Department of Ecology, Evolution, and Marine Biology, University of California Santa Barbara, Santa Barbara, CA 93106-9620, USA
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4
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Ellis EA, Goodheart JA, Hensley NM, González VL, Reda NJ, Rivers TJ, Morin JG, Torres E, Gerrish GA, Oakley TH. Sexual Signals Persist over Deep Time: Ancient Co-option of Bioluminescence for Courtship Displays in Cypridinid Ostracods. Syst Biol 2023; 72:264-274. [PMID: 35984328 PMCID: PMC10448971 DOI: 10.1093/sysbio/syac057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 07/22/2022] [Accepted: 08/08/2022] [Indexed: 11/14/2022] Open
Abstract
Although the diversity, beauty, and intricacy of sexually selected courtship displays command the attention of evolutionists, the longevity of these traits in deep time is poorly understood. Population-based theory suggests sexual selection could either lower or raise extinction risk, resulting in high or low persistence of lineages with sexually selected traits. Furthermore, empirical studies that directly estimate the longevity of sexually selected traits are uncommon. Sexually selected signals-including bioluminescent courtship-originated multiple times during evolution, allowing the empirical study of their longevity after careful phylogenetic and divergence time analyses. Here, we estimate the first transcriptome-based molecular phylogeny and divergence times of Cypridinidae. We report extreme longevity of bioluminescent courtship, a trait important in mate choice and probably under sexual selection. Our relaxed-clock estimates of divergence times coupled with stochastic character mapping show luminous courtship evolved only once in Cypridinidae-in a Sub-Tribe, we name Luxorina-at least 151 millions of years ago from cypridinid ancestors that used bioluminescence only in antipredator displays, defining a Tribe we name Luminini. This time-calibrated molecular phylogeny of cypridinids will serve as a foundation for integrative and comparative studies on the biochemistry, molecular evolution, courtship, diversification, and ecology of cypridinid bioluminescence. The persistence of luminous courtship for hundreds of millions of years suggests that sexual selection did not cause a rapid loss of associated traits, and that rates of speciation within the group exceeded extinction risk, which may contribute to the persistence of a diverse clade of signaling species. [Ancestral state reconstruction; Biodiversity; co-option; divergence time estimates; macroevolution; Ostracoda; phylogenomics; sexual selection.].
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Affiliation(s)
- Emily A Ellis
- Department of Ecology, Evolution, and Marine Biology, University of
California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Jessica A Goodheart
- Department of Ecology, Evolution, and Marine Biology, University of
California, Santa Barbara, Santa Barbara, CA 93106, USA
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of
Oceanography, University of California, San Diego, La Jolla, CA 92037,
USA
| | - Nicholai M Hensley
- Department of Ecology, Evolution, and Marine Biology, University of
California, Santa Barbara, Santa Barbara, CA 93106, USA
- Department of Neurobiology and Behavior, Cornell University,
Ithaca, NY 14850, USA
| | - Vanessa L González
- Department of Invertebrate Zoology, Smithsonian Institution, National
Museum of Natural History, 10th and Constitution NW, Washington, DC
20560-0105, USA
| | - Nicholas J Reda
- Biology Department, University of Wisconsin–La Crosse, La
Crosse, WI 54601, USA
| | - Trevor J Rivers
- Department of Ecology and Evolutionary Biology, University of Kansas
Lawrence, KS 66045, USA
| | - James G Morin
- Department of Ecology and Evolutionary Biology, Cornell
University, Ithaca, NY 14850, USA
| | - Elizabeth Torres
- Department of Biological Sciences, California State University Los
Angeles, Los Angeles, CA 90032, USA
| | - Gretchen A Gerrish
- Biology Department, University of Wisconsin–La Crosse, La
Crosse, WI 54601, USA
- Trout Lake Station, Center for Limnology, University of Wisconsin –
Madison, Boulder Junction, WI 54512, USA
| | - Todd H Oakley
- Department of Ecology, Evolution, and Marine Biology, University of
California, Santa Barbara, Santa Barbara, CA 93106, USA
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5
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Vöcking O, Macias-Muñoz A, Jaeger SJ, Oakley TH. Deep Diversity: Extensive Variation in the Components of Complex Visual Systems across Animals. Cells 2022; 11:cells11243966. [PMID: 36552730 PMCID: PMC9776813 DOI: 10.3390/cells11243966] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 11/19/2022] [Accepted: 12/02/2022] [Indexed: 12/13/2022] Open
Abstract
Understanding the molecular underpinnings of the evolution of complex (multi-part) systems is a fundamental topic in biology. One unanswered question is to what the extent do similar or different genes and regulatory interactions underlie similar complex systems across species? Animal eyes and phototransduction (light detection) are outstanding systems to investigate this question because some of the genetics underlying these traits are well characterized in model organisms. However, comparative studies using non-model organisms are also necessary to understand the diversity and evolution of these traits. Here, we compare the characteristics of photoreceptor cells, opsins, and phototransduction cascades in diverse taxa, with a particular focus on cnidarians. In contrast to the common theme of deep homology, whereby similar traits develop mainly using homologous genes, comparisons of visual systems, especially in non-model organisms, are beginning to highlight a "deep diversity" of underlying components, illustrating how variation can underlie similar complex systems across taxa. Although using candidate genes from model organisms across diversity was a good starting point to understand the evolution of complex systems, unbiased genome-wide comparisons and subsequent functional validation will be necessary to uncover unique genes that comprise the complex systems of non-model groups to better understand biodiversity and its evolution.
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Affiliation(s)
- Oliver Vöcking
- Department of Biology, University of Kentucky, Lexington, KY 40508, USA
| | - Aide Macias-Muñoz
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, CA 93106, USA
| | - Stuart J. Jaeger
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, CA 93106, USA
| | - Todd H. Oakley
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, CA 93106, USA
- Correspondence:
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Garm A, Svaerke JE, Pontieri D, Oakley TH. Corrigendum: Expression of opsins of the box jellyfish Tripedalia cystophora reveals the first photopigment in cnidarian ocelli and supports the presence of photoisomerases. Front Neuroanat 2022; 16:1028092. [PMID: 36157326 PMCID: PMC9496173 DOI: 10.3389/fnana.2022.1028092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 08/26/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
- Anders Garm
- Marine Biological Section, University of Copenhagen, Copenhagen, Denmark
- *Correspondence: Anders Garm
| | - Jens-Erik Svaerke
- Marine Biological Section, University of Copenhagen, Copenhagen, Denmark
| | - Daniela Pontieri
- Marine Biological Section, University of Copenhagen, Copenhagen, Denmark
| | - Todd H. Oakley
- Department of Biology, University of California, Santa Barbara, Santa Barbara, CA, United States
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Garm A, Svaerke JE, Pontieri D, Oakley TH. Expression of Opsins of the Box Jellyfish Tripedalia cystophora Reveals the First Photopigment in Cnidarian Ocelli and Supports the Presence of Photoisomerases. Front Neuroanat 2022; 16:916510. [PMID: 35991966 PMCID: PMC9389615 DOI: 10.3389/fnana.2022.916510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 06/24/2022] [Indexed: 11/13/2022] Open
Abstract
Cubomedusae, or box jellyfish, have a complex visual system comprising 24 eyes of four types. Like other cnidarians, their photoreceptor cells are ciliary in morphology, and a range of different techniques together show that at least two of the eye types—the image-forming upper and lower lens eyes—express opsin as the photopigment. The photoreceptors of these two eye types express the same opsin (Tc LEO), which belongs to the cnidarian-specific clade cnidops. Interestingly, molecular work has found a high number of opsin genes in box jellyfish, especially in the Caribbean species Tripedalia cystophora, most of which are of unknown function. In the current study, we raised antibodies against three out of five opsins identified from transcriptomic data from T. cystophora and used them to map the expression patterns. These expression patterns suggest one opsin as the photopigment in the slit eyes and another as a putative photoisomerase found in photoreceptors of all four eyes types. The last antibody stained nerve-like cells in the tentacles, in connection with nematocytes, and the radial nerve, in connection with the gonads. This is the first time photopigment expression has been localized to the outer segments of the photoreceptors in a cnidarian ocellus (simple eye). The potential presence of a photoisomerase could be another interesting convergence between box jellyfish and vertebrate photoreceptors, but it awaits final experimental proof.
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Affiliation(s)
- Anders Garm
- Marine Biological Section, University of Copenhagen, Copenhagen, Denmark
- *Correspondence: Anders Garm
| | - Jens-Erik Svaerke
- Marine Biological Section, University of Copenhagen, Copenhagen, Denmark
| | - Daniela Pontieri
- Marine Biological Section, University of Copenhagen, Copenhagen, Denmark
| | - Todd H. Oakley
- Department of Biology, University of California, Santa Barbara, Santa Barbara, CA, United States
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8
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Drábková M, Kocot KM, Halanych KM, Oakley TH, Moroz LL, Cannon JT, Kuris A, Garcia-Vedrenne AE, Pankey MS, Ellis EA, Varney R, Štefka J, Zrzavý J. Different phylogenomic methods support monophyly of enigmatic 'Mesozoa' (Dicyemida + Orthonectida, Lophotrochozoa). Proc Biol Sci 2022; 289:20220683. [PMID: 35858055 PMCID: PMC9257288 DOI: 10.1098/rspb.2022.0683] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Dicyemids and orthonectids were traditionally classified in a group called Mesozoa, but their placement in a single clade has been contested and their position(s) within Metazoa is uncertain. Here, we assembled a comprehensive matrix of Lophotrochozoa (Metazoa) and investigated the position of Dicyemida (= Rhombozoa) and Orthonectida, employing multiple phylogenomic approaches. We sequenced seven new transcriptomes and one draft genome from dicyemids (Dicyema, Dicyemennea) and two transcriptomes from orthonectids (Rhopalura). Using these and published data, we assembled and analysed contamination-filtered datasets with up to 987 genes. Our results recover Mesozoa monophyletic and as a close relative of Platyhelminthes or Gnathifera. Because of the tendency of the long-branch mesozoans to group with other long-branch taxa in our analyses, we explored the impact of approaches purported to help alleviate long-branch attraction (e.g. taxon removal, coalescent inference, gene targeting). None of these were able to break the association of Orthonectida with Dicyemida in the maximum-likelihood trees. Contrastingly, the Bayesian analysis and site-specific frequency model in maximum-likelihood did not recover a monophyletic Mesozoa (but only when using a specific 50 gene matrix). The classic hypothesis on monophyletic Mesozoa is possibly reborn and should be further tested.
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Affiliation(s)
- Marie Drábková
- Department of Parasitology, University of South Bohemia, České Budějovice 37005, Czech Republic,Laboratory of Molecular Ecology and Evolution, Institute of Parasitology, Biology Centre CAS, České Budějovice 37005, Czech Republic
| | - Kevin M. Kocot
- Department of Biological Sciences, The University of Alabama, Campus Box 870344, Tuscaloosa, AL 35487, USA
| | - Kenneth M. Halanych
- The Centre for Marine Science, University of North Carolina, Wilmington, 57000 Marvin K. Moss Lane, Wilmington, NC 28409, USA
| | - Todd H. Oakley
- Department of Ecology, Evolution, and Marine Biology, University of California Santa Barbara, Santa Barbara, CA 93106, USA
| | - Leonid L. Moroz
- Department of Neuroscience, and the Whitney Laboratory for Marine Bioscience, University of Florida, 9505 Ocean Shore Boulevard, St Augustine, FL 32080, USA
| | - Johanna T. Cannon
- Department of Ecology, Evolution, and Marine Biology, University of California Santa Barbara, Santa Barbara, CA 93106, USA
| | - Armand Kuris
- Department of Ecology, Evolution, and Marine Biology, University of California Santa Barbara, Santa Barbara, CA 93106, USA
| | - Ana Elisa Garcia-Vedrenne
- Department of Ecology, Evolution, and Marine Biology, University of California Santa Barbara, Santa Barbara, CA 93106, USA
| | - M. Sabrina Pankey
- Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH 03824, USA
| | - Emily A. Ellis
- Department of Ecology, Evolution, and Marine Biology, University of California Santa Barbara, Santa Barbara, CA 93106, USA
| | - Rebecca Varney
- Department of Biological Sciences, The University of Alabama, Campus Box 870344, Tuscaloosa, AL 35487, USA,Department of Ecology, Evolution, and Marine Biology, University of California Santa Barbara, Santa Barbara, CA 93106, USA
| | - Jan Štefka
- Department of Parasitology, University of South Bohemia, České Budějovice 37005, Czech Republic,Laboratory of Molecular Ecology and Evolution, Institute of Parasitology, Biology Centre CAS, České Budějovice 37005, Czech Republic
| | - Jan Zrzavý
- Department of Zoology, Faculty of Science, University of South Bohemia, České Budějovice 37005, Czech Republic
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9
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Picciani N, Kerlin JR, Jindrich K, Hensley NM, Gold DA, Oakley TH. Light modulated cnidocyte discharge predates the origins of eyes in Cnidaria. Ecol Evol 2021; 11:3933-3940. [PMID: 33976785 PMCID: PMC8093662 DOI: 10.1002/ece3.7280] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 12/06/2020] [Accepted: 01/20/2021] [Indexed: 11/07/2022] Open
Abstract
Complex biological traits often originate by integrating previously separate parts, but the organismal functions of these precursors are challenging to infer. If we can understand the ancestral functions of these precursors, it could help explain how they persisted and how they facilitated the origins of complex traits. Animal eyes are some of the best studied complex traits, and they include many parts, such as opsin-based photoreceptor cells, pigment cells, and lens cells. Eye evolution is understood through conceptual models that argue these parts gradually came together to support increasingly sophisticated visual functions. Despite the well-accepted logic of these conceptual models, explicit comparative studies to identify organismal functions of eye precursors are lacking. Here, we investigate how precursors functioned before they became part of eyes in Cnidaria, a group formed by sea anemones, corals, and jellyfish. Specifically, we test whether ancestral photoreceptor cells regulated the discharge of cnidocytes, the expensive single-use cells with various functions including prey capture, locomotion, and protection. Similar to a previous study of Hydra, we show an additional four distantly related cnidarian groups discharge significantly more cnidocytes when exposed to dim blue light compared with bright blue light. Our comparative analyses support the hypothesis that the cnidarian ancestor was capable of modulating cnidocyte discharge with light, which we speculate uses an opsin-based phototransduction pathway homologous to that previously described in Hydra. Although eye precursors might have had other functions like regulating timing of spawning, our findings are consistent with the hypothesis that photoreceptor cells which mediate cnidocyte discharge predated eyes, perhaps facilitating the prolific origination of eyes in Cnidaria.
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Affiliation(s)
- Natasha Picciani
- Department of Ecology, Evolution and Marine BiologyUniversity of California at Santa BarbaraSanta BarbaraCAUSA
- Present address:
Department of Ecology and Evolutionary BiologyYale UniversityNew HavenCTUSA
| | - Jamie R. Kerlin
- Department of Ecology, Evolution and Marine BiologyUniversity of California at Santa BarbaraSanta BarbaraCAUSA
- Present address:
Department of BiologyCalifornia State UniversityNorthridgeCAUSA
| | | | - Nicholai M. Hensley
- Department of Ecology, Evolution and Marine BiologyUniversity of California at Santa BarbaraSanta BarbaraCAUSA
| | - David A. Gold
- Department of Earth and Planetary SciencesUniversity of California at DavisDavisCAUSA
| | - Todd H. Oakley
- Department of Ecology, Evolution and Marine BiologyUniversity of California at Santa BarbaraSanta BarbaraCAUSA
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10
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Hensley NM, Ellis EA, Leung NY, Coupart J, Mikhailovsky A, Taketa DA, Tessler M, Gruber DF, De Tomaso AW, Mitani Y, Rivers TJ, Gerrish GA, Torres E, Oakley TH. Selection, drift, and constraint in cypridinid luciferases and the diversification of bioluminescent signals in sea fireflies. Mol Ecol 2021; 30:1864-1879. [PMID: 33031624 DOI: 10.1111/mec.15673] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 09/09/2020] [Accepted: 09/18/2020] [Indexed: 02/07/2023]
Abstract
Understanding the genetic causes of evolutionary diversification is challenging because differences across species are complex, often involving many genes. However, cases where single or few genetic loci affect a trait that varies dramatically across a radiation of species provide tractable opportunities to understand the genetics of diversification. Here, we begin to explore how diversification of bioluminescent signals across species of cypridinid ostracods ("sea fireflies") was influenced by evolution of a single gene, cypridinid-luciferase. In addition to emission spectra ("colour") of bioluminescence from 21 cypridinid species, we report 13 new c-luciferase genes from de novo transcriptomes, including in vitro assays to confirm function of four of those genes. Our comparative analyses suggest some amino acid sites in c-luciferase evolved under episodic diversifying selection and may be associated with changes in both enzyme kinetics and colour, two enzymatic functions that directly impact the phenotype of bioluminescent signals. The analyses also suggest multiple other amino acid positions in c-luciferase evolved neutrally or under purifying selection, and may have impacted the variation of colour of bioluminescent signals across genera. Previous mutagenesis studies at candidate sites show epistatic interactions, which could constrain the evolution of c-luciferase function. This work provides important steps toward understanding the genetic basis of diversification of behavioural signals across multiple species, suggesting different evolutionary processes act at different times during a radiation of species. These results set the stage for additional mutagenesis studies that could explicitly link selection, drift, and constraint to the evolution of phenotypic diversification.
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Affiliation(s)
- Nicholai M Hensley
- Department of Ecology, Evolution, & Marine Biology, University of California, Santa Barbara, Santa Barbara, CA, USA
| | - Emily A Ellis
- Department of Ecology, Evolution, & Marine Biology, University of California, Santa Barbara, Santa Barbara, CA, USA
| | - Nicole Y Leung
- Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA, USA
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, USA
| | - John Coupart
- Department of Ecology, Evolution, & Marine Biology, University of California, Santa Barbara, Santa Barbara, CA, USA
| | - Alexander Mikhailovsky
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, CA, USA
| | - Daryl A Taketa
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, USA
| | - Michael Tessler
- American Museum of Natural History and New York University, New York, NY, USA
- Department of Biology, St. Francis College, Brooklyn, NY, USA
| | - David F Gruber
- Department of Biology and Environmental Science, City University of New York Baruch College, New York, NY, USA
| | - Anthony W De Tomaso
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, USA
| | - Yasuo Mitani
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Japan
| | - Trevor J Rivers
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA
| | - Gretchen A Gerrish
- Department of Biology, University of Wisconsin - La Crosse, La Crosse, WI, USA
| | - Elizabeth Torres
- Department of Biological Sciences, California State University, Los Angeles, Los Angeles, CA, USA
| | - Todd H Oakley
- Department of Ecology, Evolution, & Marine Biology, University of California, Santa Barbara, Santa Barbara, CA, USA
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11
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Lau ES, Oakley TH. Multi-level convergence of complex traits and the evolution of bioluminescence. Biol Rev Camb Philos Soc 2020; 96:673-691. [PMID: 33306257 DOI: 10.1111/brv.12672] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 11/16/2020] [Accepted: 11/18/2020] [Indexed: 12/14/2022]
Abstract
Evolutionary convergence provides natural opportunities to investigate how, when, and why novel traits evolve. Many convergent traits are complex, highlighting the importance of explicitly considering convergence at different levels of biological organization, or 'multi-level convergent evolution'. To investigate multi-level convergent evolution, we propose a holistic and hierarchical framework that emphasizes breaking down traits into several functional modules. We begin by identifying long-standing questions on the origins of complexity and the diverse evolutionary processes underlying phenotypic convergence to discuss how they can be addressed by examining convergent systems. We argue that bioluminescence, a complex trait that evolved dozens of times through either novel mechanisms or conserved toolkits, is particularly well suited for these studies. We present an updated estimate of at least 94 independent origins of bioluminescence across the tree of life, which we calculated by reviewing and summarizing all estimates of independent origins. Then, we use our framework to review the biology, chemistry, and evolution of bioluminescence, and for each biological level identify questions that arise from our systematic review. We focus on luminous organisms that use the shared luciferin substrates coelenterazine or vargulin to produce light because these organisms convergently evolved bioluminescent proteins that use the same luciferins to produce bioluminescence. Evolutionary convergence does not necessarily extend across biological levels, as exemplified by cases of conservation and disparity in biological functions, organs, cells, and molecules associated with bioluminescence systems. Investigating differences across bioluminescent organisms will address fundamental questions on predictability and contingency in convergent evolution. Lastly, we highlight unexplored areas of bioluminescence research and advances in sequencing and chemical techniques useful for developing bioluminescence as a model system for studying multi-level convergent evolution.
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Affiliation(s)
- Emily S Lau
- Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, Santa Barbara, CA, 93106, U.S.A
| | - Todd H Oakley
- Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, Santa Barbara, CA, 93106, U.S.A
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12
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Goodheart JA, Minsky G, Brynjegard-Bialik MN, Drummond MS, Munoz JD, Fallon TR, Schultz DT, Weng JK, Torres E, Oakley TH. Laboratory culture of the California Sea Firefly Vargula tsujii (Ostracoda: Cypridinidae): Developing a model system for the evolution of marine bioluminescence. Sci Rep 2020; 10:10443. [PMID: 32591605 PMCID: PMC7320024 DOI: 10.1038/s41598-020-67209-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 06/04/2020] [Indexed: 11/09/2022] Open
Abstract
Bioluminescence, or the production of light by living organisms via chemical reaction, is widespread across Metazoa. Laboratory culture of bioluminescent organisms from diverse taxonomic groups is important for determining the biosynthetic pathways of bioluminescent substrates, which may lead to new tools for biotechnology and biomedicine. Some bioluminescent groups may be cultured, including some cnidarians, ctenophores, and brittle stars, but those use luminescent substrates (luciferins) obtained from their diets, and therefore are not informative for determination of the biosynthetic pathways of the luciferins. Other groups, including terrestrial fireflies, do synthesize their own luciferin, but culturing them is difficult and the biosynthetic pathway for firefly luciferin remains unclear. An additional independent origin of endogenous bioluminescence is found within ostracods from the family Cypridinidae, which use their luminescence for defense and, in Caribbean species, for courtship displays. Here, we report the first complete life cycle of a luminous ostracod (Vargula tsujii Kornicker & Baker, 1977, the California Sea Firefly) in the laboratory. We also describe the late-stage embryogenesis of Vargula tsujii and discuss the size classes of instar development. We find embryogenesis in V. tsujii ranges from 25–38 days, and this species appears to have five instar stages, consistent with ontogeny in other cypridinid lineages. We estimate a complete life cycle at 3–4 months. We also present the first complete mitochondrial genome for Vargula tsujii. Bringing a luminous ostracod into laboratory culture sets the stage for many potential avenues of study, including learning the biosynthetic pathway of cypridinid luciferin and genomic manipulation of an autogenic bioluminescent system.
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Affiliation(s)
- Jessica A Goodheart
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA.,Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Geetanjali Minsky
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA
| | - Mira N Brynjegard-Bialik
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA
| | - Michael S Drummond
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA
| | - J David Munoz
- Department of Biological Sciences, California State University, Los Angeles, CA, 90032-8201, USA
| | - Timothy R Fallon
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, 92093, USA.,Whitehead Institute for Biomedical Research, Cambridge, MA, 02142, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
| | - Darrin T Schultz
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, 95060, USA.,Department of Biomolecular Engineering and Bioinformatics, University of California, Santa Cruz, Santa Cruz, CA, 96060, USA
| | - Jing-Ke Weng
- Whitehead Institute for Biomedical Research, Cambridge, MA, 02142, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
| | - Elizabeth Torres
- Department of Biological Sciences, California State University, Los Angeles, CA, 90032-8201, USA
| | - Todd H Oakley
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, Santa Barbara, CA, 93106, USA.
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13
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Abstract
Eyes are quintessential complex traits and our understanding of their evolution guides models of trait evolution in general. A long-standing account of eye evolution argues natural selection favors morphological variations that allow increased functionality for sensing light. While certainly true in part, this focus on visual performance does not entirely explain why diffuse photosensitivity persists even after eyes evolve, or why eyes evolved many times, each time using similar building blocks. Here, we briefly review a vast literature indicating most genetic components of eyes historically responded to stress caused directly by light, including ultraviolet damage of DNA, oxidative stress, and production of aldehydes. We propose light-induced stress had a direct and prominent role in the evolution of eyes by bringing together genes to repair and prevent damage from light-stress, both before and during the evolution of eyes themselves. Stress-repair and stress-prevention genes were perhaps originally deployed as plastic responses to light and/or as beneficial mutations genetically driving expression where light was prominent. These stress-response genes sense, shield, and refract light but only as reactions to ongoing light stress. Once under regulatory-genetic control, they could be expressed before light stress appeared, evolve as a module, and be influenced by natural selection to increase functionality for sensing light, ultimately leading to complex eyes and behaviors. Recognizing the potentially prominent role of stress in eye evolution invites discussions of plasticity and assimilation and provides a hypothesis for why similar genes are repeatedly used in convergent eyes. Broadening the drivers of eye evolution encourages consideration of multi-faceted mechanisms of plasticity/assimilation and mutation/selection for complex novelties and innovations in general.
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Affiliation(s)
- Andrew J M Swafford
- Ecology, Evolution, and Marine Biology Department, University of California Santa Barbara, Santa Barbara, CA 93106, USA
| | - Todd H Oakley
- Ecology, Evolution, and Marine Biology Department, University of California Santa Barbara, Santa Barbara, CA 93106, USA
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14
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Juarez BH, Speiser DI, Oakley TH. Context‐dependent evolution of ostracod morphology along the ecogeographical gradient of ocean depth. Evolution 2019; 73:1213-1225. [DOI: 10.1111/evo.13748] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 04/07/2019] [Indexed: 11/30/2022]
Affiliation(s)
- Bryan H. Juarez
- Department of Ecology, Evolution, and Organismal Biology Iowa State University Ames Iowa 50011
| | - Daniel I. Speiser
- Department of Biological Sciences University of South Carolina Columbia South Carolina 29208
| | - Todd H. Oakley
- Santa Barbara, Department of Ecology, Evolution, and Marine Biology University of California Santa Barbara California 93106
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15
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Hensley NM, Ellis EA, Gerrish GA, Torres E, Frawley JP, Oakley TH, Rivers TJ. Phenotypic evolution shaped by current enzyme function in the bioluminescent courtship signals of sea fireflies. Proc Biol Sci 2019; 286:20182621. [PMID: 30963873 PMCID: PMC6367180 DOI: 10.1098/rspb.2018.2621] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 12/20/2018] [Indexed: 11/12/2022] Open
Abstract
Mating behaviours are diverse and noteworthy, especially within species radiations where they may contribute to speciation. Studying how differences in mating behaviours arise between species can help us understand how diversity is generated at multiple biological levels. The bioluminescent courtship displays of cypridinid ostracods (or sea fireflies) are an excellent system for this because amazing variety evolves while using a conserved biochemical mechanism. We find that the evolution of one aspect in this behavioural phenotype-the duration of bioluminescent courtship pulses-is shaped by biochemical function. First, by measuring light production from induced bioluminescence in 38 species, we discovered differences between species in their biochemical reactions. Then, for 16 species for which biochemical, phylogenetic and behavioural data are all available, we used phylogenetic comparative models to show that differences in biochemical reaction are nonlinearly correlated with the duration of courtship pulses. This relationship indicates that changes to both enzyme (c-luciferase) function and usage have shaped the evolution of courtship displays, but that they differentially contribute to these phenotypic changes. This nonlinear dynamic may have consequences for the disparity of signalling phenotypes observed across species, and demonstrates how unappreciated diversity at the biochemical level can lead to inferences about behavioural evolution.
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Affiliation(s)
- Nicholai M. Hensley
- Department of Ecology, Evolution, and Marine Biology, University of California Santa Barbara, Santa Barbara, CA 93106-9620, USA
| | - Emily A. Ellis
- Department of Ecology, Evolution, and Marine Biology, University of California Santa Barbara, Santa Barbara, CA 93106-9620, USA
| | | | - Elizabeth Torres
- Department of Biological Sciences, California State University Los Angeles, Los Angeles, CA 90032, USA
| | - John P. Frawley
- Department of Biology, University of Wisconsin, La Crosse, WI 54601, USA
| | - Todd H. Oakley
- Department of Ecology, Evolution, and Marine Biology, University of California Santa Barbara, Santa Barbara, CA 93106-9620, USA
| | - Trevor J. Rivers
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66405, USA
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16
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Picciani N, Kerlin JR, Sierra N, Swafford AJM, Ramirez MD, Roberts NG, Cannon JT, Daly M, Oakley TH. Prolific Origination of Eyes in Cnidaria with Co-option of Non-visual Opsins. Curr Biol 2018; 28:2413-2419.e4. [PMID: 30033336 DOI: 10.1016/j.cub.2018.05.055] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 03/26/2018] [Accepted: 05/17/2018] [Indexed: 11/15/2022]
Abstract
Animal eyes vary considerably in morphology and complexity and are thus ideal for understanding the evolution of complex biological traits [1]. While eyes evolved many times in bilaterian animals with elaborate nervous systems, image-forming and simpler eyes also exist in cnidarians, which are ancient non-bilaterians with neural nets and regions with condensed neurons to process information. How often eyes of varying complexity, including image-forming eyes, arose in animals with such simple neural circuitry remains obscure. Here, we produced large-scale phylogenies of Cnidaria and their photosensitive proteins and coupled them with an extensive literature search on eyes and light-sensing behavior to show that cnidarian eyes originated at least eight times, with complex, lensed-eyes having a history separate from other eye types. Compiled data show widespread light-sensing behavior in eyeless cnidarians, and comparative analyses support ancestors without eyes that already sensed light with dispersed photoreceptor cells. The history of expression of photoreceptive opsin proteins supports the inference of distinct eye origins via separate co-option of different non-visual opsin paralogs into eyes. Overall, our results show eyes evolved repeatedly from ancestral photoreceptor cells in non-bilaterian animals with simple nervous systems, co-opting existing precursors, similar to what occurred in Bilateria. Our study underscores the potential for multiple, evolutionarily distinct visual systems even in animals with simple nervous systems.
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Affiliation(s)
- Natasha Picciani
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA.
| | - Jamie R Kerlin
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Noemie Sierra
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Andrew J M Swafford
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - M Desmond Ramirez
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Nickellaus G Roberts
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Johanna T Cannon
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Marymegan Daly
- Department of Evolution, Ecology, and Organismal Biology, Ohio State University, Columbus, OH 43210, USA
| | - Todd H Oakley
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA.
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17
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Ramirez MD, Pairett AN, Pankey MS, Serb JM, Speiser DI, Swafford AJ, Oakley TH. The Last Common Ancestor of Most Bilaterian Animals Possessed at Least Nine Opsins. Genome Biol Evol 2018; 8:3640-3652. [PMID: 28172965 PMCID: PMC5521729 DOI: 10.1093/gbe/evw248] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/17/2016] [Indexed: 12/17/2022] Open
Abstract
The opsin gene family encodes key proteins animals use to sense light and has expanded dramatically as it originated early in animal evolution. Understanding the origins of opsin diversity can offer clues to how separate lineages of animals have repurposed different opsin paralogs for different light-detecting functions. However, the more we look for opsins outside of eyes and from additional animal phyla, the more opsins we uncover, suggesting we still do not know the true extent of opsin diversity, nor the ancestry of opsin diversity in animals. To estimate the number of opsin paralogs present in both the last common ancestor of the Nephrozoa (bilaterians excluding Xenoacoelomorpha), and the ancestor of Cnidaria + Bilateria, we reconstructed a reconciled opsin phylogeny using sequences from 14 animal phyla, especially the traditionally poorly-sampled echinoderms and molluscs. Our analysis strongly supports a repertoire of at least nine opsin paralogs in the bilaterian ancestor and at least four opsin paralogs in the last common ancestor of Cnidaria + Bilateria. Thus, the kernels of extant opsin diversity arose much earlier in animal history than previously known. Further, opsins likely duplicated and were lost many times, with different lineages of animals maintaining different repertoires of opsin paralogs. This phylogenetic information can inform hypotheses about the functions of different opsin paralogs and can be used to understand how and when opsins were incorporated into complex traits like eyes and extraocular sensors.
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Affiliation(s)
- M Desmond Ramirez
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA
| | - Autum N Pairett
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA
| | - M Sabrina Pankey
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH
| | - Jeanne M Serb
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA
| | - Daniel I Speiser
- Department of Biological Sciences, University of South Carolina, Columbia, SC
| | - Andrew J Swafford
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA
| | - Todd H Oakley
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA
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18
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Swafford AJM, Oakley TH. Multimodal sensorimotor system in unicellular zoospores of a fungus. ACTA ACUST UNITED AC 2018; 221:jeb.163196. [PMID: 29170260 DOI: 10.1242/jeb.163196] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 11/19/2017] [Indexed: 12/15/2022]
Abstract
Complex sensory systems often underlie critical behaviors, including avoiding predators and locating prey, mates and shelter. Multisensory systems that control motor behavior even appear in unicellular eukaryotes, such as Chlamydomonas, which are important laboratory models for sensory biology. However, we know of no unicellular opisthokonts that control motor behavior using a multimodal sensory system. Therefore, existing single-celled models for multimodal sensorimotor integration are very distantly related to animals. Here, we describe a multisensory system that controls the motor function of unicellular fungal zoospores. We found that zoospores of Allomyces arbusculus exhibit both phototaxis and chemotaxis. Furthermore, we report that closely related Allomyces species respond to either the chemical or the light stimuli presented in this study, not both, and likely do not share this multisensory system. This diversity of sensory systems within Allomyces provides a rare example of a comparative framework that can be used to examine the evolution of sensory systems following the gain/loss of available sensory modalities. The tractability of Allomyces and related fungi as laboratory organisms will facilitate detailed mechanistic investigations into the genetic underpinnings of novel photosensory systems, and how multisensory systems may have functioned in early opisthokonts before multicellularity allowed for the evolution of specialized cell types.
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Affiliation(s)
- Andrew J M Swafford
- Ecology, Evolution, and Marine Biology, University of California Santa Barbara, Santa Barbara, CA 93106, USA
| | - Todd H Oakley
- Ecology, Evolution, and Marine Biology, University of California Santa Barbara, Santa Barbara, CA 93106, USA
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19
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Lee C, Blay S, Mooers AØ, Singh A, Oakley TH. CoMET: A Mesquite Package for Comparing Models of Continuous Character Evolution on Phylogenies. Evol Bioinform Online 2017. [DOI: 10.1177/117693430600200022] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Continuously varying traits such as body size or gene expression level evolve during the history of species or gene lineages. To test hypotheses about the evolution of such traits, the maximum likelihood (ML) method is often used. Here we introduce CoMET (Continuous-character Model Evaluation and Testing), which is module for Mesquite that automates likelihood computations for nine different models offrait evolution. Due to its few restrictions on input data, CoMET is applicable to testing a wide range of character evolution hypotheses. The CoMET homepage, which links to freely available software and more detailed usage instructions, is located at http://www.lifesci.ucsb.edu/eemb/labs/oakley/software/comet.htm .
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Affiliation(s)
- Chunghau Lee
- Department of Computer Science; University of California, Santa Barbara, CA 93106 USA
| | - Sigal Blay
- Department of Biological Sciences and IRMACS, 8888 University Drive, Simon Fraser University, Burnaby, BC V5A 1S6 Canada
| | - Arne Ø. Mooers
- Department of Biological Sciences and IRMACS, 8888 University Drive, Simon Fraser University, Burnaby, BC V5A 1S6 Canada
| | - Ambuj Singh
- Department of Computer Science; University of California, Santa Barbara, CA 93106 USA
| | - Todd H. Oakley
- Department of Ecology Evolution and Marine Biology, University of California, Santa Barbara, CA 93106 USA
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20
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Jeffery NW, Ellis EA, Oakley TH, Gregory TR. The Genome Sizes of Ostracod Crustaceans Correlate with Body Size and Evolutionary History, but not Environment. J Hered 2017; 108:701-706. [PMID: 28595313 DOI: 10.1093/jhered/esx055] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 06/07/2017] [Indexed: 11/13/2022] Open
Abstract
Within animals, a positive correlation between genome size and body size has been detected in several taxa but not in others, such that it remains unknown how pervasive this pattern may be. Here, we provide another example of a positive relationship in a group of crustaceans whose genome sizes have not previously been investigated. We analyze genome size estimates for 46 species across the 2 most diverse orders of Class Ostracoda, commonly known as seed shrimps, including 29 new estimates made using Feulgen image analysis densitometry and flow cytometry. Genome sizes in this group range ~80-fold, a level of variability that is otherwise not seen in crustaceans with the exception of some malacostracan orders. We find a strong positive correlation between genome size and body size across all species, including after phylogenetic correction. We additionally detect evidence of XX/XO sex determination in 3 species of marine ostracods where male and female genome sizes were estimated. On average, genome sizes are larger but less variable in Order Myodocopida than in Order Podocopida, and marine ostracods have larger genomes than freshwater species, but this appears to be explained by phylogenetic inertia. The relationship between phylogeny, genome size, body size, and habitat is complex in this system and provides a baseline for future studies examining the interactions of these biological traits.
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Affiliation(s)
- Nicholas W Jeffery
- Department of Integrative Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada; University of California Santa Barbara, Santa Barbara, CA, USA. Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Emily A Ellis
- Department of Integrative Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada; University of California Santa Barbara, Santa Barbara, CA, USA. Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Todd H Oakley
- Department of Integrative Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada; University of California Santa Barbara, Santa Barbara, CA, USA. Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - T Ryan Gregory
- Department of Integrative Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada; University of California Santa Barbara, Santa Barbara, CA, USA. Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
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21
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Tanner AR, Fuchs D, Winkelmann IE, Gilbert MTP, Pankey MS, Ribeiro ÂM, Kocot KM, Halanych KM, Oakley TH, da Fonseca RR, Pisani D, Vinther J. Molecular clocks indicate turnover and diversification of modern coleoid cephalopods during the Mesozoic Marine Revolution. Proc Biol Sci 2017; 284:20162818. [PMID: 28250188 PMCID: PMC5360930 DOI: 10.1098/rspb.2016.2818] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 02/08/2017] [Indexed: 11/12/2022] Open
Abstract
Coleoid cephalopod molluscs comprise squid, cuttlefish and octopuses, and represent nearly the entire diversity of modern cephalopods. Sophisticated adaptations such as the use of colour for camouflage and communication, jet propulsion and the ink sac highlight the unique nature of the group. Despite these striking adaptations, there are clear parallels in ecology between coleoids and bony fishes. The coleoid fossil record is limited, however, hindering confident analysis of the tempo and pattern of their evolution. Here we use a molecular dataset (180 genes, approx. 36 000 amino acids) of 26 cephalopod species to explore the phylogeny and timing of cephalopod evolution. We show that crown cephalopods diverged in the Silurian-Devonian, while crown coleoids had origins in the latest Palaeozoic. While the deep-sea vampire squid and dumbo octopuses have ancient origins extending to the Early Mesozoic Era, 242 ± 38 Ma, incirrate octopuses and the decabrachian coleoids (10-armed squid) diversified in the Jurassic Period. These divergence estimates highlight the modern diversity of coleoid cephalopods emerging in the Mesozoic Marine Revolution, a period that also witnessed the radiation of most ray-finned fish groups in addition to several other marine vertebrates. This suggests that that the origin of modern cephalopod biodiversity was contingent on ecological competition with marine vertebrates.
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Affiliation(s)
- Alastair R Tanner
- School of Biological Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Dirk Fuchs
- Earth and Planetary System Science, Department of Natural History Sciences, Hokkaido University, Sapporo, Japan
| | - Inger E Winkelmann
- Natural History Museum of Denmark, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - M Thomas P Gilbert
- Natural History Museum of Denmark, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
- Trace and Environmental DNA Laboratory, Department of Environment and Agriculture, Curtin University, Perth, Western Australia, Australia
- NTNU University Museum, Norwegian University of Science and Technology, Trondheim, Norway
| | - M Sabrina Pankey
- Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH 03824, USA
| | - Ângela M Ribeiro
- Natural History Museum of Denmark, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Kevin M Kocot
- Department of Biological Sciences, University of Alabama, Box 870344, Tuscaloosa, AL 35487, USA
| | - Kenneth M Halanych
- Department of Biological Sciences, Auburn University, Auburn, AL 36830, USA
| | - Todd H Oakley
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, CA 93106, USA
| | - Rute R da Fonseca
- Natural History Museum of Denmark, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Davide Pisani
- School of Biological Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
- School of Earth Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Jakob Vinther
- School of Biological Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
- School of Earth Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
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22
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Ramirez MD, Oakley TH. Eye-independent, light-activated chromatophore expansion (LACE) and expression of phototransduction genes in the skin of Octopus bimaculoides. ACTA ACUST UNITED AC 2016; 218:1513-20. [PMID: 25994633 DOI: 10.1242/jeb.110908] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Cephalopods are renowned for changing the color and pattern of their skin for both camouflage and communication. Yet, we do not fully understand how cephalopods control the pigmented chromatophore organs in their skin and change their body pattern. Although these changes primarily rely on eyesight, we found that light causes chromatophores to expand in excised pieces of Octopus bimaculoides skin. We call this behavior light-activated chromatophore expansion (or LACE). To uncover how octopus skin senses light, we used antibodies against r-opsin phototransduction proteins to identify sensory neurons that express r-opsin in the skin. We hypothesized that octopus LACE relies on the same r-opsin phototransduction cascade found in octopus eyes. By creating an action spectrum for the latency to LACE, we found that LACE occurred most quickly in response to blue light. We fit our action spectrum data to a standard opsin curve template and estimated the λmax of LACE to be 480 nm. Consistent with our hypothesis, the maximum sensitivity of the light sensors underlying LACE closely matches the known spectral sensitivity of opsin from octopus eyes. LACE in isolated preparations suggests that octopus skin is intrinsically light sensitive and that this dispersed light sense might contribute to their unique and novel patterning abilities. Finally, our data suggest that a common molecular mechanism for light detection in eyes may have been co-opted for light sensing in octopus skin and then used for LACE.
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Affiliation(s)
- M Desmond Ramirez
- Department of Ecology Evolution and Marine Biology, University of California Santa Barbara, Santa Barbara, CA 93106-6150, USA
| | - Todd H Oakley
- Department of Ecology Evolution and Marine Biology, University of California Santa Barbara, Santa Barbara, CA 93106-6150, USA
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23
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Affiliation(s)
- Todd H. Oakley
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, California 93106;
| | - Daniel I. Speiser
- Department of Biological Sciences, University of South Carolina, Columbia, South Carolina 29208
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24
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Stahl BA, Gross JB, Speiser DI, Oakley TH, Patel NH, Gould DB, Protas ME. A Transcriptomic Analysis of Cave, Surface, and Hybrid Isopod Crustaceans of the Species Asellus aquaticus. PLoS One 2015; 10:e0140484. [PMID: 26462237 PMCID: PMC4604090 DOI: 10.1371/journal.pone.0140484] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 09/25/2015] [Indexed: 12/14/2022] Open
Abstract
Cave animals, compared to surface-dwelling relatives, tend to have reduced eyes and pigment, longer appendages, and enhanced mechanosensory structures. Pressing questions include how certain cave-related traits are gained and lost, and if they originate through the same or different genetic programs in independent lineages. An excellent system for exploring these questions is the isopod, Asellus aquaticus. This species includes multiple cave and surface populations that have numerous morphological differences between them. A key feature is that hybrids between cave and surface individuals are viable, which enables genetic crosses and linkage analyses. Here, we advance this system by analyzing single animal transcriptomes of Asellus aquaticus. We use high throughput sequencing of non-normalized cDNA derived from the head of a surface-dwelling male, the head of a cave-dwelling male, the head of a hybrid male (produced by crossing a surface individual with a cave individual), and a pooled sample of surface embryos and hatchlings. Assembling reads from surface and cave head RNA pools yielded an integrated transcriptome comprised of 23,984 contigs. Using this integrated assembly as a reference transcriptome, we aligned reads from surface-, cave- and hybrid- head tissue and pooled surface embryos and hatchlings. Our approach identified 742 SNPs and placed four new candidate genes to an existing linkage map for A. aquaticus. In addition, we examined SNPs for allele-specific expression differences in the hybrid individual. All of these resources will facilitate identification of genes and associated changes responsible for cave adaptation in A. aquaticus and, in concert with analyses of other species, will inform our understanding of the evolutionary processes accompanying adaptation to the subterranean environment.
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Affiliation(s)
- Bethany A. Stahl
- Department of Biological Sciences, University of Cincinnati, Cincinnati, Ohio, United States of America
- Department of Biological Sciences, Florida Atlantic University, Jupiter, FL, 33458, United States of America
| | - Joshua B. Gross
- Department of Biological Sciences, University of Cincinnati, Cincinnati, Ohio, United States of America
| | - Daniel I. Speiser
- Department of Biological Sciences, University of South Carolina, Columbia, SC, United States of America
| | - Todd H. Oakley
- Department of Ecology, Evolution, and Marine Biology, University of California Santa Barbara, Santa Barbara, CA, United States of America
| | - Nipam H. Patel
- Department of Molecular and Cell Biology & Department of Integrative Biology, University of California, Berkeley, CA, United States of America
| | - Douglas B. Gould
- Departments of Ophthalmology and Anatomy, Institute for Human Genetics, UCSF School of Medicine, San Francisco, CA, United States of America
| | - Meredith E. Protas
- Department of Natural Sciences and Mathematics, Dominican University of California, San Rafael, CA, United States of America
- * E-mail:
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Cardinale BJ, Venail P, Gross K, Oakley TH, Narwani A, Allan E, Flombaum P, Joshi J, Reich PB, Tilman D, Ruijven J. Further re‐analyses looking for effects of phylogenetic diversity on community biomass and stability. Funct Ecol 2015. [DOI: 10.1111/1365-2435.12540] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Bradley J. Cardinale
- School of Natural Resources and Environment University of Michigan 440 Church Street Ann Arbor Michigan 48109 USA
| | - Patrick Venail
- School of Natural Resources and Environment University of Michigan 440 Church Street Ann Arbor Michigan 48109 USA
- Section of Earth and Environmental Sciences Institute F.‐A. Forel University of Geneva Versoix Switzerland
| | - Kevin Gross
- Statistics Department North Carolina State University 2311 Stinson Drive Raleigh North Carolina 27695‐8203 USA
| | - Todd H. Oakley
- Department of Ecology, Evolution and Marine Biology University of California Santa Barbara California 93106‐9620 USA
| | - Anita Narwani
- School of Natural Resources and Environment University of Michigan 440 Church Street Ann Arbor Michigan 48109 USA
- Aquatic Ecology Eawag (Swiss Federal Institute of Aquatic Science and Technology) Dübendorf 8600 Switzerland
| | - Eric Allan
- Institute of Plant Sciences University of Bern Altenbergrain 21 Bern Switzerland
| | - Pedro Flombaum
- Centro de Investigaciones del Mar y la Atmósfera Conicet/Universidad de Buenos Aires C1428EGA Buenos Aires Argentina
| | - Jasmin Joshi
- Institute of Biochemistry and Biology, Biodiversity Research/Systematic Botany University of Potsdam Maulbeerallee 1 14469 Potsdam Germany
- Berlin‐Brandenburg Institute of Advanced Biodiversity Research (BBIB) Altensteinstr 6 14195 Berlin Germany
| | - Peter B. Reich
- Department of Forest Resources University of Minnesota 1530 Cleveland Avenue N Saint Paul Minnesota USA
- Hawkesbury Institute for the Environment University of Western Sydney Penrith New South Wales 2751 Australia
| | - David Tilman
- College of Biological Sciences University of Minnesota 1987 Upper Buford Circle Saint Paul Minnesota 55108USA
- Bren School of Environmental Science and Management University of California Santa Barbara California 93106USA
| | - Jasper Ruijven
- Department of Nature Conservation and Plant Ecology Wageningen University Droevendaalsesteeg 3 6708PB Wageningen The Netherlands
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Alexandrou MA, Cardinale BJ, Hall JD, Delwiche CF, Fritschie K, Narwani A, Venail PA, Bentlage B, Pankey MS, Oakley TH. Evolutionary relatedness does not predict competition and co-occurrence in natural or experimental communities of green algae. Proc Biol Sci 2015; 282:20141745. [PMID: 25473009 DOI: 10.1098/rspb.2014.1745] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The competition-relatedness hypothesis (CRH) predicts that the strength of competition is the strongest among closely related species and decreases as species become less related. This hypothesis is based on the assumption that common ancestry causes close relatives to share biological traits that lead to greater ecological similarity. Although intuitively appealing, the extent to which phylogeny can predict competition and co-occurrence among species has only recently been rigorously tested, with mixed results. When studies have failed to support the CRH, critics have pointed out at least three limitations: (i) the use of data poor phylogenies that provide inaccurate estimates of species relatedness, (ii) the use of inappropriate statistical models that fail to detect relationships between relatedness and species interactions amidst nonlinearities and heteroskedastic variances, and (iii) overly simplified laboratory conditions that fail to allow eco-evolutionary relationships to emerge. Here, we address these limitations and find they do not explain why evolutionary relatedness fails to predict the strength of species interactions or probabilities of coexistence among freshwater green algae. First, we construct a new data-rich, transcriptome-based phylogeny of common freshwater green algae that are commonly cultured and used for laboratory experiments. Using this new phylogeny, we re-analyse ecological data from three previously published laboratory experiments. After accounting for the possibility of nonlinearities and heterogeneity of variances across levels of relatedness, we find no relationship between phylogenetic distance and ecological traits. In addition, we show that communities of North American green algae are randomly composed with respect to their evolutionary relationships in 99% of 1077 lakes spanning the continental United States. Together, these analyses result in one of the most comprehensive case studies of how evolutionary history influences species interactions and community assembly in both natural and experimental systems. Our results challenge the generality of the CRH and suggest it may be time to re-evaluate the validity and assumptions of this hypothesis.
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Affiliation(s)
- Markos A Alexandrou
- Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, CA 93106, USA
| | - Bradley J Cardinale
- School of Natural Resources and Environment, University of Michigan, Ann Arbor, MI 48109, USA
| | - John D Hall
- Department of Plant Science and Landscape Architecture, University of Maryland, 2102 Plant Sciences Building, College Park, MD 20742, USA
| | - Charles F Delwiche
- Department of Cell Biology and Molecular Genetics, University of Maryland, 2107 Bioscience Research Building, College Park, MD 20742, USA
| | - Keith Fritschie
- School of Natural Resources and Environment, University of Michigan, Ann Arbor, MI 48109, USA School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA 98105, USA
| | - Anita Narwani
- School of Natural Resources and Environment, University of Michigan, Ann Arbor, MI 48109, USA Eawag, Swiss Federal Institute of Aquatic Science and Technology, ECO BU G11 Uberlandstrasse, 1338600 Dubendorf, Switzerland
| | - Patrick A Venail
- School of Natural Resources and Environment, University of Michigan, Ann Arbor, MI 48109, USA Section of Earth and Environmental Sciences, Institute F.-A. Forel, University of Geneva, Geneva, Switzerland
| | - Bastian Bentlage
- Department of Cell Biology and Molecular Genetics, University of Maryland, 2107 Bioscience Research Building, College Park, MD 20742, USA
| | - M Sabrina Pankey
- Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, CA 93106, USA
| | - Todd H Oakley
- Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, CA 93106, USA
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Narwani A, Alexandrou MA, Herrin J, Vouaux A, Zhou C, Oakley TH, Cardinale BJ. Common Ancestry Is a Poor Predictor of Competitive Traits in Freshwater Green Algae. PLoS One 2015; 10:e0137085. [PMID: 26348482 PMCID: PMC4562640 DOI: 10.1371/journal.pone.0137085] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Accepted: 08/13/2015] [Indexed: 11/25/2022] Open
Abstract
Phytoplankton species traits have been used to successfully predict the outcome of competition, but these traits are notoriously laborious to measure. If these traits display a phylogenetic signal, phylogenetic distance (PD) can be used as a proxy for trait variation. We provide the first investigation of the degree of phylogenetic signal in traits related to competition in freshwater green phytoplankton. We measured 17 traits related to competition and tested whether they displayed a phylogenetic signal across a molecular phylogeny of 59 species of green algae. We also assessed the fit of five models of trait evolution to trait variation across the phylogeny. There was no significant phylogenetic signal for 13 out of 17 ecological traits. For 7 traits, a non-phylogenetic model provided the best fit. For another 7 traits, a phylogenetic model was selected, but parameter values indicated that trait variation evolved recently, diminishing the importance of common ancestry. This study suggests that traits related to competition in freshwater green algae are not generally well-predicted by patterns of common ancestry. We discuss the mechanisms by which the link between phylogenetic distance and phenotypic differentiation may be broken.
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Affiliation(s)
- Anita Narwani
- BU-G11 Überlandstrasse 133, Department of Aquatic Ecology, Eawag (Swiss Federal Institute of Aquatic Science and Technology), 8600, Dübendorf, Switzerland
- 1556 Dana Building, 440 Church Street, School of Natural Resources and Environment, University of Michigan, Ann Arbor, MI, 48109–1041, United States of America
| | - Markos A. Alexandrou
- 4101 Life Sciences Building, UCEN Road, Department of Ecology, Evolution and Marine Biology, University of California Santa Barbara, Santa Barbara, CA, 93106, United States of America
| | - James Herrin
- 1556 Dana Building, 440 Church Street, School of Natural Resources and Environment, University of Michigan, Ann Arbor, MI, 48109–1041, United States of America
| | - Alaina Vouaux
- 1556 Dana Building, 440 Church Street, School of Natural Resources and Environment, University of Michigan, Ann Arbor, MI, 48109–1041, United States of America
| | - Charles Zhou
- 1556 Dana Building, 440 Church Street, School of Natural Resources and Environment, University of Michigan, Ann Arbor, MI, 48109–1041, United States of America
| | - Todd H. Oakley
- 4101 Life Sciences Building, UCEN Road, Department of Ecology, Evolution and Marine Biology, University of California Santa Barbara, Santa Barbara, CA, 93106, United States of America
| | - Bradley J. Cardinale
- 1556 Dana Building, 440 Church Street, School of Natural Resources and Environment, University of Michigan, Ann Arbor, MI, 48109–1041, United States of America
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29
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Venail P, Gross K, Oakley TH, Narwani A, Allan E, Flombaum P, Isbell F, Joshi J, Reich PB, Tilman D, Ruijven J, Cardinale BJ. Species richness, but not phylogenetic diversity, influences community biomass production and temporal stability in a re‐examination of 16 grassland biodiversity studies. Funct Ecol 2015. [DOI: 10.1111/1365-2435.12432] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Patrick Venail
- School of Natural Resources and Environment University of Michigan 440 Church Street Ann Arbor MI 48109 USA
- Section of Earth and Environmental Sciences Institute F.‐A. Forel University of Geneva Versoix Switzerland
| | - Kevin Gross
- Statistics Department North Carolina State University 2311 Stinson Drive Raleigh NC 27695‐8203 USA
| | - Todd H. Oakley
- Department of Ecology, Evolution and Marine Biology University of California Santa Barbara CA 93106‐9620 USA
| | - Anita Narwani
- School of Natural Resources and Environment University of Michigan 440 Church Street Ann Arbor MI 48109 USA
- Aquatic Ecology Eawag (Swiss Federal Institute of Aquatic Science and Technology) Dübendorf 8600 Switzerland
| | - Eric Allan
- Institute of Plant Sciences University of Bern Altenbergrain 21 Bern Switzerland
| | - Pedro Flombaum
- Centro de Investigaciones del Mar y la Atmósfera Conicet/Universidad de Buenos Aires C1428EGA Buenos Aires Argentina
| | - Forest Isbell
- Department of Plant Biology University of Georgia 2502 Miller Plant Sciences Athens GA 30602 USA
| | - Jasmin Joshi
- Institute of Biochemistry and Biology, Biodiversity Research/Systematic Botany University of Potsdam Maulbeerallee 1 14469 Potsdam Germany
- Berlin‐Brandenburg Institute of Advanced Biodiversity Research (BBIB) Altensteinstr 6 14195 Berlin Germany
| | - Peter B. Reich
- Department of Forest Resources University of Minnesota 1530 Cleveland Avenue N Saint Paul MN USA
- Hawkesbury Institute for the Environment University of Western Sydney Penrith NSW 2751 Australia
| | - David Tilman
- College of Biological Sciences University of Minnesota 1987 Upper Buford Circle Saint Paul MN 55108 USA
- Bren School of Environmental Science and Management University of California Santa Barbara CA 93106 USA
| | - Jasper Ruijven
- Department of Nature Conservation and Plant Ecology Wageningen University Droevendaalsesteeg 3 6708PB Wageningen The Netherlands
| | - Bradley J. Cardinale
- School of Natural Resources and Environment University of Michigan 440 Church Street Ann Arbor MI 48109 USA
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Battelle BA, Kempler KE, Saraf SR, Marten CE, Dugger DR, Speiser DI, Oakley TH. Opsins in Limulus eyes: characterization of three visible light-sensitive opsins unique to and co-expressed in median eye photoreceptors and a peropsin/RGR that is expressed in all eyes. J Exp Biol 2015; 218:466-79. [PMID: 25524988 PMCID: PMC4317242 DOI: 10.1242/jeb.116087] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 12/09/2014] [Indexed: 11/20/2022]
Abstract
The eyes of the horseshoe crab Limulus polyphemus have long been used for studies of basic mechanisms of vision, and the structure and physiology of Limulus photoreceptors have been examined in detail. Less is known about the opsins Limulus photoreceptors express. We previously characterized a UV opsin (LpUVOps1) that is expressed in all three types of Limulus eyes (lateral compound eyes, median ocelli and larval eyes) and three visible light-sensitive rhabdomeric opsins (LpOps1, -2 and -5) that are expressed in Limulus lateral compound and larval eyes. Physiological studies showed that visible light-sensitive photoreceptors are also present in median ocelli, but the visible light-sensitive opsins they express were unknown. In the current study we characterize three newly identified, visible light-sensitive rhabdomeric opsins (LpOps6, -7 and -8) that are expressed in median ocelli. We show that they are ocellar specific and that all three are co-expressed in photoreceptors distinct from those expressing LpUVOps1. Our current findings show that the pattern of opsin expression in Limulus eyes is much more complex than previously thought and extend our previous observations of opsin co-expression in visible light-sensitive Limulus photoreceptors. We also characterize a Limulus peropsin/RGR (LpPerOps1). We examine the phylogenetic relationship of LpPerOps1 with other peropsins and RGRs, demonstrate that LpPerOps1 transcripts are expressed in each of the three types of Limulus eyes and show that the encoded protein is expressed in membranes of cells closely associated with photoreceptors in each eye type. These finding suggest that peropsin was in the opsin repertoire of euchelicerates.
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Affiliation(s)
- Barbara-Anne Battelle
- Whitney Laboratory for Marine Bioscience and Departments of Neuroscience and Biology, 9505 Ocean Shore Blvd, University of Florida, St Augustine, FL 32080, USA
| | - Karen E Kempler
- Whitney Laboratory for Marine Bioscience and Departments of Neuroscience and Biology, 9505 Ocean Shore Blvd, University of Florida, St Augustine, FL 32080, USA
| | - Spencer R Saraf
- Whitney Laboratory for Marine Bioscience and Departments of Neuroscience and Biology, 9505 Ocean Shore Blvd, University of Florida, St Augustine, FL 32080, USA
| | - Catherine E Marten
- Whitney Laboratory for Marine Bioscience and Departments of Neuroscience and Biology, 9505 Ocean Shore Blvd, University of Florida, St Augustine, FL 32080, USA
| | - Donald R Dugger
- Department of Ophthalmology, University of Florida, Gainesville, FL 32080, USA
| | - Daniel I Speiser
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA 93106, USA Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
| | - Todd H Oakley
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA 93106, USA
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Speiser DI, Pankey MS, Zaharoff AK, Battelle BA, Bracken-Grissom HD, Breinholt JW, Bybee SM, Cronin TW, Garm A, Lindgren AR, Patel NH, Porter ML, Protas ME, Rivera AS, Serb JM, Zigler KS, Crandall KA, Oakley TH. Using phylogenetically-informed annotation (PIA) to search for light-interacting genes in transcriptomes from non-model organisms. BMC Bioinformatics 2014; 15:350. [PMID: 25407802 PMCID: PMC4255452 DOI: 10.1186/s12859-014-0350-x] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Accepted: 10/09/2014] [Indexed: 11/10/2022] Open
Abstract
Background Tools for high throughput sequencing and de novo assembly make the analysis of transcriptomes (i.e. the suite of genes expressed in a tissue) feasible for almost any organism. Yet a challenge for biologists is that it can be difficult to assign identities to gene sequences, especially from non-model organisms. Phylogenetic analyses are one useful method for assigning identities to these sequences, but such methods tend to be time-consuming because of the need to re-calculate trees for every gene of interest and each time a new data set is analyzed. In response, we employed existing tools for phylogenetic analysis to produce a computationally efficient, tree-based approach for annotating transcriptomes or new genomes that we term Phylogenetically-Informed Annotation (PIA), which places uncharacterized genes into pre-calculated phylogenies of gene families. Results We generated maximum likelihood trees for 109 genes from a Light Interaction Toolkit (LIT), a collection of genes that underlie the function or development of light-interacting structures in metazoans. To do so, we searched protein sequences predicted from 29 fully-sequenced genomes and built trees using tools for phylogenetic analysis in the Osiris package of Galaxy (an open-source workflow management system). Next, to rapidly annotate transcriptomes from organisms that lack sequenced genomes, we repurposed a maximum likelihood-based Evolutionary Placement Algorithm (implemented in RAxML) to place sequences of potential LIT genes on to our pre-calculated gene trees. Finally, we implemented PIA in Galaxy and used it to search for LIT genes in 28 newly-sequenced transcriptomes from the light-interacting tissues of a range of cephalopod mollusks, arthropods, and cubozoan cnidarians. Our new trees for LIT genes are available on the Bitbucket public repository (http://bitbucket.org/osiris_phylogenetics/pia/) and we demonstrate PIA on a publicly-accessible web server (http://galaxy-dev.cnsi.ucsb.edu/pia/). Conclusions Our new trees for LIT genes will be a valuable resource for researchers studying the evolution of eyes or other light-interacting structures. We also introduce PIA, a high throughput method for using phylogenetic relationships to identify LIT genes in transcriptomes from non-model organisms. With simple modifications, our methods may be used to search for different sets of genes or to annotate data sets from taxa outside of Metazoa. Electronic supplementary material The online version of this article (doi:10.1186/s12859-014-0350-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Daniel I Speiser
- Department of Ecology, Evolution, and Marine Biology, University of California Santa Barbara, Santa Barbara, CA, USA. .,Department of Biological Sciences, University of South Carolina, Columbia, SC, USA.
| | - M Sabrina Pankey
- Department of Ecology, Evolution, and Marine Biology, University of California Santa Barbara, Santa Barbara, CA, USA.
| | - Alexander K Zaharoff
- Department of Ecology, Evolution, and Marine Biology, University of California Santa Barbara, Santa Barbara, CA, USA.
| | - Barbara A Battelle
- The Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL, USA.
| | - Heather D Bracken-Grissom
- Department of Biological Sciences, Florida International University-Biscayne Bay Campus, North Miami, FL, USA.
| | - Jesse W Breinholt
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA.
| | - Seth M Bybee
- Department of Biology, Brigham Young University, Provo, UT, USA.
| | - Thomas W Cronin
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD, USA.
| | - Anders Garm
- Department of Biology, Marine Biological Section, University of Copenhagen, Copenhagen, Denmark.
| | - Annie R Lindgren
- Department of Biology, Portland State University, Portland, OR, USA.
| | - Nipam H Patel
- Department of Molecular and Cell Biology & Department of Integrative Biology, University of California, Berkeley, CA, USA.
| | - Megan L Porter
- Department of Biology, University of South Dakota, Vermillion, SD, USA.
| | - Meredith E Protas
- Department of Natural Sciences and Mathematics, Dominican University of California, San Rafael, CA, USA.
| | - Ajna S Rivera
- Department of Biology, University of the Pacific, Stockton, CA, USA.
| | - Jeanne M Serb
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA.
| | - Kirk S Zigler
- Department of Biology, Sewanee: The University of the South, Sewanee, TN, USA.
| | - Keith A Crandall
- Computational Biology Institute, George Washington University, Ashburn, VA, USA. .,Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA.
| | - Todd H Oakley
- Department of Ecology, Evolution, and Marine Biology, University of California Santa Barbara, Santa Barbara, CA, USA.
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Speiser DI, DeMartini DG, Oakley TH. The shell-eyes of the chitonAcanthopleura granulata(Mollusca, Polyplacophora) use pheomelanin as a screening pigment. J NAT HIST 2014. [DOI: 10.1080/00222933.2014.959572] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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Marxen JC, Pick C, Oakley TH, Burmester T. Occurrence of Hemocyanin in Ostracod Crustaceans. J Mol Evol 2014; 79:3-11. [DOI: 10.1007/s00239-014-9636-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Accepted: 08/02/2014] [Indexed: 12/23/2022]
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Fritschie KJ, Cardinale BJ, Alexandrou MA, Oakley TH. Evolutionary history and the strength of species interactions: testing the phylogenetic limiting similarity hypothesis. Ecology 2014; 95:1407-17. [PMID: 25000771 DOI: 10.1890/13-0986.1] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
A longstanding concept in community ecology is that closely related species compete more strongly than distant relatives. Ecologists have invoked this "limiting similarity hypothesis" to explain patterns in the structure and function of biological communities and to inform conservation, restoration, and invasive-species management. However, few studies have empirically tested the validity of the limiting similarity hypothesis. Here we report the results of a laboratory microcosm experiment in which we used a model system of 23 common, co-occurring North American freshwater green algae to quantify the strength of 216 pairwise species' interactions (the difference in population density when grown alone vs. in the presence of another species) along a manipulated gradient of evolutionary relatedness (phylogenetic distance, as the sum of branch lengths separating species on a molecular phylogeny). Interspecific interactions varied widely in these bicultures of phytoplankton, ranging from strong competition (ratio of relative yield in polyculture vs. monoculture << 1) to moderate facilitation (relative yield > 1). Yet, we found no evidence that the strength of species' interactions was influenced by their evolutionary relatedness. There was no relationship between phylogenetic distance and the average, minimum (inferior competitor), nor maximum (superior competitor) interaction strength across all biculture communities (respectively, P = 0.19, P = 0.17, P = 0.14; N = 428). When we examined each individual species, only 17% of individual species' interactions strengths varied as a function of phylogenetic distance, and none of these relationships remained significant after Bonferoni correction for multiple tests (N = 23). Last, when we grouped interactions into five qualitatively different types, the frequency of these types was not related to phylogenetic distance among species pairs (F4,422 = 1.63, P = 0.15). Our empirical study adds to several others that suggest the biological underpinnings of competition may not be evolutionarily conserved, and thus, ecologists may need to re-evaluate the previously assumed generality of the limiting similarity hypothesis.
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Abstract
Opsins mediate light detection in most animals, and understanding their evolution is key to clarify the origin of vision. Despite the public availability of a substantial collection of well-characterized opsins, early opsin evolution has yet to be fully understood, in large part because of the high level of divergence observed among opsins belonging to different subfamilies. As a result, different studies have investigated deep opsin evolution using alternative data sets and reached contradictory results. Here, we integrated the data and methods of three, key, recent studies to further clarify opsin evolution. We show that the opsin relationships are sensitive to outgroup choice; we generate new support for the existence of Rhabdomeric opsins in Cnidaria (e.g., corals and jellyfishes) and show that all comb jelly opsins belong to well-recognized opsin groups (the Go-coupled opsins or the Ciliary opsins), which are also known in Bilateria (e.g., humans, fruit flies, snails, and their allies) and Cnidaria. Our results are most parsimoniously interpreted assuming a traditional animal phylogeny where Ctenophora are not the sister group of all the other animals.
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Affiliation(s)
- Roberto Feuda
- Division of Biology and Biological Engineering, California Institute of Technology
| | - Omar Rota-Stabelli
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige (TN), Italy
| | - Todd H Oakley
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara
| | - Davide Pisani
- School of Biological Sciences and School of Earth Sciences, University of Bristol, United Kingdom
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Oakley TH, Alexandrou MA, Ngo R, Pankey MS, Churchill CKC, Chen W, Lopker KB. Osiris: accessible and reproducible phylogenetic and phylogenomic analyses within the Galaxy workflow management system. BMC Bioinformatics 2014; 15:230. [PMID: 24990571 PMCID: PMC4227113 DOI: 10.1186/1471-2105-15-230] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2013] [Accepted: 04/29/2014] [Indexed: 01/09/2023] Open
Abstract
Background Phylogenetic tools and ‘tree-thinking’ approaches increasingly permeate all biological research. At the same time, phylogenetic data sets are expanding at breakneck pace, facilitated by increasingly economical sequencing technologies. Therefore, there is an urgent need for accessible, modular, and sharable tools for phylogenetic analysis. Results We developed a suite of wrappers for new and existing phylogenetics tools for the Galaxy workflow management system that we call Osiris. Osiris and Galaxy provide a sharable, standardized, modular user interface, and the ability to easily create complex workflows using a graphical interface. Osiris enables all aspects of phylogenetic analysis within Galaxy, including de novo assembly of high throughput sequencing reads, ortholog identification, multiple sequence alignment, concatenation, phylogenetic tree estimation, and post-tree comparative analysis. The open source files are available on in the Bitbucket public repository and many of the tools are demonstrated on a public web server (http://galaxy-dev.cnsi.ucsb.edu/osiris/). Conclusions Osiris can serve as a foundation for other phylogenomic and phylogenetic tool development within the Galaxy platform.
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Affiliation(s)
- Todd H Oakley
- Ecology, Evolution, and Marine Biology, University of California-Santa Barbara, Santa Barbara, CA 93106, USA.
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Bielecki J, Zaharoff AK, Leung NY, Garm A, Oakley TH. Ocular and extraocular expression of opsins in the rhopalium of Tripedalia cystophora (Cnidaria: Cubozoa). PLoS One 2014; 9:e98870. [PMID: 24901369 PMCID: PMC4047050 DOI: 10.1371/journal.pone.0098870] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Accepted: 05/07/2014] [Indexed: 11/18/2022] Open
Abstract
A growing body of work on the neuroethology of cubozoans is based largely on the capabilities of the photoreceptive tissues, and it is important to determine the molecular basis of their light sensitivity. The cubozoans rely on 24 special purpose eyes to extract specific information from a complex visual scene to guide their behavior in the habitat. The lens eyes are the most studied photoreceptive structures, and the phototransduction in the photoreceptor cells is based on light sensitive opsin molecules. Opsins are photosensitive transmembrane proteins associated with photoreceptors in eyes, and the amino acid sequence of the opsins determines the spectral properties of the photoreceptors. Here we show that two distinct opsins (Tripedalia cystophora-lens eye expressed opsin and Tripedalia cystophora-neuropil expressed opsin, or Tc-leo and Tc-neo) are expressed in the Tripedalia cystophora rhopalium. Quantitative PCR determined the level of expression of the two opsins, and we found Tc-leo to have a higher amount of expression than Tc-neo. In situ hybridization located Tc-leo expression in the retinal photoreceptors of the lens eyes where the opsin is involved in image formation. Tc-neo is expressed in a confined part of the neuropil and is probably involved in extraocular light sensation, presumably in relation to diurnal activity.
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Affiliation(s)
- Jan Bielecki
- Ecology, Evolution and Marine Biology, University of California at Santa Barbara, Santa Barbara, California, United States of America
- * E-mail:
| | - Alexander K. Zaharoff
- Ecology, Evolution and Marine Biology, University of California at Santa Barbara, Santa Barbara, California, United States of America
| | - Nicole Y. Leung
- Ecology, Evolution and Marine Biology, University of California at Santa Barbara, Santa Barbara, California, United States of America
| | - Anders Garm
- Marine Biological Section, University of Copenhagen, Copenhagen, Denmark
| | - Todd H. Oakley
- Ecology, Evolution and Marine Biology, University of California at Santa Barbara, Santa Barbara, California, United States of America
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Churchill CKC, Ellis EA, Pique AE, Oakley TH. Two new sympatric species of Eusarsiella (Ostracoda: Myodocopida: Sarsiellidae) from the Florida Keys with a morphological phylogeny of Sarsiellinae. Zootaxa 2014:444-58. [PMID: 24871023 DOI: 10.11646/zootaxa.3802.4.3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Indexed: 11/04/2022]
Abstract
We describe two new sympatric species of Sarsiellidae from coastal Florida, USA: Eusarsiella bryanjuarezi sp. nov. and Eusarsiella eli sp. nov. We also present a morphological character matrix and maximum likelihood phylogenetic analysis for Sarsiellinae based on original species descriptions, representing 139 sarsiellins (including E. bryanjuarezi and E. eli). While support values across the phylogeny are low, E. bryanjuarezi and E. eli form a sister group pair with 68 % bootstrap support. Our phylogeny also showed support for six other sympatric sister-species pairs, distributed across Sarsiellinae's range, which may be candidates for the study of speciation and niche differentiation. Similar to other analyses of myodocopids, our Sarsiellinae phylogeny recovered only three monophyletic genera: Anscottiella, Cymbicopia, and Chelicopia, indicating that characters used in taxonomy may often be homoplasious. Because of our finding of multiple polyphyletic genera, including the two most speciose genera in the subfamily (Eusarsiella and Sarsiella, the type genus) Sarsiellinae is a strong candidate for taxonomic revision.
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Affiliation(s)
- Celia K C Churchill
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara; unknown
| | - Emily A Ellis
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara; unknown
| | - Alannah E Pique
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara; unknown
| | - Todd H Oakley
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara Marine Science Institute, University of California, Santa Barbara;
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Peyer SM, Pankey MS, Oakley TH, McFall-Ngai MJ. Eye-specification genes in the bacterial light organ of the bobtail squid Euprymna scolopes, and their expression in response to symbiont cues. Mech Dev 2014; 131:111-26. [PMID: 24157521 PMCID: PMC4000693 DOI: 10.1016/j.mod.2013.09.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Revised: 08/26/2013] [Accepted: 09/27/2013] [Indexed: 11/17/2022]
Abstract
The squid Euprymna scolopes has evolved independent sets of tissues capable of light detection, including a complex eye and a photophore or 'light organ', which houses the luminous bacterial symbiont Vibrio fischeri. As the eye and light organ originate from different embryonic tissues, we examined whether the eye-specification genes, pax6, eya, six, and dac, are shared by these two organs, and if so, whether they are regulated in the light organ by symbiosis. We obtained sequences of the four genes with PCR, confirmed orthology with phylogenetic analysis, and determined that each was expressed in the eye and light organ. With in situ hybridization (ISH), we localized the gene transcripts in developing embryos, comparing the patterns of expression in the two organs. The four transcripts localized to similar tissues, including those associated with the visual system ∼1/4 into embryogenesis (Naef stage 18) and the light organ ∼3/4 into embryogenesis (Naef stage 26). We used ISH and quantitative real-time PCR to examine transcript expression and differential regulation in postembryonic light organs in response to the following colonization conditions: wild-type, luminescent V. fischeri; a mutant strain defective in light production; and as a control, no symbiont. In ISH experiments light organs showed down regulation of the pax6, eya, and six transcripts in response to wild-type V. fischeri. Mutant strains also induced down regulation of the pax6 and eya transcripts, but not of the six transcript. Thus, luminescence was required for down regulation of the six transcript. We discuss these results in the context of symbiont-induced light-organ development. Our study indicates that the eye-specification genes are expressed in light-interacting tissues independent of their embryonic origin and are capable of responding to bacterial cues. These results offer evidence for evolutionary tinkering or the recruitment of eye development genes for use in a light-sensing photophore.
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Affiliation(s)
- Suzanne M Peyer
- School of Medicine and Public Health, Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, WI 53706, United States; McPherson Eye Research Institute, University of Wisconsin, Madison, WI 53706, United States.
| | - M Sabrina Pankey
- Department of Ecology, Evolution, and Marine Biology, University of California Santa Barbara, Santa Barbara, CA 93106-9620, United States
| | - Todd H Oakley
- Department of Ecology, Evolution, and Marine Biology, University of California Santa Barbara, Santa Barbara, CA 93106-9620, United States
| | - Margaret J McFall-Ngai
- School of Medicine and Public Health, Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, WI 53706, United States; McPherson Eye Research Institute, University of Wisconsin, Madison, WI 53706, United States.
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Venail PA, Alexandrou MA, Oakley TH, Cardinale BJ. Shared ancestry influences community stability by altering competitive interactions: evidence from a laboratory microcosm experiment using freshwater green algae. Proc Biol Sci 2013; 280:20131548. [PMID: 23945692 PMCID: PMC3757983 DOI: 10.1098/rspb.2013.1548] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Accepted: 07/17/2013] [Indexed: 11/12/2022] Open
Abstract
The impact of biodiversity on the stability of ecological communities has been debated among biologists for more than a century. Recently summarized empirical evidence suggests that biodiversity tends to enhance the temporal stability of community-level properties such as biomass; however, the underlying mechanisms driving this relationship remain poorly understood. Here, we report the results of a microcosm study in which we used simplified systems of freshwater microalgae to explore how the phylogenetic relatedness of species influences the temporal stability of community biomass by altering the nature of their competitive interactions. We show that combinations of two species that are more evolutionarily divergent tend to have lower temporal stability of biomass. In part, this is due to negative 'selection effects' in which bicultures composed of distantly related species are more likely to contain strong competitors that achieve low biomass. In addition, bicultures of distantly related species had on average weaker competitive interactions, which reduced compensatory dynamics and decreased the stability of community biomass. Our results demonstrate that evolutionary history plays a key role in controlling the mechanisms, which give rise to diversity-stability relationships. As such, patterns of shared ancestry may help us predict the ecosystem-level consequences of biodiversity loss.
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Affiliation(s)
- Patrick A Venail
- School of Natural Resources and Environment, University of Michigan, Ann Arbor, MI 48109-1041, USA.
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Narwani A, Alexandrou MA, Oakley TH, Carroll IT, Cardinale BJ. Experimental evidence that evolutionary relatedness does not affect the ecological mechanisms of coexistence in freshwater green algae. Ecol Lett 2013; 16:1373-81. [PMID: 24112458 DOI: 10.1111/ele.12182] [Citation(s) in RCA: 131] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Revised: 08/04/2013] [Accepted: 08/21/2013] [Indexed: 11/28/2022]
Abstract
The coexistence of competing species depends on the balance between their fitness differences, which determine their competitive inequalities, and their niche differences, which stabilise their competitive interactions. Darwin proposed that evolution causes species' niches to diverge, but the influence of evolution on relative fitness differences, and the importance of both niche and fitness differences in determining coexistence have not yet been studied together. We tested whether the phylogenetic distances between species of green freshwater algae determined their abilities to coexist in a microcosm experiment. We found that niche differences were more important in explaining coexistence than relative fitness differences, and that phylogenetic distance had no effect on either coexistence or on the sizes of niche and fitness differences. These results were corroborated by an analysis of the frequency of the co-occurrence of 325 pairwise combinations of algal taxa in > 1100 lakes across North America. Phylogenetic distance may not explain the coexistence of freshwater green algae.
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Affiliation(s)
- Anita Narwani
- School of Natural Resources and Environment, University of Michigan, 440 Church Street, Ann Arbor, MI, 48109-1041, USA
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Alexandrou MA, Swartz BA, Matzke NJ, Oakley TH. Genome duplication and multiple evolutionary origins of complex migratory behavior in Salmonidae. Mol Phylogenet Evol 2013; 69:514-23. [PMID: 23933489 DOI: 10.1016/j.ympev.2013.07.026] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Revised: 07/21/2013] [Accepted: 07/26/2013] [Indexed: 12/26/2022]
Abstract
Multiple rounds of whole genome duplication have repeatedly marked the evolution of vertebrates, and correlate strongly with morphological innovation. However, less is known about the behavioral, physiological and ecological consequences of genome duplication, and whether these events coincide with major transitions in vertebrate complexity. The complex behavior of anadromy - where adult fishes migrate up rivers from the sea to their natal site to spawn - is well known in salmonid fishes. Some hypotheses suggest that migratory behavior evolved as a consequence of an ancestral genome duplication event, which permitted salinity tolerance and osmoregulatory plasticity. Here we test whether anadromy evolved multiple times within salmonids, and whether genome duplication coincided with the evolution of anadromy. We present a method that uses ancestral character simulation data to plot the frequency of character transitions over a time calibrated phylogenetic tree to provide estimates of the absolute timing of character state transitions. Furthermore, we incorporate extinct and extant taxa to improve on previous estimates of divergence times. We present the first phylogenetic evidence indicating that anadromy evolved at least twice from freshwater salmonid ancestors. Results suggest that genome duplication did not coincide in time with changes in migratory behavior, but preceded a transition to anadromy by 55-50 million years. Our study represents the first attempt to estimate the absolute timing of a complex behavioral trait in relation to a genome duplication event.
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Affiliation(s)
- Markos A Alexandrou
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, CA 93106, USA
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Porter ML, Speiser DI, Zaharoff AK, Caldwell RL, Cronin TW, Oakley TH. The evolution of complexity in the visual systems of stomatopods: insights from transcriptomics. Integr Comp Biol 2013; 53:39-49. [PMID: 23727979 DOI: 10.1093/icb/ict060] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Stomatopod crustaceans have complex visual systems containing up to 16 different spectral classes of photoreceptors, more than described for any other animal. A previous molecular study of this visual system focusing on the expression of opsin genes found many more transcripts than predicted on the basis of physiology, but was unable to fully document the expressed opsin genes responsible for this diversity. Furthermore, questions remain about how other components of phototransduction cascades are involved. This study continues prior investigations by examining the molecular function of stomatopods' visual systems using new whole eye 454 transcriptome datasets from two species, Hemisquilla californiensis and Pseudosquilla ciliata. These two species represent taxonomic diversity within the order Stomatopoda, as well as variations in the anatomy and physiology of the visual system. Using an evolutionary placement algorithm to annotate the transcriptome, we identified the presence of nine components of the stomatopods' G-protein-coupled receptor (GPCR) phototransduction cascade, including two visual arrestins, subunits of the heterotrimeric G-protein, phospholipase C, transient receptor potential channels, and opsin transcripts. The set of expressed transduction genes suggests that stomatopods utilize a Gq-mediated GPCR-signaling cascade. The most notable difference in expression between the phototransduction cascades of the two species was the number of opsin contigs recovered, with 18 contigs found in retinas of H. californiensis, and 49 contigs in those of P. ciliata. Based on phylogenetic placement and fragment overlap, these contigs were estimated to represent 14 and 33 expressed transcripts, respectively. These data expand the known opsin diversity in stomatopods to clades of arthropod opsins that are sensitive to short wavelengths and ultraviolet wavelengths and confirm the results of previous studies recovering more opsin transcripts than spectrally distinct types of photoreceptors. Many of the recovered transcripts were phylogenetically placed in an evolutionary clade of crustacean opsin sequences that is rapidly expanding as the visual systems from more species are investigated. We discuss these results in relation to the emerging pattern, particularly in crustacean visual systems, of the expression of multiple opsin transcripts in photoreceptors of the same spectral class, and even in single photoreceptor cells.
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Affiliation(s)
- Megan L Porter
- Department of Biology, University of South Dakota, Vermillion, SD 57069, USA.
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Speiser DI, Lampe RI, Lovdahl VR, Carrillo-Zazueta B, Rivera AS, Oakley TH. Evasion of Predators Contributes to the Maintenance of Male Eyes in Sexually Dimorphic Euphilomedes Ostracods (Crustacea). Integr Comp Biol 2013; 53:78-88. [DOI: 10.1093/icb/ict025] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Abstract
Eyes serve as models to understand the evolution of complex traits, with broad implications for the origins of evolutionary novelty. Discussions of eye evolution are relevant at many taxonomic levels, especially within arthropods where compound eye distribution is perplexing. Either compound eyes were lost numerous times or very similar eyes evolved separately in multiple lineages. Arthropod compound eye homology is possible, especially between crustaceans and hexapods, which have very similar eye facets and may be sister taxa. However, judging homology only on similarity requires subjective decisions. Regardless of whether compound eyes were present in a common ancestor of arthropods or crustaceans + hexapods, recent phylogenetic evidence suggests that the compound eyes, today present in myodocopid ostracods (Crustacea), may have been absent in ostracod ancestors. This pattern is inconsistent with phylogenetic homology. Multiple losses of ostracod eyes are an alternative hypothesis that is statistically improbable and without clear cause. One possible evolutionary process to explain the lack of phylogenetic homology of ostracod compound eyes is that eyes may evolve by switchback evolution, where genes for lost structures remain dormant and are re-expressed much later in evolution.
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Affiliation(s)
- Todd H Oakley
- Ecology Evolution and Marine Biology, University of California-Santa Barbara, Santa Barbara, California 93106
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Oakley TH, Wolfe JM, Lindgren AR, Zaharoff AK. Phylotranscriptomics to Bring the Understudied into the Fold: Monophyletic Ostracoda, Fossil Placement, and Pancrustacean Phylogeny. Mol Biol Evol 2012; 30:215-33. [DOI: 10.1093/molbev/mss216] [Citation(s) in RCA: 184] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
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Lindgren AR, Pankey MS, Hochberg FG, Oakley TH. A multi-gene phylogeny of Cephalopoda supports convergent morphological evolution in association with multiple habitat shifts in the marine environment. BMC Evol Biol 2012; 12:129. [PMID: 22839506 PMCID: PMC3733422 DOI: 10.1186/1471-2148-12-129] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2012] [Accepted: 07/05/2012] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND The marine environment is comprised of numerous divergent organisms living under similar selective pressures, often resulting in the evolution of convergent structures such as the fusiform body shape of pelagic squids, fishes, and some marine mammals. However, little is known about the frequency of, and circumstances leading to, convergent evolution in the open ocean. Here, we present a comparative study of the molluscan class Cephalopoda, a marine group known to occupy habitats from the intertidal to the deep sea. Several lineages bear features that may coincide with a benthic or pelagic existence, making this a valuable group for testing hypotheses of correlated evolution. To test for convergence and correlation, we generate the most taxonomically comprehensive multi-gene phylogeny of cephalopods to date. We then create a character matrix of habitat type and morphological characters, which we use to infer ancestral character states and test for correlation between habitat and morphology. RESULTS Our study utilizes a taxonomically well-sampled phylogeny to show convergent evolution in all six morphological characters we analyzed. Three of these characters also correlate with habitat. The presence of an autogenic photophore (those relying upon autonomous enzymatic light reactions) is correlated with a pelagic habitat, while the cornea and accessory nidamental gland correlate with a benthic lifestyle. Here, we present the first statistical tests for correlation between convergent traits and habitat in cephalopods to better understand the evolutionary history of characters that are adaptive in benthic or pelagic environments, respectively. DISCUSSION Our study supports the hypothesis that habitat has influenced convergent evolution in the marine environment: benthic organisms tend to exhibit similar characteristics that confer protection from invasion by other benthic taxa, while pelagic organisms possess features that facilitate crypsis and communication in an environment lacking physical refuges. Features that have originated multiple times in distantly related lineages are likely adaptive for the organisms inhabiting a particular environment: studying the frequency and evolutionary history of such convergent characters can increase understanding of the underlying forces driving ecological and evolutionary transitions in the marine environment.
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Affiliation(s)
- Annie R Lindgren
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, CA 93106, USA
- Present Address: Department of Biology, Portland State University, PO Box 751, Portland, OR 97207, USA
| | - Molly S Pankey
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, CA 93106, USA
| | - Frederick G Hochberg
- Department of Invertebrate Zoology, Santa Barbara Museum of Natural History, 2559 Puesta del Sol Rd, Santa Barbara, CA, 93105, USA
| | - Todd H Oakley
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, CA 93106, USA
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Rivera AS, Ozturk N, Fahey B, Plachetzki DC, Degnan BM, Sancar A, Oakley TH. Blue-light-receptive cryptochrome is expressed in a sponge eye lacking neurons and opsin. ACTA ACUST UNITED AC 2012; 215:1278-86. [PMID: 22442365 DOI: 10.1242/jeb.067140] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Many larval sponges possess pigment ring eyes that apparently mediate phototactic swimming. Yet sponges are not known to possess nervous systems or opsin genes, so the unknown molecular components of sponge phototaxis must differ fundamentally from those in other animals, inspiring questions about how this sensory system functions. Here we present molecular and biochemical data on cryptochrome, a candidate gene for functional involvement in sponge pigment ring eyes. We report that Amphimedon queenslandica, a demosponge, possesses two cryptochrome/photolyase genes, Aq-Cry1 and Aq-Cry2. The mRNA of one gene (Aq-Cry2) is expressed in situ at the pigment ring eye. Additionally, we report that Aq-Cry2 lacks photolyase activity and contains a flavin-based co-factor that is responsive to wavelengths of light that also mediate larval photic behavior. These results suggest that Aq-Cry2 may act in the aneural, opsin-less phototaxic behavior of a sponge.
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Affiliation(s)
- Ajna S Rivera
- Department of Biological Sciences, University of the Pacific, Stockton, CA 95211, USA
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Plachetzki DC, Fong CR, Oakley TH. Cnidocyte discharge is regulated by light and opsin-mediated phototransduction. BMC Biol 2012; 10:17. [PMID: 22390726 PMCID: PMC3329406 DOI: 10.1186/1741-7007-10-17] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2011] [Accepted: 03/05/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cnidocytes, the eponymous cell type of the Cnidaria, facilitate both sensory and secretory functions and are among the most complex animal cell types known. In addition to their structural complexity, cnidocytes display complex sensory attributes, integrating both chemical and mechanical cues from the environment into their discharge behavior. Despite more than a century of work aimed at understanding the sensory biology of cnidocytes, the specific sensory receptor genes that regulate their function remain unknown. RESULTS Here we report that light also regulates cnidocyte function. We show that non-cnidocyte neurons located in battery complexes of the freshwater polyp Hydra magnipapillata specifically express opsin, cyclic nucleotide gated (CNG) ion channel and arrestin, which are all known components of bilaterian phototransduction cascades. We infer from behavioral trials that different light intensities elicit significant effects on cnidocyte discharge propensity. Harpoon-like stenotele cnidocytes show a pronounced diminution of discharge behavior under bright light conditions as compared to dim light. Further, we show that suppression of firing by bright light is ablated by cis-diltiazem, a specific inhibitor of CNG ion channels. CONCLUSIONS Our results implicate an ancient opsin-mediated phototransduction pathway and a previously unknown layer of sensory complexity in the control of cnidocyte discharge. These findings also suggest a molecular mechanism for the regulation of other cnidarian behaviors that involve both photosensitivity and cnidocyte function, including diurnal feeding repertoires and/or substrate-based locomotion. More broadly, our findings highlight one novel, non-visual function for opsin-mediated phototransduction in a cnidarian, the origins of which might have preceded the evolution of cnidarian eyes.
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Affiliation(s)
- David C Plachetzki
- Center for Population Biology, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA.
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Syme AE, Oakley TH. Dispersal between Shallow and Abyssal Seas and Evolutionary Loss and Regain of Compound Eyes in Cylindroleberidid Ostracods: Conflicting Conclusions from Different Comparative Methods. Syst Biol 2011; 61:314-36. [PMID: 21865337 DOI: 10.1093/sysbio/syr085] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Anna E. Syme
- Ecology, Evolution, Marine Biology and Marine Science Institute, University of California-Santa Barbara, Santa Barbara, CA 93106, USA; and
| | - Todd H. Oakley
- Ecology, Evolution, Marine Biology and Marine Science Institute, University of California-Santa Barbara, Santa Barbara, CA 93106, USA; and
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