Todd H Oakley

University of California, Santa Barbara, Santa Barbara, California, United States

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Publications (71)405.36 Total impact

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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 datasets 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), that 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.
    Genome Biology and Evolution 07/2014; · 4.76 Impact Factor
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    ABSTRACT: 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.
    BMC Bioinformatics 07/2014; 15(1):230. · 3.02 Impact Factor
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    ABSTRACT: A long-standing hypothesis in ecology and evolutionary biology is that closely related species are more ecologically similar to each other, and therefore, compete more strongly than distant relatives do. A recent hypothesis posits that evolutionary relatedness may also explain the prevalence of mutualisms, with facilitative interactions being more common among distantly related species. Despite the importance of these hypotheses for understanding the structure and function of ecological communities, experimental tests to determine how evolutionary relatedness influences competition and facilitation are still somewhat rare.Here, we report results of a laboratory experiment in which we assessed how competitive and facilitative interactions among eight species of freshwater green algae are influenced by their relatedness. We measured the prevalence of competition and facilitation among 28 pairs of freshwater green algal species that were chosen to span a large gradient of phylogenetic distances. For each species, we first measured its invasion success when introduced into a steady-state population of another resident species. Then, we compared its growth rate when grown alone in monoculture to its growth rate when introduced as an invader. The change in the species’ population growth rate as an invader (sensitivity) is used as a measure of the strength of its interaction with the resident species. A reduced growth rate in presence of another species indicates competition, whereas an increased growth rate indicates facilitation.Although competition between species was more frequent (75% of interactions), facilitation was common (the other 25% of interactions). We found no significant relationship between the phylogenetic distance separating two interacting species and the success of invasion, nor the prevalence or strength of either competition or facilitation. Interspecific interactions depended more on the identity of the species, with certain taxa consistently acting as good or bad competitors/facilitators. These species were not predictable a priori from their positions on a phylogeny.Synthesis. The phylogenetic relatedness of the green algae species used here did not predict the prevalence of competitive and facilitative interactions, rejecting the hypothesis that close relatives compete strongly and contesting recent evidence that facilitation is likely to occur between distant relatives.This article is protected by copyright. All rights reserved.
    Journal of Ecology 05/2014; · 5.43 Impact Factor
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    ABSTRACT: Over 95% of all metazoan (animal) species comprise the “invertebrates,” but very few genomes from these organisms have been sequenced. We have, therefore, formed a “Global Invertebrate Genomics Alliance” (GIGA). Our intent is to build a collaborative network of diverse scientists to tackle major challenges (e.g., species selection, sample collection and storage, sequence assembly, annotation, analytical tools) associated with genome/transcriptome sequencing across a large taxonomic spectrum. We aim to promote standards that will facilitate comparative approaches to invertebrate genomics and collaborations across the international scientific community. Candidate study taxa include species from Porifera, Ctenophora, Cnidaria, Placozoa, Mollusca, Arthropoda, Echinodermata, Annelida, Bryozoa, and Platyhelminthes, among others. GIGA will target 7000 noninsect/nonnematode species, with an emphasis on marine taxa because of the unrivaled phyletic diversity in the oceans. Priorities for selecting invertebrates for sequencing will include, but are not restricted to, their phylogenetic placement; relevance to organismal, ecological, and conservation research; and their importance to fisheries and human health. We highlight benefits of sequencing both whole genomes (DNA) and transcriptomes and also suggest policies for genomic-level data access and sharing based on transparency and inclusiveness. The GIGA Web site (http://giga.nova.edu) has been launched to facilitate this collaborative venture.
    Journal of Heredity 01/2014; 105(1):1-18. · 2.00 Impact Factor
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    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.
    Zootaxa 01/2014; 3802(4):444-58. · 1.06 Impact Factor
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    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 pair-wise 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 (relative yield in poly: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). Lastly, when we grouped interactions into five qualitatively different types, the frequency of these types was not related to phylogenetic distance among species pairs (F = 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.
    Ecology 01/2014; · 5.18 Impact Factor
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    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.
    PLoS ONE 01/2014; 9(6):e98870. · 3.73 Impact Factor
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    ABSTRACT: Over 95% of all metazoan (animal) species comprise the “invertebrates,” but very few genomes from these organisms have been sequenced. We have, therefore, formed a “Global Invertebrate Genomics Alliance” (GIGA). Our intent is to build a collaborative network of diverse scientists to tackle major challenges (e.g., species selection, sample collection and storage, sequence assembly, annotation, analytical tools) associated with genome/transcriptome sequencing across a large taxonomic spectrum. We aim to promote standards that will facilitate comparative approaches to invertebrate genomics and collaborations across the international scientific community. Candidate study taxa include species from Porifera, Ctenophora, Cnidaria, Placozoa, Mollusca, Arthropoda, Echinodermata, Annelida, Bryozoa, and Platyhelminthes, among others. GIGA will target 7000 noninsect/nonnematode species, with an emphasis on marine taxa because of the unrivaled phyletic diversity in the oceans. Priorities for selecting invertebrates for sequencing will include, but are not restricted to, their phylogenetic placement; relevance to organismal, ecological, and conservation research; and their importance to fisheries and human health. We highlight benefits of sequencing both whole genomes (DNA) and transcriptomes and also suggest policies for genomic-level data access and sharing based on transparency and inclusiveness. The GIGA Web site (http://giga.nova.edu) has been launched to facilitate this collaborative venture.
    Journal of Heredity 12/2013; 105(1):1-18. · 2.00 Impact Factor
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    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.
    Mechanisms of development 10/2013; · 2.83 Impact Factor
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    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.
    Ecology Letters 09/2013; · 17.95 Impact Factor
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    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.
    Molecular Phylogenetics and Evolution 08/2013; · 4.07 Impact Factor
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    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.
    Integrative and Comparative Biology 05/2013; · 3.02 Impact Factor
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    ABSTRACT: Sexual dimorphisms have long drawn the attention of evolutionary biologists. However, we still have much to learn about the evolutionary, genetic, and developmental drivers of sexual dimorphisms. Here, we introduce ostracods of the genus Euphilomedes (Myodocopida, Ostracoda, and Crustacea) as a promising new system in which to investigate why and how sexual dimorphisms evolve. First, we ask whether male-skewed selective pressure from pelagic predators may help explain a dramatic sexual dimorphism in which male Euphilomedes have compound eyes, but females do not. Manipulative experiments demonstrate that blindfolding reduces the survival rate of male Euphilomedes when they are exposed to predatory fish. Blindfolding of the female rudimentary eyes (rudiments) does not, however, similarly influence the survival rate of brooding females. Further, numerical estimates of sighting distances, based on reasonable extrapolations from Euphilomedes's eye morphology, suggest that the eyes of male Euphilomedes are useful for detecting objects roughly the size of certain pelagic predators, but not conspecifics. We conclude that eyes do not mediate direct interactions between male and female Euphilomedes, but that differences in predation pressure-perhaps associated with different reproductive behaviors-contribute to maintaining the sexually dimorphic eyes of these ostracods. Second, through transcriptome sequencing, we examined potential gene regulatory networks that could underlie sexual dimorphism in Euphilomedes' eyes. From the transcriptome of juvenile male Euphilomedes' eyes, we identified phototransduction genes and components of eye-related developmental networks that are well characterized in Drosophila and other species. The presence of suites of eye regulatory genes in our Euphilomedes juvenile male transcriptome will allow us, in future studies, to test how ostracods regulate the development of their sexually dimorphic eyes.
    Integrative and Comparative Biology 05/2013; · 3.02 Impact Factor
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    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.
    Proceedings of the Royal Society B: Biological Sciences 01/2013; 280(1768):20131548. · 5.68 Impact Factor
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    ABSTRACT: An ambitious, yet fundamental goal for comparative biology is to understand the evolutionary relationships for all of life. However, many important taxonomic groups have remained recalcitrant to inclusion into broader scale studies. Here, we focus on collection of 9 new 454 transcriptome data sets from Ostracoda, an ancient and diverse group with a dense fossil record, which is often undersampled in broader studies. We combine the new transcriptomes with a new morphological matrix (including fossils) and existing expressed sequence tag, mitochondrial genome, nuclear genome, and ribosomal DNA data. Our analyses lead to new insights into ostracod and pancrustacean phylogeny. We obtained support for three epic pancrustacean clades that likely originated in the Cambrian: Oligostraca (Ostracoda, Mystacocarida, Branchiura, and Pentastomida); Multicrustacea (Copepoda, Malacostraca, and Thecostraca); and a clade we refer to as Allotriocarida (Hexapoda, Remipedia, Cephalocarida, and Branchiopoda). Within the Oligostraca clade, our results support the unresolved question of ostracod monophyly. Within Multicrustacea, we find support for Thecostraca plus Copepoda, for which we suggest the name Hexanauplia. Within Allotriocarida, some analyses support the hypothesis that Remipedia is the sister taxon to Hexapoda, but others support Branchiopoda + Cephalocarida as the sister group of hexapods. In multiple different analyses, we see better support for equivocal nodes using slow-evolving genes or when excluding distant outgroups, highlighting the increased importance of conditional data combination in this age of abundant, often anonymous data. However, when we analyze the same set of species and ignore rate of gene evolution, we find higher support when including all data, more in line with a "total evidence" philosophy. By concatenating molecular and morphological data, we place pancrustacean fossils in the phylogeny, which can be used for studies of divergence times in Pancrustacea, Arthropoda, or Metazoa. Our results and new data will allow for attributes of Ostracoda, such as its amazing fossil record and diverse biology, to be leveraged in broader scale comparative studies. Further, we illustrate how adding extensive next-generation sequence data from understudied groups can yield important new phylogenetic insights into long-standing questions, especially when carefully analyzed in combination with other data.
    Molecular Biology and Evolution 09/2012; · 10.35 Impact Factor
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    ABSTRACT: 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. 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. 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.
    BMC Evolutionary Biology 07/2012; 12:129. · 3.29 Impact Factor
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    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.
    Journal of Experimental Biology 04/2012; 215(Pt 8):1278-86. · 3.24 Impact Factor

Publication Stats

2k Citations
405.36 Total Impact Points

Institutions

  • 2003–2014
    • University of California, Santa Barbara
      • Department of Ecology, Evolution, and Marine Biology
      Santa Barbara, California, United States
  • 2013
    • University of Michigan
      • School of Natural Resources and Environment
      Ann Arbor, Michigan, United States
    • CSU Mentor
      Long Beach, California, United States
  • 2012
    • University of California, Davis
      • Center for Population Biology
      Davis, CA, United States
  • 2007
    • University of California, Irvine
      • Department of Ecology and Evolutionary Biology
      Irvine, CA, United States
  • 2005
    • University of Chicago
      • Department of Ecology & Evolution
      Chicago, IL, United States
    • Iowa State University
      • Department of Ecology, Evolution and Organismal Biology
      Ames, IA, United States
  • 1998–2004
    • Duke University
      • Department of Biology
      Durham, NC, United States
  • 1999
    • University of Wisconsin - Milwaukee
      • Department of Biological Sciences
      Milwaukee, WI, United States