Todd H Oakley

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

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Publications (94)452.11 Total impact

  • Todd H. Oakley · Daniel I. Speiser ·

    Annual Review of Ecology Evolution and Systematics 12/2015; 46(1). DOI:10.1146/annurev-ecolsys-110512-135907 · 10.56 Impact Factor

  • PLoS ONE 10/2015; 10(10):e0140484. DOI:10.1371/journal.pone.0140484 · 3.23 Impact Factor
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    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.
    PLoS ONE 09/2015; 10(9):e0137085. DOI:10.1371/journal.pone.0137085 · 3.23 Impact Factor
  • Miriam J Henze · Todd H Oakley ·
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    ABSTRACT: Pancrustacea (Hexapoda plus Crustacea) display an enormous diversity of eye designs, including multiple types of compound eyes and single-chambered eyes, often with color vision and/or polarization vision. Although the eyes of some pancrustaceans are well-studied, there is still much to learn about the evolutionary paths to this amazing visual diversity. Here, we examine the evolutionary history of eyes and opsins across the principle groups of Pancrustacea. First, we review the distribution of lateral and median eyes, which are found in all major pancrustacean clades (Oligostraca, Multicrustacea, and Allotriocarida). At the same time, each of those three clades has taxa that lack lateral and/or median eyes. We then compile data on the expression of visual r-opsins (rhabdomeric opsins) in lateral and median eyes across Pancrustacea and find no evidence for ancient opsin clades expressed in only one type of eye. Instead, opsin clades with eye-specific expression are products of recent gene duplications, indicating a dynamic past, during which opsins often changed expression from one type of eye to another. We also investigate the evolutionary history of peropsins and r-opsins, which are both known to be expressed in eyes of arthropods. By searching published transcriptomes, we discover for the first time crustacean peropsins and suggest that previously reported odonate opsins may also be peropsins. Finally, from analyzing a reconciled, phylogenetic tree of arthropod r-opsins, we infer that the ancestral pancrustacean had four visual opsin genes, which we call LW2, MW1, MW2, and SW. These are the progenitors of opsin clades that later were variously duplicated or lost during pancrustacean evolution. Together, our results reveal a particularly dynamic history, with losses of eyes, duplication and loss of opsin genes, and changes in opsin expression between types of eyes.
    Integrative and Comparative Biology 08/2015; DOI:10.1093/icb/icv100 · 2.93 Impact Factor
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    ABSTRACT: Species richness (SR) and phylogenetic diversity (PD) are highly correlated measures of plant diversity. Each, by itself, is significantly associated with plant community biomass in biodiversity experiments. As presented by Cadotte (2015) and as we present below, reasonable but alternative analyses that attempt to control for this correlation in different ways provide contradictory or inconclusive support for the hypothesis that PD is superior to SR as a predictor of community biomass.This article is protected by copyright. All rights reserved.
    Functional Ecology 08/2015; DOI:10.1111/1365-2435.12540 · 4.83 Impact Factor
  • M Desmond Ramirez · Todd H Oakley ·
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    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. © 2015. Published by The Company of Biologists Ltd.
    Journal of Experimental Biology 05/2015; 218(Pt 10):1513-20. DOI:10.1242/jeb.110908 · 2.90 Impact Factor
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    ABSTRACT: Search String Advanced > Saved Searches > ARTICLE TOOLS Get PDF (905K) Save to My Profile E-mail Link to this Article Export Citation for this Article Get Citation Alerts Request Permissions More Sharing ServicesShare|Share on citeulikeShare on facebookShare on deliciousShare on www.mendeley.comShare on twitter Abstract Supporting Information Cited By Get PDF (905K) Keywords: Biodiversity; community biomass; data-synthesis; ecosystem functioning; grasslands; phylogenetic diversity; relatedness; stability Summary 1.Hundreds of experiments have now manipulated species richness of various groups of organisms and examined how this aspect of biological diversity influences ecosystem functioning. Ecologists have recently expanded this field to look at whether phylogenetic diversity among species, often quantified as the sum of branch lengths on a molecular phylogeny leading to all species in a community, also predicts ecological function. Some have hypothesized that phylogenetic divergence should be a superior predictor of ecological function than species richness because evolutionary relatedness represents the degree of ecological and functional differentiation among species. But studies to date have provided mixed support for this hypothesis. 2.Here, we re-analyze data from 16 experiments that have manipulated plant species richness in grassland ecosystems and examined the impact on aboveground biomass production over multiple time points. Using a new molecular phylogeny of the plant species used in these experiments, we quantified how the phylogenetic diversity of plants impacts average community biomass production as well as the stability of community biomass production through time. 3.Using four complementary analyses we show that, after statistically controlling for variation in species richness, phylogenetic diversity (the sum of branches in a molecular phylogenetic tree connecting all species in a community) is neither related to mean community biomass nor to the temporal stability of biomass. These results run counter to past claims. However, after controlling for species richness, phylogenetic diversity was positively related to variation in community biomass over time due to an increase in the variances of individual species, but this relationship was not strong enough to influence community stability. 4.In contrast to the non-significant relationships between phylogenetic diversity, biomass, and stability, our analyses show that species richness per se tends to increase the mean biomass production of plant communities, after controlling for phylogenetic diversity. The relationship between species richness and temporal variation in community biomass was either positive, non-significant or negative depending on which analysis was used. However, the increases in community biomass with species richness, independently of phylogenetic diversity, always led to increased stability. These results suggest that phylogenetic diversity is no better as a predictor of ecosystem functioning than species richness. 5.Synthesis. Our study on grasslands offers a cautionary tale when trying to relate phylogenetic diversity to ecosystem functioning suggesting that there may be ecologically important trait and functional variation among species that is not explained by phylogenetic relatedness. Our results fail to support the hypothesis that the conservation of evolutionarily distinct species would be more effective than the conservation of species richness as a way to maintain productive and stable communities under changing environmental conditions.
    Functional Ecology 03/2015; 29(5). DOI:10.1111/1365-2435.12432 · 4.83 Impact Factor
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    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.
    Journal of Experimental Biology 12/2014; 218(3). DOI:10.1242/jeb.116087 · 2.90 Impact Factor
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    ABSTRACT: Research Cite this article: Alexandrou MA et al. 2015 Evolutionary relatedness does not predict competition and co-occurrence in natural or experimental communities of green algae. 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 limit-ations: (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 labora-tory 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 lab-oratory 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 sys-tems. Our results challenge the generality of the CRH and suggest it may be time to re-evaluate the validity and assumptions of this hypothesis.
    Proceedings of the Royal Society B: Biological Sciences 12/2014; 282(1799). DOI:10.1098/rspb.2014.1745 · 5.05 Impact Factor
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    Daniel I Speiser · Daniel G DeMartini · Todd H Oakley ·
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    ABSTRACT: Certain species of chiton (Mollusca, Polyplacophora) have hundreds of small (<100 mu m) eyes embedded in their dorsal shell plates. These eyes each contain a retina, a layer of screening pigment, and a lens. Previously, we demonstrated that the eyes of chitons provide spatial vision. As in other camera-type eyes, the screening pigments in the eyes of chitons absorb off-axis light in order to preserve the contrast of images formed on the retina. Our results indicate that the red-brown, alkali-soluble screening pigment associated with the eyes of the chiton Acanthopleura granulata (Gmelin, 1791) is pheomelanin. Using high-performance liquid chromatography (HPLC) and MALDI-TOF mass spectroscopy, we find that degrading A. granulata's screening pigment with alkaline hydrogen peroxide produces 6-(2-amino-2-carboxyethyl)-2-carboxy-4-hydroxybenzothiazole (BTCA), a diagnostic marker of pheomelanin. Chitons are the first molluscs demonstrated to use pheomelanin as a screening pigment in their eyes. Our results suggest that the image-forming eyes of chitons may have evolved separately from eyes that employ different types of screening pigment, such as those of most other invertebrates. Further, we hypothesize that change in the expression pattern of tyrosinase - an enzyme responsible for melanin synthesis in many other metazoans - may have contributed to the origin of screening pigments in chitons, a critical step in the evolution of their eyes.
    Journal of Natural History 11/2014; 48(45-48-ahead-of-print):1-13. DOI:10.1080/00222933.2014.959572 · 0.88 Impact Factor

  • Zootaxa 11/2014; 3884(6):600. DOI:10.11646/zootaxa.3884.6.9 · 0.91 Impact Factor
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    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.ResultsWe 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 30 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 ( and we demonstrate PIA on a publicly-accessible web server ( 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.
    BMC Bioinformatics 11/2014; 15(1):350. DOI:10.1186/s12859-014-0350-x · 2.58 Impact Factor
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    ABSTRACT: Despite contingency in life's history, the similarity of evolutionarily convergent traits may represent predictable solutions to common conditions. However, the extent to which overall gene expression levels (transcriptomes) underlying convergent traits are themselves convergent remains largely unexplored. Here, we show strong statistical support for convergent evolutionary origins and massively parallel evolution of the entire transcriptomes in symbiotic bioluminescent organs (bacterial photophores) from two divergent squid species. The gene expression similarities are so strong that regression models of one species' photophore can predict organ identity of a distantly related photophore from gene expression levels alone. Our results point to widespread parallel changes in gene expression evolution associated with convergent origins of complex organs. Therefore, predictable solutions may drive not only the evolution of novel, complex organs but also the evolution of overall gene expression levels that underlie them.
    Proceedings of the National Academy of Sciences 10/2014; 111(44). DOI:10.1073/pnas.1416574111 · 9.67 Impact Factor
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    ABSTRACT: Hemocyanin is a copper-containing protein that transports O2 in the hemolymph of many arthropod species. Within the crustaceans, hemocyanin appeared to be restricted to Malacostraca but has recently been identified in Remipedia. Here, we report the occurrence of hemocyanin in ostracods, indicating that this respiratory protein is more widespread within crustaceans than previously thought. By analyses of expressed sequence tags and by RT-PCR, we obtained four full length and nine partial hemocyanin sequences from six of ten investigated ostracod species. Hemocyanin was identified in Myodocopida (Actinoseta jonesi, Cypridininae sp., Euphilomedes morini, Skogsbergia lerneri, Vargula tsujii) and Platycopida (Cytherelloidea californica) but not in Podocopida. We found no evidence for the presence of hemoglobin in any of these ostracod species. Like in other arthropods, we identified multiple hemocyanin subunits (up to six) to occur in a single ostracod species. Bayesian phylogenetic analyses showed that ostracod hemocyanin subunit diversity evolved independently from that of other crustaceans. Ostracod hemocyanin subunits were found paraphyletic, with myodocopid and platycopid subunits forming distinct clades within those of the crustaceans. This pattern suggests that ostracod hemocyanins originated from distinct subunits in the pancrustacean stemline.
    Journal of Molecular Evolution 08/2014; 79(1-2). DOI:10.1007/s00239-014-9636-x · 1.68 Impact Factor
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    ABSTRACT: Background/Question/Methods Darwin proposed >150-yrs ago that closely related species are more ecologically similar to each other than distantly related species. In turn, he argued closely related species should compete more strongly and be less likely to coexist. For much of the last century, Darwin's hypothesis was taken at face value, and sometimes rose to the status of dogma among those who proposed that conservation and restoration of evolutionary diversity could help maximize the resilience, stability, and ecological functioning of ecosystems. Despite its intuitive appeal, the competition-relatedness hypothesis has received surprisingly little testing. Here we present results from a suite of laboratory and field studies that used freshwater green algae to determine if evolutionary relatedness impacts species interactions, trait similarity, and patterns of co-occurrence. We cultured and sequenced ~60 of the most common species of green algae in lakes across North America to generate a robust molecular phylogeny describing evolutionary relationships. We then (a) performed laboratory competition experiments in which we manipulated the genetic distance among species and measured interaction strengths and niche overlap, (b) examined the evolutionary conservatism of biological traits that underlie interactions, and (c) explored whether patterns of species co-occurrence in real lakes are predicted by relatedness. Results/Conclusions Using lab experiments in which we grew 8 common algal species in mono- and biculture, we fit time series of population dynamics to Lotka-Volterra competition equations to estimate interaction coefficients (alphas). Even though alphas clearly predicted the winners/losers of competition, interaction strengths were independent of phylogenetic distance (F1,23 = 0.56, P = 0.46). We then expanded the species pool and ran experiments using 216 pair-wise combinations of algae, but still found no evidence that phylogenetic distance impacts species relative yields (biomass in mono- vs. biculture, P = 0.19). Following this, we experimentally quantified key biological traits thought to dictate competition for >50 algal species and found the minimum resource levels needed to sustain positive growth (R* values for N, P, light) were not evolutionarily conserved (P > 0.10 for all estimates of Bloomberg's K). Lastly, we examined patterns of species co-occurrence across >1,200 North American lakes and found that the probabilities of co-occurrence were not significantly different than the random expectation of a null model. These diverse empirical studies are all congruent, and suggest the mechanisms of competition may not always be evolutionarily conserved. Therefore, biologists may need to re-evaluate the often assumed generality of Darwin's competition-relatedness hypothesis.
    99th ESA Annual Convention 2014; 08/2014
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    Roberto Feuda · Omar Rota-Stebelli · Todd H Oakley · Davide Pisani ·
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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.
    Genome Biology and Evolution 07/2014; 6(8). DOI:10.1093/gbe/evu154 · 4.23 Impact Factor

Publication Stats

3k Citations
452.11 Total Impact Points


  • 2003-2015
    • University of California, Santa Barbara
      • Department of Ecology, Evolution, and Marine Biology
      Santa Barbara, California, United States
  • 2014
    • University of Hamburg
      • Zoological Institute
      Hamburg, Hamburg, Germany
  • 2013
    • University of California, Berkeley
      • Department of Integrative Biology
      Berkeley, California, United States
  • 2010
    • University of California, Davis
      • Department of Evolution & Ecology
      Davis, California, United States
  • 1997-2006
    • University of Wisconsin - Milwaukee
      • Department of Biological Sciences
      Milwaukee, Wisconsin, United States
    • University of Houston
      • Department of Biology and Biochemistry
      Houston, Texas, United States
  • 2004-2005
    • University of Chicago
      • Department of Ecology & Evolution
      Chicago, IL, United States
  • 1998-2004
    • Duke University
      • Department of Biology
      Durham, North Carolina, United States