Friday, January 1, 2016

SICB 2016 Schedule

Here are some #SICB2016 presentations I have marked after key word searches. What great ones am I missing?

Session/Paper#TimeRoomAuthor 1Title
Monday, Jan. 4 22-1 10:15 C125/126 SCHNITZLER, CEGenomics of Hydractinia: A Cnidarian Model for Regeneration, Allorecognition, and Developmental Biology 
Monday, Jan. 4 33-5 14:30 C125/126 VON DASSOW, MThe echinoid blastula: linking biomechanics to development-environment interactions 
Monday, Jan. 4 33-6 14:45 C125/126 SERVETNICK, MDCRISPR/Cas9-mediated excision of the brachyury gene disrupts endoderm development in the sea anemone Nematostella vectensis
Monday, Jan. 4 P1-143 15:30 Exhibit Hall A DONOHUE, M.W.Behavioral and molecular evidence for opsin-based extraocular photoreception in stomatopod crustaceans 
Monday, Jan. 4 P1-157 15:30 Exhibit Hall A ARUL NAMBI RAJAN, ANeural Determinants of Behavior in an Organism without a Nervous System 
Monday, Jan. 4 P1-162 15:30 Exhibit Hall A PRICE, C.L.The genetics of the visual system of two species of pupfishes (genus Cyprinodon) 
Monday, Jan. 4 P1-147 15:30 Exhibit Hall A PICCIANI, N.Light modulated cnidocyte firing predates the evolution of eyes in Cnidaria (Metazoa) 
Monday, Jan. 4 P1-144 15:30 Exhibit Hall A NOTAR, JCA Comparative Study of Sea Urchin Visual Ecology  
Monday, Jan. 4 P1-145 15:30 Exhibit Hall A MILLER, H.V.Pupillary responses in scallops 
Monday, Jan. 4 P1-78 15:30 Exhibit Hall A SIMMONS, SMesoglea and Muscle in Cubozoan Jellyfish Carybdea marsupialis and Tripedalia cystophora 
Monday, Jan. 4 P1-22 15:30 Exhibit Hall A MUNRO, CExploring the evolution of functional specialization in siphonophores using RNAseq 
Monday, Jan. 4 P1-148 15:30 Exhibit Hall A SWAFFORD, A.J.Gain and Loss of Sensory Modalities Alter Guidance of Allomyces Zoospores 
Tuesday, Jan. 5 S4-2 08:00 C123 PORTER, M.L.Beyond the eye: extraocular opsin evolution 
Tuesday, Jan. 5 S4-3 08:30 C123 COLLEY, N.J.Photoreception in Phytoplankton 
Tuesday, Jan. 5 40-4 08:45 B114 DALTON, B ECoexpression of opsins in each cone class spectrally tunes regions of the retina to distinct parts of the visual field 
Tuesday, Jan. 5 S4-4 09:00 C123 OAKLEY, THOpsins without eyes – precursors or derivatives? 
Tuesday, Jan. 5 40-6 09:15 B114 FAULKES, Z.Eyes under the beach: the visual system of sand crabs (Lepidopa benedicti
Tuesday, Jan. 5 S4-6 10:30 C123 KINGSTON, ACNExtraocular opsins in skin and nervous systems of aquatic animals 
Tuesday, Jan. 5 S4-7 11:00 C123 BATTELLE, B-AOcular and extraocular photosensitivity and opsin expression in the American horseshoe crabLimulus polyphemus, a chelicerate arthropod. 
Tuesday, Jan. 5 S4-8 11:30 C123 BOK, M.J.Looking with gills: The function and evolution of fan worm branchial photoreceptors 
Tuesday, Jan. 5 S4-9 13:30 C123 WALKER, Marquis T.A mouse homolog of Drosophila RDGB functions in ipRGC dim light activation 
Tuesday, Jan. 5 68-1 13:45 B118/119 DALY, MThe tree’s the thing: phylogeny as a way of understanding the diversity of venom in sea anemones 
Tuesday, Jan. 5 67-1 14:00 B117 LARSON, P.G.Evaluating taxonomic characters of Anthopleura and other sea anemones in a molecular phylogenetic context 
Tuesday, Jan. 5 S4-10 14:00 C123 SCHMIDT, T.M.New roles for ganglion cell photoreceptors 
Tuesday, Jan. 5 67-2 14:15 B117 MACRANDER, JA High-Throughput Investigation into the Tissue Specific Venom Composition and Differential Gene Expression in Three Species of Sea Anemone 
Tuesday, Jan. 5 67-3 14:30 B117 GOODHEART, J.A.Phylogenomics of Cladobranchia (Mollusca: Gastropoda: Heterobranchia) 
Tuesday, Jan. 5 S4-11 14:30 C123 SPEISER, D.I.Eyes most numerous: extracephalic visual systems in molluscs 
Tuesday, Jan. 5 67-4 14:45 B117 CHANG, J.The tempo of body shape evolution in ray-finned fishes: bringing morphology into the “phenomic era” with crowdsourced morphometrics 
Tuesday, Jan. 5 S4-12 15:00 C123 JOHNSEN, S.What Next? Unanswered questions about extraocular photoreception and how we might answer them  
Tuesday, Jan. 5 P2-136 15:30 Exhibit Hall A STABILE, F. A.Identification of four genes involved in the development of feathers but not scales in birds 
Tuesday, Jan. 5 P2-156 15:30 Exhibit Hall A MURPHY, P.J.Regional Genetic Variation of Two Ephemeral Pool Crustacean Species: Implications for Visual System Plasticity or Local Adaptation 
Wednesday, Jan. 6 74-1 08:00 B112 BABONIS, L.S.Seeing without eyes: Opsins and the evolution of photodetection in basal metazoans 
Wednesday, Jan. 6 79-2 08:15 B118/119 MCCULLOCH, KJPhotoreceptor Cell Sensitivity and Sexual Dimorphism in the Compound Eye of the ButterflyHeliconius erato 
Wednesday, Jan. 6 74-4 08:45 B112 MASON, B.M.Coral opsins: photosensitivity and partial characterization of five opsins from Acropora millepora 
Wednesday, Jan. 6 74-5 09:00 B112 SERB, J.M.Expression and spectral analysis of two Gq-opsins from the mantle and the eyes of the scallop Placopecten magellanicus  
Wednesday, Jan. 6 74-6 09:15 B112 FAGGIONATO, D.Spectra analysis of Gq-opsins from four scallop species 
Wednesday, Jan. 6 74-7 09:30 B112 BRANDLEY, NDo warning signals exploit an evolutionary constraint on insect visual acuity? 
Wednesday, Jan. 6 85-1 10:15 B112 THOMAS, K.N.The perks of being cock-eyed: Orientation and visual characteristics of histioteuthid squids 
Wednesday, Jan. 6 85-2 10:30 B112 HOLT, A.L.Light guides and open water camouflage in Galiteuthis 
Wednesday, Jan. 6 85-3 10:45 B112 CAVES, EMVisual acuity in fish: the effects of eye morphology, environment, and ecology 
Wednesday, Jan. 6 85-4 11:00 B112 JOHNSEN, S.Another beautiful hypothesis slain by an ugly fact: Polarization vision does not increase the sighting distance of silvery fish 
Wednesday, Jan. 6 85-5 11:15 B112 DODSON, TOrigins of Polydispersity In Cephalopod Photonic Systems - Are Squids Masters of RNA Editing? 
Wednesday, Jan. 6 96-2 13:45 B112 EMERLING, C.A.Spectral shifts of mammalian ultraviolet-sensitive pigments (SWS1) are associated with eye length and photic niche evolution 
Wednesday, Jan. 6 92-3 14:00 A104 CORYELL, R.L.Phylogeographic patterns in the Philippine archipelago drive symbiont diversity in the bobtail squid-Vibrio mutualism 
Wednesday, Jan. 6 101-4 14:15 B118/119 MOROZ, LLCan Synapses Evolve Independently? 
Wednesday, Jan. 6 S8-10 14:30 C124 LEWIS, C.Differential expression of genes implicated in venom, vision and sex in the aggregating box jellyfish Alatina alata 
Wednesday, Jan. 6 P3-198 15:30 Exhibit Hall A LIN, C.Neural organization of the optic lobes in the two midband-row stomatopod Squilla empusa 
Wednesday, Jan. 6 P3-16 15:30 Exhibit Hall A STERN, D.B.Comparative Vision Gene Expression in Cave Adapted Crayfish 
Thursday, Jan. 7 115-1 10:15 A107-109 ADAMS, DKEvolution of the neurosensory system mediates gain and loss of phenotypic plasticity 
Thursday, Jan. 7 114-4 11:00 A105 KELLY, MWAdaptation to heat stress reduces phenotypic and gene expression plasticity in a marine copepod 
Thursday, Jan. 7 116-6 11:30 B110-111 SCHWEIKERT, LERed Fish, Blue Fish: Wavelength Sensitivity of the Marine Fish Retina Adjusts to Transient Changes in Environmental Light Color 
Thursday, Jan. 7 115-7 11:30 A107-109 KOENIG, KMMaking an Eye: Optic Vesicle Morphogenesis in the Cephalopod Doryteuthis pealeii 
Use this button to remove checked items from your personal schedule.

Friday, November 6, 2015

Postdoctoral Position in Ecological Genomics at UCSB

Postdoctoral Researcher in Ecological and Evolutionary Genomics

We seek a researcher to lead the genomics aspects of an interdisciplinary research program on algal ecology and biofuels. The candidate will work at UCSB in the lab of Todd Oakley and collaborate with ecologists and engineers at the University of Michigan. This project was awarded by the National Science Foundation through its Emerging Frontiers in Research and Innovation (EFRI) initiative. The team is testing the hypothesis that certain naturally diverse groups of algae have complementary traits that enhance the efficiency and stability of biofuel yield beyond what any single species can achieve alone. The UCSB members of the team are testing whether gene expression differences under different ecological conditions correlate with measures biofuel yield.

The minimum requirement is a PhD in bioinformatics, genomics or a related field. Applicant should also be comfortable working in a collaborative, interdisciplinary environment, which requires excellent written and oral communication skills. The applicant should be able to handle large transcriptomic and genomic data sets, and be adept at coding (Python, PERL, or similar) and at using and implementing bioinformatics software.

Applicants should submit a cover letter, curriculum vitae, research statement, summary of research experience, publications. In addition, supply contact information for 3 colleagues willing to provide letters of recommendation (we will contact the letter writers for a short list of candidates).

We will begin to review applications immediately, but apply by Dec 1, 2015 for full consideration. Please direct questions or informal inquiries to Todd Oakley (

The department is interested in candidates who can contribute to the diversity and excellence of the academic community through research, teaching and service. The University of California is an Equal Opportunity/Affirmative Action Employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, national origin, or any other characteristic protected by law including protected Veterans and individuals with disabilities.

Wednesday, October 28, 2015

How old are fireflies?

This is an "open lab notebook" detailing an analysis I did trying to figure out how old are fireflies.

Are fireflies - beetles who use light for courtship - more diverse than expected from the age of their lineage? Answering this question in part depends on knowing the age of the clades.

In this analysis, I come up with a very rough estimate that one firefly clade is 145 MY and another is 128 MY. Divergence time estimation is notoriously error-prone and these estimates are based on a number of assumptions. They should therefore be taken with a (large) grain of salt, ie be skeptical.

I began with the phylogeny of Martin et al. (2015). They concluded adult bioluminescence was originated twice in fireflies. One clade contains Lampyrinae+Photurinae, which I call ‘firefly1’. The other clade contains Pterotinae+Luciolinae - I call this the “firefly2” clade. This tree is based on 18S, 16S, and CO1, but did not do any divergence time analyses.


In order to estimate divergence times, I needed to include clades that could be constrained with fossils. I consulted Hunt et al. (2007), a phylogeny of all beetles, with divergence times. The closest clade to fireflies with a fossil constraint is their constraint “e”. This is Elaterophanes from 196.5 MY, used as a minimum age for the Elateridae. Hunt et al. (2007) used the same genes as Martin et al. (2015) (MEA), so I concatenated the MEA data set with elaterids from HEA. I also fixed beetles to be 285 MY, after Hunt et al. (2007). This is their estimate of divergence time for beetles. Using the fossil record could lead to a ‘maximum’ age of beetles as 411 (Rhynie Chert). But if I use 285 as a minimum and 411 as a maximum, the age gets pushed up to 411, which does not seem particularly realistic. Doing that raises the age estimates by some 40 MY-  for FF1 and FF2 to 186 and 164 MY, respectively.
I also included some other outgroups. First, I used a Hydroscaphidae because the MRCA of that clade and Lampyridae is the MRCA of all beetles. In addition, I used a non-beetle, Chrysopidae. These two taxa were the only species in HEA that had all 3 genes. For divtime analyses in r8s, I pruned the Chrysopidae to leave a rooted, fully resolved tree.

I required all 3 genes to be present for each species (using phylocatenator of Osiris (Oakley et al. 2014)). My tree had some differences with HEA and MEA:

  1. Elateridae are not monophyletic. With some different outgroups, I did get monophyly. HEA also consistently got monophyly. Perhaps adding Cantheridae (a closer sister to Lampyridae) would allow recovery of the expected monyphyly of elateridae. As a result, the divtime constraint is at the base of Elateridae AND Lampyridae, and could influence final results.
  2. Firefly 2 (red taxa) is not monophyletic as in MEA. Instead, I get Pollaclasis and Cyphonocerus within the Firefly2 clade. This could influence the time estimate for this clade. I could perhaps constrain monophyly here. Also other outgroups also could influence monophyly because Pterotus is the taxon changing places, and it is fairly long branch, and may be influenced by outgroups.

Data Files:

I used Osiris (Oakley et al. 2014) to build the phylogeny, which uses phytab format. That file is here.

I used r8s for the divergence time analysis, and that file is here:


Begin TREES;

TREE 'Tree1' = ((((Oxynopterus_sp.:463.5249944,Agrypnus_murinus:526.2532825):58.07102708,(Panspaeus_guttatus:460.2987223,(Stenagostus_rhombeus:490.0649111,(Denticollis_linearis:345.0885786,Athous_haemorrhoidalis:348.234297):128.0768835):72.63022263):60.96422013):35.09443673,((((Phausis_reticulata:1662.289658,((((Lamprohiza_splendidula:544.0746241,Phosphaenus_hemipterus:229.7443014):285.1154906,Lucidota_atra:437.7055071):401.9635656,((((Photinus_australis:253.4245299,Photinus_tanytoxus:505.5902659):83.13503158,((Photinus_punctulatus:528.7843213,Photinus_pyralis:301.5064629):50.68180427,(Photinus_floridanus:473.4079674,(Ellychnia_californica:135.4824287,Ellychnia_aff._corrusca_KSH611:25.24849269):286.7912686):70.99285141):18.53357795):329.2700252,((Aspisoma_sp.:283.3096828,(Pyractomena_dispersa:29.67243287,(Pyractomena_palustris:31.23178185,(Pyractomena_angulata:517.0946069,Pyractomena_borealis:67.81801332):70.86493904):110.1146049):238.5808725):339.3010688,((Pleotomodes_needhami:426.6510094,Pleotomus_pallens:389.0211618):76.84583685,(Lampyris_noctiluca:477.2948781,((Diaphanes_formosus:371.9065228,Lychnuris_formosana:449.5272741):90.09984008,(Microphotus_angustus:406.2856534,Paraphausis_eximius:395.3158416):117.5049772):29.6282204):72.85630302):111.0228766):116.0625074):59.48984988,Micronaspis_floridana:558.9615698):107.7999852):229.3020886,(Vesta_sp.:561.4644596,(Bicellonycha_wickershamorum:491.2011309,((Photuris_tremulans:49.09336296,Photuris_aff._lucicrescens_KSH1:100.1688104):15.59686292,Photuris_quadrifulgens:50.11517938):457.7292255):121.0831356):150.8011019):163.8652632):66.19287172,((Brachylampis_blaisdelli:759.3860187,((Drilaster_axillaris:123.8337303,(Flabellotreta_sp.:171.4133031,Flabellotreta_obscuricollis:146.3672477):242.4682661):163.5674534,(Ceylonidrilus_sp.:422.4286714,(Drilaster_sp.:354.6668547,Drilaster_borneensis:394.0848821):241.6799973):72.15723681):351.5818484):270.4748514,((Luciola_sp.:326.8593145,((Luciola_parvula:576.0213995,(Curtos_okinawanus:182.2933313,Curtos_costipennis:220.7797732):214.4995191):130.4914738,Curtos_sp.:346.5873752):104.5451147):267.9094037,(Pterotus_obscuripennis:672.2005806,(Pollaclasis_bifaria:627.4316177,Cyphonocerus_ruficollis:348.7937363):198.7861435):41.84871305):52.94860049):62.12407915):680.5789337,Plateros_sp.:1002.688879):111.8242026,((Rhagophthalmus_ohbai:539.4926404,(Cebrioninae_sp.:547.7782899,Ampedus_balteatus:478.7696559):125.5329304):66.72017755,Cardiophorinae_sp.:883.3299248):39.872645):47.59526361):1043.317628,Hydroscaphidae:1499.20604);

[** Beginning of the rates block containing commands for r8s **]

begin r8s;
blformat lengths=persite nsites=6417 ultrametric=no;

MRCA beetles Hydroscaphidae Drilaster_borneensis;
MRCA elateridae Cardiophorinae_sp. Panspaeus_guttatus;
MRCA firefly1 Phausis_reticulata Pleotomus_pallens;
MRCA firefly2 Pterotus_obscuripennis Luciola_parvula;

fixage taxon=beetles age=285;
#constrain taxon=beetles min_age=280 max_age=411;
constrain taxon=elateridae min_age=196.5;

divtime method=pl algorithm=tn [cvStart=0 cvInc=0.2 cvNum=8 crossv=yes];

describe plot=chrono_description;
showage shownamed=yes;