Here are some #SICB2016 presentations I have marked after key word searches. What great ones am I missing?
Use this button to remove checked items from your personal schedule.
Friday, January 1, 2016
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 (oakley@lifesci.ucsb.edu).
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.
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 (oakley@lifesci.ucsb.edu).
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:
- 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.
- 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:
#NEXUS
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);
End;
[** 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;
end;
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);
End;
[** 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;
end;
References
Sunday, July 26, 2015
Graduating Little League
Before the actual day, I worried about
the arrival of my 40th birthday. But when that day came,
it felt like any other day. I was still me, just a day older. I
felt the same for “Y2K”, the year 2000. After months of doomsday
scenarios, January 1, 2000 was just like any other day that saw the
sun rise and saw the sun set. All our computers still turned on.
Partly because these were so normal, I am caught off-guard that today
does not feel like any other day. As strange as it may sound, the end
of my son's 12-year-old Little League year feels like I thought age
40 or Y2K might feel; like the end of an era. In many ways, my son
and his baseball buddies are no longer children. Today, our boys have
graduated Little League.
It is true that Little League goes on
past age 12. But the 12-year-old year is the privileged year. The
name of the 12U division is simply “Little League”, as if to
assert the 12-year-old division is Little League. In our town,
the 12 year-old division is top dog. It's considered first in
scheduling games and practices and batting cage time. It's the only
division without a time limit on games. At 12, Little Leaguers
traditionally play their final year on the small field, where
T-ballers and mini-minor kids also learn the game. Next comes a big
transition to a full, major-league-sized field. Many kids do not
make the transition to the more demanding field and they leave
baseball behind. There are other reasons to stop Little League after
12. Some of the best players leave to focus only on more competitive
club teams. And so the 12-year old year is the peak of Little League
participation and competition. The kids fortunate enough to be
selected to represent their league as All-Stars extend their regular
seasons with summer tournaments against other leagues. For the 12U
Little League division, the tournament is truly world-wide,
culminating in The Little League World Series in Williamsport, PA,
watched by millions each year on television.
This year, my son's 12-year-old Little
League year, he and I were especially fortunate. He represented his
league as an All-Star, with me as a coach. It was a special team that
exceeded expectations and got significant
contributions from every single player. It was a special team because the
whole was greater than the sum of the parts, with strong leadership and strong families. Most of all, it was a team of great boys who worked hard, who played hard to win,
who never gave up, and who had fun. Had these boys lost in their
district (the first tournament), not many people would have been surprised. Defying
expectations, these boys breezed to the District championship, even winning that game 11-0. Then
they went even farther. They won a Sectional championship with two
comeback, walk-off victories in a row. One of the Sectional victories
was against a power house team, last year's 11U state champions. In
so doing, our team became only the third in our league's 47-year
history to be Section champions as 12-year-olds. As Section champions, they were one
of ten teams to remain alive in all of Southern California, usually one of the very strongest regions of Little League baseball in the world.
Our team celebrates their walk-off Sectional Championship.
For all but a handful of players and
coaches, the Little League tournament ends in defeat. We know all
along that the odds of reaching a Williamsport dream are very long,
and we assume that defeat will come eventually. Yet with every win,
the dream stays alive. Why couldn't it be us? Why shouldn't it be us?
We could be the team of destiny. These boys deserve to be the
team of destiny. With every win we keep working, every day. We keep
practicing and we keep playing hard. We do not give up and we focus
on getting better. In every game, we expect to win. In every game, we
plan to win. And so we do not mentally prepare for losing. Until we
lose. Then it all changes in an instant.
It is not the loss of a game that is so
difficult. Perhaps it is the loss of an opportunity. Maybe it is the
loss of our summertime family, with whom we cheered and celebrated.
When players finish their season at age 10, they look forward to
moving up to the Little League Majors division. When they finish at
age 11, they look forward to their privileged year, when their
Williamsport dreams become most vivid. But when they are 12, and
their season comes to its inevitable end, they will never again be
little boys playing on a little diamond. My son is someone I can
still play catch with, but no longer can I play catch with my little
boy. Today, our little boys have graduated.
Even though I will miss the days of
playing baseball with a great group of boys on a perfect Santa
Barbara summer afternoon, I know that graduations are also a time to
be proud. We are so proud of what these boys accomplished. We know
they will become strong young men. These will be young men who strive
to win. These will be young men who will always do their best, and who never give up. These
will be young men who support each other and who contribute to
communities and teams in ways that maximize their individual
strengths and gifts. These will be young men who know that sometimes,
a whole can be greater than the sum of its parts. These are young men
who today graduated Little League.
Monday, April 6, 2015
Everything's comin up peropsin
(Or maybe coming up RGR). My research activities on opsin have lately led me to peropsin and RGR. These are opsins in the RGR/Go superfamily (a la Plachetzki et al 2007) [Note Porter et al 2012 named this superfamily Group IV, but I don't like that name as much because it is not clear there are actually four superfamily groups].
Below is a report I sent to the first author of a paper that just came out. The paper is here:
Battelle, B., Kempler, K., Saraf, S., Marten, C., Dugger, D., Speiser, D., & Oakley, T. (2014). 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 Journal of Experimental Biology, 218 (3), 466-479 DOI: 10.1242/jeb.116087
Battelle, B., Kempler, K., Saraf, S., Marten, C., Dugger, D., Speiser, D., & Oakley, T. (2014). 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 Journal of Experimental Biology, 218 (3), 466-479 DOI: 10.1242/jeb.116087
I've taken to writing reports for collaborations, as it focuses me to get done the work, and to share it with collaborators in a way where they can easily extract information for the publication. Below is such a report that I created for the above-cited paper:
Introduction
In 1997, (Sun et al.
1997) reported a new opsin, found in cDNA libraries of human eyes,
and shown by immunohistochemistry to be expressed in Retinal Pigment
Epithelium. Another name for peropsin is RRH (retinal pigment
epithelium-derived rhodopsin homologue). The most closely related gene to
peropsin in the human genome is RGR (RPE−retinal G protein−coupled receptor),
first discovered in 1993 (Jiang,
Pandey, and Fong 1993). Based on mouse knockout experiments, RGR is
a photoisomerase involved in the generation of 11-cis-retinal (Chen et al. 2001). Both
of these vertebrate genes belong to a large clade of opsins called “RGR/Go” (Plachetzki, Degnan, and Oakley 2007;
Feuda et al. 2012) or “Group-IV” opsins (Porter et al. 2012).
Nagata et al (2010) claimed to find the
first peropsin from a protostome, a jumping spider, Hasarius adansoni. However, their phylogenetic analysis showed only
weak support (77%) for the spider gene as the sister to peropsins and was based
on overly simplistic phylogenetic techniques (neighbor-joining based on an
unspecified distance model). Eriksson et al (2013)
discovered a gene from the spider Cupiennius
salei that is very similar to the jumping spider gene. While their
phylogenetic analysis shows good support for these spider genes in the Group IV
clade (1.0 posterior probability in Bayesian Inference), their placement with
peropsin is again tenuous (0.62). Hering and Mayer (2014) reported a third
chelicerate peropsin-like gene from the genome of the spider mite Tetranychus urticae. The three
chelicerate genes form a well-supported clade within Group IV opsins, but their
phylogenetic position was again uncertain with respect to peropsin and RGR. In
some analysis of Hering and Mayer (2014), the chelicerate
genes are weakly supported as sister to all other RGR and peropsin genes and in
one analysis they are weakly supported as sister to RGR.
Methods
I conducted phylogenetic analyses on 30 opsin sequences,
including our putative Limulus peropsin/RGR-like gene, 27 genes of the
RGR/peropsin (=RPE/peropsin) clade of Hering and Mayer (2014), plus two outgroup
opsins with solved crystal structures (Bos
taurus c-opsin (Palczewski
et al. 2000) and Todarodes r-opsin
(Murakami and Kouyama 2008)).
I conducted all phylogenetic analyses using the Osiris phylogenetics package (Oakley et al. 2014)
within Galaxy (Blankenberg et al. 2005). I first aligned all
30 sequences using MUSCLE (Edgar 2004). I next used RAxML version 7.4 (Stamatakis
2006), assuming a GTR+G model to search for the Maximum Likelihood
phylogeny, and conducted 100 bootstrap pseudoreplications to gauge node
stability.
Results
The new Limulus peropsin/RGR-like
gene forms a clade with the three “peropsins” previously described from
chelicerates (100%), and is sister to the two spider “peropsins” (93%). The
relationships within chelicerates are not consistent with taxonomy, which would
predict that Limulus, as the only
non-arachnid, should fall as the sister gene to the other three chelicerate
genes. Our results are similar to previous analyses that cannot confidently
place the chelicerate genes in a specific position between RGR and peropsin.
Discussion
We found a gene in Limulus
that is very similar to other chelicerate genes known in the literature as
protostome “peropsins”. However, a careful examination of previous studes, and
our own results, indicate that the chelicerate genes may orthologs of peropsins
or RGR genes, or that vertebrate RGR and peropsins are in paralogs compared to
the chelicerate genes. The inability of phylogenetic analyses to unequivocally
place the chelicerate genes could be caused by sparse sampling of invertebrate
genomes. In addition, many of the peropsin/RGR sequences found in invertebrate
full genome sequences have not been experimentally verified, nor has function
been demonstrated for them. Clearly, there is much to learn about this clade of
opsins.
References
Chen, P, W
Hao, L Rife, X P Wang, D Shen, J Chen, T Ogden, et al. 2001. “A Photic Visual
Cycle of Rhodopsin Regeneration Is Dependent on Rgr.” Nature
Genetics 28 (3):
256–60.
Eriksson, Bo
Joakim, David Fredman, Gerhard Steiner, and Axel Schmid. 2013.
“Characterisation and Localisation of the Opsin Protein Repertoire in the Brain
and Retinas of a Spider and an Onychophoran.” BMC
Evolutionary Biology 13
(September): 186.
Feuda,
Roberto, Sinead C Hamilton, James O McInerney, and Davide Pisani. 2012.
“Metazoan Opsin Evolution Reveals a Simple Route to Animal Vision.” Proceedings
of the National Academy of Sciences of the United States of America 109 (46): 18868–72.
Hering, Lars,
and Georg Mayer. 2014. “Analysis of the Opsin Repertoire in the Tardigrade
Hypsibius Dujardini Provides Insights into the Evolution of Opsin Genes in
Panarthropoda.” Genome Biology and Evolution, September. doi:10.1093/gbe/evu193.
Jiang, M, S
Pandey, and H K Fong. 1993. “An Opsin Homologue in the Retina and Pigment
Epithelium.” Investigative Ophthalmology & Visual Science 34 (13): 3669–78.
Murakami,
Midori, and Tsutomu Kouyama. 2008. “Crystal Structure of Squid Rhodopsin.” Nature 453 (7193): 363–67.
Nagata,
Takashi, Mitsumasa Koyanagi, Hisao Tsukamoto, and Akihisa Terakita. 2010.
“Identification and Characterization of a Protostome Homologue of Peropsin from
a Jumping Spider.” Journal of Comparative Physiology. A, Neuroethology,
Sensory, Neural, and Behavioral Physiology 196 (1): 51–59.
Oakley, Todd
H, Markos A Alexandrou, Roger Ngo, M Sabrina Pankey, Celia K C Churchill,
William Chen, and Karl B Lopker. 2014. “Osiris: Accessible and Reproducible
Phylogenetic and Phylogenomic Analyses within the Galaxy Workflow Management
System.” BMC Bioinformatics 15 (July): 230.
Palczewski,
K, T Kumasaka, T Hori, C A Behnke, H Motoshima, B A Fox, I Le Trong, et al.
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Plachetzki,
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