Rod Monochromacy and the Coevolution of Cetacean Retinal Opsins

JGM Thewissen, 2001, Whale origins as a poster child for macroevolution, BioScience, 51, 1037, 10.1641/0006-3568(2001)051[1037:WOAAPC]2.0.CO;2

JGM Thewissen, 2009, From land to water: the origin of whales, dolphins, and porpoises, Evo Edu Outreach, 2, 272, 10.1007/s12052-009-0135-2

MD Uhen, 2010, The origin(s) of whales, Annu Rev Earth Planet Sci, 38, 189, 10.1146/annurev-earth-040809-152453

J Gatesy, 2013, A phylogenetic blueprint for a modern whale, Mol Phylogenet Evol, 66, 479, 10.1016/j.ympev.2012.10.012

Y Li, 2010, The hearing gene <italic>Prestin</italic> unites echolocating bats and whales, Curr Biol, 20, R55, 10.1016/j.cub.2009.11.042

Y Liu, 2010, Cetaceans on a molecular fast track to ultrasonic hearing, Curr Biol, 20, 1834, 10.1016/j.cub.2010.09.008

KTJ Davies, 2012, Parallel signatures of sequence evolution among hearing genes in echolocating mammals: an emerging model of genetic convergence, Heredity, 108, 480, 10.1038/hdy.2011.119

MR McGowen, 2011, Phylogeny and adaptive evolution of the brain-development gene microcephalin (<italic>MCPH1</italic>) in cetaceans, BMC Evol Biol, 11, 98, 10.1186/1471-2148-11-98

S Xu, 2012, Positive selection at the ASPM gene coincides with brain size enlargements in cetaceans, Proc R Soc B, 279, 4433, 10.1098/rspb.2012.1729

Z Wang, 2009, Adaptive evolution of 5′HoxD genes in the origin and diversification of the cetacean flipper, Mol Biol Evol, 26, 613, 10.1093/molbev/msn282

T Kishida, 2007, The olfactory receptor gene repertoires in secondary-adapted marine vertebrates: evidence for reduction of the functional proportions in cetaceans, Biol Lett, 3, 428, 10.1098/rsbl.2007.0191

MR McGowen, 2008, The vestigial olfactory receptor subgenome of odontocete whales: phylogenetic congruence between gene-tree reconciliation and supermatrix methods, Syst Biol, 57, 574, 10.1080/10635150802304787

S Hayden, 2010, Ecological adaptation determines functional mammalian olfactory subgenomes, Genome Res, 20, 1, 10.1101/gr.099416.109

P Jiang, 2012, Major taste loss in carnivorous mammals, Proc Natl Acad Sci USA, 109, 4956, 10.1073/pnas.1118360109

TA Deméré, 2008, Morphological and molecular evidence for a stepwise evolutionary transition from teeth to baleen in mysticete whales, Syst Biol, 57, 15, 10.1080/10635150701884632

RW Meredith, 2009, Molecular decay of the tooth gene enamelin (<italic>ENAM</italic>) mirrors the loss of enamel in the fossil record of placental mammals, PLoS Genet, 5, e1000634, 10.1371/journal.pgen.1000634

RW Meredith, 2011, Pseudogenization of the tooth gene enamelysin (<italic>MMP20</italic>) in the common ancestor of extant baleen whales, Proc Roy Soc Lond B, 278, 993, 10.1098/rspb.2010.1280

L Yu, 2010, Characterization of <italic>TRPC2</italic>, an essential genetic component of VNS chemoreception, provides insights into the evolution of pheromonal olfaction in secondary-adapted marine mammals, Mol Biol Evol, 27, 1467, 10.1093/molbev/msq027

U Griebel, 2003, Colour vision in aquatic mammals - facts and open questions, Aquat Mamm, 29, 18, 10.1578/016754203101024040

WN McFarland, 1971, Cetacean visual pigments, Vision Res, 11, 1065, 10.1016/0042-6989(71)90113-1

JI Fasick, 2011, Estimated absorbance spectra of the visual pigments of the North Atlantic right whale (<italic>Eubalaena glacialis</italic>), Mar Mamm Sci, 27, E321, 10.1111/j.1748-7692.2011.00467.x

WIL Davies, 2012, Molecular ecology and adaptation of visual photopigments in craniates, Mol Ecol, 21, 3121, 10.1111/j.1365-294X.2012.05617.x

DH Levenson, 2003, Genetic evidence for the ancestral loss of SWS cone pigments in mysticete and odontocete cetaceans, Proc Roy Soc London B, 270, 673, 10.1098/rspb.2002.2278

L Peichl, 2005, Diversity of mammalian photoreceptor properties: adaptations to habitat and lifestyle, Anat Rec, 287A, 1001, 10.1002/ar.a.20262

N Bischoff, 2012, Deep-sea and pelagic rod visual pigments identified in the mysticete whales, Vis Neurosci, 29, 95, 10.1017/S0952523812000107

L Peichl, 2001, For whales and seals the ocean is not blue: A visual pigment loss in marine mammals, Eur J Neurosci, 13, 1520, 10.1046/j.0953-816x.2001.01533.x

LA Newman, 2005, Cone visual pigments of aquatic mammals, Vis Neurosci, 22, 873, 10.1017/S0952523805226159

H Zhao, 2009, Rhodopsin molecular evolution in mammals inhabiting low light environments, PLoS ONE, 4, e8326, 10.1371/journal.pone.0008326

JH Geisler, 2009, Hippopotamus and whale phylogeny, Nature, 458, E1, 10.1038/nature07776

M Spaulding, 2009, Relationships of Cetacea (Artiodactyla) among mammals: increased taxon sampling alters interpretations of key fossils and character evolution, PLoS ONE, 4, e7062, 10.1371/journal.pone.0007062

J Gatesy, 1996, Evidence from milk casein genes that cetaceans are close relatives of hippopotamid artiodactyls, Mol Biol Evol, 13, 954, 10.1093/oxfordjournals.molbev.a025663

J Gatesy, 1997, More DNA support for a Cetacea/Hippopotamidae clade: the blood-clotting protein gene gamma-fibrinogen, Mol Biol Evol, 14, 537, 10.1093/oxfordjournals.molbev.a025790

PD Gingerich, 2001, Origin of whales from early artiodactyls: hands and feet of Eocene Protocetidae from Pakistan, Science, 293, 2239, 10.1126/science.1063902

JGM Thewissen, 2001, Skeletons of terrestrial cetaceans and the relationship of whales to artiodactyls, Nature, 413, 277, 10.1038/35095005

JGM Thewissen, 2007, Whales originated from aquatic artiodactyls in the Eocene epoch of India, Nature, 450, 1190, 10.1038/nature06343

S Yokoyama, 2008, Evolution of dim-light and color vision pigments, Annu Rev Genomics Hum Genet, 9, 259, 10.1146/annurev.genom.9.081307.164228

JH Geisler, 2011, A supermatrix analysis of genomic, morphological, and paleontological data from crown Cetacea, BMC Evol Biol, 11, 112, 10.1186/1471-2148-11-112

Reuter T, Peichl L (2008) Structure and function of the retina in aquatic tetrapods. In: Thewissen JGM, Nummela S, eds. Sensory evolution on the threshold: adaptations in secondarily aquatic vertebrates. Berkeley and Los Angeles, California: Univ California Press. pp 149–174.

BE Bloodworth, 2008, <italic>Kogia breviceps</italic> (Cetacea: Kogiidae), Mamm Species, 819, 1, 10.1644/819.1

RE Fordyce, 1994, <italic>Waipatia maerewhenua</italic>, new genus and new species (Waipatiidae, new family), an archaic late Oligocene dolphin (Cetacea: Odontoceti: Platanistoidea) from New Zealand, Proc San Diego Soc Nat Hist, 29, 147, 10.5962/bhl.part.10662

JH Geisler, 2003, Morphological evidence for the phylogeny of Cetacea, J Mammal Evol, 10, 23, 10.1023/A:1025552007291

MR McGowen, 2009, Divergence date estimation and a comprehensive molecular tree of extant cetaceans, Mol Phylogenet Evol, 53, 891, 10.1016/j.ympev.2009.08.018

ME Steeman, 2009, Radiation of extant cetaceans driven by restructuring of the oceans, Syst Biol, 58, 573, 10.1093/sysbio/syp060

M Nozawa, 2009, Reliabilities of identifying positive selection by the branch-site and the site-prediction methods, Proc Natl Acad Sci USA, 106, 6700, 10.1073/pnas.0901855106

Z Yang, 2007, PAML 4: a program package for phylogenetic analysis by maximum likelihood, Mol Biol Evol, 24, 1586, 10.1093/molbev/msm088

Z Yang, 2005, Bayes empirical Bayes inference of amino acid sites under positive selection, Mol Biol Evol, 22, 1107, 10.1093/molbev/msi097

J Zhang, 2005, Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level, Mol Biol Evol, 22, 2472, 10.1093/molbev/msi237

Z Yang, 2009, In defense of statistical methods for detecting positive selection, Proc Natl Acad Sci USA, 106, E95, 10.1073/pnas.0904550106

T Sugawara, 2010, Vertebrate rhodopsin adaptation to dim light via rapid meta-II intermediate formation, Mol Biol Evol, 27, 506, 10.1093/molbev/msp252

AJ Rader, 2004, Identification of core amino acids stabilizing rhodopsin, Proc Natl Acad Sci USA, 101, 7246, 10.1073/pnas.0401429101

U Gether, 1997, Agonists induce conformational changes in transmembrane domains III an VI of the β₂ adrenoceptor, EMBO J, 16, 6737, 10.1093/emboj/16.22.6737

Walls GL (1942) The vertebrate eye and its adaptive radiation. Bloomfield Hills, Michigan: Cranbrook Institute of Science.

HH Woollard, 1927, The differentiation of the retina in the primates, Proc Zool Soc Lond, 97, 1, 10.1111/j.1096-3642.1927.tb02243.x

HH Woollard, 1927, The comparative anatomy of the lateral geniculate body, J Anat, 61, 414

SR Detwiler, 1941, The eye of the owl monkey (<italic>Nyctipithecus</italic>), Anat Rec, 80, 233, 10.1002/ar.1090800209

SR Detwiler, 1941, Some biological aspects of vision, Sigma Xi Quart, 29, 112

SR Detwiler, 1956, The eye and its structural adaptations, Am Sci, 44, 45

K Nagao, 2005, Coupling and decoupling of evolutionary mode between X- and Y-Chromosomal red-green opsin genes in owl monkeys, Gene, 352, 32, 10.1016/j.gene.2005.04.008

Y Tan, 2005, Evidence from opsin genes rejects nocturnality in ancestral primates, Proc Natl Acad Sci USA, 102, 14712, 10.1073/pnas.0507042102

B Müller, 2007, Cone photoreceptor diversity in the retinas of fruit bats (Megachiroptera), Brain Behav Evol, 70, 90, 10.1159/000102971

JK Bowmaker, 2008, Evolution of vertebrate visual pigments, Vision Res, 48, 2022, 10.1016/j.visres.2008.03.025

EB Kim, 2011, Genome sequencing reveals insights into physiology and longevity of the naked mole rat, Nature, 479, 223, 10.1038/nature10533

GH Jacobs, 1992, Cone photopigments in nocturnal and diurnal procyonids, J Comp Physiol A, 171, 351, 10.1007/BF00223965

GH Jacobs, 1993, Photopigments and color vision in the nocturnal monkey, <italic>Aotus</italic>, Vision Res, 33, 1773, 10.1016/0042-6989(93)90168-V

GH Jacobs, 1996, Mutations in S-cone pigment genes and the absence of colour vision in two species of nocturnal primate, Proc Royal Soc London B, 263, 705, 10.1098/rspb.1996.0105

DF Deegan II, 1996, Spectral sensitivity and photopigments of a nocturnal prosimian, the bushbaby (<italic>Otolemur crassicaudatus</italic>), Am J Primatol, 40, 55, 10.1002/(SICI)1098-2345(1996)40:1<55::AID-AJP4>3.0.CO;2-#

L Peichl, 1998, Absence of short-wavelength sensitive cones in the retinae of seals (Carnivora) and African giant rats (Rodentia), Eur J Neurosci, 10, 2586, 10.1046/j.1460-9568.1998.00265.x

MA Crognale, 1998, Cone spectral sensitivity in the harbor seal (<italic>Phoca vitulina</italic>) and implications for color vision, Can J Zool, 76, 2114, 10.1139/z98-129

S Kawamura, 2004, Ancestral loss of short wave-sensitive cone visual pigment in Lorisiform prosimians, contrasting with its strict conservation in other prosimians, J Mol Evol, 58, 314, 10.1007/s00239-003-2553-z

LPS Carvalho, 2006, Shortwave visual sensitivity in tree and flying squirrels reflects changes in life style, Curr Biol, 16, R81, 10.1016/j.cub.2006.01.045

GH Jacobs, 2009, Evolution of colour vision in mammals, Phil Trans R Soc B, 364, 2957, 10.1098/rstb.2009.0039

U Griebel, 2002, Spectral sensitivity and color vision in the bottlenose dolphin (<italic>Tursiops truncatus</italic>), Mar Fresh Behav Physiol, 35, 129, 10.1080/1023624021000014716

JC Partridge, 1989, Interspecific variation in the visual pigments of deep-sea fishes, J Comp Physiol A, 164, 513, 10.1007/BF00610445

H Ripps, 1991, Structural features and adaptive properties of photoreceptors in the skate retina, J Exp Zool, Suppl 5, 46

RH Douglas, 1995, Visual and lenticular pigments in the eyes of demersal deep-sea fishes, J Comp Physiol A, 177, 111, 10.1007/BF00243403

J O'Brien, 1997, Molecular cloning of a rod opsin cDNA from the skate retina, Gene, 193, 141, 10.1016/S0378-1119(97)00079-6

A Bozzano, 2001, The photoreceptor system in the retinae of two dogfishes, <italic>Scyliorhinus canicula</italic> and <italic>Galeus melastomus</italic>: possible relationship with depth distribution and predatory lifestyle, J Fish Biol, 59, 1258, 10.1111/j.1095-8649.2001.tb00190.x

A Bozzano, 2004, Retinal specialisations in the dogfish Centroscymnus coelolepis from the Mediterranean deep-sea, Scientia Marina, 68, 185, 10.3989/scimar.2004.68s3185

NS Hart, 2011, Microspectrophotometric evidence for cone monochromacy in sharks, Naturwissenschaften, 98, 193, 10.1007/s00114-010-0758-8

TJ Lisney, 2012, Vision in elasmobranchs and their relatives: 21^st century advances, J Fish Biol, 80, 2024, 10.1111/j.1095-8649.2012.03253.x

NL Schieber, 2012, Comparative retinal anatomy in four species of elasmobranch, J Morphol, 273, 423, 10.1002/jmor.11033

SM Mohun, 2010, Identification and characterization of visual pigments in caecilians (Amphibia: Gymnophiona), an order of limbless vertebrates with rudimentary eyes, J Exp Biol, 213, 3586, 10.1242/jeb.045914

M Kos, 2001, Immunocytochemical demonstration of visual pigments in the degenerate retinal and pineal photoreceptors of the blind cave salamander (Proteus anguinus), Cell Tissue Res, 303, 15, 10.1007/s004410000298

JF Schreer, 1997, Allometry of diving capacity in air-breathing vertebrates, Can J Zool, 75, 339, 10.1139/z97-044

S Panigada, 1999, How deep can baleen whales dive?, Mar Ecol Prog Ser, 187, 309, 10.3354/meps187309

M Amano, 2003, Sperm whale diving behavior monitored using a suction-cup-attached TDR tag, Mar Ecol Prog Ser, 258, 291, 10.3354/meps258291

DA Croll, 2005, From wind to whales: trophic links in a coastal upwelling system, Mar Ecol Prog Ser, 289, 117, 10.3354/meps289117

SL Watwood, 2006, Deep-diving foraging behavior of sperm whales (<italic>Physeter macrocephalus</italic>), J Anim Ecol, 75, 814, 10.1111/j.1365-2656.2006.01101.x

Jerlov NG (1968) Optical oceanography. Amsterdam, The Netherlands: Elsevier Sci Publ Co.

EJ Warrant, 2004, Vision in the deep sea, Biol Rev, 79, 671, 10.1017/S1464793103006420

Y Fu, 2008, Quantal noise from human red cone pigment, Nature Neurosci, 11, 565, 10.1038/nn.2110

DR Lindberg, 2007, Things that go bump in the night: evolutionary interactions between cephalopods and cetaceans in the tertiary, Lethaia, 40, 335, 10.1111/j.1502-3931.2007.00032.x

C Ware, 2010, Shallow and deep lunge feeding of humpback whales in fjords of the West Antarctic Peninsula, Mar Mamm Sci, 27, 587, 10.1111/j.1748-7692.2010.00427.x

JA Goldbogen, 2011, Mechanics, hydrodynamics and energetics of blue whale lunge feeding: efficiency dependence on krill density, J Exp Biol, 214, 131, 10.1242/jeb.048157

Rambaut A (1996) Se-Al: sequence alignment editor, version 2.0a11. Available: <ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://tree.bio.ed.ac.uk/software/seal/" xlink:type="simple">http://tree.bio.ed.ac.uk/software/seal/</ext-link>.

A Stamatakis, 2006, RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models, Bioinformatics, 22, 2688, 10.1093/bioinformatics/btl446

Gatesy J (2009) Whales and even-toed ungulates (Cetartiodactyla). In: Hedges SB, Kumar S, eds. The timetree of life. Oxford, UK: Oxford Univ Press. pp 511–515.

Maddison WP, Maddison DR (2010) Mesquite: a modular system for evolutionary analysis, version 2.73. Available: <ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://mesquiteproject.org" xlink:type="simple">http://mesquiteproject.org</ext-link>.

JI Fasick, 1998, Mechanism of spectral tuning in the dolphin visual pigments, Biochemistry, 37, 433, 10.1021/bi972500j

Z Yang, 2011, Statistical properties of the branch-site test of positive selection, Mol Biol Evol, 28, 1217, 10.1093/molbev/msq303

RW Meredith, 2011, Impacts of the Cretaceous terrestrial revolution and KPg extinction on mammal diversification, Science, 334, 521, 10.1126/science.1211028