Critical amino acid replacements in the rhodopsin ... - Springer Link

Environ Biol Fish (2015) 98:193–200 DOI 10.1007/s10641-014-0249-4

Critical amino acid replacements in the rhodopsin gene of 19 teleost species occupying different light environments from shallow-waters to the deep-sea Andrea I. Varela & Peter A. Ritchie

Received: 26 August 2013 / Accepted: 24 February 2014 / Published online: 19 March 2014 # Springer Science+Business Media Dordrecht 2014

Abstract Critical amino acid replacements in opsin proteins shift the maximal absorbance of visual pigments to perceive different photic environments (spectral tuning). Here we studied the molecular basis for spectral tuning of the rhodopsin (RH1) pigment in 19 species of marine teleosts inhabiting different light environments, from shallow waters to the deep-sea. We identified replacements at the critical sites 194, 195, 292 and 299, which have been defined relative to the bovine RH1 gene and are known to be involved in shifting the λmax value of RH1 pigments towards the blue light. All the species had the substitutions P194R and H195A. However, we detected a relationship between the combination of amino acids at the critical sites 292 and 299 and the maximum depth of the species under study. The combination 292S/299A was only found in the deep-sea congeners Hoplostethus atlanticus and H. mediterraneus. This may reflects an adaptation of these species to the bathypelagic light environment. All the epipelagic species studied and the epi-mesopelgic species Parapercis colias, had the combination 292A/299S, except Chelidonichthys kumu (292A/299A) and Notolabrus celidotus (292S/299S). It is possible that the combination 292A/299S is an adaptation A. I. Varela : P. A. Ritchie School of Biological Sciences, Victoria University of Wellington, Wellington 6140, New Zealand A. I. Varela (*) Departamento de Biología Marina, Facultad de Ciencias del Mar, Universidad Católica del Norte, Larrondo, 1281 Coquimbo, Chile e-mail: [email protected]

to longer wavelengths of light in comparison with the deeper species. This is the first study in the rhodopsin gene sequence in all the species under study, except for Macruronus novaezelandiae and H. mediterraneus. Keywords RH1 gene . Spectral tuning . Photic environment . Marine fishes

Introduction Within the vast research of visual science, one area of increasing development has been the study of the evolution of fish’s visual systems adapted to see in a range of marine environments (e.g. Levine and MacNichol 1982; Crescitelli 1991; Bowmaker 1995; Douglas et al. 1998; Turner et al. 2009; Larmuseau et al. 2009, 2011). In this sense, the diversity of visual pigments reflects the adaptations of organisms to perceive different photic environments (see Yokoyama 2008). Visual pigments consist of an opsin protein attached to a chromophore via a Schiff base linkage and a conserved lysine residue. The opsin protein in vertebrates is composed of a single polypeptide chain of 340–370 amino acids that forms seven α-helical transmembrane (TM) regions connected by cytoplasmic and luminal loops (Dratz and Hargrave 1983; see Fig. 1 in Bowmaker 1995). Each pigment shows a characteristic peak of maximal absorbance (λmax); the location of this peak depends on the chromophore (11-cis-retinal or 11cis-3,4-dehydroretinal) and the interactions between the chromophore and the specific amino acid sequence of the opsin protein (Bowmaker 1995). In most vertebrates, rod

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photoreceptors are highly sensitive to dim-light and cone photoreceptors mediate vision at higher light intensities (reviewed by Yokoyama 2008). For example, one typical feature in deep-sea fishes is the loss of cone photoreceptors resulting in rod-only retina (see Hunt et al. 2001). In terrestrial environments and in the surface of the oceans, the sun radiation is dominated by photons of the visual spectrum from ultraviolet with wavelengths of ~300 nm, to infrared with wavelengths of ~1,100 nm (Levine and MacNichol 1982; Bowmaker 1995). In clear oceanic waters, the intensity and spectral composition of the light decreases with depth due to absorption by water molecules and suspended particles; the light becomes monochromatic towards blue region of the human visual spectrum (~470 nm), while ultraviolet and infrared light are reduced (Bowmaker 1995; Warrant and Locket 2004). The epipelagic zone from shallow waters up to ~150–200 m receives relatively bright sunlight; further down to about 1,000 m, the mesopelagic zone is characterized by dim-light and bioluminescence (Warrant and Locket 2004). After 1,000 m, in the dark bathypelagic zone, the light comes from organisms with point-source bioluminescent flashes (Warrant and Locket 2004). Over 80 % of the marine species living deeper than 200 m produce some type of bioluminescence, which has a range of uses, including intra- and inter-specific communication, camouflage, startling predators and attracting prey (Douglas et al. 1998). Organisms usually produce blue/green bioluminescence; however, some produce far-red illumination (Douglas et al. 1998; Turner et al. 2009). Many marine fishes have evolved visual pigments adapted to perceive the limited spectrum of light of the environment in which they inhabit (e.g. Levine and MacNichol 1982; Crescitelli 1991; Yokoyama 1999; Yokoyama and Takenaka 2004; Yokoyama et al. 2008, among others). The opsin genes were first isolated and characterized in bovines and later in humans (Nathans and Hogness 1983, 1984). Since then, many opsin genes from a variety of vertebrate species have been studied including the measure of the λmaxs of the corresponding visual pigments (see Yokoyama 2008). Modifications of λmaxs have been suggested as an adaptive strategy to exploit different light environments. These pigments are divided into five groups: rhodopsins (RH1, λmax =~500 nm), RH1-like (RH2, λmax =470−510 nm), short wavelength-sensitive type 1 (SWS1, λmax = 360 − 420 nm), SWS type 2 (SWS2, λmax =440−455 nm), and middle and long wavelength-sensitive (M/LWS, λmax =510−570 nm)

Environ Biol Fish (2015) 98:193–200

(Yokoyama 1999 and references therein). RH1 pigments are usually expressed in rods and the four other classes of pigments in cones (Yokoyama et al. 1999). Particular amino acid changes in the opsin protein shift the λmax values of the visual pigments, enabling a phenomenon known as “spectral tuning” in which a chromophore attains different absorption spectra when attached to different opsins (Yokoyama 2008). The critical amino acid sites (tuning sites) that shift λmax values have been defined relative to the site positions in the bovine RH1 gene. Specific replacements in the opsin protein in many marine fishes shift the λmax values of the RH1 pigments towards the blue to match the spectral quality of oceanic waters (e.g. Yokoyama 1999, 2008; Yokoyama et al. 1999; Hunt et al. 2001; Yokoyama and Takenaka 2004). Hunt et al. (2001) investigated the rhodopsin gene sequence of 28 deep-sea fish species; most of the λmax values of the rod pigments of those species vary from 477 to 490 nm. The aim of this study was to determine critical amino acid replacements that are known to cause a shift in the λmax value of RH1 pigments in species of marine teleosts inhabiting a range of depths and, therefore, different light environments. To achieve this, we sequenced a partial sequence of the rhodopsin gene of 19 species occurring from shallow-waters to the deep-sea. We hypothesized that 1) all the species would have amino acid replacements that are known to be implicated in shift the λmax of RH1 pigments towards the blue, compared with the bovine RH1 gene, and 2) particular amino acid replacements will be correlated with the maximum depth of the species under study.

Materials and methods Sampling and DNA extractions Tissue samples from a total of 127 specimens were obtained from 19 teleost species belonging to 16 families (Table 1). Sample size per species ranged from 2 to 19; sampling areas included New Zealand, Australia, Namibia, Chile, the Mediterranean Sea and the Northeast Atlantic Ocean (Table 1). Muscle samples were collected from fresh fish and frozen at −20 °C or stored in 95 % ethanol. DNA extractions were performed using proteinase K digestion followed by salt extraction (protocol modified from Aljanabi and Martinez 1997). The remaining pellet


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Table 1 Depth range, sample size (n) and sampling area of the 19 teleots species used for partial amplification of the rhodopsin gene. The depth range, scientific and common names were obtained from

FishBase (www.fishbase.org, version 10/2013) and the literature as indicated. Total n=127

Scientific names (Family)

Common names Depth range (m) n

Sampling area

References

Odax pullus (Odacidae)

Butterfish

0–40

5

New Zealand

Trip et al. (2011) NZ Ministry of Fisheries (2011)

Arripis trutta (Arripidae)

Kahawai

10–40

2

New Zealand

Duffy and Petherick (1999) Francis et al. (2002)

Rhombosolea leporina (Pleuronectidae)

Yellowbelly flounder

1–50

3

New Zealand

Ayling and Cox (1982) Glova and Sagar (2000)

Rhombosolea plebeia (Pleuronectidae)

Sand flounder

22–100

3

New Zealand

Ayling and Cox (1982) Glova and Sagar (2000)

Peltorhamphus latus (Pleuronectidae) Latridopsis ciliaris (Latridae) Notolabrus celidotus (Labridae) Chelidonichthys kumu (Triglidae) Pagrus auratus (Sparidae)

Sole

1–100

3

New Zealand

Ayling and Cox (1982)

Blue moki

10–120

5

New Zealand

Smith et al. (2001)

Spotty

0–145

10 New Zealand

Francis et al. (2002)

Red gurnard

1–200

4

New Zealand

Francis et al. (2002)

Snapper

3–200

10 New Zealand

Francis et al. (2002) Stewart (2008)

Trachurus murphyi (Carangidae)

Jack mackerel

20–300

10 Chile

Francis et al. (2002) Bertrand et al. (2004)

Parapercis colias (Pinguipedidae)

Blue cod

5–360

13 New Zealand

Francis et al. (2002) Carbines (2003)

Nemadactylus macropterus (Cheilodactylidae)

Tarakihi

40–400

4

New Zealand

Francis et al. (2002) Thresher et al. (2007)

Seriolella brama (Centrolophidae)

Blue warehou

100–600

4

New Zealand

Francis et al. (2002) Robinson et al. (2008)

Polyprion oxygeneios (Polyprionidae)

Hapuku

50–850

5

New Zealand

Francis et al. (2002) Wakefield et al. (2010)

Macruronus novaezelandiae Hoki (Merlucciidae)

10–900

12 New Zealand, Australia, Chile

Connell et al. (2010) Olavarria et al. (2006)

Kathetostoma giganteum (Uranoscopidae) Pseudophycis bachus (Moridae)

Giant stargazer

12–1000

5

New Zealand

Smith et al. (2006)

Red cod

26–1000

5

New Zealand

Beentjes and Renwick (2001) Francis et al. (2002)

Hoplostethus mediterraneus Silver roughy (Trachichthyidae)

100–1175

5

New Zealand, Mediterranean Sea, NE Atlantic

Francis et al. (2002) Madurell and Cartes (2005)

Hoplostethus atlanticus (Trachichthyidae)

450–1800

19 New Zealand, Australia, Branch (2001) Namibia, Chile, NE Atlantic Francis et al. (2002)

Orange roughy

was washed twice with ethanol and resuspended in 100 μL TE buffer. DNA samples were stored at 4 °C. PCR amplification, DNA sequencing and alignment Six-primer pairs developed for teleost species (Chen et al. 2003) were tested for partial amplification of the rhodopsin gene. Non-specific DNA fragments were observed in gel electrophoresis for all primer pairs. The

primer pair: Rh545-5′-GCAAGCCCATCAGCAACT TCCG-3′ and Rh1073r -5′- CCRCAGCACA RCGTGGTGATCATG-3′ (Chen et al. 2003) was successfully optimized and used in this study. PCR was conducted in 10 μL total volume consisting of ~20 ng of DNA, 1X PCR buffer (160 mM (NH4)2SO4, 670 mM Tris–HCl, 0.1 % stabilizer), 1.5 mM MgCl2, 0.6 μM of each primer, 0.2 mM of each dNTPs, 1.5 U of Taq polymerase, and 0.4 mg mL−1 of

196


Bovine Serum Albumin (BSA). Thermal cycling was performed on an Eppendorf Mastercycler ep gradient S, as follows: Initial denaturing at 95 °C for 2 min, followed by 35 cycles of denaturing at 95 °C for 30 s, annealing at 58 °C for 1 min, extension at 72 °C for 1 min and a final extension at 72 °C for 5 min. PCR products were purified with ExoSAP-IT following the manufacturer’s instructions. The nucleotide sequences were determined using an ABI3730 Genetic Analyzer. The software Geneious 5.1.7 (Biomatters Ltd.) was used to align the sequences using the Geneious alignment option (Drummond et al. 2010). Each species had a unique nucleotide sequence (except for within H. atlanticus, see results). Seven of the 19 species had one or two heterozygous sites (see Table 2). The nucleotide sequence of each species was translated into amino acid sequences using the standard genetic code. The amino acid sequences of the 19 species were aligned to the bovine rhodopsin sequence (Bos taurus, GenBank accession number: NP_001014890) to determine potential sites for spectral tuning.

Results A 477-bp nucleotide fragment was obtained for all 127 individuals analyzed. Sequences were deposited in GenBank under Accession Numbers: JX049165JX049193. There were 177 variable sites among all the samples, but intra-specific variation was low. A few sites in the sequences appeared to be heterozygous in seven species (Table 2). There were no fixed nucleotide differences within each species, except in H. atlanticus at site 190. From the total number of H. atlanticus samples, at site 190 two individuals had cytosine, 11 had thymine (homozygotes) and six were heterozygous (see Table 2). Table 2 Heterozygous positions in the 477-bp nucleotide fragment identified in 14 individuals of seven species. The number of individuals with heterozygous sites per species is indicated by (n)s Species (n)

Positions

Bases

R. leporina (1)

166

A/G

R. plebeia (2)

130–307

C/T–G/T

T. murphyi (1)

37

C/T

P. colias (2)

97–208

C/T–C/T

M. novaezelandiae (1)

121

C/T

P. bachus (1)

205

C/T

H. atlanticus (6)

190

C/T

The translation of the nucleotide sequences into amino acids resulted in a unique amino acid sequence for each species, with a total length of 158 amino acids. An alignment with the bovine reference amino acid sequence was used to identify potential sites for spectral tuning, and it showed that the amino acid sequences obtained started at site 161 and ended at site 318, from the α-helix IV to the luminal loop after α-helix VII. In the total length of the amino acid sequences, 60 sites were variable (Table 3). Among these variable sites, four are known to be involved in shift the λmax value of RH1 pigments. The potential sites for spectral tuning were P194R, H195A, A292S and A299S (the letters represent the code of the amino acid in the bovine/teleost species and the number indicates the site according to the site numbers of the bovine RH1 gene). The critical amino acid changes P194R and H195A were determined for all the teleost species. The change A292S occurred only in Notolabrus celidotus, Hoplostethus mediterraneus and H. atlanticus. The replacement A299S was identified in nine species: Odax pullus, Arripis trutta, Rhombosolea leporina, Rhombosolea plebeia, Peltorhamphus latus, Latridopsis ciliaris, Notolabrus celidotus, Pagrus auratus and Parapercis colias (Table 3). The grouping of the species according to the combination of the critical sites 292 and 299 shows a relationship between the maximum depth of the species and the amino acids at these two sites (polynomial regression, r2 =0.77). The combination 292A/299S was found in species that have a maximum depth of 40–360 m. The combination 292S/299S was only found in N. celidotus, which has a maximum depth of 145 m. The combination 292A/299A was determined for species that have a maximum depth of 200–1,000 m. Finally, the combination 292S/299A was only found in the species capable of reaching depths of 1,175 and 1,800 m, Hoplostethus mediterraneus and H. atlanticus, respectively (Table 4).

Discussion As hypothesized, we detected amino acid replacements in the rhodopsin sequences of 19 species of marine teleosts that are known to be involved in shifting the λmax of RH1 pigments towards the blue light. Hunt et al. (2001), Yokoyama and Takenaka (2004), Yokoyama (2008) and Yokoyama et al. (2008) summarized critical amino acid changes in marine fishes.


197

Table 3 Variable amino acid sites among the 19 teleost species analysed using the bovine (B. taurus) sequence as a reference. The site numbers are those of the bovine RH1 gene. Highlighted sites

1 6 2 Species Bovine V O. pullus L A. trutta V R. leporina F R. plebeia F P. latus F L. ciliaris L N. celidotus F C. kumu T P. auratus T T. murphyi F P. colias L N. macropterus L S. brama L P. oxygeneios L M. novaezelandiae I K. giganteum L P. bachus V H. mediterraneus L H. atlanticus L

1 6 3 M M M G G G M M M M M M M M M M M M M M

1 6 5 L L S C S C S S L M S N C S S N C N C L

1 6 7 C C C C C C C C C C C C C C C S C C C C

1 6 8 A S A A A A A A S A A A A A A A A A S S

1 6 9 A V V V V V V V V A V V V V V A V F V V

1 7 3 V V V L F V V V V V V V V V V V V V V F

1 8 6 S S S S S S S S S S S S S S S S S S A S

1 8 9 I V I V V V V V V I I V V V V I V V I I

1 9 4 P R R R R R R R R R R R R R R R R R R R

1 9 5 H A A A A A A A A A A A A A A A A A A A

1 9 6 E E E E E E E E E E E E E E E A E P P P

indicate changes that are known to cause a shift in the λmax value of the RH1 pigments

1 9 7 E G G G G G G G G G G G G G G G G G G G

1 9 8 T F F F F F F F F F F F F F F Y F I V V

2 0 5 I I I I I V V V I V L I V V I V V I I V

2 0 9 V T V T T V V T T T S C I C I T T V V V

2 1 0 V C C C C C C C C C C C C C C C C C C C

2 1 3 I L L C C C L L M L C M S C S C L T S S

2 1 4 I I I I I I T I T T I T I I I V I V I I

2 1 6 L L L L L L L M L L L L L L L L L L L L

2 1 7 I T L C C I T A T T V T T I T V T T T T

2 1 8 V I V I I I I I I I I V I V V V I V I I

2 1 9 I V V V V V V V I V V V V I V V V I I I

2 2 0 F F F G A G F F F F F F F F F F F F F F

2 2 5 Q R R R R R R R R R R R R R R R R R R R

2 2 7 V L L L L L L L L L L L L L L L L L L L

2 2 8 F C C C C C C C C C C C C C C C C C C C

2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 3 3 3 3 4 4 4 5 5 5 5 6 6 6 7 7 7 7 7 8 8 8 9 9 9 9 9 0 0 0 0 Species 2 5 8 1 5 6 9 0 3 6 0 3 4 7 8 1 2 6 0 2 7 8 9 0 4 8 9 Bovine T K K T I I I A I L G F Y T H S D I I A T S A V V M M O. pullus T R R T V I V G V C G W W T H S E V L A S S S I M C M A. trutta T R R T V I I A V V S W W T H S D V L A S S S I M C M R. leporina T R R T V I I A V V S W Y I N S D L I A S S S I L L M R. plebeia T R R T V I I A V V S W Y I N S D L I A S S S I L L M P. latus T R R T V I I A V V S W Y I N S D L I A S S S I L F M L. ciliaris T R R T V L I A V C G W Y T H S E V F A S S S I M C M N. celidotus T R R T V I I A V V G W W T H S E V I S S S S I M C M C. kumu T R R S V I I A V V S W Y L N S E V I A S S A V M C M P. auratus T R R T V L I A V I S W W T H S E V I A S S S I M C M T. murphyi T R R T V I V A V C G W F T H S E V I A S S A I M C M P. colias T R R T V L I A V C G W W T H S E V I A S S S I M C M N. macropterus T R R T V I I G V C G W F T H S E V F A S S A I M C M S. brama T R R T V I I G V V S W F T H S E V V A S S A I M C M P. oxygeneios T R R S V L V A V L G W W T H S E V V A S S A I M C M M. novaezelandiaeT R R T I I I G I C G W F T H I T L V A A A A V M C L K. giganteum T R R T V L I A V L G W W T N S E V I A S S A I M C M P. bachus T R R T I I V G V C G W F T H S T V I A S A A I M C L H. mediterraneus S R R T V L I A I L S W Y T H S E V L S S S A I M C M H. atlanticus S R R S V L I A I L G W Y T H S E V I S S S A I L F M A alanine, C cysteine, D aspartic acid, E glutamic acid, F phenylalanine, G glycine, H histidine, I isoleucine, K lysine, methionine, N asparagine, P proline, Q glutamine, R arginine, S serine, T threonine, V valine, W tryptophan, Y tyrosine

Hunt et al. (2001) determined that a specific λmax value is not always explained by a particular set of amino acid substitutions; rather, the same λmax value results from different combinations of amino acids at specific sites. In the present study, all the species had the substitutions P194R, H195A which decreases the λmax of RH1 pigments (Yokoyama et al. 2008); however, the combination of the replacements P194R, H195A and A292S was only found in three species: N. celidotus, H. mediterraneus and H. atlanticus (but N. celidotus differed from H. mediterraneus and H. atlanticus in the

2 2 9 T A A A A A A A A A A A A A A A A A A A

2 3 6 Q A A A A A A A A A A A A A A A A A A A

2 4 1 A E E E E E E E E E E E E E E E E E E E

3 3 3 1 1 1 1 5 8 K N V K H I K Q I K H I K H I K H I K H I K N I K T I K H I K H I K H I K H I K N I K H I K H I K N I K H I K N I R N I L leucine, M

critical amino acid site 299, which is discussed further below). The combination 194R/195A/292S decreases the λmax value of the RH1 pigment by 14–20 nm (Yokoyama 2008); and for a fish of the family Congridae this combination resulted in a λmax value of 486 nm (Yokoyama 2008). The same decrease in the λmax value could be achieved by the combination 83 N/ 292S and by a unique replacement at site 122 (E122Q) (Yokoyama 2008). Because the sequences that we obtained started at site 161, it could not been ruled out that the same functional change is presented by some of the

198


Table 4 Grouping of the 19 teleost species according to the combination at the critical sites 292 and 299. The maximum depth recorded for each species is indicated Critical sites

Species

Max depth (m)

292A/299S

O. pullus

40

A. trutta

40

R. leporina

50

R. plebeia

100

P. latus

100

L. ciliaris

120

P. auratus

200

P. colias

360

292S/299S

N. celidotus

145

292A/299A

C. kumu

200

T. murphyi

300

N. macropterus

400

S. brama

600

P. oxygeneios

850

M. novaezelandiae

900

K. giganteum

1,000

P. bachus

1,000

H. mediterraneus

1,175

H. atlanticus

1,800

292S/299A

other species studied. The replacement A292S was already detected in H. mediterraneus by Hope et al. (1997). Other marine fishes living at depths of more than 200 m had the substitution A292S, such as the coelacanth, Latimeria chalumnae (Yokoyama et al. 1999). Also, Hunt et al. (2001) detected this replacement in 18 deep-sea teleosts from six different orders: Beryciformes, Ophidiiformes, Gadiformes, Aulopiformes, Stomiiformes and Osmeriformes. The same replacement has also been detected in species living in shallower waters. Yokoyama and Takenaka (2004) found the A292S change in three species of squirrelfishes inhabiting depths of less than 70 m, and it was also detected in the bottlenose dolphin, Tursiops truncatus (Fasick and Robinson 1998). Mutation experiments in the bovine rod pigment performed by Fasick and Robinson (1998) indicated that the change A292S alone is capable of shifting the λmax value by 10 nm towards the blue. Another site involved in shortwave shifts is the site 299 (Fasick and Robinson 1998; Hunt et al. 2001). As stated before, the deep-sea species H. atlanticus and H. mediterraneus and the epipelagic species N. celidotus had the change A292S; however,

the combination 292S/299A was only found in the deepsea species, instead, N. celidotus presented the combination 292S/299S. Hunt et al. (2001) noted that the combination 292S/299A in H. mediterraneus was related to a λmax value of 479 nm, but a higher λmax value of 485 nm was detected in Anoplogaster cornuta, which has the combination 292S/299S. Similarly, studying the rod visual pigments of mysticete whales, Bischoff et al. (2012) determined that the combination 83 N/292S/ 299A was related to a λmax value of 479 nm, whereas the combination 83 N/292S/299S resulted in a λmax value of 484 nm. Considering the findings of Hunt et al. (2001) and Bischoff et al. (2012), it is likely that the amino acids found at the critical sites 292 and 299 result in a shorter λmax value of the RH1 pigments in H. atlanticus and H. mediterraneus in comparison with N. celidotus; which may be an adaptation to the bathypelagic light environment. It is worth noting that the combination 292S/299A detected here in H. atlanticus and H. mediterraneus was also found by Hunt et al. (2001) in species that have a maximum depth of ~600– 5,000 m (recorded maximum depths were obtained from www.fishbase.org, version 10/2013). Moreover, our second hypothesis was supported by a relationship between the combination of the amino acids at the critical sites 292 and 299 and the maximum depth of the species studied. Interestingly, we found that all the epipelagic species and the epi-mesopelgic species P. colias, had the combination 292A/299S. The exceptions were Chelidonichthys kumu (292A/299A), and, as previous stated, N. celidotus (292S/299S). The combination 83 N/292A/299S was detected in the rhodopsin sequence of mysticete whales with a λmax value of 493 nm (Bischoff et al. 2012). Therefore, it is likely that the combination 292A/299S detected here in most of the epipelagic species is related to an adaptation to longer wavelengths of light in comparison with the deeper species. To the best of our knowledge, this is the first study to determine partial rhodopsin sequences in all the species under study, except for Macruronus novaezelandiae (Prado et al., unpublished data at GenBank number: FR832604) and H. mediterraneus (Hope et al. 1997; Chen et al. 2003). Further studies about the molecular basis of rod pigments in the species studied here should attempt to obtain a larger or complete rhodopsin sequence to identify if there are other replacements at critical sites that have been shown to be involved in spectral tuning in marine fishes (e.g. sites 83, 122, 124, 132). These data


will also allow for an investigation of the combinations at different critical sites that correlate with depth distribution. To better understand how these and potentially other critical amino acid replacements are involved in the visual adaptations of these species, it is also necessary to determine the λmax value of their rod pigments. This is important because the maximal absorbance of visual pigments might closely correlate with the wavelengths of light at which animals can see.

Conclusion In summary, we identified four critical amino acid changes in partial rhodopsin sequences of 19 teleost species that are involved in the spectral tuning of rod pigments. Hoplostethus atlanticus presented the same amino acid combination at the critical sites 292 and 299 already reported for H. mediterraneus, which was not found in any of the other species studied. This may reflect an adaptation to the dim-light available in the bathypelagic environment. Moreover, we detected a relationship between the combination of the amino acids at these two sites and the maximum depth of the species under study. Acknowledgments This work was carried out under a PhD scholarship awarded to A. I. Varela by CONICYT (Comisión Nacional de Investigación Científica y Tecnológica, Gobierno de Chile) and Victoria University of Wellington. Our research was conducted in accordance with the guidelines set by the Victoria University Animal Ethics Committee. We thank Milan Barbarich and Khush Mistry from Anton’s Seafoods Ltd, Jim Fitzgerald from Sanford Ltd, and to Kris Ramm, Ministry of Fisheries Observer, for assisting with H. atlanticus sample collection in Northern New Zealand. Hoplostethus atlanticus samples from around central and southern New Zealand and H. mediterraneus samples were provided by Peter Smith from a frozen tissue collection held at NIWA. Edwin Niklitschek, Universidad de Los Lagos, Chile, Jamie Coughlan, University College Cork, Ireland and Sergio Stefanni, University of the Azores, Portugal provided H. atlanticus samples from Chile and the Northeast Atlantic Ocean, respectively. Samples from all the other fish species used in this study were provided by students/associates at Victoria University of Wellington: Hayden Smith, Heather Constable, Sebastien Rioux Paquette, Jack Du, Henry Lane, David Ashton and Brenton Hodgson.

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