Evolution of ultraviolet vision in shorebirds (Charadriiformes)

Abstract

Diurnal birds belong to one of two classes of colour vision. These are distinguished by the maximum absorbance wavelengths of the SWS1 visual pigment sensitive to violet (VS) and ultraviolet (UVS). Shifts between the classes have been rare events during avian evolution. Gulls (Laridae) are the only shorebirds (Charadriiformes) previously reported to have the UVS type of opsin, but too few species have been sampled to infer that gulls are unique among shorebirds or that Laridae is monomorphic for this trait. We have sequenced the SWS1 opsin gene in a broader sample of species. We confirm that cysteine in the key amino acid position 90, characteristic of the UVS class, has been conserved throughout gull evolution but also that the terns Anous minutus, A. tenuirostris and Gygis alba, and the skimmer Rynchops niger carry this trait. Terns, excluding Anous and Gygis, share the VS conferring serine in position 90 with other shorebirds but it is translated from a codon more similar to that found in UVS shorebirds. The most parsimonious interpretation of these findings, based on a molecular gene tree, is a single VS to UVS shift and a subsequent reversal in one lineage.

1. Introduction

There is a categorical, physiological difference in colour vision between groups of diurnal birds (Cuthill et al. 2000). These have short-wavelength sensitive type 1 (SWS1) cone-opsin-based visual pigments of either an ultraviolet sensitive (UVS) type with maximum absorbance wavelengths (λ_max) between 355 and 380 nm or a violet sensitive (VS) type with λ_max between 402 and 426 nm (reviewed by Ödeen et al. 2009). The VS type appears to be ancestral (Yokoyama 2002) and phylogenetically most widespread (Ödeen & Håstad 2003) in birds. Independent shifts to UVS may have occurred only three or four times (Håstad et al. 2009): in shorebirds (Charadriiformes), in a common ancestor of passerines and psittaciforms, in Rhea americana and possibly in trogons (Carvalho et al. 2007). Gulls are the only shorebirds reported to be UVS—demonstrated through the presence of cysteine in amino acid (aa) position 90 (bovine rod opsin numbering) in their SWS1 opsin gene and ocular media with spectral transmission similar to that of other UVS birds (Ödeen & Håstad 2003; Håstad et al. 2005, 2009).

There is an increased cost of UV transmittance owing to photo-oxidation of the retina (e.g. Boulton et al. 2001), making the presence of UV tuning in gulls rather puzzling. Unlike other UVS birds, no selective advantage of UV vision has been demonstrated in gulls, whether for detecting sexual signals (e.g. Bennett et al. 1997) or foraging (e.g. Church et al. 1998). It has been suggested to allow eavesdropping on UV communication in schools of fish swimming close to the surface (Ödeen & Håstad 2003) but evidence seems weak. All auks, waders and terns investigated so far have SWS1 opsins of the VS type (Håstad et al. 2005), and some, especially terns, are ecologically similar to gulls. However, too few species have been sampled to safely infer that no other charadriiforms have UV-tuned visual pigments, or that this character state does not vary within Laridae.

The SWS1 λ_max pigments in avian retinae closely follows aa sequence variation in the SWS1 opsin gene. In vitro studies have demonstrated that λ_max can be predicted on the basis of the opsin's aa sequence (Wilkie et al. 2000; Yokoyama et al. 2000; Carvalho et al. 2007). The cone sensitivity can then be estimated from the opsin sequence, owing to covariance between the visual pigment's λ_max and the spectral absorptance properties of the cone oil droplets (Hart & Vorobyev 2005). As spectral tuning of the SWS1 single cone is under direct genetic control, it becomes possible to identify the type of short-wavelength sensitivity in a bird from a sample of genomic DNA. This method was conceived by Ödeen & Håstad (2003) and validated by Ödeen et al. (2009). We have used it here to search for gross differences in colour vision in a significantly widened sample of gulls and other shorebirds. The aim has been to assess how stable the SWS1 pigment sensitivity has been during the evolution of shorebirds in general and gulls in particular. As the basis for this analysis, we have inferred a phylogeny, mainly using GenBank sequence data.

2. Material and methods

We studied a broad selection of species in the order Charadriiformes (table 1) with special emphasis on including a representative sample of various Laridae taxa. We sequenced a fragment of the SWS1 opsin gene containing the aa residues of positions 84–94 in up to six species each of seven shorebird families (table 1). We estimated λ_max from three key positions, as outlined by Ödeen et al. (2009).

Table 1.

SWS1 opsin gene fragments from shorebirds. The spectral tuning amino acid (aa) sites 86, 90 and 93 are marked in bold. Type of SWS1 opsin is either VS (violet sensitive) or UVS (UV-sensitive), as predicted from the gene fragment aa sequences. NRM, Swedish Museum of Natural History; LSUMZ, LSU Museum of Natural Science; UWBM, Burke Museum, University of Washington; ZMUC, Zoological Museum, University of Copenhagen.

family	species	common name	aa seq. 84–94	aa90 codon	type	unknown effect	origin/voucher no.	tissue no.	GenBank acc. no.	reference
Scolopacidae	Tringa glareola	Wood Sandpiper	FIACIFSVFTV	agc	VS		Department of Animal Ecology, U. U.	031218-2	GU129664	this study
	Actitis hypoleucos	Common Sandpiper	FIACIFSVFTV	agc	VS				AY960716	Håstad et al. (2005)
	Phalaropus fulicarius	Red Phalarope	FIACIFSVFTV	agc	VS				AY960718	Håstad et al. (2005)
	Gallinago gallinago	Common Snipe	FIACIFSVFTV	agc	VS				AY960717	Håstad et al. (2005)
	Philomachus pugnax	Ruff	FIACIFSVFTV	agc	VS		F. Widemo	11 individuals	GU129665	this study
Thinocoridae	Thinocorus orbignyianus	Grey-breasted Seedsnipe	FIACIFSVFTV	agc	VS		UWBM 54407	DAB 808	GU129666	this study
Laridae	Larus atlanticus	Olrog's Gull	FIICVFCISIV	tgc	UVS	Ile86, 93	P. Yorio, J.-M. Pons		GU129667	this study
	Larus marinus	Great Black-backed Gull	FIICVFCISIV	tgc	UVS	Ile86, 93			AY227162	Ödeen & Håstad (2003)
	Larus argentatus	European Herring Gull	FIICVFCISIV	tgc	UVS	Ile86, 93			AY227160	Ödeen & Håstad (2003)
	Larus michahellis	Yellow-legged Gull	FIICVFCISIV	tgc	UVS	Ile86, 93			FJ790325	Håstad et al. (2009)
	Larus fuscus	Lesser Black-backed Gull	FIICVFCISIV	tgc	UVS	Ile86, 93			AY227161	Ödeen & Håstad (2003)
	Ichthyaetus hemprichii	Sooty Gull	FIICVFCISIV	tgc	UVS	Ile86, 93			AY960710	Håstad et al. (2005)
	Leucophaeus pipixcan	Franklin's Gull	FIICVFCISIV	tgc	UVS	Ile86, 93	UWBM 80595	CSW 6795	GU129668	this study
	Chroicocephalus hartlaubii	Hartlaub's Gull	FIICVLCISIV	tgc	UVS	Ile86, 93			AY960709	Håstad et al. (2005)
	Chroicocephalus ridibundus	Black-headed Gull	FIICVLCISIV	tgc	UVS	Ile86, 93			AY960711	Håstad et al. (2005)
	Rhodostethia rosea	Ross's Gull	FVICVFCISLV	tgc	UVS	Ile86, Leu93	ZMUC 139640		GU129669	this study
	Rissa tridactyla	Black-legged Kittiwake	FIICVFCISIV	tgc	UVS	Ile86, 93			AY960712	Håstad et al. (2005)
	Pagophila eburnea	Ivory Gull	FIICVFCISIV	tgc	UVS	Ile86, 93	ZMUC 132130		GU129670	this study
	Xema sabini	Sabine's Gull	FIICVFCISIV	tgc	UVS	Ile86, 93	LSUMZ B-4066		GU129671	this study
	Creagrus furcatus	Shallow-tailed Gull	FIICVFCISIV	tgc	UVS	Ile86, 93	LSUMZ B-15450		GU129672	this study
Rynchopidae	Rynchops niger	Black Skimmer	FVACVFCIFTV	tgc	UVS		LSUMZ B-2457		GU129673	this study
Sternidae	Anous minutus	Black Noddy	FIACIFCIFTV	tgc	UVS		ZMUC 137802		GU129674	this study
	Anous tenuirostris	Lesser Noddy	FIACIFCIFTV	tgc	UVS		ZMUC 113339		GU129675	this study
	Onychoprion anaethetus	Bridled Tern	FVTCVFSIFTV	tcc	VS	Thr86	ZMUC 112708		GU129676	this study
	Onychoprion fuscatus	Sooty Tern	FVTCVFSIFTV	tcc	VS	Thr86	ZMUC 113320		GU129677	this study
	Gygis alba	White Tern	FIACIFCIFTV	tgc	UVS		ZMUC 113340		GU129678	this study
	Sternula albifrons	Little Tern	FVTCIFSIFTV	tcc	VS	Thr86	NRM 20076398		GU129679	this study
	Chlidonias niger	Black Tern	FVTCIFSIFTV	tcc	VS	Thr86	NRM 20066936		GU129680	this study
	Chlidonias hybrida	Whiskered Tern	FVTCIFSIFTV	tcc	VS	Thr86	ZMUC 131916		GU129681	this study
	Sterna hirundo	Common Tern	FVTCIFSIFTV	tcc	VS	Thr86	Department of Animal Ecology, U. U.	031218-9	GU129682	this study
	Thalasseus sandvicensis	Sandwich Tern	FVTCIFSIFTV	tcc	VS	Thr86			AY960720	Håstad et al. (2005)
	Sterna paradisaea	Arctic Tern	FVTCIFSIFTV	tcc	VS	Thr86			AY960719	Håstad et al. (2005)
Alcidae	Uria aalge	Common Murre	FLACIFSVFTV	agc	VS				AY227163	Ödeen & Håstad (2003)
	Alca torda	Razorbill	FVACIFSVFTV	agc	VS				AY227159	Ödeen & Håstad (2003)
Stercorariidae	Stercorarius longicaudus	Long-tailed Jaeger	FVACIFSVFTV	agc	VS		NRM 976537		GU129683	this study
	Stercorarius parasiticus	Parasitic Jaeger	FVACIFSVFTV	agc	VS		NRM 20066101		GU129684	this study
	Stercorarius maccormicki	South Polar Skua	FVACIFSVFTV	agc	VS		ZMUC 131807		GU129685	this study
Glareolidae	Glareola pratincola	Collared Pratincole	FLACVFSVFTV	agc	VS		M. Wilson, A.Ö.	Ug35	GU129686	this study
	Glareola nuchalis	Rock Pratincole	FLACIFSVFTV	agc	VS		ZMUC 113386		GU129687	this study
	Rhinoptilus chalcopterus	Bronze-winged Courser	CLACLFSVFTV	agc	VS		ZMUC 131583		GU129688	this study
Recurvirostridae	Himantopus himantopus	Black-winged Stilt	FVACIFSVFTV	agc	VS				AY227156	Ödeen & Håstad (2003)
Haematopodidae	Haematopus ostralegus	Eurasian Oystercatcher	FIACIFSVFTV	agc	VS				AY227155	Ödeen & Håstad (2003)
Charadriidae	Pluvialis apricaria	Eurasian Golden Plover	FIACIFSVFTV	agc	VS		Department of Animal Ecology, U. U.	Ljungpipare98	GU129689	this study
	Charadrius dubius	Little Ringed Plover	FIACIFSVFTV	agc	VS				AY227154	Ödeen & Håstad (2003)

For the phylogenetic analyses, we used GenBank sequences of three mitochondrial and three nuclear loci, plus own β fibrinogen (FGB7) and myoglobin sequences of Anous tenuirostris and Gygis alba. Phylogenetic trees were constructed by maximum likelihood for one locus at a time and by Bayesian inference in the following combinations: (i) mitochondrial CO1, ND2 and cytochrome b, (ii) nuclear RAG-1, FGB7 and myoglobin intron 2 (myoglobin), and (iii) all loci together. For details, see the electronic supplementary material.

3. Results

(a). Opsin gene analysis

All gull species investigated in this and previous studies (table 1) carry the UVS-pigment-conferring Ser to Cys substitution at aa position 90 (Ser90Cys: Wilkie et al. 2000; Yokoyama et al. 2000), as specified by the codon TGC in the SWS1 opsin gene. We found this trait in four other shorebirds, namely A. minutus, A. tenuirostris, G. alba (Sternidae) and Rynchops niger (Rynchopidae). All other species examined carry Ser90, which is ancestral to Charadriiformes (Ödeen & Håstad 2003; Håstad et al. 2005), but translated from different synonymous codons. In general, VS shorebirds carry AGC; the exception is Sternidae (excluding Anous and Gygis), where all sequences read TCC instead. The distribution of these traits on the phylogeny is shown in figure 1 (and the electronic supplementary material, figures S1 and S2).

Figure 1.

Bayesian inference tree of shorebirds based on mitochondrial ND2, cytochrome b and CO1, and nuclear RAG-1, FGB7 and myoglobin (approx. 7.4 kbp). The species having the UVS-pigment-conferring Ser90Cys substitution in their SWS1 opsin are in bold. The most parsimonious reconstruction of the sequence of mutations in the corresponding codon is shown in boxes. Numbers at nodes are posterior probabilities (values of 1.00 indicated by *). The name of the family Thinocoridae (comprising Thinocorus) is not marked owing to lack of space.

(b). Phylogeny

All analyses produced results largely in agreement with previous studies (Ericson et al. 2003; Paton et al. 2003; Paton & Baker 2006; Baker et al. 2007; Fain & Houde 2007), and identify three main clades corresponding to Lari, Scolopaci and Charadrii. Only the tree based on all loci (figure 1) is shown (combined nuclear and mitochondrial gene trees in the electronic supplementary material, figures S1 and S2). All trees recover a strongly supported clade comprising Laridae, Sternidae and Rynchops. Within this clade, in the tree based on all loci, Laridae, Rynchops and Sterna form a poorly supported clade, which is sister to an insufficiently supported clade comprising Anous and Gygis. The nuclear tree has the same topology, but even weaker support. In contrast, in the mitochondrial tree, Laridae, Rynchops and Anous form a moderately well-supported trichotomy that is sister to a strongly supported clade containing Gygis as sister to the rest of Sternidae (excluding Anous).

4. Discussion

Our results agree with previous studies in showing that gulls have Cys90 in their SWS1 opsins, characteristic of the UVS class of colour vision. This trait has been conserved during gull evolution, as revealed by the denser taxon sampling of this study compared with previous ones (Håstad et al. 2005). Another new finding is that gulls are not unique among shorebirds in being UVS, as the terns A. minutus, A. tenuirostris and G. alba and the skimmer R. niger share the UVS opsin forming Ser90Cys substitution.

The evolutionary interpretation of our results hinges on the correct inference of the phylogeny. As the relationships in the Laridae/Sternidae/Rynchopidae clade are somewhat uncertain, different interpretations are possible. However, the most parsimonious reconstruction suggests a Ser90Cys substitution in the common ancestor to Laridae/Sternidae/Rynchopidae, and a subsequent reversal to Ser in the Sternidae lineage (except Anous and Gygis), in all formed by two consecutive point mutations in the codon at aa position 90, from AGC to TGC to TCC. This is true even if the uncertainty in the gene tree is taken into account by considering the Sternidae branch (except Anous and Gygis) in alternative positions. For example, the posterior probability that Sterna is outside the clade comprising Laridae, Rynchops, Anous and Gygis—which would support a single Ser90Cys substitution but no subsequent reversal—is lesser than 0.06. Accordingly, our favoured hypothesis based on the available data is a single shift from VS to UVS in the common ancestor to Laridae/Sternidae/Rynchopidae and a subsequent reversal in the Sternidae lineage (except Anous and Gygis).

All key aas we report in positions 86, 90 and 93 have already been described (Wilkie et al. 2000; Yokoyama et al. 2000; Ödeen & Håstad 2003), but the spectral tuning effects of some of them are still unknown. The effect of Cys86 in birds is probably negligible (Ödeen et al. 2009), but neither the effects of Thr86 or Ile86 nor Ile93 has been investigated in vitro. However, the λ_max of SWS1 pigment of Anas platyrhynchos, which carries Ile93, is not significantly different from that of species with aas of known effect in this position (Ödeen et al. 2009).

In one aspect, avian colour vision is under simple genetic control: the VS/UVS pigment opsin character depends on the Ser90Cys substitution, which can be caused by a single nucleotide mutation. Still, this character is surprisingly conserved among birds, indicating strong stabilizing selection. This is a rare example of a system where two very similar and well-understood variants of the same gene, which have a significantly different effect on the phenotype and ecology of the carrier, have been equally successful in a large taxon.