Rapid evolution and selection inferred from the transcriptomes of sympatric crater lake cichlid fishes


  • K. R. ELMER,

    1. Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätstrasse 10, 78457 Konstanz, Germany
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  • S. FAN,

    1. Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätstrasse 10, 78457 Konstanz, Germany
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  • H. M. GUNTER,

    1. Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätstrasse 10, 78457 Konstanz, Germany
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  • J. C. JONES,

    1. Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätstrasse 10, 78457 Konstanz, Germany
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    1. Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätstrasse 10, 78457 Konstanz, Germany
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  • S. KURAKU,

    1. Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätstrasse 10, 78457 Konstanz, Germany
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  • A. MEYER

    1. Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätstrasse 10, 78457 Konstanz, Germany
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  • The Meyer Laboratory (AM, KRE, JCJ, HGM, SF) is interested in the molecular basis of the vast ecological adaptations and evolutionary radiations of cichlid fishes, both African and neotropical. The Kuraku Laboratory (SK, SB) studies the evolution of gene repertoires, especially in early vertebrates, and the integration of bioinformatics and molecular evolutionary developmental biology.

Axel Meyer, Fax: +49 7531 88 3018;
E-mail: axel.meyer@uni-konstanz.de


Crater lakes provide a natural laboratory to study speciation of cichlid fishes by ecological divergence. Up to now, there has been a dearth of transcriptomic and genomic information that would aid in understanding the molecular basis of the phenotypic differentiation between young species. We used next-generation sequencing (Roche 454 massively parallel pyrosequencing) to characterize the diversity of expressed sequence tags between ecologically divergent, endemic and sympatric species of cichlid fishes from crater lake Apoyo, Nicaragua: benthic Amphilophus astorquii and limnetic Amphilophus zaliosus. We obtained 24 174 A. astorquii and 21 382 A. zaliosus high-quality expressed sequence tag contigs, of which 13 106 pairs are orthologous between species. Based on the ratio of nonsynonymous to synonymous substitutions, we identified six sequences exhibiting signals of strong diversifying selection (Ka/Ks > 1). These included genes involved in biosynthesis, metabolic processes and development. This transcriptome sequence variation may be reflective of natural selection acting on the genomes of these young, sympatric sister species. Based on Ks ratios and p-distances between 3′-untranslated regions (UTRs) calibrated to previously published species divergence times, we estimated a neutral transcriptome-wide substitutional mutation rate of ∼1.25 × 10−6 per site per year. We conclude that next-generation sequencing technologies allow us to infer natural selection acting to diversify the genomes of young species, such as crater lake cichlids, with much greater scope than previously possible.


Cichlid fishes are one of the most species-rich vertebrate families and much of this richness is reflected in morphological adaptations related to trophic niche, such as body shape, mouth and jaw form (Rüber et al. 1999; Clabaut et al. 2007; Salzburger 2009). The Midas cichlids in Nicaragua have evolved rapidly into different trophic niches in young crater lakes (Barlow & Munsey 1976; Wilson et al. 2000; Vivas & McKaye 2001; Stauffer & McKaye 2002; Barluenga et al. 2006; Stauffer et al. 2008). In crater lake Apoyo, such eco-morphological speciation has occurred in sympatry: a trophically and genetically distinct endemic limnetic species, Amphilophus zaliosus, evolved from a benthic or generalist ancestor in the past 10 000 years (Barlow & Munsey 1976; Barluenga et al. 2006) (Fig. 1). Amphilophus astorquii, a recently described benthic species, is also strictly endemic to crater lake Apoyo (Stauffer et al. 2008), where it is the most abundant species in the lake (McCrary & López 2008). Disruptive natural selection within the crater lake environment is likely to have driven species’ divergent ecologies and morphologies (Barlow & Munsey 1976; Parsons et al. 2003; Barluenga et al. 2006; Elmer et al. in press), resulting in reproductive isolation (Baylis 1976) and population differentiation at putatively neutral genetic regions (microsatellites, amplified fragment length polymorphisms, mitochondrial DNA) (Barluenga et al. 2006). Given the Lake Apoyo Midas cichlid species flock’s genetic monophyly (Wilson et al. 2000; Barluenga & Meyer 2004; Barluenga et al. 2006; Bunje et al. 2007), the species’ strict endemism, and trophic differentiation (Stauffer et al. 2008), it is highly probable that not only A. zaliosus (Barlow & Munsey 1976; Barluenga et al. 2006) but also A. astorquii arose in lake Apoyo by sympatric speciation (Stauffer et al. 2008). Despite the established ecological and neutral genetic differences, we lack estimates of gene sequence diversity between the benthic and limnetic species. Further, we have no information about how divergent natural selection may have affected these species’ genomes within the very short evolutionary time span since their divergence from a common ancestor.

Figure 1.

 Lake Apoyo is a crater lake in western Nicaragua and has no water connection with neighbouring crater or great lakes. Amphilophus zaliosus is a limnetic endemic species that evolved in sympatry in Lake Apoyo (lower above). Amphilophus astorquii is an endemic benthic species (lower below).

Emerging techniques based on ‘next generation’ sequencing or massively parallel sequencing, such as low-pass shotgun genome sequencing and expressed sequence tag (EST) analyses, are proving to be valuable additions to evolutionary and ecological research (Ellegren 2008; Rokas & Abbot 2009). Research areas such as population genetics (Lynch et al. 2008), experimental evolution (Shendure et al. 2005) and phylogenetics (Moore et al. 2006, 2007) have successfully synthesized genome data to address biologically meaningful questions. The spearhead for research on the genomic bases of species differences is work on human genome comparisons, which seek to identify the features that distinguish us from our primate relatives and to quantify the variability between human populations. For example, a comparison between the human and chimp genomes indicated that they are 98.4% similar (Chen & Li 2001), and that genes related to immune functions, spermatogenesis, olfaction and sensory perception are probably under positive selection in the human lineage (Bustamante et al. 2005; Nielsen et al. 2007). This human research has driven the development of cost-effective techniques, which have opened the door for genome research on nonmodel organisms: the ‘new frontiers’ of genomics research (Collins et al. 2003). There are specific challenges that are encountered when using massively parallel sequencing technologies on nonmodel organisms because a reference genome is rarely available. In some cases, a close relative provides a scaffold for read assembly: for example, having a sequenced honeybee genome facilitated wasp transcriptome research (Toth et al. 2007), the silkworm genome aided analysis of Glanville fritillary butterfly ESTs (Vera et al. 2008) and chicken and zebra finch genomes inform transcriptome research on non-model bird species (Kunstner et al. 2010; Wolf et al. 2010). Sufficiently long sequence reads from massively parallelized sequencing can compensate for the lack of a reference genome so 454 pyrosequencing, with currently the longest available read lengths, is the platform favoured for such scenarios (Rokas & Abbot 2009). In the context of our research, a completely sequenced cichlid genome is underway (International Cichlid Genome Consortium 2006) but is not yet complete.

Expressed sequence tags represent a sample of the spatiotemporally expressed genome: the transcriptome. EST studies can be used as an entry into gene expression and comparative genome-level questions in nonmodel organisms when other genomic resources, such as a sequenced genome, are not yet developed (Bouck & Vision 2007; Hudson 2007). EST studies – one of the most cost-effective methods for gene discovery (Bouck & Vision 2007) – are made even more robust and efficient using massively parallelized sequencing. This has eliminated the need for cloning ESTs, which introduces bias, and has greatly increased the quantity of data that can be generated in a short time at a reduced cost compared with traditional Sanger sequencing of cDNA libraries (Weber et al. 2007; Wheat, in press). Parallelized sequencing of transcriptomes allows us to identify candidate genes without imposing strong a priori expectations or biases (although most studies restrict their starting material to pertinent tissues and/or developmental stages when resources are limited). Implicit in this approach to identify transcriptome differences between species is the expectation that gene (or transcript) sequence differences may be relevant to some interspecific phenotypic variation.

In this study, we use massively parallelized pyrosequencing (454 GS FLX) to characterize the transcriptome sequence diversity between two young, endemic and ecologically divergent sympatric species of Midas cichlid fish from the neotropical crater lake Apoyo, Nicaragua. A. zaliosus is an open water, elongate limnetic species. A. astorquii is a high-bodied, short benthic species. Both species breed in the littoral zone during the same breeding season, with A. zaliosus breeding in solitary pairs and A. astorquii in colonies of pairs. We aim to identify interspecific EST sequence variation and infer orthologous genes that may be showing signs of diversifying natural selection (a non-neutral rate of synonymous and nonsynonymous substitutions between sequence pairs). We identify transcriptome sequence variation that reflects the impact of natural selection on the genome. Using the neutral substitutional mutation rate inferred from Ks and the similarities in 3′-untranslated regions (UTR), we estimate a transcriptome-wide substitutional mutation rate for these neotropical cichlids. By using pyrosequencing technology, we infer mutation rates and the effects of natural selection across the genome and transcriptome with greater speed and scope than previously possible.

Materials and methods

Generating samples

Intraspecific crosses were established between pairs of Amphilophus astorquii and Amphilophus zaliosus. These adults have been laboratory-reared under common conditions since they were collected in Lake Apoyo as fry 2–4 years before. When a clutch was successfully produced, three time points were sampled from each species: day of hatching (1 dph), 1 week post-hatching (1 wph) and 1 month post-hatching (1 mph). Samples were collected in a standardized manner and time of day. Fry and juvenile fish were killed following approved protocols and placed in RNALater (Qiagen). These were held at 4 °C for less than 1 month before being stored at −20 °C. A portion of each sample not stored in RNALater was fixed in 4% paraformaldehyde overnight, stepped into methanol, and then stored at −20 °C to provide an archive of the stage-specific morphologies.

RNA extraction

RNA extractions were performed simultaneously. For each species, sample sizes were: 6 individuals of 1 dph, 10 individuals of 1 wph, and 2 individuals of 1 mph. Fewer individuals were included in 1 dph than 1 wph because the high quantity of yolk in the 1 dph samples was found to cause poor quality and quantity of total RNA. Only the head (cut immediately behind the gill cover) was used for 1 mph samples to avoid contaminating the sample with gut flora and fauna. After removing RNALater, samples were homogenized in 1 mL of Trizol (Invitrogen) in an MP Biosciences homogenizer at intensity 5.0 for 20 s. RNA extraction was performed using the manufacturer’s protocol and re-precipitated for 3 h with one volume of 4M LiCl. Pellets were recovered by centrifugation and dissolved in 20 μL pH 8.0 diethylpyrocarbonate water (DEPC). The quantity and quality of total RNA was assessed by spectrophotometry and gel electrophoresis. Between 1 and 2 μg of each sample was requested for commercial normalized library construction, and equal quantities of RNA from each stage were pooled per species.

Normalized library development

We commissioned a 3′-fragment normalized cDNA library to be constructed by a third-party service provider (Eurofins MWG GmbH, Ebersberg, Germany). Briefly, from total RNA, first-strand cDNA was synthesized using reverse transcriptase and an oligo(dT)-adapter primer. Second-strand synthesis was performed with a N6 random adapter primer. cDNAs were then amplified with 17 (A. zaliosus) or 18 (A. astorquii) cycles of long and accurate polymerase chain reaction (PCR) (Barnes 1994). Libraries were normalized by hydroxylapatite chromatography and the ss-cDNA was then amplified by PCR. cDNA was size selected for 450–550 bp including the 5′- and 3′-454 and cDNA adapters.

454 Sequencing and assembly quality control

The normalized cDNA library was sequenced in one GS FLX (Roche 454) Standard Chemistry run (half a plate per species at equimolar concentrations) by Eurofins MWG. Reads were assembled using the Eurofins MWG in-house bioinformatics pipeline. Adapter sequences were clipped and contigs were assembled using MIRA 2.9.15 (Chevreux et al. 2004) based on 40 bp overlap, 90% homology and a minimum of five reads deep on average. Singleton raw reads were excluded.

We subjected all contigs to an extensive quality control procedure. First, sequences were screened for contamination by blastn searches (E-value E-20) against Escherichia coli genome and human and mouse EST databases (downloaded December 2008). Two E. coli contamination sequences were identified in the A. astorquii pool and excluded. Second, low-quality bases were masked using an in-house Perl script (S. Fan) given a quality score threshold of Q > 20. Third, contigs with interspersed repeats and low-complexity DNA sequences were excluded using an in-house script (S. Fan) parsing the results of RepeatMasker (version 3.2.6 with repeat library 20090120) (Smit et al. 1996), since such sequences would impede orthologous EST identification. Contigs <200 bp long were excluded from further analyses.

Transcriptome functional annotation

Functional annotation was performed online using Blast2GO (Version 2.3.4) (Conesa et al. 2005; Götz et al. 2008), which performs a blastx search against the nonredundant database on NCBI (default parameters were used). Annotated accession numbers and Gene Ontology (GO) (The Gene Ontology Consortium 2000) numbers were derived from NCBI QBLAST (Altschul et al. 1997) based on an E-value ≤1E-5 and a high-scoring segment pair cut-off greater than 33. The annotation procedure was conducted using the following parameters: a pre-E-value-Hit-Filter of 10−6, a pro-Similarity-Hit-Filter of 15, an annotation cut-off of 55, and a GO weight of 5.

Identifying orthologous ESTs

We used the bidirectional best hit method in blast with a bit score threshold of >300 to identify ESTs that are putatively orthologous between the two species. Bidirectional best hit has been found to out-perform more complex orthology identification algorithms (Altenhoff & Dessimoz 2009). Our bidirectional best hit threshold ensures that the alignment of two ESTs is longer than 150 bp.

Predicting the open reading frame and the untranslated region

Open reading frames (ORF) for the putatively orthologous ESTs were determined by blastx (NCBI blast version, 2.2.19) (Altschul et al. 1997) against all known vertebrate proteins from the Universal Protein Resource (The UniProt Consortium 2008) and protein data sets for five teleost fishes (fugu, medaka, green spotted pufferfish, stickleback and zebrafish) in the Ensembl database (Hubbard et al. 2005) (Ensembl 52) using a threshold of <1E-5. If both orthologous ESTs could be annotated, the coding regions were extracted according to the blastx results. The coding sequences were aligned by ClustalW version 2.0 (Larkin et al. 2007).

The 3′-untranslated region (UTR) of each contig was identified based on the results of the ORF prediction. We searched downstream of the coding region to identify the stop codon (TAG, TAA or TGA). If the number of base pairs between the stop codon and end of the coding region were divisible by three (i.e. matched a reading frame by being the length of an amino acid), then downstream of the stop codon was considered a ‘true 3′-UTR’. If the number of base pairs between the coding region and the stop codon was not divisible by three, then downstream of the ORF was considered a ‘pseudo-UTR’ and excluded from further analyses.

Estimating substitution rates

We estimated the rate of nonsynonymous substitutions per nonsynonymous site (Ka) to the number of synonymous substitutions per synonymous site (Ks) between putatively orthologous coding regions using a maximum-likelihood method (Yang & Nielsen 2000) implemented by yn00 in the PAML toolkit (vers. 4.0) (Yang 2007). Orthologous ESTs with a Ks rate >0.1 were excluded from further analyses to avoid analysing paralogous genes (Bustamante et al. 2005).

Estimating the overall substitutional mutation rate

We estimated an overall substitution rate for the cichlid genome based on divergence between orthologous EST pairs (entire EST, including coding region and UTRs > 50 bp long) and synonymous mutations calibrated with a maximum age of crater Lake Apoyo (Kutterolf et al. 2007). Only UTRs contiguous with orthologous coding regions were used in distance calculations to avoid including artefacts of assembly. The rate (r) (in substitutions/site/year) is calculated from the mean genetic distance between sequences (d) divided by the divergence time between two species (2t). d for coding regions is based on the Ks rate, since under the neutral theory of evolution Ks should be proportional to the neutral mutation rate (Hurst 2002). d for UTRs was estimated by a Jukes-Cantor (Jukes & Cantor 1969) corrected pairwise distance.


Sequencing and assembly quality control

We received a total of 114 Mb from one run, approximately evenly represented in both species (Table 1). Sequences are deposited in the NCBI Short Read Archive (Accession no. SRA009759.2). The average read length was just over 200 bp (Table 1). This is shorter than the 220–270 average read length expected from the GS FLX technology and may be because of the 3′-library construction method. Our total number of base pairs meets Roche 454 expectations of 100 Mb per run for GS FLX standard chemistry. Raw reads were assembled into 57 566 contigs. Fewer than 100 hits per pool could be attributed to the mitochondrial genome (from neotropical cichlids: NCBI Accession nos NC_009058, NC_011168). After quality control (see Methods and materials), our sample consisted of 24 174 Amphilophus astorquii and 21 382 Amphilophus zaliosus‘high-quality ESTs’ ranging in length from 200 to 1277 bp. These sequences were used for further analysis.

Table 1.   Sequencing coverage was approximately equal in both species, suggesting that there was no bias towards any particular pool of RNA
 Amphilophus astorquiiAmphilophus zaliosusTotal
  1. ‘High quality’ ESTs are those used for subsequent analyses. Total represents the two species combined. Numbers of bases and read length are trimmed of tags and low quality bases. EST, expressed sequence tags.

Total number of reads300 610262 494563 104
Total number of bases60 732 54754 132 058114 864 605
Average read length202206 
Assembly results
 Number assembled231 293199 628 
 Number too short and excluded13 74911 567 
 Number of all contigs30 56926 99757 566
 Total number of bases8 143 4297 167 69915 311 128
‘High quality’ ESTs
 Total number of contigs24 17421 38245 556
 Average length300299 
 Median length275277 
 Maximum length1 2771 271 

A total of 2289 A. astorquii and 2119 A. zaliosus ESTs showed homology (i.e. significant e-values) with known proteins from the vertebrate protein database (Universal Protein Resource) and five fish protein databases (Ensembl). This represents about 10% of the ESTs being successfully annotated, a proportion that is less than the 20% to 40% of ESTs often annotated from a traditional Sanger sequenced EST library (e.g. Cerda et al. 2008; Salzburger et al. 2008) but similar in absolute numbers. By proportion our annotation success is lower because 454 reads tend to be biased towards the 3′-transcript end (Shin et al. 2008) and are shorter than traditional Sanger sequences. Also, we used a 3′-fragment extension library protocol that should maximize depth but at the cost of 5′ ends, which makes annotation more difficult (G. Gradl, personal communication).

Functional annotation

Of our data, 3152 (13%) of the A. astorquii and 2673 (12%) of the A. zaliosus contigs were annotated with an inferred biological function based on currently known proteins in the NCBI nonredundant protein database (blastx). Approximately equal numbers of the EST sequences for A. astorquii and A. zaliosus had GO resource assignments relating to three major divisions. The first, ‘biological process’, refers to the ‘biological objective to which the gene or gene product contributes’ (The Gene Ontology Consortium 2000). Within the function of ‘biological process’, 15 categories were identified and these were perfectly paired between species. The two most abundant categories were: (i) ‘cellular and metabolic processes’, to which 46% of both species’ ESTs were dedicated (2810 A. astorquii and 2705 A. zaliosus ESTs); and (ii) ‘development process’, to which 10% of ESTs were dedicated (627 A. astorquii and 593 A. zaliosus ESTs) (Fig. 2). The second major division is ‘molecular function’, which refers to some biochemical activity that is performed by the gene, without a temporal or spatial context (The Gene Ontology Consortium 2000). EST coverage of this division was similar between species: 10 categories of ‘molecular function’ were found in A. astorquii and nine categories in A. zaliosus (genes corresponding to auxiliary transport protein activity function could only be found in the A. astorquii transcriptome) (Fig. 2). Of these ESTs ascribed to ‘molecular function’, most A. astorquii (71%, 2347 sequences) and A. zaliosus (75%, 2222 sequences) ESTs were dedicated to binding functions and catalytic activity. The third division is ‘cellular component’, which describes the sub-cellular location where a gene product is active (The Gene Ontology Consortium 2000). Again, coverage is similar between species: nine categories were found in the A. astorquii transcriptome and 11 categories were found in the A. zaliosus transcriptome. Gene products were mainly expressed intracellularly (A. astorquii: 3456 sequences or 51%; A. zaliosus: 3274 sequences or 50%) or in the organelle (A. astorquii 1241 sequences or 18%; A. zaliosus: 1202 sequences or 18%). The matched proportion of GO categories between A. astorquii and A. zaliosus suggests that our library and 454 sequencing covered both species’ transcriptomes equally.

Figure 2.

 Blast2GO assignment for 3152 Amphilophus astorquii and 2673 Amphilophus zaliosus ESTs. The proportion of ESTs assigned to different categories is approximately equal.

Orthologous EST identification

We identified 13 106 pairs of ESTs that are putatively orthologous between the two species (hereafter referred to as ‘orthologous ESTs’). The median length of sequence shared by the orthologous ESTs (i.e. alignment length) is 264 bp, ranging from 153 to 767 bp. A total of 1721 pairs of orthologous ESTs matched to the ORFs of known or unknown proteins.

Untranslated region identification

The untranslated region of each orthologous EST was identified based on the predicted coding region. Thirty-three pairs (median length 78 bp, ranging from 51 to 153 bp) of UTRs that are informative for divergence were found in the orthologous ESTs.

Estimated Ka/Ks

Based on a data set of 1721 pairs of ESTs that were orthologous and had an ORF that could be predicted (criterion 1E-5), divergence was sufficiently high for 44 ESTs (3%) of which both a Ka and a Ks rate could be calculated. Of these, six orthologous ESTs have a Ka/Ks > 1 and eight orthologous ESTs have a Ka/Ks between 0.5 and 1 (Fig. 3). For the remainder of the orthologous ESTs, we could calculate either only Ka (175 orthologous ESTs, 10%), only Ks (103 orthologous ESTs, 6%), or the orthologous ESTs were identical (1399 or 81%), making a ratio incalculable. Ka/Ks > 1 suggests that strong positive selection has acted to change the protein DNA sequence (Yang & Bielawski 2000) while Ka/Ks above 0.5 is a less conservative cut-off that has also proven useful for identifying genes under positive selection (Swanson et al. 2004). EST pairs with Ka/Ks > 1 function in biosynthetic and metabolic processes, brain development and cognition, response to hormone stimuli, and nervous system development. Those ESTs with Ka/Ks between 0.5 and 1 related to metabolic processes, tissue, blood and hormone regulation and regeneration (Table 2).

Figure 3.

 Distribution of Ka and Ks. A nonzero Ka and a Ks ratio could be calculated for 44 ESTs. ESTs with Ka/Ks > 1 fall above the grey line while ESTs with Ka/Ks = 0.5–1 fall between the black and grey lines.

Table 2.   Ratio of nonsynonymous (Ka) to synonymous (Ks) substitutions, number of polymorphisms (SNPs), bit scores, E-values, Gene Ontology (F, molecular function, P, biological process, C, cellular components), hit sequence name, the species of origin for this hit and the accession identification numbers for homologues in other species of the 14 candidate genes (ESTs) showing a signal of evolution by diversifying natural selection
Ka/KsNumber of SNPsAmphilophus astorquii Bit scoreAmphilophus zaliosus Bit scoreAmphilophus astorquii E-valueAmphilophus zaliosus E-valueGene ontologyHit sequence nameSpecies of originAccession IDs
  1. EST, expressed sequence tags; SNP, single nucleotide polymorphism.

7.682488.21483.00E-172.00E-35F: isomerase activity; P: biosynthetic processPhenazine biosynthesis-like domain-containing protein 2Salmo salartr|B5X8N7|B5X8N7_SALSA
2.836582.81271.00E-155.00E-29P: amino acid metabolic process; P: ATP metabolic process; C: lysosomal membrane; C: integral to membrane; F: l-cystine transmembrane transporter activity; P: brain development; P: cognition; P: l-cystine transport; P: glutathione metabolic process; C: late endosome; C: early endosomeCystinosinOryzias latipesENSORLP00000003583
2.453770.11207.00E-126.00E-27Not availableNovel protein codingOryzias latipesENSORLP00000003819
1.32041431257.00E-341.00E-28Not availableConserved domainGasterosteus aculeatusENSGACP00000016806
1.0408871316.00E-173.00E-30C: cytoplasm; P: response to hormone stimulus; P: epithelial cell differentiation; C: polysome; P: nervous system development; F: poly(U) binding; C: nucleus; F: nucleotide bindingRNA-binding protein Musashi homologue 1Oryzias latipesENSORLP00000024802
1.03549258.22.00E-183.00E-08P: cell redox homeostasis; P: transportThioredoxin domainBombina orientalistr|B6VFL5|B6VFL5_BOMOR
0.79041011452.00E-211.00E-34P: lipid metabolic process; P: induction of apoptosis; F: endopeptidase inhibitor activity; F: calcium ion binding; P: negative regulation of angiogenesis; P: tissue remodelling; P: fibrinolysis; P: lipid transport; P: proteolysis; F: apolipoprotein binding; P: myoblast differentiation; P: muscle maintenance; F: serine-type endopeptidase activity; C: extracellular region; F: plasmin activity; P: blood circulation; P: tissue regenerationPlasminogenDanio reriotr|Q8AVB0|Q8AVB0_DANRE
0.71451471623.00E-352.00E-39P: response to organic nitrogen; P: multidrug transport; F: xenobiotic-transporting ATPase activity; P: canalicular bile acid transport; F: ATP binding; F: bile acid-exporting ATPase activity; P: response to organic cyclic substance; P: response to estradiol stimulus; C: basolateral plasma membrane; P: response to lipopolysaccharide; C: integral to plasma membraneCanalicular multispecific organic anion transporter 1Gasterosteus aculeatusENSGACP00000009848
0.70241191221.00E-261.00E-27F: actin monomer binding; P: cardiac muscle contraction; P: regulation of the force of heart contraction; C: myosin complex; P: regulation of striated muscle contraction; F: calcium ion binding; P: ventricular cardiac muscle morphogenesis; F: motor activity; C: A band; C: I bandMyosin light chain 4Oryzias latipesENSORLP00000021991
0.66841421951.00E-331.00E-49C: proteasome core complex; P: ubiquitin-dependent protein catabolic process; C: nucleus; C: cytosol; F: threonine endopeptidase activityProteasome subunit beta type-6 PrecursorTakifugu rubripesENSTRUP00000003687
0.632398.21392.00E-208.00E-33Not availableA-kinase anchor protein 13Gasterosteus aculeatusENSGACP00000000813
0.62151791627.00E-451.00E-39C: proteasome core complex; P: ubiquitin-dependent protein catabolic process; C: nucleus; C: cytosol; F: threonine endopeptidase activity; P: immune responseProteasome subunit beta type-9 precursorGasterosteus aculeatusENSGACP00000000192
0.59821431585.00E-342.00E-38Not availableNovel protein-coding sticklebackGasterosteus aculeatusENSGACP00000024881
0.54831161051.00E-252.00E-22F: molecular_function; C: cellular_componentCoiled-coil domain containing 93Gasterosteus aculeatusENSGACP00000001928

Substitution rate estimation

The average Ks rate for 147 orthologous ESTs is 0.0250 ± 0.015 (mean ± SD). The average divergence between orthologous and informative UTRs is 0.0252 ± 0.020 (Fig. 4). Substitutions in the synonymous sites and 3′-UTR are putatively neutral, especially among very closely related taxa (Hurst 2002) (but see Hellmann et al. 2003, who find 5′-UTR in humans may be under positive selection). The similarity of the two means strongly suggests that our coding region and UTR analyses are valid and represent equal and approximately neutral evolutionary change.

Figure 4.

 Mean (±1 SD) Ks value and corrected p-distance of 3′-untranslated regions for orthologous ESTs. The means of these mutation rates are the same, suggesting that they both indicate neutral and consistent substitution.

Based on a species divergence time of 10 000 years ago estimated from mitochondrial DNA (Barluenga et al. 2006), we used the substitution rate estimated above to calculate a transcriptome-wide substitution rate of 1.25 × 10−6 per site per year. The geological age of Lake Apoyo is 23 890 ± 120 years (Kutterolf et al. 2007). Using that as a maximum species divergence time, we infer a minimum transcriptome-wide substitution rate of 6.3 × 10−7 mutations per site per year (calibrated to 20 000 years).


Transcriptome variation in the Midas cichlid species complex

We have identified genes under balancing and positive selection in the extremely young crater lake cichlid species Amphilophus astorquii and Amphilophus zaliosus. These species are model systems for understanding the ecology and evolution of adaptive radiations and sympatric speciation (Barluenga et al. 2006; Elmer et al. in press). A. astorquii is endemic to crater lake Apoyo (Stauffer et al. 2008), which houses a monophyletic Midas cichlid species flock (Bunje et al. 2007). Thus, although the ecology and evolutionary history of the recently described A. astorquii have not yet been extensively studied (but see Elmer et al. in press; Stauffer et al. 2008; Oldfield 2009) it is very likely that, like A. zaliosus (Barluenga et al. 2006), A. astorquii arose by sympatric speciation (Stauffer et al. 2008). Because of the young ages of these species, we anticipated that genetic differences between species would be very small. This expectation was borne out and in this initial screen we find only 14 candidate genes that show signs of positive selection while most of the transcriptome is either identical between species or was only sampled in one species. This is in agreement with previous research indicating that A. zaliosus is only weakly diverged at neutral loci from the other Midas cichlids in Lake Apoyo (Barluenga et al. 2006). Nonetheless, this transcriptome-wide approach has provided the first indication of putatively functional genome divergences between these sympatric species.

Transcriptome sequencing and annotation of ESTs for a nonmodel organism

Pyrosequencing of our normalized cDNA library resulted in 24 174 ESTs for A. astorquii and 21 382 ESTs for A. zaliosus. We found that 13 106 pairs of ESTs were putatively orthologous between species. This represents a significant increase in the number of available cichlid ESTs (generated primarily by a few traditional EST studies using Sanger sequencing technology for East African cichlids, e.g. Renn et al. 2004; Watanabe et al. 2004; Salzburger et al. 2008) and inferred from chimeric genomic sequences from the cichlid genome project (Loh et al. 2008). Currently, approximately 45 000 ESTs are available for three African cichlid species, Astatotilapia burtoni, Haplochromis chilotes and Haplochromis‘redtail sheller’ (http://compbio.dfci.harvard.edu/tgi/tgipage.html and NCBI dbEST; accessed 9 June 2009). Thus, our study contributes both a greater number of new cichlid ESTs to the research domain and, to our knowledge, the first neotropical cichlid ESTs.

Because of its relatively long read lengths, 454 pyrosequencing is the best method for de novo assembly (Rokas & Abbot 2009), although transcriptome assembly is nonetheless difficult and requires deep coverage (Weber et al. 2007; Wheat in press). Given that there is a constant upper limit (approximately 100 Mb for GS FLX standard chemistry) to the total number of base pairs generated per run, we sequenced normalized cDNA to try and maximize coverage of transcripts and reduce sequences of abundant transcripts. There will inevitably be a trade-off in cDNA preparation methods: whether or not to normalize, and the type of normalization approach to use. Largely, this depends on the experimental question being pursued, the diversity of input material and the number of sequence reads to be returned (Hale et al. 2009; Wheat in press). In this study, we used a 3′ extension approach, which purports to maximize depth and overall number of base pairs although at a cost of ORF length relative to random priming approaches. The equal coverage between species, the comparably high number of total base pairs, and the 3′-UTR bias in our results are because of our choice of library preparation. Nonetheless, more sequencing to gain deeper coverage and greater assembly power will be required to generate full-length ESTs for these cichlid species. Additionally, without high-coverage genomic sequences, we cannot confirm that our orthologous ESTs are in fact derived from the orthologous locus (i.e. expressed from the identical location in the genome) in both species. In the near future, with bacterial artificial chromosome (BAC) resources (K. Stölting, F. Henning, M. Lang, S. Fukamachi, A. Meyer, in preparation) and an emerging cichlid genome as a reference sequence, we will be able to more confidently identify genes important in the divergence of these two species and aim to map their functional importance.

Natural selection and the transcriptome

Of the 44 EST orthologues for which Ka and Ks could be calculated, six have Ka/Ks > 1, suggestive of positive selection acting on those genes by elevating the number of nonsynonymous substitutions. Ours may be a very conservative estimate because of the strict criteria we used for included orthologues. Eight candidate loci have Ka/Ks between 0.5 and 1. We included ESTs with Ka/Ks > 0.5 in our candidate genes of interest because we lack full-length genes, which will artefactually decrease Ka/Ks and cause one to overlook genic information relevant for positive selection (Swanson et al. 2004). The ESTs we identified as being under strong positive selection (Ka/Ks > 1) function in biosynthetic and metabolic processes, cognition, response to hormone stimuli and in the nervous system. Eight ESTs with Ka/Ks between 0.5 and 1 function in metabolic processes, tissue, blood and hormone regulation and regeneration. These genes under natural selection will be of particular interest for future research (Jensen et al. 2007), although molecular laboratory approaches such as RACE PCR will probably be needed to get full-length sequences. Putatively, Darwinian selection or adaptive molecular evolution has resulted in important sequence differences between species in these genomic regions (Hurst 2009) and/or these regions are relevant to speciation (Noor & Feder 2006).

The ratio of nonsynonymous to synonymous substitutions is considered to be a good indicator of selective pressure at the sequence level (Yang & Bielawski 2000; Bustamante et al. 2005) and has been used to identify protein-coding genes under positive and purifying selection in a breadth of organisms (Hurst 2009). Evolutionary factors may limit the ability to detect signals of selection on a gene. For example, selection may act on putatively silent sites, selection pressures along a gene or gene fragment may be heterogeneous, and adaptive evolution may be limited to few functional sites (Yang & Bielawski 2000; Hurst 2002; Ellegren 2008). Additionally, evolutionarily important changes may lie in the gene regulatory region rather than the protein-coding region itself (Prud’homme et al. 2007). Further, gene sequence variation between species only demonstrates selection that has occurred in the past; to detect on-going or recent selection, population genetic data and comparisons are needed (Nielsen et al. 2007). These population- vs. species-level differences will be a focus of our future research.

Genome-wide mutation rate estimate of neotropical and African cichlids

We used our interspecific distance estimates based on neutral substitution (Ks and UTR) to calculate a transcriptome-wide estimate of substitution rate in these Midas cichlids. Thus, the minimum substitution rate would be 0.63 × 10−6 per site per year when calibrated to the maximal age of crater lake Apoyo (c. 20 000 years; Kutterolf et al. 2007). Based on a more biologically probable speciation time between A. zaliosus and Amphilophus ‘citrinellus’ (which includes all benthic morphs in the lake: A. astorquii, Amphilophus chancho and Amphilophus flaveolus) of 10 000 years (Barluenga et al. 2006), the substitution rate would be 1.25 × 10−6 per site per year. If the true divergence time is less than that estimated from mitochondrial DNA then the substitution rate would be faster. To our knowledge, this is the first transcriptome-wide inference of substitution rate for cichlid fishes.

The rate we inferred between Midas sympatric cichlid species based on substitution in protein-coding genes is considerably faster than the few previously published genome-wide estimates available across taxa (e.g. mammals generally: ∼2.2 × 10−9 per site per year (Kumar & Subramanian 2002); humans specifically: ∼3.0 × 10−8 per site per generation (Xue et al. 2009). Little consensus or knowledge exists regarding true genome- or transcriptome-level molecular clocks in vertebrates (Kumar 2005; Pulquerio & Nichols 2007). Our rate may be elevated by population-level polymorphism and therefore fall into the much debated possible discrepancy between population genetic and phylogenetic mutation rate estimates (e.g. Ho et al. 2005; Bandelt 2008) that has evidence in fish mitochondrial DNA (e.g. Burridge et al. 2008). Regardless, the substitution rates per year that we have generated will be useful to researchers of adaptive radiations of fish in general and cichlids in particular, for which interspecific divergences are characteristically shallow.

Although our estimates may be elevated by population polymorphism, the molecular evolutionary rate of fish is known to be fast: protein sequences in fish evolve significantly faster than their orthologues in mammals, both for duplicated genes and those retained in single copy (Ravi & Venkatesh 2008). For example, protein sequences between the two pufferfish species with sequenced genomes (Takifugu rubripes and Tetraodon nigroviridis) are more divergent than their homologues in mammals, although the pufferfishes diverged 32 million years ago whereas the mammals (human and mouse) diverged 61 million years ago (reviewed in Ravi & Venkatesh 2008).

Studying adaptive radiations with massively parallel sequencing

Based on the phenotypic diversity of cichlids, many have pondered whether there are some unusual properties in cichlid molecular evolution, genome size or plasticity (e.g. lineage-specific genome duplications, karyotypic dynamism, accelerated mutation rate) that allows for such spectacular diversification: yet all information to date indicates there is not (Kuraku & Meyer 2008). Studies seeking to understand adaptive sequence evolution as a source of variation to explain the diversity of cichlids have met with mixed success. Some cichlid studies have found signs of positive selection in genes involved in ecologically important traits, for example, MHC and fertilization (Gerrard & Meyer 2007), egg-dummy colour (Salzburger et al. 2007), colour perception genes (Terai et al. 2002a; Terai et al. 2006; Seehausen et al. 2008; Spady et al. 2005) and jaw bone development (Terai et al. 2002b). Others have found a lack of species-specific sequence differentiation (Watanabe et al. 2004; Loh et al. 2008; Kobayashi et al. 2009), which suggests that genomic or transcriptomic factors other than protein-coding sequence variation are responsible for extant cichlid diversity, such as expression levels (Kijimoto et al. 2005; Kobayashi et al. 2006) or regulatory variation (Terai et al. 2003; Sanetra et al. 2009). Using a single pyrosequencing experiment, we have identified more genes putatively under natural selection than any of the above studies.

Genomic tools such as pyrosequencing offer a breadth of new, exciting avenues for research into the genetic basis underlying this great range of cichlid diversity, both in sequence polymorphisms and gene expression variation. By using genome- or transcriptome-wide techniques, we can now identify a greater number of candidate genes more quickly, with fewer biases, and at less cost than ever before (Fontanillas et al. 2010, Wheat in press). We can also have better success at discerning molecular differences between very closely related species, such as these recently diverged cichlid fish. Coupled with studies of parallel evolution, functional effects and fitness experiments, we are embarking on a new era of understanding how natural selection on the genome drives speciation. Hopefully, by integrating ecological speciation theory (Schluter 2000; Nosil et al. 2009) and emerging genomic and transcriptomic resources, we will begin to understand how genetic and ecological factors interact and might drive speciation.


This research was funded by a University of Konstanz Young Scholar’s Award and a Natural Sciences and Engineering Research Council fellowship to KRE, University of Konstanz Zukunftskolleg fellowships to HMG and JCJ, and grants of the Deutsche Forschungsgemeinschaft to AM. We thank T. Lehtonen, M. Barluenga, and W. Salzburger for photographs used in Fig. 1 and three anonymous reviewers for suggestions on the manuscript. AM thanks the Institute for Advanced Study Berlin for a fellowship that supported him during this study and Wissenshaftskollge fellows J. Feder, J. Mallet and P. Nosil for fruitful discussions.

Conflicts of interest

The authors have no conflict of interest to declare and note that the sponsors of the issue had no role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript.