Background
The guppy, Poecilia reticulata, is a well-known model organism for studying inheritance and variation of male ornamental traits as well as adaptation to different river habitats. However, genomic resources for studying this important model were not previously widely available.
Results
With the aim of generating molecular markers for genetic mapping of the guppy, cDNA libraries were constructed from embryos and different adult organs to generate expressed sequence tags (ESTs). About 18,000 ESTs were annotated according to BLASTN and BLASTX results and the sequence information from the 3' UTRs was exploited to generate PCR primers for re-sequencing of genomic DNA from different wild type strains. By comparison of EST-linked genomic sequences from at least four different ecotypes, about 1,700 polymorphisms were identified, representing about 400 distinct genes. Two interconnected MySQL databases were built to organize the ESTs and markers, respectively. A robust phylogeny of the guppy was reconstructed, based on 10 different nuclear genes.
Conclusion
Our EST and marker databases provide useful tools for genetic mapping and phylogenetic studies of the guppy.

Background
The diversity of visual systems in fish has long been of interest for evolutionary biologists and neurophysiologists, and has recently begun to attract the attention of molecular evolutionary geneticists. Several recent studies on the copy number and genomic organization of visual pigment proteins, the opsins, have revealed an increased opsin diversity in fish relative to most vertebrates, brought about through recent instances of opsin duplication and divergence. However, for the subfamily of opsin genes that mediate vision at the long-wavelength end of the spectrum, the LWS opsins, it appears that most fishes possess only one or two loci, a value comparable to most other vertebrates. Here, we characterize the LWS opsins from cDNA of an individual guppy, Poecilia reticulata, a fish that is known exhibit variation in its long-wavelength sensitive visual system, mate preferences and colour patterns.
Results
We identified six LWS opsins expressed within a single individual. Phylogenetic analysis revealed that these opsins descend from duplication events both pre-dating and following the divergence of the guppy lineage from that of the bluefin killifish, Lucania goodei, the closest species for which comparable data exists. Numerous amino acid substitutions exist among these different LWS opsins, many at sites known to be important for visual pigment function, including spectral sensitivity and G-protein activation. Likelihood analyses using codon-based models of evolution reveal significant changes in selective constraint along two of the guppy LWS opsin lineages.
Conclusion
The guppy displays an unusually high number of LWS opsins compared to other fish, and to vertebrates in general. Observing both substitutions at functionally important sites and the persistence of lineages across species boundaries suggests that these opsins might have functionally different roles, especially with regard to G-protein activation. The reasons why are currently unknown, but may relate to aspects of the guppy's behavioural ecology, in which both male colour patterns and the female mate preferences for these colour patterns experience strong, highly variable selection pressures.

Background
Comparisons of functionally important changes at the molecular level in model systems have identified key adaptations driving isolation and speciation. In cichlids, for example, long wavelength-sensitive (LWS) opsins appear to play a role in mate choice and male color variation within and among species. To test the hypothesis that the evolution of elaborate coloration in male guppies (Poecilia reticulata) is also associated with opsin gene diversity, we sequenced long wavelength-sensitive (LWS) opsin genes in six species of the family Poeciliidae.
Results
Sequences of four LWS opsin genes were amplified from the guppy genome and from mRNA isolated from adult guppy eyes. Variation in expression was quantified using qPCR. Three of the four genes encode opsins predicted to be most sensitive to different wavelengths of light because they vary at key amino acid positions. This family of LWS opsin genes was produced by a diversity of duplication events. One, an intronless gene, was produced prior to the divergence of families Fundulidae and Poeciliidae. Between-gene PCR and DNA sequencing show that two of the guppy LWS opsins are linked in an inverted orientation. This inverted tandem duplication event occurred near the base of the poeciliid tree in the common ancestor of Poecilia and Xiphophorus. The fourth sequence has been uncovered only in the genus Poecilia. In the guppies surveyed here, this sequence is a hybrid, with the 5' end most similar to one of the tandem duplicates and the 3' end identical to the other.
Conclusion
Enhanced wavelength discrimination, a possible consequence of opsin gene duplication and divergence, might have been an evolutionary prerequisite for color-based sexual selection and have led to the extraordinary coloration now observed in male guppies and in many other poeciliids.

Well-studied model systems present ideal opportunities to understand the relative roles of contemporary selection versus historical processes in determining population differentiation and speciation. Although guppy populations in Trinidad have been a model for studies of evolutionary ecology and sexual selection for more than 50 years, this work has been conducted with little understanding of the phylogenetic history of this species. We used variation in nuclear (X-src) and mitochondrial DNA (mtDNA) sequences to examine the phylogeographic history of Poecilia reticulata Peters (the guppy) across its entire natural range, and to test whether patterns of morphological divergence are a consequence of parallel evolution. Phylogenetic, nested clade, population genetic, and demographic analyses were conducted to investigate patterns of genetic structure at several temporal scales and are discussed in relation to vicariant events, such as tectonic activity and glacial cycles, shaping northeast South American river drainages. The mtDNA phylogeny defined five major lineages, each associated with one or more river drainages, and analysis of molecular variance also detected geographic structuring among these river drainages in an evolutionarily conserved nuclear (X-src) locus. Nested clade and other demographic analyses suggest that the eastern Venezuela/ western Trinidad region is likely the center of origin of P. reticulata. Mantel tests show that the divergence of morphological characters, known to differentiate on a local scale in response to natural and sexual selection pressures, is not associated with mtDNA genetic distance; however, TreeScan analysis identified several significant associations of these characters with the haplotype tree. Parallel upstream/downstream patterns of morphological adaptation in response to selection pressures reported in P. reticulata within Trinidad rivers appears to persist across the natural range. Our results together with previous studies suggest that, although morphological variation in P. reticulata is primarily attributed to selection, phylogeographic history may also play a role.

Heat denaturation experiments revealed heat stability differences at a locus encoding glucosephosphate isomerase (GPI) in the guppy. Inheritance experiments indicated that the observed differences in heat stability are controlled by a single incomplete dominant autosomal locus.

Visual pigments initiate vision and are characterized by their wavelengths of maximal absorption (λmax). Modifications of the λmax values of visual pigments have allowed organisms to adapt to diverse light environments. The availability of the functional assays of these visual pigments using cultured cells makes vision an ideal genetic system to study the molecular bases of adaptation and genetics of color vision in vertebrates. The visual pigments in vertebrate retinas are distinguished into five evolutionarily distinct groups RH1 (λmax = 490-500 nm), RH2 (470-510 nm), SWS1 (360-420 nm), SWS2 (440-455), and LWS/MWS (510-570 nm). Here, we review amino acid replacements that are associated with the shifts in the λmax values of these visual pigments.
The λmax-shifts in several RH1 pigments seem to reflect adaptive changes to blue environments of the organisms and are explained mostly by amino acid replacements D83N (D → N at residue 83), E122Q, and A292S. Similarly, the blue-shifts in the λmax values of the RH2 pigments can be explained by D83N, E122Q, A164S, and M207L. For the SWS1 pigments of birds, only one amino acid replacement S84C seems to be responsible for the transformation of ultraviolet pigments from the violet pigment. For the LWS/MWS pigments, the additive effects of amino acid differences at 180, 197, 277, 285, and 308 fully explain the red-green color vision in a wide range of vertebrates. All of these observations suggest that the evolution of the extant visual pigments can be explained by amino acid replacements at only a small number of sites.
Visual pigments, a group of G-protein-coupled receptors, initiate visual excitation (Wald 1968). Each visual pigment consists of a transmembrane protein, opsin, and the chromophore, 11-cis-retinal, and can be characterized by its wavelength of maximal absorption (λmax). Human color vision is mediated by `blue', `green', and `red' visual pigments. The `blue' pigments absorb wavelengths ranging from about 370 nm to 570 nm with a λmax at 420 nm, while both `green' and `red' pigments are sensitive to wavelength about 450-620 nm with λmax values at 530 nm and 560 nm, respectively (Nathans 1989). The molecular bases of the spectral tuning of these and other visual pigments in vertebrates are still not well understood. Recently, however, some significant progress has been made on this subject.
To evaluate the mechanisms of the functional properties of visual pigments, a large number of amino acid changes have been introduced into the bovine rod-specific visual pigment (rhodopsin) by several groups of vision scientists (for a review, see Yokoyama 1997). In most of these analyses, charged amino acids have been considered. For example, an amino acid change from glutamic acid at residue 113 (E113) to glutamine (E113Q) shifts the λmax of the pigment from 500 nm to 380 nm (Sakmar et al. 1989; Zhukovsky and Oprian 1989; Nathans 1990a, b). E113 is the negatively charged counterion to the positively charged protonated Schiff base and the modification of this opsin structure causes a drastic shift in the λmax value of the pigment. Unfortunately, most of these amino acid changes, including E113Q, have not been found in nature. Thus, it is not immediately clear how these mutagenesis results are helpful in elucidating the molecular basis for the divergence of λmax values of visual pigments in nature (Yokoyama 1995, 1997).

Response to low temperature was measured in different strains in the guppy, Poecilia reticulata. The responses of each strain were measured as survival rates, which were calculated from the survived fish after 24 h at 12°C for fishes acclimated at 23°C. The values for response measurements demonstrate the survival rates that were very different among strains, and among females and males within each strain.
The progeny tests for resistant (R) and susceptible (r) to the low temperature treatment in intra-crosses indicated a mode of sex-linked inheritance.

Sexual selection may favour the evolution of elaborated genital traits in males, particularly when phenotypic variation in such traits results in corresponding variation in reproductive success among males in the population. Compared with insects, very little is known about the natural variation in any male genital trait, and its causes, in vertebrates. Here we report on variation in a male intromittent organ both within and between natural populations of a vertebrate, the Trinidadian guppy (Poecilia reticulata). Male guppies inseminate females using an intromittent organ called the gonopodium. We demonstrate that males from populations that have evolved under high fish-predation intensity have, on average, a relatively longer gonopodium than males originating from populations under low fish-predation intensity. Compared with body coloration, the gonopodium exhibited relatively low phenotypic variation, but nonetheless was within the range of known variation for sexually selected traits. The male gonopodium was positively allometric in general. To our knowledge, this is the first report of within-species variation in an intromittent organ and of a positive allometric relationship between male genitalia and body size in a vertebrate species. Our results suggest that the length of the male intromittent organ in the guppy is under selection, which varies geographically.

The empirical study of natural selection reveals that adaptations often involve trade-offs between competing functions. Because natural selection acts on whole organisms rather than isolated traits, adaptive evolution may be constrained by the interaction between traits that are functionally integrated. Yet, few attempts have been made to characterize how and when such constraints are manifested or whether they limit the adaptive divergence of populations. Here we examine the consequences of adaptive life-history evolution on locomotor performance in the live-bearing guppy. In response to increased predation from piscivorous fish, Trinidadian guppies evolve an increased allocation of resources toward reproduction. These populations are also under strong selection for rapid fast-start swimming performance to evade predators. Because embryo development increases a female’s wet mass as she approaches parturition, an increased investment in reproductive allocation should impede faststart performance. We find evidence for adaptive but constrained evolution of fast-start swimming performance in laboratory trials conducted on second-generation lab-reared fish. Female guppies from high-predation localities attain a faster acceleration and velocity and travel a greater distance during fast-start swimming trials. However, velocity and distance traveled decline more rapidly over the course of pregnancy in these same females, thus reducing the magnitude of divergence in swimming performance between high- and low-predation populations. This functional trade-off between reproduction and swimming performance reveals how different aspects of the phenotype are integrated and highlights the complexity of adaptation at the whole-organism level.
Keywords: adaptation, constraint, life-history evolution, swimming performance, fast start, trade-offs.