Sequence Analysis Methods Research Articles

PERSEPSI DAN PREFERENSI MASYARAKAT TERHADAP FASAD BANGUNAN DI KORIDOR JALAN KI SAMAUN KOTA TANGERANG

This research aims to discover people’s perceptions and preferences towards building façade. This research has used a mixed-method approach with the triangulation of data validation. In the analysis, a sequence-analysis method has been utilized, beginning from qualitative descriptive to quantitative one. Data were collected from in-depth-interview with several key persons like district official, officers of certain governmental departments, and questionnaire distribution to the people who have their daily activities in Ki SamaunStreet, which is part of Kota Lama area in Tangerang City. The findings of this study show that colors; architectural design; width and height of the buildings and building-‘s’ ornaments are the most important elements in building façade that can be used to comprehend the people’s perceptions and preferences. This study has found that there are similarities between people’s perceptions and preferences with the Kota Lama’s development plans. Both sides are of the opinion that the colors of the buildings are similar, unpleasant, and there are some buildings more stand out than the others. Both sides also perceive that the architectural style of the buildings no longer represents the Chinese culture. This makes the restoration work to reverse the façade back into its original form is essential. Both sides also recognize that building-‘s’ height and width are not in harmony, although the people think that renovation is not needed. Both sides also observe that there are no buildingswith similar ornaments; whilesignage is the main source of visual pollution and rearrangement of signage is needed.

Site-Specific Amino Acid Preferences Are Mostly Conserved in Two Closely Related Protein Homologs.

Evolution drives changes in a protein’s sequence over time. The extent to which these changes in sequence lead to shifts in the underlying preference for each amino acid at each site is an important question with implications for comparative sequence-analysis methods, such as molecular phylogenetics. To quantify the extent that site-specific amino acid preferences shift during evolution, we performed deep mutational scanning on two homologs of human influenza nucleoprotein with 94% amino acid identity. We found that only a modest fraction of sites exhibited shifts in amino acid preferences that exceeded the noise in our experiments. Furthermore, even among sites that did exhibit detectable shifts, the magnitude tended to be small relative to differences between nonhomologous proteins. Given the limited change in amino acid preferences between these close homologs, we tested whether our measurements could inform site-specific substitution models that describe the evolution of nucleoproteins from more diverse influenza viruses. We found that site-specific evolutionary models informed by our experiments greatly outperformed nonsite-specific alternatives in fitting phylogenies of nucleoproteins from human, swine, equine, and avian influenza. Combining the experimental data from both homologs improved phylogenetic fit, partly because measurements in multiple genetic contexts better captured the evolutionary average of the amino acid preferences for sites with shifting preferences. Our results show that site-specific amino acid preferences are sufficiently conserved that measuring mutational effects in one protein provides information that can improve quantitative evolutionary modeling of nearby homologs.

Design and application of a core genome multilocus sequence typing scheme for investigation of Legionnaires' disease incidents.

Sequence-based typing (SBT) for Legionella pneumophila (Lp) has dramatically improved Legionnaires’ disease (LD) cluster investigation. Microbial whole genome sequencing (WGS) is a promising modality for investigation but sequence analysis methods are neither standardised, nor agreed. We sought to develop a WGS-based typing scheme for Lp using de novo assembly and a genome-wide gene-by-gene approach (core genome multilocus sequence typing, cgMLST). We analysed 17 publicly available Lp genomes covering the whole species variation to define a core genome (1,521 gene targets) which was validated using 21 additional published genomes. The genomes of 12 Lp strains implicated in three independent cases of paediatric humidifier-associated LD were subject to cgMLST together with three 'outgroup' strains. cgMLST was able to resolve clustered strains and clearly identify related and unrelated strains. Thus, a cgMLST scheme was readily achievable and provided high-resolution analysis of Lp strains. cgMLST appears to have satisfactory discriminatory power for LD cluster analysis and is advantageous over mapping followed by single nucleotide polymorphism (SNP) calling as it is portable and easier to standardise. cgMLST thus has the potential for becoming a gold standard tool for LD investigation. Humidifiers pose an ongoing risk as vehicles for LD and should be considered in cluster investigation and control efforts.

Investigation of ganciclovir resistance in CMV UL54 and UL97 gene regions in immunocompromised patients receiving gancyclovir treatment

Cytomegalovirus (CMV) is a main cause of severe morbidity and mortality in immunocompromised patients. Ganciclovir (GCV) is used for both prophylaxis and treatment of CMV disease with successful results, however GCV resistance has been increasingly reported. The aim of this study was to investigate the GCV resistance in patients whose viral loads did not decline (≥1000 copies/mL) despite of receiving GCV treatment, by using sequence analysis method. A total of 30 patients, 25 of them were bone marrow transplant (BMT) and five who were followed in hematology clinics (non-Hodgkin lymphoma, lung cancer, diffuse large B cell lymphoma, combined immune deficiency, chronic lymphocytic leukemia) were included in the study. CMV-DNA levels were monitored by real-time polymerase chain reaction (QIAsymphony, Artus® CMV QS-RGQ kit, Qiagen, Germany), and DNA sequence analysis (ABI 310 Genetic Analyzer, Applied Biosystems, USA) was performed to detect the mutations leading to CMV antiviral drug resistance in following gene regions: 420-664 codons in UL97 gene region and 261 to 588 and 740 to 987 codons in UL54 gene region. Of 30 patients included, M460V mutation in CMV UL97 gene region was detected in one (3.3%) (1st case) and L802M mutation in UL54 gene region, in addition to P887S and S897L variant sequences in another patient (3.3%) (2nd case). The first patient was a 20-year-old male with acute myeloid leukemia who underwent BMT. The blood sample for the investigation of antiviral drug resistance was taken on the 117th day of transplantation (with simultaneous viral load 4470 copies/mL) and the patient has been using GCV for 70 days when the sample was taken. Valganciclovir (VGCV) and foscarnet (FOS) were used for the therapy of the first patient and monitored. The second patient was a 19-year-old male with acute lymphoblastic leukemia who underwent BMT. The blood sample for the investigation of antiviral drug resistance was taken on the 109th day of transplantation (with simultaneous viral load 4830 copies/mL) and the patient received GCV for 26 days and VGCV for 40 days when the sample was taken. FOS and cidofovir were used for the therapy of the second patient but the patient was lost due to the underlying diseases. In conclusion, mutations responsible for GCV resistance was detected in 6.6% (2/30) of immunocompromised patients receiving GCV, indicating that the determination of CMV antiviral drug resistance may help clinicians for planning the antiviral therapy.

Determination of HER2 and p53 Mutations by Sequence Analysis Method and EGFR/Chromosome 7 Gene Status by Fluorescence in Situ Hybridization for the Predilection of Targeted Therapy Modalities in Immunohistochemically Triple Negative Breast Carcinomas in Turkish Population

Triple negative breast cancer (TNBC), an agressive subtype accounts nearly 15 % of all breast carcinomas. Conventional chemotherapy is the only treatment modality thus new, effective targeted therapy methods have been investigated. Epidermal growth factor receptor (EGFR) inhibitors give hope according to the recent studies results. Also therapeutic agents have been tried against aberrant p53 signal activity as TNBC show high p53 mutation rates. Our aim was to detect the incidence of mutations/amplifications identified in TNBC in our population. Here we used sequence analysis to detect HER2 (exon 18-23), p53 (exon 5-8) mutations; fluorescence in situ hybridization (FISH) method to analyse EGFR/chromosome 7 centromere gene status in 82 immunohistochemically TNBC. Basaloid phenotype was identified in 49 (59.8 %) patients. EGFR amplification was noted in 5 cases (6.1 %). All EGFR amplified cases showed EGFR overexpression by immunohistochemistry (IHC). p53 mutations were identified in 33 (40.2 %) cases. Almost 60 % of the basal like breast cancer cases showed p53 mutation. Only one case showed HER2 mutation (exon 20:g.36830_3). Our results showed that gene amplification is not the unique mechanism in EGFR overexpression. IHC might be used in the decision of anti-EGFR therapy in routine practice. p53 mutation rate was lower than the rates reported in the literature probably due to ethnic differences and low sensitivity of sanger sequences in general mutation screening. We also established the rarity of HER2 mutation in TNBC. In conclusion EGFR and p53 are the major targets in TNBC also for our population.

Re-sequencing and assembly of chicken T cell receptor gamma locus

The genomic organization of the animal T cell receptor (TCR) loci is characterized by different gene families with high homology, and it is quite difficult to obtain accurate gene sequences and arrangements of these gene families. In this study, we identified the location of chicken TCR gamma chain (TCRγ or TRG) genes by comparing those TRG gene sequences with the chicken reference genome, and the corresponding bacterial artificial chromosome (BAC) clone, CH261-174P24, was chosen for further high-throughput DNA re-sequencing and assembly. As a result, a draft genome assembly containing ten scaffolds was obtained, which almost covered the chicken TRG gene locus and the flanking regions. Subsequently, the internal structure of these scaffolds was confirmed by PCR amplification and Sanger sequencing. Our analysis corrected two errors in the sequence-one near a TRG variable gene and one close to a gap, respectively, and several errors in the TRG variable genes in the chicken reference genome. In conclusion, our work has partially corrected the erroneously assembled sequences of the TRG gene locus in the chicken reference genome and thus provides a new method for genome sequence analysis of chicken TRA/D and TRB gene loci.

Prediction of multi-drug resistance transporters using a novel sequence analysis method.

There are many examples of groups of proteins that have similar function, but the determinants of functional specificity may be hidden by lack of sequence similarity, or by large groups of similar sequences with different functions. Transporters are one such protein group in that the general function, transport, can be easily inferred from the sequence, but the substrate specificity can be impossible to predict from sequence with current methods. In this paper we describe a linguistic-based approach to identify functional patterns from groups of unaligned protein sequences and its application to predict multi-drug resistance transporters (MDRs) from bacteria. We first show that our method can recreate known patterns from PROSITE for several motifs from unaligned sequences. We then show that the method, MDRpred, can predict MDRs with greater accuracy and positive predictive value than a collection of currently available family-based models from the Pfam database. Finally, we apply MDRpred to a large collection of protein sequences from an environmental microbiome study to make novel predictions about drug resistance in a potential environmental reservoir.

Global Diversity within and between Human Herpesvirus 1 and 2 Glycoproteins.

Human herpes simplex viruses 1 and 2 (HSV-1 and HSV-2) are large-genome DNA viruses that establish a persistent infection in sensory neurons and commonly manifest with recurring oral or genital erosions that transmit virus. HSV encodes 12 predicted glycoproteins that serve various functions, including cellular attachment, entry, and egress. Glycoprotein G is currently the target of an antibody test to differentiate HSV-1 from HSV-2; however, this test has shown reduced capacity to differentiate HSV strains in East Africa. Until the recent availability of 26 full-length HSV-1 and 36 full-length HSV-2 sequences, minimal comparative information was available for these viruses. In this study, we use a variety of sequence analysis methods to compare all available sequence data for HSV-1 and HSV-2 glycoproteins, using viruses isolated in Europe, Asia, North America, the Republic of South Africa, and East Africa. We found numerous differences in diversity, nonsynonymous/synonymous substitution rates, and recombination rates between HSV-1 glycoproteins and their HSV-2 counterparts. Phylogenetic analysis revealed that while most global HSV-2 glycoprotein G sequences did not form clusters within or between continents, one clade (supported at 60.5%) contained 37% of the African sequences analyzed. Accordingly, sequences from this African subset contained unique amino acid signatures, not only in glycoprotein G, but also in glycoproteins I and E, which may account for the failure of sensitive antibody tests to distinguish HSV-1 from HSV-2 in some African individuals. Consensus sequences generated in the study can be used to improve diagnostic assays that differentiate HSV-1 from HSV-2 in global populations. Human herpes simplex viruses 1 and 2 (HSV-1 and HSV-2) are large DNA viruses associated with recurring oral or genital erosions that transmit virus. Up to 12 HSV-1 and HSV-2 glycoproteins are involved in HSV cell entry or are required for viral spread in animals, albeit some are dispensable for replication in vitro. The recent availability of comparable numbers of full-length HSV-1 and HSV-2 sequences enabled comparative analysis of gene diversity of glycoproteins within and between HSV types. Overall, we found less glycoprotein sequence diversity within HSV-2 than within the HSV-1 strains studied, while at the same time, several HSV-2 glycoproteins were evolving under less selective pressure. Because HSV glycoproteins are the focus of antibody tests to detect and differentiate between infections with the two strains and are constituents of vaccines in clinical-stage development, these findings will aid in refining the targets for diagnostic tests and vaccines.

Synthesis and use of universal sequence probes in fluorogenic multi-strand hybridisation complexes for economical nucleic acid testing

Analysis of nucleic acid amplification products has become the gold standard for applications such as pathogen detection and characterisation of single nucleotide polymorphisms and short tandem repeat sequences. The development of real-time PCR and melting curve analysis using fluorescent probes has simplified nucleic acid analyses. However, the cost of probe synthesis can be prohibitive when developing large panels of tests. We describe an economic two-stage method for probe synthesis, and a new method for nucleic acid sequence analysis which together considerably reduce costs. The analysis method utilises three-strand and four-strand hybridisation complexes for the detection and identification of nucleic acid target sequences by real-time PCR and fluorescence melting.

Prediction of multi-drug resistance transporters using a novel sequence analysis method

There are many examples of groups of proteins that have similar function, but the determinants of functional specificity may be hidden by lack of sequence similarity, or by large groups of similar sequences with different functions. Transporters are one such protein group in that the general function, transport, can be easily inferred from the sequence, but the substrate specificity can be impossible to predict from sequence with current methods. In this paper we describe a linguistic-based approach to identify functional patterns from groups of unaligned protein sequences and its application to predict multi-drug resistance transporters (MDRs) from bacteria. We first show that our method can recreate known patterns from PROSITE for several motifs from unaligned sequences. We then show that the method, MDRpred, can predict MDRs with greater accuracy and positive predictive value than a collection of currently available family-based models from the Pfam database. Finally, we apply MDRpred to a large collection of protein sequences from an environmental microbiome study to make novel predictions about drug resistance in a potential environmental reservoir.

SimSeq: a nonparametric approach to simulation of RNA-sequence datasets.

RNA sequencing analysis methods are often derived by relying on hypothetical parametric models for read counts that are not likely to be precisely satisfied in practice. Methods are often tested by analyzing data that have been simulated according to the assumed model. This testing strategy can result in an overly optimistic view of the performance of an RNA-seq analysis method. We develop a data-based simulation algorithm for RNA-seq data. The vector of read counts simulated for a given experimental unit has a joint distribution that closely matches the distribution of a source RNA-seq dataset provided by the user. We conduct simulation experiments based on the negative binomial distribution and our proposed nonparametric simulation algorithm. We compare performance between the two simulation experiments over a small subset of statistical methods for RNA-seq analysis available in the literature. We use as a benchmark the ability of a method to control the false discovery rate. Not surprisingly, methods based on parametric modeling assumptions seem to perform better with respect to false discovery rate control when data are simulated from parametric models rather than using our more realistic nonparametric simulation strategy. The nonparametric simulation algorithm developed in this article is implemented in the R package SimSeq, which is freely available under the GNU General Public License (version 2 or later) from the Comprehensive R Archive Network (http://cran.rproject.org/). sgbenidt@gmail.com Supplementary data are available at Bioinformatics online.

ChemInform Abstract: Reading Polymers: Sequencing of Natural and Synthetic Macromolecules

AbstractReview: [81 refs.

Forensic Analysis of Mitochondrial and Autosomal Markers Using Pyrosequencing®.

Forensic casework analyses often face challenges, such as limited genetic material with or without fragmentation and damage. To compensate for low amounts and degradation, shorter amplicons are often applied in the analysis. Also, a change of markers might be necessary using mitochondrial instead of autosomal markers. In addition, forensic research often involves analysis of large number of samples for marker evaluation and population-database compilation. Therefore, a flexible, robust but also rapid method for the detection of variation is highly useful. Pyrosequencing(®) is a rapid, reliable, easy-to-use method for sequence analysis. The method is well suited for rapid forensic analysis of a few targets or analysis of a single target in many samples. It allows sequencing of very short amplicons, which facilitates analysis of degraded DNA. Here we present the use of Pyrosequencing, a robust method for sensitive forensic analysis of mitochondrial DNA, autosomal STRs, and Y-chromosome STRs and SNPs.

What does Evolution Tell us about the Structure of a Functional Amyloid Protein?

Amyloids are insoluble fibrillar protein aggregates. While they are commonly found in human diseases, it is becoming increasingly clear that this type of structure is essential for a range of biological functions, with prominent examples in organisms ranging from bacteria to human. Functional amyloid and pathogenic amyloid share similar physical and chemical properties. Unlike pathological amyloids, however, the structures of functional amyloids are formed by polypeptide sequences whose amyloid structure has been under a positive evolutionary selection pressure. This important distinction provides us with an opportunity to obtain structural insights from an unexpected source: the covariation of amino acids among sequences within the same family of a functional amyloid protein. There is a long history for the idea of using coevolution for molecular structure prediction, but recent growth in sequence databases and new, efficient algorithms to disentangle indirect couplings in a network, have dramatically improved our ability to predict residue-residue contacts. We used recently developed sequence analysis methods (EVcoupling, PSICOV and GREMLIN) to extract distance restraints from a multiple sequence alignment of a functional amyloid protein. Together with an efficient force field, these restraints allow us to determine atomic resolution structural models. We find that the protein forms a beta-helical structure, where each turn corresponds to previously identified repeat sequences. The proposed structure is validated by previously published solid-state NMR, electron microscopy and X-ray diffraction data, and confirms an earlier proposed model derived by complementary means. To our knowledge, this is the first time the analysis of correlated mutations and computer simulations have been used together to study the structure of a functional amyloid. The current study therefore serves as a probe into the potential applicability of the approach in this domain.

Familial Mediterranean fever in children from the Aegean region of Turkey:gene mutation frequencies and phenotype–genotype correlation

Familial Mediterranean fever (FMF) is diagnosed by fever episodes with sterile peritonitis, arthritis, pleurisy, and erysipelas-like erythema. The relationship between phenotype and genotype in FMF has not been adequately explained. The aim of this study was to characterize the phenotype and genotype correlation in FMF. Clinical diagnosis of FMF was conducted according to the Tel Hashomer criteria. Pras scoring was used to determine clinical severity. FMF strip assay analysis was used, and the hotspot regions were observed with PCR amplification and automatic DNA sequence analysis method. We showed commonly seen mutations (most frequently M694V) in a study group of 191 patients. The disease severity score of patients with M694V mutation was high on the Pras scoring system. Patients with M694V mutation needed high colchicine dosages to control disease activity. R202Q was the most commonly seen polymorphism in 70 patients. The coexpression of R314R single nucleotide polymorphism on third exon was shown in our study. Moreover, D102D, G138G, and A165A subhaplotypes and E474E, Q476Q, and D510D subhaplotypes were also shown. DNA sequence analysis should be a commonly used method for progress in the field of molecular genetics and for the better understanding of the FMF phenotype and genotype relationships in all populations.

Group interactive network and behavioral patterns in online English-to-Chinese cooperative translation activity

This study investigated the group interactive network of students and the behavioral patterns of knowledge construction in online cooperative translation activities without teacher intervention. Participants in this study consisted of 48 EFL learners from a Chinese university who major in educational technology. The following are determined by combining the methods of social network analysis and lag sequence analysis: (1) The group interactive network generated in this activity was reciprocal and balanced, and high cohesiveness and tight interaction relationship exist among groups. (2) In different cooperation phases, the behavioral sequences of knowledge construction of students presented different characteristics. (3) The behavioral sequences between the high-score groups and low-score groups also showed distinct differences. In addition, this study also revealed certain problems in cooperative translation, such as uneven contribution and unrelated chats. Finally, some implications for specialized English translation instruction, the limitations, and future research plan were presented.

Genetic variants of genital mycoplasmas and their relation to the clinical course of inflammatory diseases of the urogenital system in women

Goal of the study. To study genetic variability of M. hominis (based on the vaa gene) and M. genitalium (based on the mg192 gene) derived from biological material samples taken from women with different clinical manifestations of inflammatory diseases of the urogenital system and clinically healthy women (for M. hominis). Materials and methods. Genetic variability of twenty M. hominis samples taken from patients with inflammatory diseases of the urogenital system and twenty M. hominis samples taken from patients without clinical and laboratory signs of inflammatory processes of the urogenital system was studied by the sequence analysis method. Genetic variability of eight M. genitalium samples taken from patients with different clinical signs of inflammatory diseases of the urogenital system was also examined by the sequence analysis method. Results. Three genetic variants of M. hominis based on the vaa gene were found; variant I was revealed more often in patients with clinical manifestations of inflammatory diseases (65.0%), and variant II - in clinically healthy women (60.0%). Three phylogenetic M. gentium groups based on the mg192 gene were revealed; two samples were referred to Groups I and II, and four samples were referred to Group III. Samples from each phylogenetic groups were taken from patients with clinical and laboratory manifestations of cervicitis and urethritis. Conclusion. The study data demonstrate a potential effect of the VAA surface protein on the virulence of opportunistic M. hominis pathogens.

Integrating protein structural dynamics and evolutionary analysis with Bio3D.

BackgroundPopular bioinformatics approaches for studying protein functional dynamics include comparisons of crystallographic structures, molecular dynamics simulations and normal mode analysis. However, determining how observed displacements and predicted motions from these traditionally separate analyses relate to each other, as well as to the evolution of sequence, structure and function within large protein families, remains a considerable challenge. This is in part due to the general lack of tools that integrate information of molecular structure, dynamics and evolution.ResultsHere, we describe the integration of new methodologies for evolutionary sequence, structure and simulation analysis into the Bio3D package. This major update includes unique high-throughput normal mode analysis for examining and contrasting the dynamics of related proteins with non-identical sequences and structures, as well as new methods for quantifying dynamical couplings and their residue-wise dissection from correlation network analysis. These new methodologies are integrated with major biomolecular databases as well as established methods for evolutionary sequence and comparative structural analysis. New functionality for directly comparing results derived from normal modes, molecular dynamics and principal component analysis of heterogeneous experimental structure distributions is also included. We demonstrate these integrated capabilities with example applications to dihydrofolate reductase and heterotrimeric G-protein families along with a discussion of the mechanistic insight provided in each case.ConclusionsThe integration of structural dynamics and evolutionary analysis in Bio3D enables researchers to go beyond a prediction of single protein dynamics to investigate dynamical features across large protein families. The Bio3D package is distributed with full source code and extensive documentation as a platform independent R package under a GPL2 license from http://thegrantlab.org/bio3d/.Electronic supplementary materialThe online version of this article (doi:10.1186/s12859-014-0399-6) contains supplementary material, which is available to authorized users.

A novel method for comparative analysis of DNA sequences by Ramanujan-Fourier transform.

Alignment-free sequence analysis approaches provide important alternatives over multiple sequence alignment (MSA) in biological sequence analysis because alignment-free approaches have low computation complexity and are not dependent on high level of sequence identity. However, most of the existing alignment-free methods do not employ true full information content of sequences and thus can not accurately reveal similarities and differences among DNA sequences. We present a novel alignment-free computational method for sequence analysis based on Ramanujan-Fourier transform (RFT), in which complete information of DNA sequences is retained. We represent DNA sequences as four binary indicator sequences and apply RFT on the indicator sequences to convert them into frequency domain. The Euclidean distance of the complete RFT coefficients of DNA sequences are used as similarity measures. To address the different lengths of RFT coefficients in Euclidean space, we pad zeros to short DNA binary sequences so that the binary sequences equal the longest length in the comparison sequence data. Thus, the DNA sequences are compared in the same dimensional frequency space without information loss. We demonstrate the usefulness of the proposed method by presenting experimental results on hierarchical clustering of genes and genomes. The proposed method opens a new channel to biological sequence analysis, classification, and structural module identification.

Sexual selection and genetic colour polymorphisms in animals.

Genetic colour polymorphisms are widespread across animals and often subjected to complex selection regimes. Traditionally, colour morphs were used as simple visual markers to measure allele frequency changes in nature, selection, population divergence and speciation. With advances in sequencing technology and analysis methods, several model systems are emerging where the molecular targets of selection are being described. Here, we discuss recent studies on the genetics of sexually selected colour polymorphisms, aiming at (i) reviewing the evidence of sexual selection on colour polymorphisms, (ii) highlighting the genetic architecture, molecular and developmental basis underlying phenotypic colour diversification and (iii) discuss how the maintenance of such polymorphisms might be facilitated or constrained by these. Studies of the genetic architecture of colour polymorphism point towards the importance of tight clustering of colour loci with other trait loci, such as in the case of inversions and supergene structures. Other interesting findings include linkage between colour loci and mate preferences or sex determination, and the role of introgression and regulatory variation in fuelling polymorphisms. We highlight that more studies are needed that explicitly integrate fitness consequences of sexual selection on colour with the underlying molecular targets of colour to gain insights into the evolutionary consequences of sexual selection on polymorphism maintenance.