scholarly journals A novel locus on chromosome 1 underlies the evolution of a melanic plumage polymorphism in a wild songbird

2017 ◽  
Vol 4 (2) ◽  
pp. 160805 ◽  
Author(s):  
Yann X. C. Bourgeois ◽  
Boris Delahaie ◽  
Mathieu Gautier ◽  
Emeline Lhuillier ◽  
Pierre-Jean G. Malé ◽  
...  
Keyword(s):  
Balancing Selection ◽  
Phenotypic Diversity ◽  
Intermediate Frequency ◽  
Chromosome 1 ◽  
Ancestral Population ◽  
Naturally Occurring ◽  
Plumage Polymorphism ◽  
Phenotypic Diversification ◽  
Colour Patterns ◽  
Colour Morphs

Understanding the mechanisms responsible for phenotypic diversification within and among species ultimately rests with linking naturally occurring mutations to functionally and ecologically significant traits. Colour polymorphisms are of great interest in this context because discrete colour patterns within a population are often controlled by just a few genes in a common environment. We investigated how and why phenotypic diversity arose and persists in the Zosterops borbonicus white-eye of Reunion (Mascarene archipelago), a colour polymorphic songbird in which all highland populations contain individuals belonging to either a brown or a grey plumage morph. Using extensive phenotypic and genomic data, we demonstrate that this melanin-based colour polymorphism is controlled by a single locus on chromosome 1 with two large-effect alleles, which was not previously described as affecting hair or feather colour. Differences between colour morphs appear to rely upon complex cis -regulatory variation that either prevents the synthesis of pheomelanin in grey feathers, or increases its production in brown ones. We used coalescent analyses to show that, from a ‘brown’ ancestral population, the dominant ‘grey’ allele spread quickly once it arose from a new mutation. Since colour morphs are always found in mixture, this implies that the selected allele does not go to fixation, but instead reaches an intermediate frequency, as would be expected under balancing selection.

scholarly journals Heritable variation in colour patterns mediating individual recognition

2017 ◽  
Vol 4 (2) ◽  
pp. 161008 ◽  
Author(s):  
Michael J. Sheehan ◽  
Juanita Choo ◽  
Elizabeth A. Tibbetts
Keyword(s):  
Genetic Diversity ◽  
Balancing Selection ◽  
Phenotypic Diversity ◽  
Individual Recognition ◽  
Genetic Correlations ◽  
Colour Pattern ◽  
Heritable Variation ◽  
Pattern Diversity ◽  
Selection For ◽  
Colour Patterns

Understanding the developmental and evolutionary processes that generate and maintain variation in natural populations remains a major challenge for modern biology. Populations of Polistes fuscatus paper wasps have highly variable colour patterns that mediate individual recognition. Previous experimental and comparative studies have provided evidence that colour pattern diversity is the result of selection for individuals to advertise their identity. Distinctive identity-signalling phenotypes facilitate recognition, which reduces aggression between familiar individuals in P. fuscatus wasps. Selection for identity signals may increase phenotypic diversity via two distinct modes of selection that have different effects on genetic diversity. Directional selection for increased plasticity would greatly increase phenotypic diversity but decrease genetic diversity at associated loci. Alternatively, heritable identity signals under balancing selection would maintain genetic diversity at associated loci. Here, we assess whether there is heritable variation underlying colour pattern diversity used for facial recognition in a wild population of P. fuscatus wasps. We find that colour patterns are heritable and not Mendelian, suggesting that multiple loci are involved. Additionally, patterns of genetic correlations among traits indicated that many of the loci underlying colour pattern variation are unlinked and independently segregating. Our results support a model where the benefits of being recognizable maintain genetic variation at multiple unlinked loci that code for phenotypic diversity used for recognition.

scholarly journals Long-term balancing selection in LAD1 maintains a missense trans-species polymorphism in humans, chimpanzees and bonobos

2014 ◽  
Author(s):  
João C. Teixeira ◽  
Cesare de Filippo ◽  
Antje Weihmann ◽  
Juan R. Meneu ◽  
Fernando Racimo ◽  
...  
Keyword(s):  
Balancing Selection ◽  
Phenotypic Diversity ◽  
Intermediate Frequency ◽  
High Genetic Diversity ◽  
Protein Coding ◽  
Missense Change ◽  
Linear Iga Disease ◽  
Filament Protein

Balancing selection maintains advantageous genetic and phenotypic diversity in populations. When selection acts for long evolutionary periods selected polymorphisms may survive species splits and segregate in present-day populations of different species. Here, we investigate the role of long-term balancing selection in the evolution of protein-coding sequences in the Homo-Pan clade. We sequenced the exome of 20 humans, 20 chimpanzees and 20 bonobos and detected eight coding trans-species polymorphisms (trSNPs) that are shared among the three species and have segregated for approximately 14 million years of independent evolution. While the majority of these trSNPs were found in three genes of the MHC cluster, we also uncovered one coding trSNP (rs12088790) in the gene LAD1. All these trSNPs show clustering of sequences by allele rather than by species and also exhibit other signatures of long-term balancing selection, such as segregating at intermediate frequency and lying in a locus with high genetic diversity. Here we focus on the trSNP in LAD1, a gene that encodes for Ladinin-1, a collagenous anchoring filament protein of basement membrane that is responsible for maintaining cohesion at the dermal-epidermal junction; the gene is also an autoantigen responsible for linear IgA disease. This trSNP results in a missense change (Leucine257Proline) and, besides altering the protein sequence, is associated with changes in gene expression of LAD1.

scholarly journals Reproduction in Trypanosomatids: Past and Present

Biology ◽  
2021 ◽  
Vol 10 (6) ◽  
pp. 471
Author(s):  
Camino Gutiérrez-Corbo ◽  
Bárbara Domínguez-Asenjo ◽  
María Martínez-Valladares ◽  
Yolanda Pérez-Pertejo ◽  
Carlos García-Estrada ◽  
...  
Keyword(s):  
Low Income ◽  
Phenotypic Diversity ◽  
Natural Populations ◽  
Genetic Exchange ◽  
Health Concern ◽  
Current Debate ◽  
Naturally Occurring ◽  
Experimental Works ◽  
Genomic Recombination ◽  
The Impact

Diseases caused by trypanosomatids (Sleeping sickness, Chagas disease, and leishmaniasis) are a serious public health concern in low-income endemic countries. These diseases are produced by single-celled parasites with a diploid genome (although aneuploidy is frequent) organized in pairs of non-condensable chromosomes. To explain the way they reproduce through the analysis of natural populations, the theory of strict clonal propagation of these microorganisms was taken as a rule at the beginning of the studies, since it partially justified their genomic stability. However, numerous experimental works provide evidence of sexual reproduction, thus explaining certain naturally occurring events that link the number of meiosis per mitosis and the frequency of mating. Recent techniques have demonstrated genetic exchange between individuals of the same species under laboratory conditions, as well as the expression of meiosis specific genes. The current debate focuses on the frequency of genomic recombination events and its impact on the natural parasite population structure. This paper reviews the results and techniques used to demonstrate the existence of sex in trypanosomatids, the inheritance of kinetoplast DNA (maxi- and minicircles), the impact of genetic exchange in these parasites, and how it can contribute to the phenotypic diversity of natural populations.

scholarly journals A Naturally Occurring Rgg Variant in Serotype M3 Streptococcus pyogenes Does Not Activate speB Expression Due to Altered Specificity of DNA Binding

2009 ◽  
Vol 77 (12) ◽  
pp. 5411-5417 ◽  
Author(s):  
Kyle V. Kappeler ◽  
Srivishnupriya Anbalagan ◽  
Alexander V. Dmitriev ◽  
Emily J. McDowell ◽  
Melody N. Neely ◽  
...  
Keyword(s):  
Amino Acid ◽  
Streptococcus Pyogenes ◽  
Murine Model ◽  
Cysteine Protease ◽  
Phenotypic Diversity ◽  
Transcriptional Regulator ◽  
Amino Acid Position ◽  
Invasive Disease ◽  
Naturally Occurring

ABSTRACT The transcriptional regulator Rgg of Streptococcus pyogenes is essential for expression of the secreted cysteine protease SpeB. Although all isolates of S. pyogenes possess the speB gene, not all of them produce the protein in vitro. In a murine model of infection, the absence of SpeB production is associated with invasive disease. We speculated that naturally occurring mutations in rgg, which would also abrogate SpeB production, may be present in invasive isolates of S. pyogenes. Examination of the inferred Rgg sequences available in public databases revealed that the rgg gene in strain MGAS315 (a serotype M3 strain associated with invasive disease) encodes a proline at amino acid position 103 (Rgg103P); in contrast, all other strains encode a serine at this position (Rgg103S). A caseinolytic assay and Western blotting indicated that strain MGAS315 does not produce SpeB in vitro. Gene-swapping experiments showed that the rgg gene of MGAS315 is solely responsible for the lack of SpeB expression. In contrast to Rgg103S, Rgg103P does not bind to the speB promoter in gel shift assays, which correlates with a lack of speB expression. Despite its inability to activate speB expression, Rgg103P retains the ability to bind to DNA upstream of norA and to influence its expression. Overall, this study illustrates how variation at the rgg locus may contribute to the phenotypic diversity of S. pyogenes.

scholarly journals A New Catalog of Structural Variants in 1,301 A. thaliana Lines from Africa, Eurasia, and North America Reveals a Signature of Balancing Selection at Defense Response Genes

2020 ◽  
Author(s):  
Mehmet Göktay ◽  
Andrea Fulgione ◽  
Angela M Hancock
Keyword(s):  
North America ◽  
Defense Response ◽  
Balancing Selection ◽  
Natural Populations ◽  
Housekeeping Genes ◽  
Intermediate Frequency ◽  
Genomic Variation ◽  
Nucleotide Polymorphisms ◽  
Structural Variants ◽  
Defense Response Genes

Abstract Genomic variation in the model plant Arabidopsis thaliana has been extensively used to understand evolutionary processes in natural populations, mainly focusing on single-nucleotide polymorphisms. Conversely, structural variation has been largely ignored in spite of its potential to dramatically affect phenotype. Here, we identify 155,440 indels and structural variants ranging in size from 1 bp to 10 kb, including presence/absence variants (PAVs), inversions, and tandem duplications in 1,301 A. thaliana natural accessions from Morocco, Madeira, Europe, Asia, and North America. We show evidence for strong purifying selection on PAVs in genes, in particular for housekeeping genes and homeobox genes, and we find that PAVs are concentrated in defense-related genes (R-genes, secondary metabolites) and F-box genes. This implies the presence of a “core” genome underlying basic cellular processes and a “flexible” genome that includes genes that may be important in spatially or temporally varying selection. Further, we find an excess of intermediate frequency PAVs in defense response genes in nearly all populations studied, consistent with a history of balancing selection on this class of genes. Finally, we find that PAVs in genes involved in the cold requirement for flowering (vernalization) and drought response are strongly associated with temperature at the sites of origin.

scholarly journals Coevolution is linked with phenotypic diversification but not speciation in avian brood parasites

2015 ◽  
Vol 282 (1821) ◽  
pp. 20152056 ◽  
Author(s):  
Iliana Medina ◽  
Naomi E. Langmore
Keyword(s):  
Egg Size ◽  
Biological Diversity ◽  
Phenotypic Diversity ◽  
Arms Race ◽  
Phenotypic Evolution ◽  
Brood Parasites ◽  
Parasitic Species ◽  
Extinction Rates ◽  
Rates Of Evolution ◽  
Phenotypic Diversification

Coevolution is often invoked as an engine of biological diversity. Avian brood parasites and their hosts provide one of the best-known examples of coevolution. Brood parasites lay their eggs in the nests of other species, selecting for host defences and reciprocal counteradaptations in parasites. In theory, this arms race should promote increased rates of speciation and phenotypic evolution. Here, we use recently developed methods to test whether the three largest avian brood parasitic lineages show changes in rates of phenotypic diversity and speciation relative to non-parasitic lineages. Our results challenge the accepted paradigm, and show that there is little consistent evidence that lineages of brood parasites have higher speciation or extinction rates than non-parasitic species. However, we provide the first evidence that the evolution of brood parasitic behaviour may affect rates of evolution in morphological traits associated with parasitism. Specifically, egg size and the colour and pattern of plumage have evolved up to nine times faster in parasitic than in non-parasitic cuckoos. Moreover, cuckoo clades of parasitic species that are sympatric (and share similar host genera) exhibit higher rates of phenotypic evolution. This supports the idea that competition for hosts may be linked to the high phenotypic diversity found in parasitic cuckoos.

Polymorphic HSRs in chromosome 1 of the two semispecies Mus musculus musculus and M. m. domesticus have a common origin in an ancestral population

Chromosoma ◽  
1991 ◽  
Vol 100 (3) ◽  
pp. 147-151 ◽  
Author(s):  
H. Winking ◽  
A. Weith ◽  
B. Boldyreff ◽  
K. Moriwaki ◽  
K. Fredga ◽  
...  
Keyword(s):  
Mus Musculus ◽  
Common Origin ◽  
Chromosome 1 ◽  
Ancestral Population ◽  
Mus Musculus Musculus

scholarly journals Genetics and evidence for balancing selection of a sex-linked colour polymorphism in a songbird

2018 ◽  
Author(s):  
Kang-Wook Kim ◽  
Benjamin C. Jackson ◽  
Hanyuan Zhang ◽  
David P. L. Toews ◽  
Scott A. Taylor ◽  
...  
Keyword(s):  
Balancing Selection ◽  
Regulatory Region ◽  
Intermediate Frequency ◽  
Colour Polymorphism ◽  
Z Chromosome ◽  
Coalescent Simulations ◽  
Putative Regulatory Region ◽  
History Of ◽  
Gouldian Finch ◽  
Selection Of

AbstractColour polymorphisms play a key role in sexual selection and speciation, yet the mechanisms that generate and maintain them are not fully understood. Here, we use genomic and transcriptomic tools to identify the precise genetic architecture and evolutionary history of a sex-linked colour polymorphism in the Gouldian finch Erythrura gouldiae that is also accompanied by remarkable differences in behaviour and physiology. We find that differences in colour are associated with an ~72-kbp region of the Z chromosome in a putative regulatory region for follistatin, an antagonist of the TGF-β superfamily genes. The region is highly differentiated between morphs, unlike the rest of the genome, yet we find no evidence that an inversion is involved in maintaining the distinct haplotypes. Coalescent simulations confirm that there is elevated nucleotide diversity and an excess of intermediate frequency alleles at this locus. We conclude that this pleiotropic colour polymorphism is most probably maintained by balancing selection.

scholarly journals Pervasive Linked Selection and Intermediate-Frequency Alleles Are Implicated in an Evolve-and-Resequencing Experiment of Drosophila simulans

Genetics ◽  
2018 ◽  
Vol 211 (3) ◽  
pp. 943-961 ◽  
Author(s):  
John K. Kelly ◽  
Kimberly A. Hughes
Keyword(s):  
Balancing Selection ◽  
Parallel Evolution ◽  
Rapid Evolution ◽  
Natural Populations ◽  
Intermediate Frequency ◽  
Drosophila Simulans ◽  
Data Sets ◽  
Sequencing Data ◽  
Simulation Tools ◽  
Genome Wide

We develop analytical and simulation tools for evolve-and-resequencing experiments and apply them to a new study of rapid evolution in Drosophila simulans. Likelihood test statistics applied to pooled population sequencing data suggest parallel evolution of 138 SNPs across the genome. This number is reduced by orders of magnitude from previous studies (thousands or tens of thousands), owing to differences in both experimental design and statistical analysis. Whole genome simulations calibrated from Drosophila genetic data sets indicate that major features of the genome-wide response could be explained by as few as 30 loci under strong directional selection with a corresponding hitchhiking effect. Smaller effect loci are likely also responding, but are below the detection limit of the experiment. Finally, SNPs showing strong parallel evolution in the experiment are intermediate in frequency in the natural population (usually 30–70%) indicative of balancing selection in nature. These loci also exhibit elevated differentiation among natural populations of D. simulans, suggesting environmental heterogeneity as a potential balancing mechanism.

Genetic-Evidence for Sympatric Differentiation Between 2 Color Morphs of the Skink Egernia-Whitii

1990 ◽  
Vol 38 (2) ◽  
pp. 117 ◽  
Author(s):  
DA Milton
Keyword(s):  
Low Frequency ◽  
Mate Recognition ◽  
Colour Pattern ◽  
Linkage Disequilibria ◽  
Color Morphs ◽  
The Status ◽  
Colour Patterns ◽  
Colour Morphs ◽  
Granite Rocks ◽  
Two Populations

The viviparous skink Egernia whitii is dimorphic for dorsal colour pattern. Both patterned and plain morphs coexist throughout the species' range. Adults live in family groups beneath exfoliating granite rocks. The closely related E. modesta also coexists in similar habitats in the northern part of the range of E. whitii. The plain E. whitii morph is intermediate in colour pattern between patterned E. whitii and E. modesta. Three populations of E. whitii and two populations of E. modesta were examined electrophoretically to assess the status of the plain morph of E. whitii. There were no fixed differences between the two morphs of E. whitii at any of the 55 loci examined, and loci polymorphic in both rnorphs of E. whitii showed no evidence of linkage disequilibria. Although heterozygosity values (H=0.017�0.002) and the level of polymorphism (P 0.95=0.015) were low, there were highly significant allele frequency differences between sympatric samples of the two morphs of E. whitii. This indicated that the two morphs were conspecific, yet they were not interbreeding at random. The established frequency of gene exchange between the two colour morphs in the three populations sampled varied from 3.6 to 6 individuals per generation. Reproductive data confirmed that both colour morphs of E. whitii produced young of the same dorsal colour pattern as their own in much greater frequency than random. However, females of both colours can and do breed with males of the other colour in very low frequency. Analysis of the lateral colour pattern of the two E. whitii morphs and E. modesta suggests that the colour patterns of the two E. whitii morphs are very similar, yet differ slightly from the colour pattern of E. modesta in the region of geographic overlap of these species. These results suggest that behavioural or microhabit differences between the two morphs may be involved in mate recognition.

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