scholarly journals Mutation accumulation in chromosomal inversions maintains wing pattern polymorphism in a butterfly

2019 ◽  
Author(s):  
Paul Jay ◽  
Mathieu Chouteau ◽  
Annabel Whibley ◽  
Héloïse Bastide ◽  
Violaine Llaurens ◽  
...  
Keyword(s):  
Chromosomal Rearrangements ◽  
Mutational Load ◽  
Wing Pattern ◽  
Numerous Species ◽  
Chromosomal Inversions ◽  
Population Genomic ◽  
Genomic Analyses ◽  
Wing Patterns ◽  
Pattern Polymorphism ◽  
Genome Assemblies

While natural selection favours the fittest genotype, polymorphisms are maintained over evolutionary timescales in numerous species. Why these long-lived polymorphisms are often associated with chromosomal rearrangements remains obscure. Combining genome assemblies, population genomic analyses, and fitness assays, we studied the factors maintaining multiple mimetic morphs in the butterfly Heliconius numata. We show that the polymorphism is maintained because three chromosomal inversions controlling wing patterns express a recessive mutational load, which prevents their fixation despite their ecological advantage. Since inversions suppress recombination and hamper genetic purging, their formation fostered the capture and accumulation of deleterious variants. This suggests that many complex polymorphisms, instead of representing adaptations to the existence of alternative ecological optima, could be maintained primarily because chromosomal rearrangements are prone to carrying recessive harmful mutations.

scholarly journals Dissecting supergene: evidence for recombination suppression among multiple functional loci within inversions.

2021 ◽  
Author(s):  
Paul Jay ◽  
Manon Leroy ◽  
Yann Le Poul ◽  
Annabel Whibley ◽  
Monica Arias ◽  
...  
Keyword(s):  
Association Studies ◽  
Chromosomal Rearrangements ◽  
Genome Wide Association Studies ◽  
Wing Pattern ◽  
Multiple Traits ◽  
Recombination Suppression ◽  
Adaptive Mutations ◽  
Wing Patterns ◽  
Pattern Polymorphism ◽  
The Individual

Supergenes are genetic architectures associated with discrete and concerted variation in multiple traits. It has long been suggested that supergenes control these complex polymorphisms by suppressing recombination between set of coadapted genes. However, because recombination suppression hinders the dissociation of the individual effects of genes within supergenes, there is still little evidence that supergenes evolve by tightening linkage between coadapted genes. Here, combining an landmark-free phenotyping algorithm with multivariate genome wide association studies, we dissected the genetic basis of wing pattern variation in the butterfly Heliconius numata. We showed that the supergene controlling the striking wing-pattern polymorphism displayed by this species contains many independent loci associated with different features of wing patterns. The three chromosomal inversions of this supergene suppress recombination between these loci, supporting the hypothesis that they may have evolved because they captured beneficial combinations of alleles. Some of these loci are associated with colour variations only in morphs controlled by inversions, indicating that they were recruited after the formation of these inversions. Our study shows that supergenes and clusters of adaptive loci in general may form via the evolution of chromosomal rearrangements suppressing recombination between co-adapted loci but also via the subsequent recruitment of linked adaptive mutations.

scholarly journals Genome evolution of the psammophyte Pugionium for desert adaptation and further speciation

2021 ◽  
Vol 118 (42) ◽  
pp. e2025711118
Author(s):  
Quanjun Hu ◽  
Yazhen Ma ◽  
Terezie Mandáková ◽  
Sheng Shi ◽  
Chunlin Chen ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Stress Responses ◽  
De Novo ◽  
Lignin Biosynthesis ◽  
Gene Families ◽  
Population Genomic ◽  
Interspecific Divergence ◽  
Genomic Analyses ◽  
Environmental Adaptations ◽  
Genome Assemblies

Deserts exert strong selection pressures on plants, but the underlying genomic drivers of ecological adaptation and subsequent speciation remain largely unknown. Here, we generated de novo genome assemblies and conducted population genomic analyses of the psammophytic genus Pugionium (Brassicaceae). Our results indicated that this bispecific genus had undergone an allopolyploid event, and the two parental genomes were derived from two ancestral lineages with different chromosome numbers and structures. The postpolyploid expansion of gene families related to abiotic stress responses and lignin biosynthesis facilitated environmental adaptations of the genus to desert habitats. Population genomic analyses of both species further revealed their recent divergence with continuous gene flow, and the most divergent regions were found to be centered on three highly structurally reshuffled chromosomes. Genes under selection in these regions, which were mainly located in one of the two subgenomes, contributed greatly to the interspecific divergence in microhabitat adaptation.

scholarly journals Chromosome arm specific patterns of polymorphism associated with chromosomal inversions in the major African malaria vector, Anopheles funestus

2016 ◽  
Author(s):  
Colince Kamdem ◽  
Caroline Fouet ◽  
Bradley J. White
Keyword(s):  
Chromosomal Rearrangements ◽  
Anopheles Funestus ◽  
Sequence Divergence ◽  
Sub Saharan Africa ◽  
Chromosomal Inversions ◽  
Genomic Analyses ◽  
Chromosome Arm ◽  
Sub Saharan ◽  
Moisture Conditions ◽  
Two Populations

AbstractChromosomal inversions facilitate local adaptation of beneficial mutations and modulate genetic polymorphism, but the extent of their effects within the genome is still insufficiently understood. The genome of Anopheles funestus, a malaria mosquito endemic to sub-Saharan Africa, contains an impressive number of paracentric polymorphic inversions, which are unevenly distributed among chromosomes and provide an excellent framework for investigating the genomic impacts of chromosomal rearrangements. Here we present results of a fine-scale analysis of genetic variation within the genome of two weakly differentiated populations of Anopheles funestus inhabiting contrasting moisture conditions in Cameroon. Using population genomic analyses, we found that genetic divergence between the two populations is centered on regions of the genome corresponding to three inversions, which are characterized by high values of FST, absolute sequence divergence and fixed differences. Importantly, in contrast to the 2L chromosome arm, which is collinear, nucleotide diversity is significantly reduced along the entire length of three autosome arms bearing multiple overlapping chromosomal rearrangements. These findings support the idea that interactions between reduced recombination and natural selection within inversions contribute to sculpt nucleotide polymorphism across chromosomes in An. funestus.

scholarly journals Admixture can readily lead to the formation of supergenes

2020 ◽  
Author(s):  
Paul Jay ◽  
Thomas G. Aubier ◽  
Mathieu Joron
Keyword(s):  
Gene Flow ◽  
Population Genetic ◽  
Chromosomal Rearrangements ◽  
Theoretical Research ◽  
Mutational Load ◽  
Genetic Origin ◽  
Chromosomal Inversions ◽  
Complex Phenotypes ◽  
History Of ◽  
And Inversion

Supergenes are genetic architectures allowing the segregation of alternative combinations of alleles underlying complex phenotypes. The co-segregation of sets of alleles at linked loci is determined by polymorphic chromosomal rearrangements suppressing recombination locally. Supergenes are involved in many complex polymorphisms, including sexual, color or behavioral polymorphisms in numerous plants, fungi, mammals, fish, and insects. Despite a long history of empirical and theoretical research, the genetic origin of supergenes remains poorly understood. Here, using a population genetic two-island model, we explore how the evolution of overdominant chromosomal inversions may lead to the formation of supergenes. We show that the evolution of inversions in differentiated populations connected by gene flow leads to an increase in frequency of poorly adapted, immigrant haplotypes. When inversions are associated with recessive fitness cost hampering their fixation (such as a mutational load), this results in the formation of supergenes. These results provide a realistic scenario for the evolution of supergenes and inversion polymorphisms in general, and bring new light into the importance of admixture in the formation of new genetic architectures.

Revision of Hista Oiticica (Lepidoptera: Castniidae) and discussion on the validity of its subspecies

Zootaxa ◽  
2010 ◽  
Vol 2421 (1) ◽  
pp. 1 ◽  
Author(s):  
SIMEÃO S. MORAES ◽  
MARCELO DUARTE ◽  
JORGE M. GONZÁLEZ
Keyword(s):  
Taxonomic Structure ◽  
Wing Pattern ◽  
New Synonyms ◽  
New Synonym ◽  
Wing Patterns ◽  
The Stability

Diurnal Lepidoptera tend to have colorful and conspicuous wing patterns, which is the reason the first classifications of day-flying moths and butterflies were based mainly on wing color and pattern characters. This is the case with the Neotropical Castniidae, which are usually large and colorful day-flying moths. One classification listed 134 species in 32 genera while an alternate classification recognized 81 species. In this paper we examine the taxonomic structure of the genus Hista Oiticica. It is the purpose of this paper to evaluate taxonomically useful characters besides wing pattern with the goal of classifying the taxa of Hista rather than classifying the variation of its wing pattern. In so doing, the results resolve the differences between the two proposed classifications of Hista. In addition, a lectotype is designated for Castnia boisduvalii Walker, 1854 (new synonym of Castnia fabricii Swainson, 1823) to ensure the stability of the name. Other new synonyms are proposed for C. fabricii (C. papagaya Westwood, 1877) and Castnia hegemon Kollar, 1839 (C. menetriesi Boisduval, [1875] and C. hegemon variegata Rothschild, 1919).

scholarly journals Genome sequencing of four culinary herbs reveals terpenoid genes underlying chemodiversity in the Nepetoideae

DNA Research ◽  
2020 ◽  
Vol 27 (3) ◽  
Author(s):  
Nolan Bornowski ◽  
John P Hamilton ◽  
Pan Liao ◽  
Joshua C Wood ◽  
Natalia Dudareva ◽  
...  
Keyword(s):  
Leaf Tissue ◽  
Terpene Synthases ◽  
Genomic Analyses ◽  
Genes Encoding ◽  
Medicinal Properties ◽  
Culinary Herbs ◽  
Rosmarinus Officinalis L ◽  
Origanum Majorana ◽  
Genome Assemblies ◽  
High Quality Genome

Abstract Species within the mint family, Lamiaceae, are widely used for their culinary, cultural, and medicinal properties due to production of a wide variety of specialized metabolites, especially terpenoids. To further our understanding of genome diversity in the Lamiaceae and to provide a resource for mining biochemical pathways, we generated high-quality genome assemblies of four economically important culinary herbs, namely, sweet basil (Ocimum basilicum L.), sweet marjoram (Origanum majorana L.), oregano (Origanum vulgare L.), and rosemary (Rosmarinus officinalis L.), and characterized their terpenoid diversity through metabolite profiling and genomic analyses. A total 25 monoterpenes and 11 sesquiterpenes were identified in leaf tissue from the 4 species. Genes encoding enzymes responsible for the biosynthesis of precursors for mono- and sesqui-terpene synthases were identified in all four species. Across all 4 species, a total of 235 terpene synthases were identified, ranging from 27 in O. majorana to 137 in the tetraploid O. basilicum. This study provides valuable resources for further investigation of the genetic basis of chemodiversity in these important culinary herbs.

A new species of the genus Teratozephyrus Sibatani, 1946 from China (Lepidoptera, Lycaenidae, Theclinae)

Zootaxa ◽  
2021 ◽  
Vol 4963 (1) ◽  
pp. 187-192
Author(s):  
SI-YAO HUANG ◽  
FAN JIANG ◽  
HAI-TIAN SONG
Keyword(s):  
New Species ◽  
Male Genitalia ◽  
The Other ◽  
Southwestern China ◽  
Wing Pattern ◽  
Southeastern China ◽  
Wing Patterns ◽  
A New Species

A new species, T. yaolihuoi Huang, Jiang & Song sp. nov. of the genus Teratozephyrus Sibatani, 1946 is described from southeastern China. Among the other representatives of the genus, the new species resembles only T. hinomaru Fujioka, 1994 from southwestern China, from which the new species can be separated easily by examining details in both wing pattern and the male genitalia. Wing patterns and genitalia of the new species and T. hinomaru are illustrated and compared.

scholarly journals The Popgen Pipeline Platform: A Software Platform for Facilitating Population Genomic Analyses

2019 ◽  
Author(s):  
Andrew Webb ◽  
Jared Knoblauch ◽  
Nitesh Sabankar ◽  
Apeksha Sukesh Kallur ◽  
Jody Hey ◽  
...  
Keyword(s):  
Open Source ◽  
Development Time ◽  
End Users ◽  
File Format ◽  
Software Platform ◽  
Format Conversion ◽  
Link Type ◽  
Population Genomic ◽  
Genomic Analyses ◽  
File Format Conversion

AbstractHere we present the Pop-Gen Pipeline Platform (PPP), a software platform with the goal of reducing the computational expertise required for conducting population genomic analyses. The PPP was designed as a collection of scripts that facilitate common population genomic workflows in a consistent and standardized Python environment. Functions were developed to encompass entire workflows, including: input preparation, file format conversion, various population genomic analyses, output generation, and visualization. By facilitating entire workflows, the PPP offers several benefits to prospective end users - it reduces the need of redundant in-house software and scripts that would require development time and may be error-prone, or incorrect. The platform has also been developed with reproducibility and extensibility of analyses in mind. The PPP is an open-source package that is available for download and use at https://ppp.readthedocs.io/en/latest/PPP_pages/install.html

scholarly journals Improved Understanding of the Role of Gene and Genome Duplications in Chordate Evolution With New Genome and Transcriptome Sequences

2021 ◽  
Vol 9 ◽  
Author(s):  
Madeleine E. Aase-Remedios ◽  
David E. K. Ferrier
Keyword(s):  
Chromosomal Rearrangements ◽  
Expression Patterns ◽  
Gene Families ◽  
Evolutionary Transitions ◽  
Whole Genome Duplications ◽  
Chordate Evolution ◽  
Genome Duplications ◽  
The Many ◽  
Genome Assemblies ◽  
The Impact

Comparative approaches to understanding chordate genomes have uncovered a significant role for gene duplications, including whole genome duplications (WGDs), giving rise to and expanding gene families. In developmental biology, gene families created and expanded by both tandem and WGDs are paramount. These genes, often involved in transcription and signalling, are candidates for underpinning major evolutionary transitions because they are particularly prone to retention and subfunctionalisation, neofunctionalisation, or specialisation following duplication. Under the subfunctionalisation model, duplication lays the foundation for the diversification of paralogues, especially in the context of gene regulation. Tandemly duplicated paralogues reside in the same regulatory environment, which may constrain them and result in a gene cluster with closely linked but subtly different expression patterns and functions. Ohnologues (WGD paralogues) often diversify by partitioning their expression domains between retained paralogues, amidst the many changes in the genome during rediploidisation, including chromosomal rearrangements and extensive gene losses. The patterns of these retentions and losses are still not fully understood, nor is the full extent of the impact of gene duplication on chordate evolution. The growing number of sequencing projects, genomic resources, transcriptomics, and improvements to genome assemblies for diverse chordates from non-model and under-sampled lineages like the coelacanth, as well as key lineages, such as amphioxus and lamprey, has allowed more informative comparisons within developmental gene families as well as revealing the extent of conserved synteny across whole genomes. This influx of data provides the tools necessary for phylogenetically informed comparative genomics, which will bring us closer to understanding the evolution of chordate body plan diversity and the changes underpinning the origin and diversification of vertebrates.

scholarly journals Author Correction: Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch

2019 ◽  
Vol 51 (7) ◽  
pp. 1187-1189
Author(s):  
Jarkko Salojärvi ◽  
Olli-Pekka Smolander ◽  
Kaisa Nieminen ◽  
Sitaram Rajaraman ◽  
Omid Safronov ◽  
...  
Keyword(s):  
Genome Sequencing ◽  
Silver Birch ◽  
Adaptive Landscape ◽  
Population Genomic ◽  
Genomic Analyses
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