scholarly journals Introgression of wing pattern alleles and speciation via homoploid hybridization in Heliconius butterflies: a review of evidence from the genome

2013 ◽  
Vol 280 (1752) ◽  
pp. 20122302 ◽  
Author(s):  
Andrew V. Z. Brower
Keyword(s):  
Apparent Paradox ◽  
Closely Related Species ◽  
Adaptive Introgression ◽  
Wing Patterns ◽  
Interspecific Recognition ◽  
Homoploid Hybrid ◽  
Aposematic Signals ◽  
Close Relatives ◽  
Allelic Differentiation ◽  
Trait Introgression

The diverse Müllerian mimetic wing patterns of neotropical Heliconius (Nymphalidae) have been proposed to be not only aposematic signals to potential predators, but also intra- and interspecific recognition signals that allow the butterflies to maintain their specific identities, and which perhaps drive the process of speciation, as well. Adaptive features under differential selection that also serve as cues for assortative mating have been referred to as ‘magic traits’, which can drive ecological speciation. Such traits are expected to exhibit allelic differentiation between closely related species with ongoing gene flow, whereas unlinked neutral traits are expected to be homogenized to a greater degree by introgression. However, recent evidence suggests that interspecific hybridization among Heliconius butterflies may have resulted in adaptive introgression of these very same traits across species boundaries, and in the evolution of new species by homoploid hybrid speciation. The theory and data supporting various aspects of the apparent paradox of ‘magic trait’ introgression are reviewed, with emphasis on population genomic comparisons of Heliconius melpomene and its close relatives.

Genetic variation for monomer–dimer equilibria of esterase-5 in Drosophila pseudoobscura, Drosophila persimilis, and Drosophila miranda

1984 ◽  
Vol 26 (3) ◽  
pp. 374-381 ◽  
Author(s):  
David R. Townsend ◽  
Rama S. Singh
Keyword(s):  
Electrophoretic Mobility ◽  
Enzyme Stability ◽  
Good Deal ◽  
The Other ◽  
Drosophila Pseudoobscura ◽  
Closely Related Species ◽  
Speciation Event ◽  
Population Polymorphism ◽  
Drosophila Persimilis ◽  
Close Relatives

Esterase-5 is a highly polymorphic enzyme in Drosophila pseudoobscura and its close relatives. Numerous alleles have been identified by employing a number of physicochemical properties of the enzyme (e.g. electrophoretic mobility, enzyme stability, subunit dimerization, and variation in monomer–dimer equilibrium). Variation in the monomer–dimer equilibrium of esterase-5 leads to differences in electrophoretic mobility of monomers produced by dimers all of which have the same mobility. In this report we have used this criterion to study variation within, as well as between, four closely related species: D. pseudoobscura pseudoobscura, D. pseudoobscura bogotana. D. persimilis, and D. miranda. All lines were characterized for esterase-5 monomer and dimer mobility at a number of gel concentrations and the comparison was made by plotting log10 monomer – dimer mobility as a function of gel concentration. No variation was found within D. p. pseudoobscura or D. p. bogotana but some variation (two distinct alleles) did occur in D. persimilis. Drosophila miranda is segregating for two alleles, one of which is fixed in D. pseudoobscura and the other one is common in D. persimilis. Thus it seems that the variation in monomer–dimer equilibrium is a rather conservative criterion and that the variation in D. miranda is a good deal older than the speciation event(s) which gave rise to D. miranda and the lineage leading to D. pseudoobscura and D. persimilis.Key words: esterase-5, Drosophila pseudoobscura, monomer–dimer equilibrium, population, polymorphism, speciation, electrophoresis.

scholarly journals Classic and introgressed selective sweeps shape mimicry loci across a butterfly adaptive radiation

2019 ◽  
Author(s):  
Markus Moest ◽  
Steven M. Van Belleghem ◽  
Jennifer E. James ◽  
Camilo Salazar ◽  
Simon H. Martin ◽  
...  
Keyword(s):  
Adaptive Radiation ◽  
Sequence Data ◽  
Colour Pattern ◽  
Stabilizing Selection ◽  
High Coverage ◽  
Adaptive Introgression ◽  
Wing Patterns ◽  
History Of ◽  
Colour Patterns ◽  
Turn Over

AbstractNatural selection leaves distinct signatures in the genome that can reveal the targets and history of adaptive evolution. By analysing high-coverage genome sequence data from four major colour pattern loci sampled from nearly 600 individuals in 53 populations, we show pervasive selection on wing patterns across the Heliconius adaptive radiation. The strongest signatures correspond to loci with the greatest phenotypic effects, consistent with visual selection by predators, and are found in colour patterns with geographically restricted distributions. These recent sweeps are similar between co-mimics and indicate colour pattern turn-over events despite strong stabilizing selection. Using simulations we compare sweep signatures expected under classic hard sweeps with those resulting from adaptive introgression, an important aspect of mimicry evolution in Heliconius. Simulated recipient populations show a distinct ‘volcano’ pattern with peaks of increased genetic diversity around the selected target, consistent with patterns found in some populations. Our genomic data provide unprecedented insights into the recent history of selection across the Heliconius adaptive radiation.

Ribosomal internal transcribed spacer regions are not suitable for intra- or inter-specific phylogeny reconstruction in haplosclerid sponges (Porifera: Demospongiae)

2009 ◽  
Vol 89 (6) ◽  
pp. 1251-1256 ◽  
Author(s):  
Niamh E. Redmond ◽  
Grace P. McCormack
Keyword(s):  
Internal Transcribed Spacer ◽  
Phylogenetic Trees ◽  
Population Level ◽  
Single Species ◽  
Its Sequences ◽  
Closely Related Species ◽  
Internal Transcribed Spacer Regions ◽  
Species Specific ◽  
Close Relatives ◽  
Number Of Individuals

Sequences of the ribosomal internal transcribed spacer regions 1 and 2 (ITS-1 and ITS-2) were employed to investigate relationships between putatively very closely related species of marine haplosclerids and to investigate the species status of Haliclona cinerea. Results indicate that intra-genomic and intra-specific levels of diversity are equivalent, and sequences from multiple clones from a number of individuals of a single species could not be separated on phylogenetic trees. As a result, the ITS regions are not suitable markers for population level studies in marine haplosclerids. Sequences of these regions were highly species specific, and large differences were found between species. ITS sequences from three Callyspongia and three Haliclona species could not be aligned successfully and therefore this locus could not be used to investigate relationships between these putative close relatives. However, ITS sequences retrieved from one H. cinerea were very different from sequences generated from other H. cinerea individuals indicating that this species comprises more than one taxon.

scholarly journals Morphology captures diet and locomotor types in rodents

2017 ◽  
Vol 4 (1) ◽  
pp. 160957 ◽  
Author(s):  
Luis D. Verde Arregoitia ◽  
Diana O. Fisher ◽  
Manuel Schweizer
Keyword(s):  
Evolutionary History ◽  
Morphological Features ◽  
Museum Specimens ◽  
Museum Collections ◽  
Morphological Similarity ◽  
Closely Related Species ◽  
Phylogenetic Relatedness ◽  
Ecological Relevance ◽  
Ecological Literature ◽  
Close Relatives

To understand the functional meaning of morphological features, we need to relate what we know about morphology and ecology in a meaningful, quantitative framework. Closely related species usually share more phenotypic features than distant ones, but close relatives do not necessarily have the same ecologies. Rodents are the most diverse group of living mammals, with impressive ecomorphological diversification. We used museum collections and ecological literature to gather data on morphology, diet and locomotion for 208 species of rodents from different bioregions to investigate how morphological similarity and phylogenetic relatedness are associated with ecology. After considering differences in body size and shared evolutionary history, we find that unrelated species with similar ecologies can be characterized by a well-defined suite of morphological features. Our results validate the hypothesized ecological relevance of the chosen traits. These cranial, dental and external (e.g. ears) characters predicted diet and locomotion and showed consistent differences among species with different feeding and substrate use strategies. We conclude that when ecological characters do not show strong phylogenetic patterns, we cannot simply assume that close relatives are ecologically similar. Museum specimens are valuable records of species' phenotypes and with the characters proposed here, morphology can reflect functional similarity, an important component of community ecology and macroevolution.

scholarly journals IroN, a Novel Outer Membrane Siderophore Receptor Characteristic of Salmonella enterica

1998 ◽  
Vol 180 (6) ◽  
pp. 1446-1453 ◽  
Author(s):  
Andreas J. Bäumler ◽  
Tracy L. Norris ◽  
Todd Lasco ◽  
Wolfgang Voigt ◽  
Rolf Reissbrodt ◽  
...  
Keyword(s):  
Outer Membrane ◽  
Salmonella Enterica ◽  
Mutational Analysis ◽  
Iron Acquisition ◽  
Bacterial Species ◽  
Receptor Protein ◽  
Closely Related Species ◽  
E Coli ◽  
Phylogenetic Lineages ◽  
Close Relatives

ABSTRACT Speciation in enterobacteria involved horizontal gene transfer. Therefore, analysis of genes acquired by horizontal transfer that are present in one species but not its close relatives is expected to give insights into how new bacterial species were formed. In this study we characterize iroN, a gene located downstream of theiroBC operon in the iroA locus ofSalmonella enterica serotype Typhi. Like iroBC, the iroN gene is present in all phylogenetic lineages ofS. enterica but is absent from closely related species such as Salmonella bongori or Escherichia coli. Comparison of the deduced amino acid sequence of iroN with other proteins suggested that this gene encodes an outer membrane siderophore receptor protein. Mutational analysis in S. enterica and expression in E. coli identified a 78-kDa outer membrane protein as the iroN gene product. When introduced into an E. coli fepA cir fiu aroB mutant on a cosmid, iroN mediated utilization of structurally related catecholate siderophores, includingN-(2,3-dihydroxybenzoyl)-l-serine, myxochelin A, benzaldehyde-2,3-dihydroxybenzhydrazone, 2-N,6-N-bis(2,3-dihydroxybenzoyl)-l-lysine, 2-N,6-N-bis(2,3-dihydroxybenzoyl)-l-lysine amide, and enterochelin. These results suggest that theiroA locus functions in iron acquisition in S. enterica.

scholarly journals Building a Reference Transcriptome for the Hexaploid Hard Fescue Turfgrass (Festuca brevipila) Using a Combination of PacBio Iso-Seq and Illumina Sequencing

2020 ◽  
Author(s):  
Yinjie Qiu ◽  
Ya Yang ◽  
Cory D. Hirsch ◽  
Eric Watkins
Keyword(s):  
Full Length ◽  
Gene Trees ◽  
Illumina Platform ◽  
Closely Related Species ◽  
Festuca Ovina ◽  
Reference Transcriptome ◽  
Sequencing Errors ◽  
Festuca Valesiaca ◽  
Close Relatives ◽  
Breeding And Genetics

AbstractBackgroundHard fescue (Festuca brevipila Tracey, 2n=6x=42) is a cool season turfgrass with a fine leaf texture that performs well under low-input management. Breeding and genetics studies of F. brevipila have been limited due to the complexity of its hexaploid genome. To advance our knowledge of F. brevipila genomics, we used PacBio isoform sequencing to develop a reference transcriptome for this species.ResultsHere, we report the F. brevipila reference transcriptome generated from root, crown, leaf, and inflorescence tissues. We obtained 59,510 full-length transcripts, of which 38,556 were non-redundant full-length transcripts. The longest and shortest transcripts were 11,487 and 58 bp, respectively. Distribution of synonymous distances among paralogs within F. brevipila suggested highly similar subgenomes that are difficult to distinguish from sequencing errors. To evaluate the phylogenetic relationships among F. brevipila and close relatives, we sequenced three additional transcriptomes using closely related species on an Illumina platform. The results of our phylotranscriptomic analysis supported the close relationships among F. brevipila (6x), Festuca ovina (4x), Festuca ovina subsp. ovina (2x), and Festuca valesiaca (2x), with high levels of discordance among gene trees.ConclusionsOverall, the F. brevipila PacBio Isoseq reference transcriptome provided the foundation for transcriptome studies and allowed breeders a resource for gene discovery in this important turfgrass species.

scholarly journals Evolution of a mimicry supergene from a multilocus architecture

2011 ◽  
Vol 279 (1727) ◽  
pp. 316-325 ◽  
Author(s):  
Robert T. Jones ◽  
Patricio A. Salazar ◽  
Richard H. ffrench-Constant ◽  
Chris D. Jiggins ◽  
Mathieu Joron
Keyword(s):  
Morphometric Analysis ◽  
Related Species ◽  
Quantitative Trait ◽  
Colour Pattern ◽  
Wing Pattern ◽  
Model Species ◽  
Closely Related Species ◽  
Origin And Evolution ◽  
Wing Patterns ◽  
First Time

The origin and evolution of supergenes have long fascinated evolutionary biologists. In the polymorphic butterfly Heliconius numata , a supergene controls the switch between multiple different forms, and results in near-perfect mimicry of model species. Here, we use a morphometric analysis to quantify the variation in wing pattern observed in two broods of H. numata with different alleles at the supergene locus, ‘ P ’. Further, we genotype the broods to associate the variation we capture with genetic differences. This allows us to begin mapping the quantitative trait loci that have minor effects on wing pattern. In addition to finding loci on novel chromosomes, our data, to our knowledge, suggest for the first time that ancestral colour-pattern loci, known to have major effects in closely related species, may contribute to the wing patterns displayed by H. numata , despite the large transfer of effects to the supergene.

Development of a Reference Standard Library of Chloroplast Genome Sequences, GenomeTrakrCP

Planta Medica ◽  
2017 ◽  
Vol 83 (18) ◽  
pp. 1420-1430 ◽  
Author(s):  
Ning Zhang ◽  
Padmini Ramachandran ◽  
Jun Wen ◽  
James Duke ◽  
Helen Metzman ◽  
...  
Keyword(s):  
Dietary Supplements ◽  
Chloroplast Genome ◽  
Related Species ◽  
Sequencing Data ◽  
Genome Sequences ◽  
Closely Related Species ◽  
Chloroplast Genomes ◽  
Processed Products ◽  
Species Specific ◽  
Close Relatives

AbstractPrecise, species-level identification of plants in foods and dietary supplements is difficult. While the use of DNA barcoding regions (short regions of DNA with diagnostic utility) has been effective for many inquiries, it is not always a robust approach for closely related species, especially in highly processed products. The use of fully sequenced chloroplast genomes, as an alternative to short diagnostic barcoding regions, has demonstrated utility for closely related species. The U. S. Food and Drug Administration (FDA) has also developed species-specific DNA-based assays targeting plant species of interest by utilizing chloroplast genome sequences. Here, we introduce a repository of complete chloroplast genome sequences called GenomeTrakrCP, which will be publicly available at the National Center for Biotechnology Information (NCBI). Target species for inclusion are plants found in foods and dietary supplements, toxin producers, common contaminants and adulterants, and their close relatives. Publicly available data will include annotated assemblies, raw sequencing data, and voucher information with each NCBI accession associated with an authenticated reference herbarium specimen. To date, 40 complete chloroplast genomes have been deposited in GenomeTrakrCP (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA325670/), and this will be expanded in the future.

scholarly journals Genomes reveal drastic and recurrent phenotypic divergence in firetip skipper butterflies (Hesperiidae: Pyrrhopyginae)

2019 ◽  
Vol 286 (1903) ◽  
pp. 20190609 ◽  
Author(s):  
Jing Zhang ◽  
Qian Cong ◽  
Jinhui Shen ◽  
Ernst Brockmann ◽  
Nick V. Grishin
Keyword(s):  
Molecular Mechanisms ◽  
Phenotypic Diversity ◽  
Genomic Analysis ◽  
Phenotypic Divergence ◽  
Representative Species ◽  
Whole Genomes ◽  
Wing Patterns ◽  
Similar Appearance ◽  
Close Relatives ◽  
Five Tribes

Biologists marvel at the powers of adaptive convergence, when distantly related animals look alike. While mimetic wing patterns of butterflies have fooled predators for millennia, entomologists inferred that mimics were distant relatives despite similar appearance. However, the obverse question has not been frequently asked. Who are the close relatives of mimetic butterflies and what are their features? As opposed to close convergence, divergence from a non-mimetic relative would also be extreme. When closely related animals look unalike, it is challenging to pair them. Genomic analysis promises to elucidate evolutionary relationships and shed light on molecular mechanisms of divergence. We chose the firetip skipper butterfly as a model due to its phenotypic diversity and abundance of mimicry. We sequenced and analysed whole genomes of nearly 120 representative species. Genomes partitioned this subfamily Pyrrhopyginae into five tribes (1 new), 23 genera and, additionally, 22 subgenera (10 new). The largest tribe Pyrrhopygini is divided into four subtribes (three new). Surprisingly, we found five cases where a uniquely patterned butterfly was formerly placed in a genus of its own and separately from its close relatives. In several cases, extreme and rapid phenotypic divergence involved not only wing patterns but also the structure of the male genitalia. The visually striking wing pattern difference between close relatives frequently involves disappearance or suffusion of spots and colour exchange between orange and blue. These differences (in particular, a transition between unspotted black and striped wings) happen recurrently on a short evolutionary time scale, and are therefore probably achieved by a small number of mutations.

scholarly journals Rampant genome-wide admixture across the Heliconius radiation

2021 ◽  
Author(s):  
Krzysztof M Kozak ◽  
Mathieu Joron ◽  
W Owen McMillan ◽  
Chris D Jiggins
Keyword(s):  
Gene Flow ◽  
Phylogenetic Networks ◽  
Adaptive Traits ◽  
Closely Related Species ◽  
Interspecific Gene Flow ◽  
Genomic Representation ◽  
Genome Wide ◽  
Wing Patterns ◽  
New Evidence ◽  
Complete Genomic

Abstract How frequent is gene flow between species? The pattern of evolution is typically portrayed as a phylogenetic tree, yet gene flow between good species may be an important mechanism in diversification, spreading adaptive traits and leading to a complex pattern of phylogenetic incongruence. This process has thus far been studied mainly among a few closely related species, or in geographically restricted areas such as islands, but not on the scale of a continental radiation. Using a nearly complete genomic representation of 47 species in the genus, we demonstrate that admixture has played a role throughout the evolution of the charismatic Neotropical butterflies Heliconius. Modeling of phylogenetic networks based on the exome uncovers up to 13 instances of interspecific gene flow. Admixture is detected among the relatives of H. erato, as well as between the ancient lineages leading to modern clades. Interspecific gene flow played a role throughout the evolution of the genus, although the process has been most frequent in the clade of H. melpomene and relatives. We identify H. hecalesia and relatives as putative hybrids, including new evidence for introgression at the loci controlling the mimetic wing patterns. Models accounting for interspecific gene flow yield a more complete picture of the radiation as a network, which will improve our ability to study trait evolution in a realistic comparative framework.

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