A CYC-RAD-DIV-DRIF interaction likely pre-dates the origin of floral monosymmetry in Lamiales

2021 ◽  
Author(s):  
Aniket Sengupta ◽  
Lena C. Hileman
Keyword(s):  
Evolutionary Biology ◽  
De Novo ◽  
Tomato Fruit ◽  
Regulatory Interaction ◽  
En Bloc ◽  
Regulatory Interactions ◽  
Developmental Program ◽  
Novel Traits ◽  
Carpel Development ◽  
Outstanding Question

Abstract BackgroundAn outstanding question in evolutionary biology is how genetic interactions defining novel traits evolve. They may evolve either by de novo assembly of previously non-interacting genes or by en bloc co-option of interactions from other functions. We tested these hypotheses in the context of a novel phenotype—Lamiales flower monosymmetry—defined by a developmental program that relies on regulatory interaction among CYCLOIDEA , RADIALIS , DIVARICATA , and DRIF gene products. In Antirrhinum majus (snapdragon), representing Lamiales, we tested whether components of this program likely function beyond their previously known role in petal and stamen development. In Solanum lycopersicum (tomato), representing Solanales which diverged from Lamiales before the origin of Lamiales floral monosymmetry, we additionally tested for regulatory interactions in this program. ResultsWe found that RADIALIS , DIVARICATA , and DRIF are expressed in snapdragon ovaries and developing fruit, similar to their homologs during tomato fruit development. Additionally, we found that a tomato CYCLOIDEA ortholog positively regulates a tomato RADIALIS ortholog. ConclusionOur results provide preliminary support to the hypothesis that the developmental program defining floral monosymmetry in Lamiales was co-opted en bloc from a function in carpel development. This expands our understanding of novel trait evolution facilitated by co-option of existing regulatory interactions.

scholarly journals A121 UNDERWATER EMR FOR NON-LIFTING SESSILE COLORECTAL LESIONS

2021 ◽  
Vol 4 (Supplement_1) ◽  
pp. 102-103
Author(s):  
C Galts ◽  
R Barclay ◽  
D Percy
Keyword(s):  
Surgical Resection ◽  
De Novo ◽  
Lesion Size ◽  
Colorectal Polyps ◽  
Invasive Cancer ◽  
Previous Attempt ◽  
Tubular Adenoma ◽  
En Bloc ◽  
Clinical Role ◽  
Submucosal Injection

Abstract Background Sessile colorectal lesions which do not elevate with submucosal injection — “non-lifting” lesions — are considered poor candidates for EMR due to concerns of possible invasive cancer and increased procedural risk. However, a non-lifting sign is an unreliable predictor of malignancy, relegating many benign lesions to surgical resection. Underwater EMR (UEMR), which obviates submucosal injection, is effective for sessile colorectal polyps but has not been evaluated specifically for non-lifting lesions. Aims The aim of this study was to assess the efficacy of UEMR for “non-lifting” large sessile colorectal lesions with the hypothesis that UEMR may have a clinical role in managing complex lesions. Methods We reviewed our database from 2016 to 2019 for patients referred for large (≥ 20 mm) non-lifting colorectal lesions without overt signs of invasive cancer, who subsequently underwent UEMR. Results Thirty-two cases were successfully treated with single session UEMR. 18 (56%) were de novo lesions whereas the remainder had undergone previous attempt(s) at conventional EMR. The mean lesion size was 37 ± 17 mm. 4 cases (13%) were resected en bloc; the remainder piecemeal. Final pathology was T1 adenocarcinoma, N=3 (9%); tubulovillous adenoma, N=15 (47%); tubular adenoma, N=8 (25%); sessile serrated, N=6 (19%); high-grade dysplasia, N=2 (6%). One patient with cancer underwent surgical resection (T1N0); the remainder had endoscopic follow-up over 8 ± 3 months with benign recurrent/residual lesions in 8%, all amenable to UEMR. There were no procedural complications. Conclusions In this series of large sessile non-lifting colorectal lesions, UEMR was effective for both de novo and previously treated lesions, obviating surgery in the majority of cases. Funding Agencies None

scholarly journals The Rubisco small subunits in the green algal genus Chloromonas provide insights into evolutionary loss of the eukaryotic carbon-concentrating organelle, the pyrenoid

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Ryo Matsuzaki ◽  
Shigekatsu Suzuki ◽  
Haruyo Yamaguchi ◽  
Masanobu Kawachi ◽  
Yu Kanesaki ◽  
...  
Keyword(s):  
Evolutionary Biology ◽  
De Novo ◽  
Small Subunit ◽  
Plant Evolution ◽  
Reaction Products ◽  
Photosynthetic Organisms ◽  
Green Algal ◽  
Interesting Study ◽  
Algal Genus ◽  
The Relationship

Abstract Background Pyrenoids are protein microcompartments composed mainly of Rubisco that are localized in the chloroplasts of many photosynthetic organisms. Pyrenoids contribute to the CO2-concentrating mechanism. This organelle has been lost many times during algal/plant evolution, including with the origin of land plants. The molecular basis of the evolutionary loss of pyrenoids is a major topic in evolutionary biology. Recently, it was hypothesized that pyrenoid formation is controlled by the hydrophobicity of the two helices on the surface of the Rubisco small subunit (RBCS), but the relationship between hydrophobicity and pyrenoid loss during the evolution of closely related algal/plant lineages has not been examined. Here, we focused on, the Reticulata group of the unicellular green algal genus Chloromonas, within which pyrenoids are present in some species, although they are absent in the closely related species. Results Based on de novo transcriptome analysis and Sanger sequencing of cloned reverse transcription-polymerase chain reaction products, rbcS sequences were determined from 11 strains of two pyrenoid-lacking and three pyrenoid-containing species of the Reticulata group. We found that the hydrophobicity of the RBCS helices was roughly correlated with the presence or absence of pyrenoids within the Reticulata group and that a decrease in the hydrophobicity of the RBCS helices may have primarily caused pyrenoid loss during the evolution of this group. Conclusions Although we suggest that the observed correlation may only exist for the Reticulata group, this is still an interesting study that provides novel insight into a potential mechanism determining initial evolutionary steps of gain and loss of the pyrenoid.

scholarly journals The effect of autopolyploidy on population genetic signals of hard sweeps

2019 ◽  
Author(s):  
Patrick Monnahan ◽  
Yaniv Brandvain
Keyword(s):  
Evolutionary Biology ◽  
Fundamental Parameter ◽  
Ploidy Levels ◽  
Natural Systems ◽  
Left Behind ◽  
Sequencing Technologies ◽  
Coalescent Simulations ◽  
Outstanding Question ◽  
Genomic Signals ◽  
Systems Studies

AbstractSearching for population genomic signals left behind by positive selection is a major focus of evolutionary biology, particularly as sequencing technologies develop and costs decline. The effect of the number of chromosome copies (i.e. ploidy) on the manifestation of these signals remains an outstanding question, despite a wide appreciation of ploidy being a fundamental parameter governing numerous biological processes. We clarify the principal forces governing the differential manifestation and persistence of the signal of selection by separating the effects of polyploidy on rates of fixation versus rates of diversity (i.e. mutation and recombination) with a set of coalescent simulations. We explore what the major consequences of polyploidy, such as a more localized signal, greater dependence on dominance, and longer persistence of the signal following fixation, mean for within- and across-ploidy inference on the strength and prevalence of selective sweeps. As genomic advances continue to open doors for interrogating natural systems, studies such as this aid our ability to anticipate, interpret, and compare data across ploidy levels.

scholarly journals Contingency in the convergent evolution of a regulatory network: Dosage compensation in Drosophila

2018 ◽  
Author(s):  
Doris Bachtrog ◽  
Chris Ellison
Keyword(s):  
Transposable Element ◽  
Dosage Compensation ◽  
Sex Chromosomes ◽  
Binding Sites ◽  
Evolutionary Biology ◽  
De Novo ◽  
Binding Motif ◽  
Sequence Motif ◽  
X Chromosomes ◽  
Msl Complex

The repeatability or predictability of evolution is a central question in evolutionary biology, and most often addressed in experimental evolution studies. Here, we infer how genetically heterogeneous natural systems acquire the same molecular changes, to address how genomic background affects adaptation in natural populations. In particular, we take advantage of independently formed neo-sex chromosomes in Drosophila species that have evolved dosage compensation by co-opting the dosage compensation (MSL) complex, to study the mutational paths that have led to the acquisition of 100s of novel binding sites for the MSL complex in different species. This complex recognizes a conserved 21-bp GA-rich sequence motif that is enriched on the X chromosome, and newly formed X chromosomes recruit the MSL complex by de novo acquisition of this binding motif. We identify recently formed sex chromosomes in the Drosophila repleta and robusta species groups by genome sequencing, and generate genomic occupancy maps of the MSL complex to infer the location of novel binding sites. We find that diverse mutational paths were utilized in each species to evolve 100s of de novo binding motifs along the neo-X, including expansions of microsatellites and transposable element insertions. However, the propensity to utilize a particular mutational path differs between independently formed X chromosomes, and appears to be contingent on genomic properties of that species, such as simple repeat or transposable element density. This establishes the “genomic environment” as an important determinant in predicting the outcome of evolutionary adaptations.

The Nature and Analysis of Phenotypic Transitions

2003 ◽  
Author(s):  
Mary Jane West-Eberhard
Keyword(s):  
Evolutionary Biology ◽  
Adopted Children ◽  
Psychological Traits ◽  
Origin Of Species ◽  
Classical Mythology ◽  
Biological Parents ◽  
Novel Traits ◽  
Famous Book ◽  
The Common ◽  
Vertebrate Eye

Part II is about origins: how do new traits arise from old phenotypes? People of all ages are fascinated by the question of origins. Origins are the common concern of evolutionists and creationists, of ethnic historians, of Mormon geneologists and the Daughters of the American Revolution, of adopted children searching for their biological parents— indeed, of all who have wondered where Johnny got his patience, his sense of humor, or his big nose. Darwin was a clever publicist when he titled his most famous book The Origin of Species. He touched deep human chords by discussing not only the origin of species but the origin of marvellously complex morphological and psychological traits—specialized limbs, sexual behavior, intelligence, heroism, and the vertebrate eye, to mention just a few. Research on selection and adaptation may tell us why a trait persisted and spread, but it will not tell us where a trait came from. This is why evolutionary biology inevitably intersects with developmental biology, and why satisfactory explanations of ultimate (evolutionary) causation must always include both proximate causes and the study of selection. Novel traits originate via the transformation of ancestral phenotypes during development. This transformational aspect of evolutionary change has been oddly neglected in modern evolutionary biology, even though it is an integral part of human curiosity about origins in other fields. From classical mythology to modern-day childrens’ books, origins are explained in terms of transformations of the phenotype, alongside attention to developmental mechanisms and adaptive functions. Consider this excerpt from The Apeman’s Secret (Dixon, 1980), a Hardy Boys adventure book: . . . [T]he Apeman hated cruelty of any kind. Whenever he saw crooks or villians do something nasty to a helpless victim, he would fly into a rage. This would change his body chemistry and cause him to revert to the savage state. . . .

scholarly journals Disentangling Population History and Character Evolution among Hybridizing Lineages

2020 ◽  
Vol 37 (5) ◽  
pp. 1295-1305 ◽  
Author(s):  
Sean P Mullen ◽  
Nicholas W VanKuren ◽  
Wei Zhang ◽  
Sumitha Nallu ◽  
Evan B Kristiansen ◽  
...  
Keyword(s):  
Evolutionary Biology ◽  
De Novo ◽  
Balancing Selection ◽  
Incomplete Lineage Sorting ◽  
Introgressive Hybridization ◽  
Character Evolution ◽  
Population History ◽  
Lineage Sorting ◽  
Evolutionary Origins ◽  
Whole Genome Resequencing

Abstract Understanding the origin and maintenance of adaptive phenotypic novelty is a central goal of evolutionary biology. However, both hybridization and incomplete lineage sorting can lead to genealogical discordance between the regions of the genome underlying adaptive traits and the remainder of the genome, decoupling inferences about character evolution from population history. Here, to disentangle these effects, we investigated the evolutionary origins and maintenance of Batesian mimicry between North American admiral butterflies (Limenitis arthemis) and their chemically defended model (Battus philenor) using a combination of de novo genome sequencing, whole-genome resequencing, and statistical introgression mapping. Our results suggest that balancing selection, arising from geographic variation in the presence or absence of the unpalatable model, has maintained two deeply divergent color patterning haplotypes that have been repeatedly sieved among distinct mimetic and nonmimetic lineages of Limenitis via introgressive hybridization.

scholarly journals Origin and evolution of developmental enhancers in the mammalian neocortex

2016 ◽  
Vol 113 (19) ◽  
pp. E2617-E2626 ◽  
Author(s):  
Deena Emera ◽  
Jun Yin ◽  
Steven K. Reilly ◽  
Jake Gockley ◽  
James P. Noonan
Keyword(s):  
De Novo ◽  
Regulatory Elements ◽  
Evolutionary Constraint ◽  
Regulatory Sequences ◽  
En Bloc ◽  
Origin And Evolution ◽  
Stem Lineage ◽  
Coexpressed Genes ◽  
Human And Mouse ◽  
Insight Into

Morphological innovations such as the mammalian neocortex may involve the evolution of novel regulatory sequences. However, de novo birth of regulatory elements active during morphogenesis has not been extensively studied in mammals. Here, we use H3K27ac-defined regulatory elements active during human and mouse corticogenesis to identify enhancers that were likely active in the ancient mammalian forebrain. We infer the phylogenetic origins of these enhancers and find that ∼20% arose in the mammalian stem lineage, coincident with the emergence of the neocortex. Implementing a permutation strategy that controls for the nonrandom variation in the ages of background genomic sequences, we find that mammal-specific enhancers are overrepresented near genes involved in cell migration, cell signaling, and axon guidance. Mammal-specific enhancers are also overrepresented in modules of coexpressed genes in the cortex that are associated with these pathways, notably ephrin and semaphorin signaling. Our results also provide insight into the mechanisms of regulatory innovation in mammals. We find that most neocortical enhancers did not originate by en bloc exaptation of transposons. Young neocortical enhancers exhibit smaller H3K27ac footprints and weaker evolutionary constraint in eutherian mammals than older neocortical enhancers. Based on these observations, we present a model of the enhancer life cycle in which neocortical enhancers initially emerge from genomic background as short, weakly constrained “proto-enhancers.” Many proto-enhancers are likely lost, but some may serve as nucleation points for complex enhancers to evolve.

scholarly journals GiantDe NovoPleomorphic Adenoma Arising from the Parapharyngeal Space

2013 ◽  
Vol 2013 ◽  
pp. 1-3
Author(s):  
Sang Hwang ◽  
Sim Choroomi ◽  
Ben McArdle ◽  
Ian Jacobson
Keyword(s):  
Pleomorphic Adenoma ◽  
Surgical Management ◽  
De Novo ◽  
Parapharyngeal Space ◽  
Wisdom Tooth ◽  
En Bloc ◽  
Pleomorphic Adenomas ◽  
Oral Approach ◽  
Difficult Area ◽  
Gland Tumour

Introduction.De novopleomorphic adenomas in the parapharyngeal space are rare and cause difficulties in its surgical management. We report the largestde novopleomorphic adenoma arising from the parapharyngeal space and discuss its surgical management.Presentation of Case. A 34-year-old male presented with a giantde novopleomorphic adenoma arising from the parapharyngeal space, which was initially misdiagnosed as an impacted wisdom tooth. Measuring8.4×6.5×3.9 cm in size and weighing 87.3 g, this is the largest primary salivary gland tumour arisingde novofrom the parapharyngeal space reported in the literature, presenting challenges in its surgical management.Discussion. Parapharyngeal space tumours cause nonspecific symptoms and may be difficult to diagnose, which can allow the tumours to become very large and cause obstructive and compressive symptoms in an anatomically difficult area. A combined trans-cervical and trans-oral approach can be used to safely perform anen blocresection.Conclusion. We report the diagnosis and surgical management of the largest pleomorphic adenoma arisingde novofrom the parapharyngeal space reported in the literature.

scholarly journals An evaluation of pool-sequencing transcriptome-based exon capture for population genomics in non-model species

2019 ◽  
Author(s):  
Emeline Deleury ◽  
Thomas Guillemaud ◽  
Aurélie Blin ◽  
Eric Lombaert
Keyword(s):  
Evolutionary Biology ◽  
High Throughput Sequencing ◽  
Harmonia Axyridis ◽  
Population Genomics ◽  
De Novo ◽  
Cost Effective ◽  
Allele Frequencies ◽  
Technical Solution ◽  
Model Species ◽  
Exon Capture

AbstractExon capture coupled to high-throughput sequencing constitutes a cost-effective technical solution for addressing specific questions in evolutionary biology by focusing on expressed regions of the genome preferentially targeted by selection. Transcriptome-based capture, a process that can be used to capture the exons of non-model species, is use in phylogenomics. However, its use in population genomics remains rare due to the high costs of sequencing large numbers of indexed individuals across multiple populations. We evaluated the feasibility of combining transcriptome-based capture and the pooling of tissues from numerous individuals for DNA extraction as a cost-effective, generic and robust approach to estimating the variant allele frequencies of any species at the population level. We designed capture probes for ∼5 Mb of chosen de novo transcripts from the Asian ladybird Harmonia axyridis (5,717 transcripts). We called ∼300,000 bi-allelic SNPs for a pool of 36 non-indexed individuals. Capture efficiency was high, and pool-seq was as effective and accurate as individual-seq for detecting variants and estimating allele frequencies. Finally, we also evaluated an approach for simplifying bioinformatic analyses by mapping genomic reads directly to targeted transcript sequences to obtain coding variants. This approach is effective and does not affect the estimation of SNP allele frequencies, except for a small bias close to some exon ends. We demonstrate that this approach can also be used to predict the intron-exon boundaries of targeted de novo transcripts, making it possible to abolish genotyping biases near exon ends.

scholarly journals Extensivede novomutation rate variation between individuals and across the genome ofChlamydomonas reinhardtii

2015 ◽  
Author(s):  
Rob W Ness ◽  
Andrew D Morgan ◽  
Radhakrishnan B Vasanthakrishnan ◽  
Nick Colegrave ◽  
Peter D Keightley
Keyword(s):  
Mutation Rate ◽  
Evolutionary Biology ◽  
De Novo ◽  
Spontaneous Mutation ◽  
Gc Content ◽  
Rate Variation ◽  
De Novo Mutations ◽  
Local Sequence ◽  
Wild Strains ◽  
Genomic Regions

Describing the process of spontaneous mutation is fundamental for understanding the genetic basis of disease, the threat posed by declining population size in conservation biology, and in much evolutionary biology. However, directly studying spontaneous mutation is difficult because of the rarity of de novo mutations. Mutation accumulation (MA) experiments overcome this by allowing mutations to build up over many generations in the near absence of natural selection. In this study, we sequenced the genomes of 85 MA lines derived from six genetically diverse wild strains of the green algaChlamydomonas reinhardtii. We identified 6,843 spontaneous mutations, more than any other study of spontaneous mutation. We observed seven-fold variation in the mutation rate among strains and that mutator genotypes arose, increasing the mutation rate dramatically in some replicates. We also found evidence for fine-scale heterogeneity in the mutation rate, driven largely by the sequence flanking mutated sites, and by clusters of multiple mutations at closely linked sites. There was little evidence, however, for mutation rate heterogeneity between chromosomes or over large genomic regions of 200Kbp. Using logistic regression, we generated a predictive model of the mutability of sites based on their genomic properties, including local GC content, gene expression level and local sequence context. Our model accurately predicted the average mutation rate and natural levels of genetic diversity of sites across the genome. Notably, trinucleotides vary 17-fold in rate between the most mutable and least mutable sites. Our results uncover a rich heterogeneity in the process of spontaneous mutation both among individuals and across the genome.

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