scholarly journals rgenesconverged : An R Package for the Exploration of Molecular Convergent Evolution

2019 ◽  
Author(s):  
Dina Issakova
Keyword(s):  
Convergent Evolution ◽  
Genetic Similarity ◽  
R Package ◽  
Genetic Mechanisms ◽  
Genetic Sequences

AbstractSequence convergence is a type of convergent evolution that results in similarity between orthologous genetic sequences. However, this can be difficult to evaluate statistically given classical paradigms for convergent evolution, which rest on the assumption that convergent phenotypes are achieved by unrelated genetic mechanisms. While sophisticated models exist to model this process and to evaluate the probability of this explanation of genetic similarity across two different species, no tool has currently been implemented in R to carry out these analyses. Here we present rgenesconverged, an R package allowing the exploration of sequence convergence hypotheses in a given phylogeny.

scholarly journals The variability of Venturia inaequalis CKE. races in the Czech republic and the accumulation of resistance genes in apple germplasm

2011 ◽  
Vol 50 (No. 9) ◽  
pp. 416-423 ◽  
Author(s):  
M. Melounová ◽  
P. Vejl ◽  
P. Sedlák ◽  
A. Reznerová ◽  
M. Tesařová ◽  
...  
Keyword(s):  
Czech Republic ◽  
Genetic Similarity ◽  
Venturia Inaequalis ◽  
Pcr Markers ◽  
The Czech Republic ◽  
Resistant Genotype ◽  
Vf Gene ◽  
Apple Varieties ◽  
Specific Pcr ◽  
Genetic Mechanisms

The growing of resistant apple varieties against the scab, impacts the Venturia inaequalis CKE. races development that can overcome the resistance. For this reason the main breeders object is to cumulate the different genetic mechanisms of resistance against this disease. Presented in this paper is the first genetic study of monosporic isolates in the Czech Republic. By means of RAPD and UPGMA methods which characterised the variability of 10 monosporic isolates from different localities and apple varieties. The monosporic isolate derived from the resistant genotype (Vf gene) proved a 79% genetic similarity with the isolate derived from sensitive variety Top Red. The genetic similarity of other isolates did not prove the dependence either on a locality or a host variety. The Vf and Vm genes accumulation in apple germplasm by means of specific PCR markers was studied. It was confirmed that Vf gene donors are always heterozygous. Concurrently it was statistically confirmed that the donor of Vm gene (OR-45-T-132) is heterozygous, too. The accumulation of Vf and Vm major genes against the scab was validated in 25% of seedlings of the cross.  

scholarly journals genBaRcode: a comprehensive R-package for genetic barcode analysis

2019 ◽  
Vol 36 (7) ◽  
pp. 2189-2194 ◽  
Author(s):  
Lars Thielecke ◽  
Kerstin Cornils ◽  
Ingmar Glauche
Keyword(s):  
User Interface ◽  
Next Generation Sequencing ◽  
Error Correction ◽  
Graphical User Interface ◽  
R Package ◽  
Next Generation ◽  
Analysis Strategies ◽  
Genetic Sequences ◽  
Reproducible Analysis ◽  
Generation Sequencing

Abstract Motivation Genetic barcodes have been established as an efficient method to trace clonal progeny of uniquely labeled cells by introducing artificial genetic sequences into the corresponding genomes. The assessment of those sequences relies on next generation sequencing and the subsequent analysis aiming to identify sequences of interest and correctly quantifying their abundance. Results We developed the genBaRcode package as a toolbox combining the flexibility of digesting next generation sequencing reads with or without a sophisticated barcode structure, with a variety of error-correction approaches and the availability of several types of visualization routines. Furthermore, a graphical user interface was incorporated to allow also less experienced R users package-based analyses. Finally, the provided tool is intended to bridge the gap between generating and analyzing barcode data and thereby supporting the establishment of standardized and reproducible analysis strategies. Availability and implementation The genBaRcode package is available at CRAN (https://cran.r-project.org/package=genBaRcode).

scholarly journals Introduction to ‘Homology and convergence in nervous system evolution’

2016 ◽  
Vol 371 (1685) ◽  
pp. 20150034 ◽  
Author(s):  
Nicholas J. Strausfeld ◽  
Frank Hirth
Keyword(s):  
Nervous System ◽  
Convergent Evolution ◽  
Neural Circuit ◽  
Cambrian Explosion ◽  
Developmental Genetics ◽  
Society Meeting ◽  
Nervous Systems ◽  
System Evolution ◽  
Genetic Mechanisms ◽  
Nervous System Evolution

The origin of brains and central nervous systems (CNSs) is thought to have occurred before the Palaeozoic era 540 Ma. Yet in the absence of tangible evidence, there has been continued debate whether today's brains and nervous systems derive from one ancestral origin or whether similarities among them are due to convergent evolution. With the advent of molecular developmental genetics and genomics, it has become clear that homology is a concept that applies not only to morphologies, but also to genes, developmental processes, as well as to behaviours. Comparative studies in phyla ranging from annelids and arthropods to mammals are providing evidence that corresponding developmental genetic mechanisms act not only in dorso–ventral and anterior–posterior axis specification but also in segmentation, neurogenesis, axogenesis and eye/photoreceptor cell formation that appear to be conserved throughout the animal kingdom. These data are supported by recent studies which identified Mid-Cambrian fossils with preserved soft body parts that present segmental arrangements in brains typical of modern arthropods, and similarly organized brain centres and circuits across phyla that may reflect genealogical correspondence and control similar behavioural manifestations. Moreover, congruence between genetic and geological fossil records support the notion that by the ‘Cambrian explosion’ arthropods and chordates shared similarities in brain and nervous system organization. However, these similarities are strikingly absent in several sister- and outgroups of arthropods and chordates which raises several questions, foremost among them: what kind of natural laws and mechanisms underlie the convergent evolution of such similarities? And, vice versa: what are the selection pressures and genetic mechanisms underlying the possible loss or reduction of brains and CNSs in multiple lineages during the course of evolution? These questions were addressed at a Royal Society meeting to discuss homology and convergence in nervous system evolution. By integrating knowledge ranging from evolutionary theory and palaeontology to comparative developmental genetics and phylogenomics, the meeting covered disparities in nervous system origins as well as correspondences of neural circuit organization and behaviours, all of which allow evidence-based debates for and against the proposition that the nervous systems and brains of animals might derive from a common ancestor.

scholarly journals Integrating natural history-derived phenomics with comparative genomics to study the genetic architecture of convergent evolution

2019 ◽  
Author(s):  
Sangeet Lamichhaney ◽  
Daren C. Card ◽  
Phil Grayson ◽  
João F.R. Tonini ◽  
Gustavo A. Bravo ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Natural History ◽  
Convergent Evolution ◽  
Phenotypic Diversity ◽  
Taxonomic Diversity ◽  
Gold Rush ◽  
Phenotypic Data ◽  
Natural History Collection ◽  
Genomic Studies ◽  
Genetic Mechanisms

AbstractEvolutionary convergence has been long considered primary evidence of adaptation driven by natural selection and provides opportunities to explore evolutionary repeatability and predictability. In recent years, there has been increased interest in exploring the genetic mechanisms underlying convergent evolution, in part due to the advent of genomic techniques. However, the current ‘genomics gold rush’ in studies of convergence has overshadowed the reality that most trait classifications are quite broadly defined, resulting in incomplete or potentially biased interpretations of results. Genomic studies of convergence would be greatly improved by integrating deep ‘vertical’, natural history knowledge with ‘horizontal’ knowledge focusing on the breadth of taxonomic diversity. Natural history collections have and continue to be best positioned for increasing our comprehensive understanding of phenotypic diversity, with modern practices of digitization and databasing of morphological traits providing exciting improvements in our ability to evaluate the degree of morphological convergence. Combining more detailed phenotypic data with the well-established field of genomics will enable scientists to make progress on an important goal in biology: to understand the degree to which genetic or molecular convergence is associated with phenotypic convergence. Although the fields of comparative biology or comparative genomics alone can separately reveal important insights into convergent evolution, here we suggest that the synergistic and complementary roles of natural history collection-derived phenomic data and comparative genomics methods can be particularly powerful in together elucidating the genomic basis of convergent evolution among higher taxa.

scholarly journals Anther cones increase pollen release in buzz-pollinated Solanum flowers

2021 ◽  
Author(s):  
Mario Vallejo-Marín ◽  
Carlos Eduardo Pereira Nunes ◽  
Avery Leigh Russell
Keyword(s):  
Functional Significance ◽  
Convergent Evolution ◽  
Adaptive Significance ◽  
Buzz Pollination ◽  
Mechanical Connection ◽  
Genetic Mechanisms ◽  
Conical Structure ◽  
Pollen Release ◽  
Plant Families

AbstractThe widespread evolution of tube-like anthers releasing pollen from apical pores is associated with buzz pollination, in which bees vibrate flowers to remove pollen. The mechanical connection among anthers in buzz-pollinated species varies from loosely held conformations, to anthers tightly held together with trichomes or bio-adhesives forming a functionally joined conical structure (anther cone). Joined anther cones in buzz-pollinated species have evolved independently across plant families and via different genetic mechanisms, yet their functional significance remains mostly untested. We used experimental manipulations to compare vibrational and functional (pollen release) consequences of joined anther cones in three buzz-pollinated species of Solanum (Solanaceae). We applied bee-like vibrations to focal anthers in flowers with (“joined”) and without (“free”) experimentally created joined anther cones, and characterised vibrations transmitted to other anthers and the amount of pollen released. We found that joined anther architectures cause non-focal anthers to vibrate at higher amplitudes than free architectures. Moreover, in the two species with naturally loosely held anthers, anther fusion increases pollen release, while in the species with a free but naturally compact architecture it does not. We discuss hypotheses for the adaptive significance of the convergent evolution of joined anther cones.

scholarly journals Estimating Genetic Similarity Matrices using Phylogenies

2020 ◽  
Author(s):  
Shijia Wang ◽  
Shufei Ge ◽  
Caroline Coljin ◽  
Liangliang Wang ◽  
Lloyd T Elliott
Keyword(s):  
Genetic Similarity ◽  
Phylogenetic Trees ◽  
Genetic Relatedness ◽  
Poor Quality ◽  
Morphological Data ◽  
Inner Product ◽  
Simulation Studies ◽  
Genetic Traits ◽  
Genetic Sequences ◽  
Similarity Matrices

AbstractGenetic similarity is a measure for the genetic relatedness among individuals. The standard method for computing similarity matrices involves the inner product of observed genetic variant matrices. Such an approach is inaccurate or impossible if genotypes are not available, or not densely sampled, or of poor quality (for example, genetic analysis of extinct species). We provide a new method for computing genetic similarities among individuals using phylogenetic trees. Our method can supplement (or stand in for) computations based on genetic sequences. We show that the genetic similarity matrices computed from trees are consistent with those computed from genotypes. Quantitative analysis on genetic traits and analysis of heritability and co-heritability can be conducted directly using genetic similarity matrices and so in the absence of genotype data, and the presence of phylogenetic trees derived from morphological data or geological dates, such analyses can be undertaken using our methods. We use simulation studies to demonstrate the advantages of our method, and we provide an application to ancient hominin data.

scholarly journals Genomic Insights into the Adaptive Convergent Evolution

2019 ◽  
Vol 20 (2) ◽  
pp. 81-89 ◽  
Author(s):  
Yan Hao ◽  
Yanhua Qu ◽  
Gang Song ◽  
Fumin Lei
Keyword(s):  
Amino Acid ◽  
Convergent Evolution ◽  
Biological Functions ◽  
Future Perspectives ◽  
Protein Coding ◽  
Selective Pressures ◽  
Genomic Technologies ◽  
Long Time ◽  
Genetic Mechanisms ◽  
Phenotypic Convergence

Adaptive convergent evolution, which refers to the same or similar phenotypes produced by species from independent lineages under similar selective pressures, has been widely examined for a long time. Accumulating studies on the adaptive convergent evolution have been reported from many different perspectives (cellular, anatomical, morphological, physiological, biochemical, and behavioral). Recent advances in the genomic technologies have demonstrated that adaptive convergence can arise from specific genetic mechanisms in different hierarchies, ranging from the same nucleotide or amino acid substitutions to the biological functions or pathways. Among these genetic mechanisms, the same amino acid changes in protein-coding genes play an important role in adaptive phenotypic convergence. Methods for detecting adaptive convergence at the protein sequence level have been constantly debated and developed. Here, we review recent progress on using genomic approaches to evaluate the genetic mechanisms of adaptive convergent evolution, summarize the research methods for identifying adaptive amino acid convergence, and discuss the future perspectives for researching adaptive convergent evolution.

scholarly journals genBaRcode – a comprehensive R package for genetic barcode analysis

2019 ◽  
Author(s):  
Lars Thielecke ◽  
Kerstin Cornils ◽  
Ingmar Glauche
Keyword(s):  
User Interface ◽  
Next Generation Sequencing ◽  
Error Correction ◽  
Graphical User Interface ◽  
R Package ◽  
Next Generation ◽  
Analysis Strategies ◽  
Genetic Sequences ◽  
Reproducible Analysis ◽  
Generation Sequencing

AbstractMotivationGenetic barcodes have been established as an efficient method to trace clonal progeny of uniquely labeled cells by introducing artificial genetic sequences into the corresponding genomes. The assessment of those sequences, relies on next generation sequencing and the subsequent analysis aiming to identify sequences of interest and correctly quantifying their abundance.ResultsWe developed the genBaRcode package as a toolbox combining the flexibility of digesting next generation sequencing reads with or without a sophisticated barcode structure, with a variety of error correction approaches and the availability of several types of visualization routines. Furthermore, a graphical user interface was incorporated to allow also less experienced R users package-based analyses. Finally, the provided tool is intended to bridge the gap between generating and analyzing barcode data and thereby supporting the establishment of standardized and reproducible analysis strategies.AvailabilityThe genBaRcode package is available at CRAN (https://cran.r-project.org/pack-age=genBaRcode)[email protected]

scholarly journals Who’s your daddy? On the identity and distribution of the paternal hybrid ancestor of the parthenogenetic gecko Lepidodactylus lugubris (Reptilia: Squamata: Gekkonidae)

Zootaxa ◽  
2021 ◽  
Vol 4999 (1) ◽  
pp. 87-100
Author(s):  
BENJAMIN R. KARIN ◽  
PAUL M. OLIVER ◽  
ALEXANDER L. STUBBS ◽  
UMILAELA ARIFIN ◽  
DJOKO T. ISKANDAR ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Genetic Similarity ◽  
Small Islands ◽  
Central Pacific ◽  
Biogeographic History ◽  
Caroline Islands ◽  
Lepidodactylus Lugubris ◽  
Kei Islands ◽  
Genetic Sequences ◽  
Remote Islands

The widespread parthenogenetic gecko Lepidodactylus lugubris is comprised of several clonal lineages, at least one of which has been known for some time to have originated from hybridization between its maternal ancestor, Lepidodactylus moestus, and a putatively undescribed paternal ancestor previously known only from remote islands in the Central Pacific. By integrating new genetic sequences from multiple studies on Lepidodactylus and incorporating new genetic sequences from previously sampled populations, we recovered a phylogenetic tree that shows a close genetic similarity between the generally hypothesized paternal hybrid ancestor and a recently described species from Maluku (Indonesia), Lepidodactylus pantai. Our results suggest that the paternal hybrid ancestor of at least one parthenogenetic clone of L. lugubris is conspecific with L. pantai and that the range of this species extends to Palau, the Caroline Islands, the Kei Islands, Wagabu, and potentially other small islands near New Guinea. Deeper genetic structure in the western (Palau, Maluku) versus eastern (eastern Melanesia, Micronesia, Polynesia) part of this species’ range suggests that the western populations likely dispersed via natural colonization, whereas the eastern populations may be the result of human-mediated dispersal. The potential taxonomic affinities and biogeographic history should be confirmed with further morphological and genetic analyses, including research on L. woodfordi from its type locality, which would have nomenclatural priority if found to be conspecific with L. pantai. We recommend referring to the wide-ranging sexual species as Lepidodactylus pantai until such a comparison can be made.  

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