scholarly journals A quantitative model for characterizing the evolutionary history of mammalian gene expression

2017 ◽  
Author(s):  
Jenny Chen ◽  
Ross Swofford ◽  
Jeremy Johnson ◽  
Beryl B. Cummings ◽  
Noga Rogel ◽  
...  
Keyword(s):  
Gene Expression ◽  
Evolutionary History ◽  
Selective Pressure ◽  
Mammalian Species ◽  
Quantitative Model ◽  
Process Models ◽  
Stabilizing Selection ◽  
Expression Data ◽  
Evolutionary Forces ◽  
History Of

AbstractCharacterizing the evolutionary history of a gene’s expression profile is a critical component for understanding the relationship between genotype, expression, and phenotype. However, it is not well-established how best to distinguish the different evolutionary forces acting on gene expression. Here, we use RNA-seq across 7 tissues from 17 mammalian species to show that expression evolution across mammals is accurately modeled by the Ornstein-Uhlenbeck (OU) process. This stochastic process models expression trajectories across time as Gaussian distributions whose variance is parameterized by the rate of genetic drift and strength of stabilizing selection. We use these mathematical properties to identify expression pathways under neutral, stabilizing, and directional selection, and quantify the extent of selective pressure on a gene’s expression. We further detect deleterious expression levels outside expected evolutionary distributions in expression data from individual patients. Our work provides a statistical framework for interpreting expression data across species and in disease.One Sentence SummaryWe demonstrate the power of a stochastic model for quantifying selective pressure on expression and estimating evolutionary distributions of optimal gene expression.

scholarly journals A Novel Rubi-Like Virus in the Pacific Electric Ray (Tetronarce californica) Reveals the Complex Evolutionary History of the Matonaviridae

Viruses ◽  
2021 ◽  
Vol 13 (4) ◽  
pp. 585
Author(s):  
Rebecca M. Grimwood ◽  
Edward C. Holmes ◽  
Jemma L. Geoghegan
Keyword(s):  
Evolutionary History ◽  
Mammalian Species ◽  
Virus Transmission ◽  
Health Concern ◽  
Virus Species ◽  
Vast Number ◽  
The Pacific ◽  
Positive Sense ◽  
History Of ◽  
Fish Viruses

Rubella virus (RuV) is the causative agent of rubella (“German measles”) and remains a global health concern. Until recently, RuV was the only known member of the genus Rubivirus and the only virus species classified within the Matonaviridae family of positive-sense RNA viruses. Recently, two new rubella-like matonaviruses, Rustrela virus and Ruhugu virus, have been identified in several mammalian species, along with more divergent viruses in fish and reptiles. To screen for the presence of additional novel rubella-like viruses, we mined published transcriptome data using genome sequences from Rubella, Rustrela, and Ruhugu viruses as baits. From this, we identified a novel rubella-like virus in a transcriptome of Tetronarce californica—order Torpediniformes (Pacific electric ray)—that is more closely related to mammalian Rustrela virus than to the divergent fish matonavirus and indicative of a complex pattern of cross-species virus transmission. Analysis of host reads confirmed that the sample analysed was indeed from a Pacific electric ray, and two other viruses identified in this animal, from the Arenaviridae and Reoviridae, grouped with other fish viruses. These findings indicate that the evolutionary history of the Matonaviridae is more complex than previously thought and highlights the vast number of viruses that remain undiscovered.

scholarly journals The diverging evolutionary history of opsin genes in Diptera

2020 ◽  
Author(s):  
Roberto Feuda ◽  
Matthew Goulty ◽  
Nicola Zadra ◽  
Tiziana Gasparetti ◽  
Ezio Rosato ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Turnover Rate ◽  
Selective Pressure ◽  
Ecological Factors ◽  
Peculiar Behaviour ◽  
Opsin Genes ◽  
History Of ◽  
Phylogenetic Framework ◽  
Independent Expansion ◽  
Dipteran Species

AbstractOpsin receptors mediate the visual process in animals and their evolutionary history can provide precious hints on the ecological factors that underpin their diversification. Here we mined the genomes of more than 60 Dipteran species and reconstructed the evolution of their opsin genes in a phylogenetic framework. Our phylogenies indicate that dipterans possess an ancestral set of five core opsins which have undergone several lineage-specific events including an independent expansion of low wavelength opsins in flies and mosquitoes and numerous family specific duplications and losses. Molecular evolutionary studies indicate that gene turnover rate, overall mutation rate, and site-specific selective pressure are higher in Anopheles than in Drosophila; we found signs of positive selection in both lineages, including events possibly associated with their peculiar behaviour. Our findings indicate an extremely variable pattern of opsin evolution in dipterans, showcasing how two similarly aged radiations - Anopheles and Drosophila - can be characterized by contrasting dynamics in the evolution of this gene family.

scholarly journals A quantitative framework for characterizing the evolutionary history of mammalian gene expression

2018 ◽  
Vol 29 (1) ◽  
pp. 53-63 ◽  
Author(s):  
Jenny Chen ◽  
Ross Swofford ◽  
Jeremy Johnson ◽  
Beryl B. Cummings ◽  
Noga Rogel ◽  
...  
Keyword(s):  
Gene Expression ◽  
Evolutionary History ◽  
Mammalian Gene ◽  
History Of ◽  
Mammalian Gene Expression

scholarly journals Evolutionary history of host use, rather than plant phylogeny, determines gene expression in a generalist butterfly

2016 ◽  
Vol 16 (1) ◽  
Author(s):  
Maria de la Paz Celorio-Mancera ◽  
Christopher W. Wheat ◽  
Mikael Huss ◽  
Francesco Vezzi ◽  
Ramprasad Neethiraj ◽  
...  
Keyword(s):  
Gene Expression ◽  
Evolutionary History ◽  
Host Use ◽  
Plant Phylogeny ◽  
History Of

Evolution of physiological dormancy multiple times in Melastomataceae from Neotropical montane vegetation

2011 ◽  
Vol 22 (1) ◽  
pp. 37-44 ◽  
Author(s):  
Fernando A.O. Silveira ◽  
Rafaella C. Ribeiro ◽  
Denise M.T. Oliveira ◽  
G. Wilson Fernandes ◽  
José P. Lemos-Filho
Keyword(s):  
Phylogenetic Tree ◽  
Seed Dormancy ◽  
Rainy Season ◽  
Evolutionary History ◽  
Selective Pressure ◽  
Strong Selective Pressure ◽  
Montane Vegetation ◽  
Physiological Dormancy ◽  
History Of ◽  
Seed Coats

AbstractWe investigated seed dormancy among species of Melastomataceae from Neotropical montane vegetation of Brazil. Four out of 50 studied species had dormant seeds:Miconia corallina(Miconieae), Tibouchina cardinalis(Melastomeae), Comolia sertularia(Melastomeae) andChaetostoma armatum(Microlicieae). For these four species, germinability of seeds collected in different years was always < 10% and the percentages of embryoless seeds and non-viable embryos were both insufficient to explain low or null germinability. This is the first unequivocal report of seed dormancy in tropical Melastomataceae. The production of seeds with permeable seed coats and fully developed, differentiated embryos indicates the occurrence of physiological dormancy. The reconstructed phylogenetic tree of the 50 species suggests that physiological dormancy evolved multiple times during the evolutionary history of Melastomataceae in this vegetation. Physiological dormancy evolved in species and populations associated with xeric microhabitats, where seeds are dispersed in unfavourable conditions for establishment. Therefore, drought-induced mortality may have been a strong selective pressure favouring the evolution of physiological dormancy in Melastomataceae. We argue that dormancy may have been independently selected in other lineages of Cerrado plants colonizing xeric microhabitats and dispersing seeds at the end of the rainy season. The contributions of our data to the understanding of seed dormancy in tropical montane vegetation are discussed.

scholarly journals Discovery of diverse polyomaviruses in bats and the evolutionary history of the Polyomaviridae

2013 ◽  
Vol 94 (4) ◽  
pp. 738-748 ◽  
Author(s):  
Ying Tao ◽  
Mang Shi ◽  
Christina Conrardy ◽  
Ivan V. Kuzmin ◽  
Sergio Recuenco ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Evolutionary History ◽  
Evolutionary Rate ◽  
Mammalian Species ◽  
Evolutionary Analysis ◽  
Viral Pathogens ◽  
Genomic Features ◽  
Wide Range ◽  
History Of ◽  
Multiple Species

Polyomaviruses (PyVs) have been identified in a wide range of avian and mammalian species. However, little is known about their occurrence, genetic diversity and evolutionary history in bats, even though bats are important reservoirs for many emerging viral pathogens. This study screened 380 specimens from 35 bat species from Kenya and Guatemala for the presence of PyVs by semi-nested pan-PyV PCR assays. PyV DNA was detected in 24 of the 380 bat specimens. Phylogenetic analysis revealed that the bat PyV sequences formed 12 distinct lineages. Full-genome sequences were obtained for seven representative lineages and possessed similar genomic features to known PyVs. Strikingly, this evolutionary analysis revealed that the bat PyVs were paraphyletic, suggestive of multiple species jumps between bats and other mammalian species, such that the theory of virus–host co-divergence for mammalian PyVs as a whole could be rejected. In addition, evidence was found for strong heterogeneity in evolutionary rate and potential recombination in a number of PyV complete genomes, which complicates both phylogenetic analysis and virus classification. In summary, this study revealed that bats are important reservoirs of PyVs and that these viruses have a complex evolutionary history.

The floral genome: an evolutionary history of gene duplication and shifting patterns of gene expression

2007 ◽  
Vol 12 (8) ◽  
pp. 358-367 ◽  
Author(s):  
Douglas E. Soltis ◽  
Hong Ma ◽  
Michael W. Frohlich ◽  
Pamela S. Soltis ◽  
Victor A. Albert ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Duplication ◽  
Evolutionary History ◽  
History Of

scholarly journals Inferences on the Evolutionary History of theDrosophila americanaPolymorphicX/4Fusion From Patterns of Polymorphism at theX-LinkedparalyticandelavGenes

Genetics ◽  
2003 ◽  
Vol 164 (4) ◽  
pp. 1459-1469 ◽  
Author(s):  
Cristina P Vieira ◽  
Paula A Coelho ◽  
Jorge Vieira
Keyword(s):  
X Chromosome ◽  
Evolutionary History ◽  
Strong Association ◽  
Fourth Chromosome ◽  
Data Set ◽  
Evolutionary Forces ◽  
Local Selection ◽  
The Status ◽  
History Of ◽  
Polymorphism Data

AbstractIn Drosophila there is limited evidence on the nature of evolutionary forces affecting chromosomal arrangements other than inversions. The study of the X/4 fusion polymorphism of Drosophila americana is thus of interest. Polymorphism patterns at the paralytic (para) gene, located at the base of the X chromosome, suggest that there is suppressed crossing over in this region between fusion and nonfusion chromosomes but not within fusion and nonfusion chromosomes. These data are thus compatible with previous claims that within fusion chromosomes the amino acid clines found at fused1 (also located at the base of the X chromosome) are likely maintained by local selection. The para data set also suggests a young age of the X/4 fusion. Polymorphism data on para and elav (located at the middle region of the X chromosome) suggest that there is no population structure other than that caused by the X/4 fusion itself. These findings are therefore compatible with previous claims that selection maintains the strong association observed between the methionine/threonine variants at fused1 and the status of the X chromosome as fused or unfused to the fourth chromosome.

scholarly journals Drift and directional selection are the evolutionary forces driving gene expression divergence in eye and brain tissue ofHeliconiusbutterflies

2018 ◽  
Author(s):  
Ana Catalán ◽  
Adriana Briscoe ◽  
Sebastian Höhna
Keyword(s):  
Gene Expression ◽  
Brownian Motion ◽  
Brain Tissue ◽  
Directional Selection ◽  
Stabilizing Selection ◽  
Expression Levels ◽  
Evolutionary Forces ◽  
Expression Evolution ◽  
Species Specific ◽  
Gene Expression Evolution

AbstractInvestigating gene expression evolution over micro- and macroevolutionary timescales will expand our understanding of the role of gene expression in adaptation and speciation. In this study, we characterized which evolutionary forces are acting on gene expression levels in eye and brain tissue of fiveHeliconiusbutterflies with divergence times of ~5-12 MYA. We developed and applied Brownian motion and Ornstein-Uhlenbeck models to identify genes whose expression levels are evolving through drift, stabilizing selection, or a lineage-specific shift. We find that 81% of the genes evolve under genetic drift. When testing for branch-specific shifts in gene expression, we detected 368 (16%) shift events. Genes showing a shift towards up-regulation have significantly lower gene expression variance than those genes showing a shift leading towards down-regulation. We hypothesize that directional selection is acting in shifts causing up-regulation, since transcription is costly. We further uncover through simulations that parameter estimation of Ornstein-Uhlenbeck models is biased when using small phylogenies and only becomes reliable with phylogenies having at least 50 taxa. Therefore, we developed a new statistical test based on Brownian motion to identify highly conserved genes (i.e., evolving under strong stabilizing selection), which comprised 3% of the orthoclusters. In conclusion, we found that drift is the dominant evolutionary force driving gene expression evolution in eye and brain tissue inHeliconius. Nevertheless, the higher proportion of genes evolving under directional than under stabilizing selection might reflect species-specific selective pressures on vision and brain necessary to fulfill species-specific requirements.

scholarly journals Subdivision of ancestral scale genetic program underlies origin of feathers and avian scutate scales

2018 ◽  
Author(s):  
Jacob M. Musser ◽  
Günter P. Wagner ◽  
Cong Liang ◽  
Frank A. Stabile ◽  
Alison Cloutier ◽  
...  
Keyword(s):  
Gene Expression ◽  
Evolutionary History ◽  
Theropod Dinosaurs ◽  
Skin Appendages ◽  
Key Factor ◽  
History Of ◽  
Tetrapod Evolution ◽  
Similar Gene ◽  
Complex Evolutionary History

AbstractBirds and other reptiles possess a diversity of feather and scale-like skin appendages. Feathers are commonly assumed to have originated from ancestral scales in theropod dinosaurs. However, most birds also have scaled feet, indicating birds evolved the capacity to grow both ancestral and derived morphologies. This suggests a more complex evolutionary history than a simple linear transition between feathers and scales. We set out to investigate the evolution of feathers via the comparison of transcriptomes assembled from diverse skin appendages in chicken, emu, and alligator. Our data reveal that feathers and the overlapping ‘scutate’ scales of birds share more similar gene expression to each other, and to two types of alligator scales, than they do to the tuberculate ‘reticulate’ scales on bird footpads. Accordingly, we propose a history of skin appendage diversification, in which feathers and bird scutate scales arose from ancestral archosaur body scales, whereas reticulate scales arose earlier in tetrapod evolution. We also show that many “feather-specific genes” are also expressed in alligator scales. In-situ hybridization results in feather buds suggest that these genes represent ancestral scale genes that acquired novel roles in feather morphogenesis and were repressed in bird scales. Our findings suggest that the differential reuse, in feathers, and suppression, in bird scales, of genes ancestrally expressed in archosaur scales has been a key factor in the origin of feathers – and may represent an important mechanism for the origin of evolutionary novelties.

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