Integration of abundances and chromatin state data of Long INterspersed Elements reveals dynamics transitions during evolution in mammalian genomes

Mapping Intimacies ◽

10.1101/513572 ◽

2019 ◽

Author(s):

Silvia Vitali ◽

Enrico Giampieri ◽

Steven Criscione ◽

Claudia Sala ◽

Italo do Valle ◽

...

Keyword(s):

Evolutionary Biology ◽

Chromatin State ◽

Death Process ◽

Specific Element ◽

Competition Mechanism ◽

Long Interspersed Elements ◽

Interdisciplinary Approaches ◽

Mammalian Genomes ◽

Chromatin Configuration ◽

Taxonomic Order

AbstractGenome ecology and evolutionary biology have being increasingly investigated by interdisciplinary approaches, complementing experimental techniques with advanced modeling and statistical methods. Both disciplines, with distinct perspectives, have been successful in giving theoretical insights of the processes that happen inside and shape the genomes. Distinguishing between evolutionary and ecological origin of genomes patterns is not easy, and often the two approaches dedicate to well separated topics. Here, we integrate data of Long-INterspersed Elements (LINEs) abundances in 46 mammalian genomes with the insertions chromatin configuration, and their estimated age of amplification, to study the evolution of LINEs ecosystem inside and together with the genome landscape. We describe LINEs amplification dynamics by a birth-death process with assumption of competitive neutrality. Then, a competition mechanism for the internal promoter is introduced, spontaneously breaking the neutral assumption. We show that LINEs abundances, as well as the inherent model rates, cluster according to the host taxonomic order. The temporal variation of these rates combined with the average abundances and chromatin state of LINEs copies highlights host-elements interaction and taxa-specific element appearance, such as Lx, associated to the radiation of the murine subfamily, and LIMA/LPB sub-families, related to primates evolution.

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The Effect of Fossil Sampling on the Estimation of Divergence Times with the Fossilized Birth–Death Process

Systematic Biology ◽

10.1093/sysbio/syz037 ◽

2019 ◽

Vol 69 (1) ◽

pp. 124-138 ◽

Cited By ~ 5

Author(s):

Joseph E O’Reilly ◽

Philip C J Donoghue

Keyword(s):

Evolutionary Biology ◽

Empirical Bayes ◽

Divergence Time ◽

Death Process ◽

Divergence Times ◽

Simulation Framework ◽

Occurrence Data ◽

Empirical Bayes Approach ◽

Taxonomic Groups ◽

Birth Death

Abstract Timescales are of fundamental importance to evolutionary biology as they facilitate hypothesis tests of historical evolutionary processes. Through the incorporation of fossil occurrence data, the fossilized birth–death (FBD) process provides a framework for estimating divergence times using more paleontological data than traditional node calibration approaches have allowed. The inclusion of more data can refine evolutionary timescale estimates, but for many taxonomic groups it is computationally infeasible to include all available fossil occurrence data. Here, we utilize both empirical data and a simulation framework to identify approaches to subsampling fossil occurrence data that result in the most accurate estimates of divergence times. To achieve this we assess the performance of the FBD-Skyline model when implementing multiple approaches to incorporating subsampled fossil occurrence data. Our results demonstrate that it is necessary to account for all available fossil occurrence data to achieve the most accurate estimates of clade age. We show that this can be achieved if an empirical Bayes approach, accounting for fossil sampling through time, is applied to the FBD process. Random subsampling of occurrence data can lead to estimates of clade age that are incompatible with fossil evidence if no control over the affinities of fossil occurrences is enforced. Our results call into question the accuracy of previous divergence time studies incorporating the FBD process that have used only a subsample of all available fossil occurrence data.

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Nasal airflow simulations suggest convergent adaptation in Neanderthals and modern humans

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1703790114 ◽

2017 ◽

Vol 114 (47) ◽

pp. 12442-12447 ◽

Cited By ~ 15

Author(s):

S. de Azevedo ◽

M. F. González ◽

C. Cintas ◽

V. Ramallo ◽

M. Quinto-Sánchez ◽

...

Keyword(s):

Fluid Dynamics ◽

Evolutionary Biology ◽

Climatic Conditions ◽

Cold Climate ◽

Stabilizing Selection ◽

Modern Humans ◽

Interdisciplinary Approaches ◽

Climate Simulations ◽

The Many ◽

Species Specific

Both modern humans (MHs) and Neanderthals successfully settled across western Eurasian cold-climate landscapes. Among the many adaptations considered as essential to survival in such landscapes, changes in the nasal morphology and/or function aimed to humidify and warm the air before it reaches the lungs are of key importance. Unfortunately, the lack of soft-tissue evidence in the fossil record turns difficult any comparative study of respiratory performance. Here, we reconstruct the internal nasal cavity of a Neanderthal plus two representatives of climatically divergent MH populations (southwestern Europeans and northeastern Asians). The reconstruction includes mucosa distribution enabling a realistic simulation of the breathing cycle in different climatic conditions via computational fluid dynamics. Striking across-specimens differences in fluid residence times affecting humidification and warming performance at the anterior tract were found under cold/dry climate simulations. Specifically, the Asian model achieves a rapid air conditioning, followed by the Neanderthals, whereas the European model attains a proper conditioning only around the medium-posterior tract. In addition, quantitative-genetic evolutionary analyses of nasal morphology provided signals of stabilizing selection for MH populations, with the removal of Arctic populations turning covariation patterns compatible with evolution by genetic drift. Both results indicate that, departing from important craniofacial differences existing among Neanderthals and MHs, an advantageous species-specific respiratory performance in cold climates may have occurred in both species. Fluid dynamics and evolutionary biology independently provided evidence of nasal evolution, suggesting that adaptive explanations regarding complex functional phenotypes require interdisciplinary approaches aimed to quantify both performance and evolutionary signals on covariation patterns.

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The Dynamics, Causes, and Impacts of Mammalian Evolutionary Rates Revealed by the Analyses of Capybara Draft Genome Sequences

Genome Biology and Evolution ◽

10.1093/gbe/evaa157 ◽

2020 ◽

Vol 12 (8) ◽

pp. 1444-1458

Author(s):

Isaac Adeyemi Babarinde ◽

Naruya Saitou

Keyword(s):

Litter Size ◽

Evolutionary Rate ◽

Expression Patterns ◽

Draft Genome ◽

Evolutionary Rates ◽

Gestation Length ◽

Generation Interval ◽

Rate Acceleration ◽

Mammalian Genomes ◽

Taxonomic Order

Abstract Capybara (Hydrochoerus hydrochaeri) is the largest species among the extant rodents. The draft genome of capybara was sequenced with the estimated genome size of 2.6 Gb. Although capybara is about 60 times larger than guinea pig, comparative analyses revealed that the neutral evolutionary rates of the two species were not substantially different. However, analyses of 39 mammalian genomes revealed very heterogeneous evolutionary rates. The highest evolutionary rate, 8.5 times higher than the human rate, was found in the Cricetidae–Muridae common ancestor after the divergence of Spalacidae. Muridae, the family with the highest number of species among mammals, emerged after the rate acceleration. Factors responsible for the evolutionary rate heterogeneity were investigated through correlations between the evolutionary rate and longevity, gestation length, litter frequency, litter size, body weight, generation interval, age at maturity, and taxonomic order. The regression analysis of these factors showed that the model with three factors (taxonomic order, generation interval, and litter size) had the highest predictive power (R2 = 0.74). These three factors determine the number of meiosis per unit time. We also conducted transcriptome analysis and found that the evolutionary rate dynamics affects the evolution of gene expression patterns.

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Comprehensive analysis of endogenous bornavirus-like elements in eukaryote genomes

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2012.0499 ◽

2013 ◽

Vol 368 (1626) ◽

pp. 20120499 ◽

Cited By ~ 47

Author(s):

Masayuki Horie ◽

Yuki Kobayashi ◽

Yoshiyuki Suzuki ◽

Keizo Tomonaga

Keyword(s):

Dna Sequences ◽

Cell Biology ◽

Evolutionary Biology ◽

Driving Forces ◽

Biological Significance ◽

Comprehensive Analysis ◽

Retroviral Integration ◽

Host Interactions ◽

Mammalian Genomes ◽

Borna Disease

Bornaviruses are the only animal RNA viruses that establish a persistent infection in their host cell nucleus. Studies of bornaviruses have provided unique information about viral replication strategies and virus–host interactions. Although bornaviruses do not integrate into the host genome during their replication cycle, we and others have recently reported that there are DNA sequences derived from the mRNAs of ancient bornaviruses in the genomes of vertebrates, including humans, and these have been designated endogenous borna-like (EBL) elements. Therefore, bornaviruses have been interacting with their hosts as driving forces in the evolution of host genomes in a previously unexpected way. Studies of EBL elements have provided new models for virology, evolutionary biology and general cell biology. In this review, we summarize the data on EBL elements including what we have newly identified in eukaryotes genomes, and discuss the biological significance of EBL elements, with a focus on EBL nucleoprotein elements in mammalian genomes. Surprisingly, EBL elements were detected in the genomes of invertebrates, suggesting that the host range of bornaviruses may be much wider than previously thought. We also review our new data on non-retroviral integration of Borna disease virus.

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The extinction time of a general birth and death process with catastrophes

Journal of Applied Probability ◽

10.1017/s0021900200116031 ◽

1986 ◽

Vol 23 (04) ◽

pp. 851-858 ◽

Cited By ~ 1

Author(s):

P. J. Brockwell

Keyword(s):

Laplace Transform ◽

Size Distribution ◽

Sufficient Conditions ◽

Necessary And Sufficient Conditions ◽

Death Process ◽

Extinction Time ◽

Birth And Death Process ◽

Different Types ◽

The Laplace Transform ◽

Necessary And Sufficient

The Laplace transform of the extinction time is determined for a general birth and death process with arbitrary catastrophe rate and catastrophe size distribution. It is assumed only that the birth rates satisfyλ0= 0,λj> 0 for eachj> 0, and. Necessary and sufficient conditions for certain extinction of the population are derived. The results are applied to the linear birth and death process (λj=jλ, µj=jμ) with catastrophes of several different types.

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Normal approximations to discrete unimodal distributions

Journal of Applied Probability ◽

10.1017/s0021900200115931 ◽

1986 ◽

Vol 23 (04) ◽

pp. 1013-1018

Author(s):

B. G. Quinn ◽

H. L. MacGillivray

Keyword(s):

Stationary Distribution ◽

Sufficient Conditions ◽

Random Variables ◽

Hypergeometric Distribution ◽

Death Process ◽

Normal Approximations ◽

Discrete Random Variables ◽

Birth Death

Sufficient conditions are presented for the limiting normality of sequences of discrete random variables possessing unimodal distributions. The conditions are applied to obtain normal approximations directly for the hypergeometric distribution and the stationary distribution of a special birth-death process.

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