scholarly journals New exon ignites accelerated evolution of placental gene Nrk in the ancestral lineage of eutherians

2021 ◽  
Author(s):  
Guopeng Liu ◽  
Chunxiao Zhang ◽  
Yuting Wang ◽  
Guangyi Dai ◽  
Shu-Qun Liu ◽  
...  
Keyword(s):  
Positive Selection ◽  
Fitness Landscape ◽  
Induction Of Labor ◽  
Placental Development ◽  
Terrestrial Vertebrates ◽  
Regulatory Domains ◽  
Ancestral Lineage ◽  
Accelerated Evolution ◽  
Rate Test ◽  
Chorioallantoic Placenta

AbstractAccelerated evolution is often driven by the interaction between environmental factors and genes. However, it remains unclear whether accelerated evolution can be ignited. Here, we focused on adaptive events during the emergence of chorioallantoic placenta. We scanned the chromosome X and identified eight accelerated regions in the ancestral lineage of eutherian mammals. Five of these regions (P = 5.61 × 10−11 ~ 9.03 × 10−8) are located in the five exons of Nik-related kinase (Nrk), which is essential in placenta development and fetoplacental induction of labor. Moreover, a eutherian-specific exogenous exon lack of splice variant was found to be conserved. Structure modelling of NRK suggests that the accelerated exons and the eutherian-specific exon could change the enzymatic activity of eutherian NRK. Since the eutherian-specific exon was surrounded by accelerated exons, it indicates that the accelerated evolution of Nrk may be ignited by the emergence of the new exon in the ancestral lineage of eutherian mammals. The new exon might shift the function of Nrk and provide a new fitness landscape for eutherian species to explore. Although multiple exons were accelerated in both of the Nrk catalytic and regulatory domains, positive selection can only be revealed on the regulatory domain if the branch specific nonsynonymous and synonymous rate test was performed by PAML. Thus, it may be important to detect accelerated evolution when studying positive selection on coding regions. Overall, this work suggests that the fundamental process of placental development and fetoplacental induction of labor has been targeted by positive Darwinian selection. Identifying positively selected placental genes provides insights into how eutherian mammals gain benefits from the invasive chorioallantoic placenta to form one of the most successful groups among terrestrial vertebrates.

scholarly journals Evolution of gene regulatory networks by means of selection and random genetic drift

2018 ◽  
Author(s):  
Antonios Kioukis ◽  
Pavlos Pavlidis
Keyword(s):  
Natural Selection ◽  
Positive Selection ◽  
Genetic Drift ◽  
Regulatory Networks ◽  
Fitness Landscape ◽  
Random Genetic Drift ◽  
Maturation Period ◽  
Evolutionary Forces ◽  
Gene Regulatory

The evolution of a population by means of genetic drift and natural selection operating on a gene regulatory network (GRN) of an individual has not been scrutinized in depth. Thus, the relative importance of various evolutionary forces and processes on shaping genetic variability in GRNs is understudied. Furthermore, it is not known if existing tools that identify recent and strong positive selection from genomic sequences, in simple models of evolution, can detect recent positive selection when it operates on GRNs. Here, we propose a simulation framework, called EvoNET, that simulates forward-in-time the evolution of GRNs in a population. Since the population size is finite, random genetic drift is explicitly applied. The fitness of a mutation is not constant, but we evaluate the fitness of each individual by measuring its genetic distance from an optimal genotype. Mutations and recombination may take place from generation to generation, modifying the genotypic composition of the population. Each individual goes through a maturation period, where its GRN reaches equilibrium. At the next step, individuals compete to produce the next generation. As time progresses, the beneficial genotypes push the population higher in the fitness landscape. We examine properties of the GRN evolution such as robustness against the deleterious effect of mutations and the role of genetic drift. We confirm classical results from Andreas Wagner’s work that GRNs show robustness against mutations and we provide new results regarding the interplay between random genetic drift and natural selection.

scholarly journals Crossing fitness valleys via double substitutions within codons

BMC Biology ◽  
2019 ◽  
Vol 17 (1) ◽  
Author(s):  
Frida Belinky ◽  
Itamar Sela ◽  
Igor B. Rogozin ◽  
Eugene V. Koonin
Keyword(s):  
Amino Acid ◽  
Positive Selection ◽  
Fitness Landscape ◽  
Purifying Selection ◽  
Second Step ◽  
Nucleotide Substitutions ◽  
Protein Coding ◽  
Synonymous Substitutions ◽  
Ancestral States ◽  
Double Substitution

Abstract Background Single nucleotide substitutions in protein-coding genes can be divided into synonymous (S), with little fitness effect, and non-synonymous (N) ones that alter amino acids and thus generally have a greater effect. Most of the N substitutions are affected by purifying selection that eliminates them from evolving populations. However, additional mutations of nearby bases potentially could alleviate the deleterious effect of single substitutions, making them subject to positive selection. To elucidate the effects of selection on double substitutions in all codons, it is critical to differentiate selection from mutational biases. Results We addressed the evolutionary regimes of within-codon double substitutions in 37 groups of closely related prokaryotic genomes from diverse phyla by comparing the fractions of double substitutions within codons to those of the equivalent double S substitutions in adjacent codons. Under the assumption that substitutions occur one at a time, all within-codon double substitutions can be represented as “ancestral-intermediate-final” sequences (where “intermediate” refers to the first single substitution and “final” refers to the second substitution) and can be partitioned into four classes: (1) SS, S intermediate–S final; (2) SN, S intermediate–N final; (3) NS, N intermediate–S final; and (4) NN, N intermediate–N final. We found that the selective pressure on the second substitution markedly differs among these classes of double substitutions. Analogous to single S (synonymous) substitutions, SS double substitutions evolve neutrally, whereas analogous to single N (non-synonymous) substitutions, SN double substitutions are subject to purifying selection. In contrast, NS show positive selection on the second step because the original amino acid is recovered. The NN double substitutions are heterogeneous and can be subject to either purifying or positive selection, or evolve neutrally, depending on the amino acid similarity between the final or intermediate and the ancestral states. Conclusions The results of the present, comprehensive analysis of the evolutionary landscape of within-codon double substitutions reaffirm the largely conservative regime of protein evolution. However, the second step of a double substitution can be subject to positive selection when the first step is deleterious. Such positive selection can result in frequent crossing of valleys on the fitness landscape.

scholarly journals Positive selection drives accelerated evolution of mosquito salivary genes associated with blood-feeding

2013 ◽  
Vol 23 (1) ◽  
pp. 122-131 ◽  
Author(s):  
B. Arcà ◽  
C. J. Struchiner ◽  
V. M. Pham ◽  
G. Sferra ◽  
F. Lombardo ◽  
...  
Keyword(s):  
Positive Selection ◽  
Blood Feeding ◽  
Accelerated Evolution

scholarly journals Molecular evolution of PCSK family: Analysis of natural selection rate and gene loss

PLoS ONE ◽  
2021 ◽  
Vol 16 (10) ◽  
pp. e0259085
Author(s):  
Najmeh Parvaz ◽  
Zahra Jalali
Keyword(s):  
Molecular Evolution ◽  
Positive Selection ◽  
Gene Loss ◽  
Experimental Studies ◽  
Bile Acid Metabolism ◽  
Future Studies ◽  
Accelerated Evolution ◽  
Family Analysis ◽  
Bioinformatics Study ◽  
Functional Relevance

Proprotein convertases subtilisin kexins are serine endoproteases, playing critical roles in the biological functions, including lipid, glucose, and bile acid metabolism, as well as cell proliferation, migration, and metastasis. Experimental studies have demonstrated the physiological functions of PCSKs and their association with diseases; however, studies on the evolutionary history and diversification of these proteins are missing. In the present research, a bioinformatics study was conducted on the molecular evolution of several PCSKs family members and gene loss events across placental mammalian. In order to detect evolutionary constraints and positive selection, the CodeML program of the PAML package was used. The results showed the positive selection to occur in PCSK1, PCSK3, PCSK5, and PCSK7. A decelerated rate of evolution was observed in PCSK7, PCSK3, and MBTPS1 in Carnivores compared to the rest of phylogeny, and an accelerated evolution of PCSK1, PCSK7, and MBTPS1 in Muridae family of rodents was found. Additionally, our results indicated pcsk9 gene loss in 12 species comprising Carnivores and bats (Chiroptera). Future studies are required to evaluate the functional relevance and selective evolutionary advantages associated with these modifications in PCSK proteins during evolution.

scholarly journals Recent advances in understanding evolution of the placenta: insights from transcriptomics

F1000Research ◽  
2018 ◽  
Vol 7 ◽  
pp. 89 ◽  
Author(s):  
Anthony M. Carter
Keyword(s):  
Gene Expression ◽  
Fine Structure ◽  
Gene Transcription ◽  
Comparative Studies ◽  
Convergent Evolution ◽  
Reproductive Strategies ◽  
Chorioallantoic Membrane ◽  
Placental Development ◽  
Chorioallantoic Placenta ◽  
Future Work

The mammalian placenta shows an extraordinary degree of variation in gross and fine structure, but this has been difficult to interpret in physiological terms. Transcriptomics offers a path to understanding how structure relates to function. This essay examines how studies of gene transcription can inform us about placental evolution in eutherian and marsupial mammals and more broadly about convergent evolution of viviparity and placentation in vertebrates. Thus far, the focus has been on the chorioallantoic placenta of eutherians at term, the reproductive strategies of eutherians and marsupials, and the decidual response of the uterus at implantation. Future work should address gene expression during early stages of placental development and endeavor to cover all major groups of mammals. Comparative studies across oviparous and viviparous vertebrates have centered on the chorioallantoic membrane and yolk sac. They point to the possibility of defining a set of genes that can be recruited to support commonalities in reproductive strategies. Further advances can be anticipated from single-cell transcriptomics if those techniques are applied to a range of placental structures and in species other than humans and mice.

scholarly journals Evolution of hypothalamus-pituitary growth axis among fish, amphibian, birds and mammals

Genetika ◽  
2015 ◽  
Vol 47 (2) ◽  
pp. 665-677 ◽  
Author(s):  
M. Moaeen-Ud-Din ◽  
G. Bilal ◽  
James Reecy
Keyword(s):  
Molecular Evolution ◽  
Comparative Genomics ◽  
Positive Selection ◽  
Evolutionary History ◽  
Relative Rate ◽  
Relative Rate Test ◽  
Synonymous Substitutions ◽  
Growth Axis ◽  
Synonymous Sites ◽  
Rate Test

Hypothalamus-pituitary growth axis (HP growth axis) regulates animal growth and development in pre-natal and post natal life governed by many factors. However, until recently, the evolutionary history of this axis among lineages is not understood. Aim of the present study was to understand the major events in evolution and evolutionary history and trend of HP growth axis. The diversity among Homo sapience, Mus musculus, Rattus norvegicus, Gallus gallus, Danio rerio and Xenopus laevis was determined for genes involved in HP growth axis in current study. Sequences of HP growth axis genes were retrieved from NCBI (http://www.ncbi.nlm.nih.gov/). Nucleotide diversity using Kimura?s two-parameter method; codon-based test of positive selection using the Nei-Gojobori; equality of evolutionary rate with Tajima's relative rate test and phylogenetic history using the RelTime method were estimated in MEGA6. Estimates of the coefficients of evolutionary differentiation based on nucleotides and amino acids substitution patterns of HP growth axis genes showed contrasting evolutionary patterns among the lineages. The results demonstrated that although these genes might have crucial functional roles in each of the species, however, their sequence divergence did not necessarily reflect similar molecular evolution among the species. Codon-based test of positive selection revealed that Human vs Mouse, Chicken vs Rat, Human vs Rat and Mouse vs Rat had similar and higher non synonymous substitutions (P > 0.05). Higher rate of non-synonymous substitutions at similar orthologs level among species indicated a similar positive selection pressure in these species. Results for relative rate test assessed with the chi-squared test showed difference on unique mutations among lineages at synonymous and non synonymous sites except Chicken vs Mouse, Human vs Mouse, Chicken vs Rat, Human vs Rat and Mouse vs Rat. This indicated that the mutagenic process that generates substitutional mutation is taking place at approximately the same rate at synonymous and non-synonymous sites these lineages. Moreover, despite of common ancestry, our results indicate a different divergent time among genes of these species. This is the first demonstration that variable rates of molecular evolution may be present within HP growth axis genes among different species. This difference could be of interest for comparative genomics analysis and physiological genes functions identification among tho comparative genomics, evolution rate, HP growth axis, positive selection se species whose HP growth axis is not explored.

scholarly journals The evolution of brain size among the Homininae and selection at ASPM and MCPH1 genes

2021 ◽  
Vol 2 (2) ◽  
pp. 293-310
Author(s):  
Sandra Leyva-Hernández ◽  
Ricardo Fong-Zazueta ◽  
Luis Medrano-González ◽  
Ana Julia Aguirre-Samudio
Keyword(s):  
Positive Selection ◽  
Nucleotide Substitution ◽  
Brain Size ◽  
Phylogenetic Analyses ◽  
Evolutionary Relationship ◽  
Brain Evolution ◽  
Haplotype Blocks ◽  
Accelerated Evolution ◽  
Relationship Of ◽  
The Brain

We examined the evolutionary relationship of the ASPM (abnormal spindle-like microcephaly associated) and MCPH1 (microcephalin-1) genes with brain volume among humans and other primates. We obtained sequences of these genes from 14 simiiform species including hominins. Two phylogenetic analyses of ASPM exon 3 and MCPH1 exons 8 and 11 were performed to maximize taxon sampling or sequence extension to compare the nucleotide substitution and encephalization rates, and examine signals of selection. Further assessment of selection among humans was done through the analysis of non-synonymous and synonymous substitutions (dN/dS), and linkage disequilibrium (LD) patterns. We found that the accelerated evolution of brain size in hominids, is related to synchronic acceleration in the substitution rates of ASPM and MCPH1, and to signals of positive selection, especially in hominins. The dN/dS and LD analyses in Homo detected sites under positive selection and some regions with haplotype blocks at several candidate sites surrounded by blocks in LD-equilibrium. Accelerations and signals of positive selection in ASPM and MCPH1 occurred in different lineages and periods being ASPM more closely related with the brain evolution of hominins. MCPH1 evolved under positive selection in different lineages of the Catarrhini, suggesting independent evolutionary roles of this gene among primates.

scholarly journals Histology Atlas of the Developing Mouse Placenta

2021 ◽  
pp. 019262332110422
Author(s):  
Susan A. Elmore ◽  
Robert Z. Cochran ◽  
Brad Bolon ◽  
Beth Lubeck ◽  
Beth Mahler ◽  
...  
Keyword(s):  
Model Organism ◽  
Placental Development ◽  
Maternal Cell ◽  
Cell Lineages ◽  
Extraembryonic Endoderm ◽  
Mouse Placenta ◽  
Inner Surface ◽  
Chorioallantoic Placenta ◽  
Key Features ◽  
Timing Of Death

The use of the mouse as a model organism is common in translational research. This mouse–human similarity holds true for placental development as well. Proper formation of the placenta is vital for development and survival of the maturing embryo. Placentation involves sequential steps with both embryonic and maternal cell lineages playing important roles. The first step in placental development is formation of the blastocyst wall (approximate embryonic days [E] 3.0-3.5). After implantation (∼E4.5), extraembryonic endoderm progressively lines the inner surface of the blastocyst wall (∼E4.5-5.0), forming the yolk sac that provides histiotrophic support to the embryo; subsequently, formation of the umbilical vessels (∼E8.5) supports transition to the chorioallantoic placenta and hemotrophic nutrition. The fully mature (“definitive”) placenta is established by ∼E12.5. Abnormal placental development often leads to embryonic mortality, with the timing of death depending on when placental insufficiency takes place and which cells are involved. This comprehensive macroscopic and microscopic atlas highlights the key features of normal and abnormal mouse placental development from E4.5 to E18.5. This in-depth overview of a transient (and thus seldom-analyzed) developmental tissue should serve as a useful reference to aid researchers in identifying and describing mouse placental changes in engineered, induced, and spontaneous disease models.

scholarly journals Detecting positive selection within genomes: the problem of biased gene conversion

2010 ◽  
Vol 365 (1552) ◽  
pp. 2571-2580 ◽  
Author(s):  
Abhirami Ratnakumar ◽  
Sylvain Mousset ◽  
Sylvain Glémin ◽  
Jonas Berglund ◽  
Nicolas Galtier ◽  
...  
Keyword(s):  
Positive Selection ◽  
Gene Conversion ◽  
Evolutionary Genetics ◽  
Synonymous Substitution ◽  
Nucleotide Substitutions ◽  
Accelerated Evolution ◽  
A Genome ◽  
Biased Gene Conversion ◽  
Synonymous Substitution Rates ◽  
Wide Scale

The identification of loci influenced by positive selection is a major goal of evolutionary genetics. A popular approach is to perform scans of alignments on a genome-wide scale in order to find regions evolving at accelerated rates on a particular branch of a phylogenetic tree. However, positive selection is not the only process that can lead to accelerated evolution. Notably, GC-biased gene conversion (gBGC) is a recombination-associated process that results in the biased fixation of G and C nucleotides. This process can potentially generate bursts of nucleotide substitutions within hotspots of meiotic recombination. Here, we analyse the results of a scan for positive selection on genes on branches across the primate phylogeny. We show that genes identified as targets of positive selection have a significant tendency to exhibit the genomic signature of gBGC. Using a maximum-likelihood framework, we estimate that more than 20 per cent of cases of significantly elevated non-synonymous to synonymous substitution rates ratio ( d N / d S ), particularly in shorter branches, could be due to gBGC. We demonstrate that in some cases, gBGC can lead to very high d N / d S (more than 2). Our results indicate that gBGC significantly affects the evolution of coding sequences in primates, often leading to patterns of evolution that can be mistaken for positive selection.

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