Molecular evolution of the Bovini tribe (Bovidae, Bovinae): Is there evidence of rapid evolution or reduced selective constraint in Domestic cattle?

Using an elaborate set of cis-regulatory sequences, the decapentaplegic (dpp) gene displays a dynamic pattern of gene expression during development. The C-terminal portion of the DPP protein is processed to generate a secreted signaling molecule belonging to the transforming growth factor-β (TGF-β) family. This signal, the DPP ligand, is able to influence the developmental fates of responsive cells in a concentration-dependent fashion. Here we examine the sequence level organization of a significant portion of the dpp locus in Drosophila melanogaster and use interspecific comparisons with D. simulans, D. pseudoobscura and D.virilis to explore the molecular evolution of the gene. Our interspecific analysis identified significant selective constraint on both the nucleotide and amino acid sequences. As expected, interspecific comparison of protein coding sequences shows that the C-terminal ligand region is highly conserved. However, the central portion of the protein is also conserved, while the N-terminal third is quite variable. Comparison of noncoding regions reveals significant stretches of nucleotide identity in the 3′ untranslated portion of exon 3 and in the intron between exons 2 and 3. An examination of cDNA sequences representing five classes of dpp transcripts indicates that these transcripts encode the same polypeptide.

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Molecular Evolution of Duplicated Amylase Gene Regions in Drosophila melanogaster: Evidence of Positive Selection in the Coding Regions and Selective Constraints in the cis-Regulatory Regions

Genetics ◽

10.1093/genetics/157.2.667 ◽

2001 ◽

Vol 157 (2) ◽

pp. 667-677

Author(s):

Hitoshi Araki ◽

Nobuyuki Inomata ◽

Tsuneyuki Yamazaki

Keyword(s):

Drosophila Melanogaster ◽

Molecular Evolution ◽

Positive Selection ◽

Natural Populations ◽

Sliding Window ◽

Selective Constraint ◽

Proximal Region ◽

Coding Regions ◽

Asian Populations ◽

Flanking Region

Abstract In this study, we randomly sampled Drosophila melanogaster from Japanese and Kenyan natural populations. We sequenced duplicated (proximal and distal) Amy gene regions to test whether the patterns of polymorphism were consistent with neutral molecular evolution. Fst between the two geographically distant populations, estimated from Amy gene regions, was 0.084, smaller than reported values for other loci, comparing African and Asian populations. Furthermore, little genetic differentiation was found at a microsatellite locus (DROYANETSB) in these samples (Gst′=−0.018). The results of several tests (Tajima's, Fu and Li's, and Wall's tests) were not significantly different from neutrality. However, a significantly higher level of fixed replacement substitutions was detected by a modified McDonald and Kreitman test for both populations. This indicates that positive selection occurred during or immediately after the speciation of D. melanogaster. Sliding-window analysis showed that the proximal region 1, a part of the proximal 5′ flanking region, was conserved between D. melanogaster and its sibling species, D. simulans. An HKA test was significant when the proximal region 1 was compared with the 5′ flanking region of Alcohol dehydrogenase (Adh), indicating a severe selective constraint on the Amy proximal region 1. These results suggest that natural selection has played an important role in the molecular evolution of Amy gene regions in D. melanogaster.

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Inferring the frequency spectrum of derived variants to quantify adaptive molecular evolution in protein-coding genes of Drosophila melanogaster

10.1101/039404 ◽

2016 ◽

Cited By ~ 1

Author(s):

Peter D. Keightley ◽

Jose Campos ◽

Tom Booker ◽

Brian Charlesworth

Keyword(s):

Amino Acid ◽

Molecular Evolution ◽

Frequency Spectrum ◽

Population Genomics ◽

Selective Constraint ◽

Accurate Estimation ◽

Protein Coding ◽

Protein Coding Genes ◽

Adaptive Molecular Evolution ◽

Amino Acid Mutations

Many approaches for inferring adaptive molecular evolution analyze the unfolded site frequency spectrum (SFS), a vector of counts of sites with different numbers of copies of derived alleles in a sample of alleles from a population. Accurate inference of the high copy number elements of the SFS is difficult, however, because of misassignment of alleles as derived versus ancestral. This is a known problem with parsimony using outgroup species. Here, we show that the problem is particularly serious if there is variation in the substitution rate among sites brought about by variation in selective constraint levels. We present a new method for inferring the SFS using one or two outgroups, which attempts to overcome the problem of misassignment. We show that two outgroups are required for accurate estimation of the SFS if there is substantial variation in selective constraints, which is expected to be the case for nonsynonymous sites of protein-coding genes. We apply the method to estimate unfolded SFSs for synonymous and nonsynonymous sites from Phase 2 of the Drosophila Population Genomics Project. We use the unfolded spectra to estimate the frequency and strength of advantageous and deleterious mutations, and estimate that ~50% of amino acid substitutions are positively selected, but that less than 0.5% of new amino acid mutations are beneficial, with a scaled selection strength of Nes ≈ 12.

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Selection constrains high rates of satellite DNA mutation in Daphnia pulex

10.1101/156554 ◽

2017 ◽

Author(s):

Jullien M. Flynn ◽

Ian Caldas ◽

Melania E. Cristescu ◽

Andrew G. Clark

Keyword(s):

Satellite Dna ◽

Related Species ◽

Rapid Evolution ◽

Daphnia Pulex ◽

Selective Constraint ◽

Mutation Rates ◽

Stabilizing Selection ◽

Closely Related Species ◽

Dna Mutation ◽

Evolutionary Forces

AbstractA long-standing evolutionary puzzle is that all eukaryotic genomes contain large amounts of tandemly-repeated satellite DNA whose composition varies greatly among even closely related species. To elucidate the evolutionary forces governing satellite dynamics, quantification of the rates and patterns of mutations in satellite DNA copy number and tests of its selective neutrality are necessary. Here we used whole-genome sequences of 28 mutation accumulation (MA) lines of Daphnia pulex in addition to six isolates from a non-MA population originating from the same progenitor to both estimate mutation rates of abundances of satellite sequences and evaluate the selective regime acting upon them. We found that mutation rates of individual satellite sequence “kmers” were both high and highly variable, ranging from additions/deletions of 0.29 – 105 copies per generation (reflecting changes of 0.12 - 0.80 percent per generation). Our results also provide evidence that new kmer sequences are often formed from existing ones. The non-MA population isolates showed a signal of either purifying or stabilizing selection, with 33 % lower variation in kmer abundance on average than the MA lines, although the level of selective constraint was not evenly distributed across all kmers. The changes between many pairs of kmers were correlated, and the pattern of correlations was significantly different between the MA lines and the non-MA population. Our study demonstrates that kmer sequences can experience extremely rapid evolution in abundance, which can lead to high levels of divergence in genome-wide satellite DNA composition between closely related species.

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Synergistic coevolution accelerates genome evolution

10.1101/2021.05.19.444833 ◽

2021 ◽

Author(s):

Daniel Preussger ◽

Alexander Herbig ◽

Christian Kost

Keyword(s):

Molecular Evolution ◽

Rapid Evolution ◽

Ecological Interactions ◽

Metabolic Cooperation ◽

Interacting Species ◽

Long Run ◽

Speed Up ◽

Key Drivers ◽

Evolutionary Consequences ◽

Rapid Emergence

Ecological interactions are key drivers of evolutionary change. Although it is welldocumented that antagonistic coevolution can accelerate molecular evolution, the evolutionary consequences of synergistic coevolution remain poorly understood. Here we show experimentally that also synergistic coevolution can speed up the rate of molecular evolution. Pairs of auxotrophic genotypes of the bacterium Escherichia coli, whose growth depended on a reciprocal exchange of amino acids, were experimentally coevolved, and compared to two control groups of independently growing cells. Coevolution drove the rapid emergence of a strong metabolic cooperation that correlated with a significantly increased number of mutations in coevolved auxotrophs as compared to monoculture controls. These results demonstrate that synergistic coevolution can cause rapid evolution that in the long run may drive diversification of mutualistically interacting species.

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High Variability and Rapid Evolution of a Nanovirus

Journal of Virology ◽

10.1128/jvi.00607-10 ◽

2010 ◽

Vol 84 (18) ◽

pp. 9105-9117 ◽

Cited By ~ 49

Author(s):

Ioana Grigoras ◽

Tatiana Timchenko ◽

Ana Grande-Pérez ◽

Lina Katul ◽

Heinrich-Josef Vetten ◽

...

Keyword(s):

Molecular Evolution ◽

Nucleotide Substitution ◽

Rapid Evolution ◽

Plant Viruses ◽

High Variability ◽

Nucleotide Substitution Rate ◽

Virus Propagation ◽

The Family ◽

Leguminous Crops ◽

Ssdna Viruses

ABSTRACT Nanoviruses are multipartite single-stranded DNA (ssDNA) plant viruses that cause important diseases of leguminous crops and banana. Little has been known about the variability and molecular evolution of these viruses. Here we report on the variability of faba bean necrotic stunt virus (FBNSV), a nanovirus from Ethiopia. We found mutation frequencies of 7.52 × 10−4 substitutions per nucleotide in a field population of the virus and 5.07 × 10−4 substitutions per nucleotide in a laboratory-maintained population derived thereof. Based on virus propagation for a period of more than 2 years, we determined a nucleotide substitution rate of 1.78 × 10−3 substitutions per nucleotide per year. This high molecular evolution rate places FBNSV, as a representative of the family Nanoviridae, among the fastest-evolving ssDNA viruses infecting plants or vertebrates.

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Molecular Evolution of APP family proteins: Rapid Evolution of the Mammalian APLP1 as a Synaptic Adhesion Molecule

10.21203/rs.3.rs-267698/v1 ◽

2021 ◽

Author(s):

Wataru Onodera ◽

Toru Asahi ◽

Naoya Sawamura

Keyword(s):

Phylogenetic Analysis ◽

Molecular Evolution ◽

Rapid Evolution ◽

Family Members ◽

Docking Simulation ◽

Brain Evolution ◽

Mammalian Brain ◽

Heparin Binding ◽

Family Based ◽

App Gene

Abstract Amyloid precursor protein (APP) family members are involved in essential neuronal activities, and dysfunction of APP family members leads to neurodegenerative diseases such as Alzheimer’s disease. Among the APP gene family members, amyloid precursor-like protein 1 (APLP1) is selectively expressed in neurons and has specialized functions during synaptogenesis. Although a potential role for APLP1 in neuronal evolution has been indicated, its precise evolutionary and functional contributions are unknown. This study shows the molecular evolution of the vertebrate APP family based on phylogenetic analysis, while contrasting the evolutionary differences within the APP family. Phylogenetic analysis showed 15 times higher substitution rate that is driven by positive selection at the stem branch of the mammalian APLP1, resulting in dissimilar protein sequences compared to APP/APLP2. Docking simulation identified one positively selected site in APLP1 that alters the heparin-binding site, which could affect its function, and dimerization rate. Furthermore, the evolutionary rate covariation between the mammalian APP family and synaptic adhesion molecules (SAMs) was confirmed, indicating that only APLP1 has evolved to gain synaptic adhesion property. Overall, our results suggest that the enhanced synaptogenesis property of APLP1 as one of the SAMs may have played a role in mammalian brain evolution.

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The molecular evolution of spermatogenesis across mammals

10.1101/2021.11.08.467712 ◽

2021 ◽

Author(s):

Florent Murat ◽

Noe Mbengue ◽

Sofia Boeg Winge ◽

Timo Trefzer ◽

Evgeny Leushkin ◽

...

Keyword(s):

Molecular Evolution ◽

Sex Chromosome ◽

Rapid Evolution ◽

Cell Types ◽

Reproductive Organ ◽

Egg Laying ◽

General Mechanism ◽

Meiotic Sex Chromosome Inactivation ◽

Selective Forces ◽

Species Specific

The testis is a key male reproductive organ that produces gametes through the process of spermatogenesis. Testis morphologies and spermatogenesis evolve rapidly in mammals, presumably due to the evolutionary pressure on males to be reproductively successful. The rapid evolution of the testis was shown to be reflected at the molecular level based on bulk-tissue work, but the molecular evolution of individual spermatogenic cell types across mammalian lineages remains largely uncharacterized. Here we report evolutionary analyses of single-nucleus transcriptome data for testes from eleven species that cover the three major mammalian lineages (eutherians, marsupials, egg-laying monotremes) and birds (the evolutionary outgroup), and include seven key primates. Our analyses reveal that the rapid evolution of the testis is driven by accelerated fixation rates of gene expression changes, amino acid altering substitutions, and newly emerged genes in late spermatogenic stages - likely facilitated by reduced pleiotropic constraints, haploid selection, and a transcriptionally permissive chromatin environment. We identify temporal expression changes of individual genes across species, which may have contributed to the emergence of species-specific phenotypes, but also conserved expression programs underlying ancestral spermatogenic processes. Sex chromosome analyses show that genes predominantly expressed in spermatogonia (i.e., germ cells fueling spermatogenesis) and Sertoli cells (i.e., somatic supporting cells) independently accumulated on X chromosomes across mammals during evolution, presumably due to male-beneficial selective forces. Further work uncovered that the process of meiotic sex chromosome inactivation (MSCI) also occurs in monotremes and hence is common to the different mammalian sex chromosome systems, contrary to previous inferences. Thus, the general mechanism of meiotic silencing of unsynapsed chromatin (MSUC), which underlies MSCI, represents an ancestral mammalian feature. Together, our study illuminates the cellular and molecular evolution of mammalian spermatogenesis and associated selective forces, and provides a resource for investigating the biology of the testis across mammals.

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Cloning and characterisation of the gene encoding red deer (Cervus elaphus) growth hormone: implications for the molecular evolution of growth hormone in artiodactyls

Journal of Molecular Endocrinology ◽

10.1677/jme.0.0190259 ◽

1997 ◽

Vol 19 (3) ◽

pp. 259-266 ◽

Cited By ~ 13

Author(s):

A Lioupis ◽

OC Wallis ◽

M Wallis

Keyword(s):

Growth Hormone ◽

Molecular Evolution ◽

Cervus Elaphus ◽

Red Deer ◽

Signal Sequence ◽

Rapid Evolution ◽

Gene Encoding ◽

Rate Of Evolution ◽

Gh Gene ◽

Polymerase Chain

In mammals the structure of pituitary GH is generally strongly conserved, indicating a slow basal rate of molecular evolution. However, on two occasions, during the evolution of primates and of artiodactyls, the rate of evolution has increased dramatically (25- to 50-fold) so that the sequences of human and ruminant GHs differ markedly from those of other mammalian GHs. In order to define further the burst of GH evolution that occurred in artiodactyls we have cloned and characterised the GH gene of red deer (Cervus elaphus) using genomic DNA and a polymerase chain reaction technique. The deduced sequence for the mature GH from red deer is identical to that of bovine GH, indicating that the burst of rapid evolution of GH that occurred in Artiodactyla must have been completed before the divergence of Cervidae and Bovidae and suggesting that the rate of evolution during this burst must have been greater than previously estimated. In other aspects (signal sequence, 5' and 3' sequences, introns and synonymous substitutions in the coding sequence) the red deer GH gene differs considerably from the GH genes of other ruminants. Differences between the signal peptide sequences of red deer and bovid GHs probably explain why N-terminal heterogeneity is seen in bovine, ovine and caprine GHs but not GH from red deer, pig or most other mammals.

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Are sex-biased genes more dispensable?

Biology Letters ◽

10.1098/rsbl.2008.0732 ◽

2009 ◽

Vol 5 (3) ◽

pp. 409-412 ◽

Cited By ~ 41

Author(s):

Judith E. Mank ◽

Hans Ellegren

Keyword(s):

Gene Expression ◽

Sexual Selection ◽

Molecular Evolution ◽

Gene Expression Pattern ◽

Selective Constraint ◽

Sexually Dimorphic ◽

Males And Females ◽

Natural And Sexual Selection ◽

Rates Of Molecular Evolution

Many genes show different expression levels in males and females, and these form the basis of sexually dimorphic phenotypes. Sex-biased genes experience accelerated rates of protein evolution, which has been attributed to sexual selection. However, it is possible that the increased rates of molecular evolution, and more importantly the sex-biased gene expression pattern itself, are due to decreased selective constraint. This notion may explain many of the patterns associated with sex-biased gene expression, and changes how we should view the role of natural and sexual selection in relation to these genes.

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