The examples given so far mainly pertain to protecting the cell or species and keeping the genome uncorrupted. But sometimes, in new situations, genetic changes are needed. There is plenty of evidence that programs can be optimized to suit changed conditions. A familiar example is the color vision of coelacanths, living 200 meters underwater where only dim blue light is available. In each of two color-receptors, only two amino acids are changed from the orthologous receptors in species living in brighter light. Each of these changes could be accomplished by one nucleotide substitution, not forbiddingly unlikely. Examples of similar optimization are everywhere in the tree of life.
Of course, random nucleotide substitutions are usually harmful and sometimes fatal. Therefore, it would be better if the tinkering were supressed until a need arises. There is programming to initiate the tinkering. The phenomenon is called "adaptive mutation." By one account, ...the newly identified mutases, present in all cells, produce mutations only when a genetic or metabolic stress triggers their induction and activation. (2.6)
It would also help if the mutations were focussed on the appropriate nucleotides only, the ones needing to change. Indeed, "directed mutation" often confines the point mutations to positions where they may be useful. Among prokaryotes,
diversity-generating retroelements (DGRs) use mutagenic reverse transcription and retrohoming to generate myriad variants of a target gene. ...Crucially, the reverse transcriptase (RT) used is error-prone at template adenine bases, but has high fidelity at other template bases.... Massive and low-risk protein diversification offers clear advantages to any organism. (4.5)
Adaptation to changing environments often requires only microevolution — evolution attainable with minor tweaking and optimizing of existing proteins. Macroevolution, by contrast, requires wholly new programs or subroutines. It is best illustrated by example. Examples would include the first earthly appearances of [a long list]. These evolutionary features depend on the first deployment of genetic sequences that contain the programming for [the long list]. This first deployment requires (1) that the programming is available, and (2) that the regulatory system is appropriate for it and synchronized with it. But where does the programming come from?
Horizontal Gene Transfer
is the whole story among bacteria
can be accelerated
can be initiated by the recipient species (5). bacteria can kill to steal
"the amoeba replaced it with another gene with the same function from bacteria." (4)
viral infection can transform whole eukaryotic species in few generations (3.5)
Gene Conversion for restoration, optimization or exploration
If the mainstream theory of evolution is correct, we would expect to read about the evolution of the genetic programming behind the complex systems mentioned here. Where are those accounts?
Evidence supporting a viral origin of the eukaryotic nucleus by Philip J.L. Bell, doi:10.1016/j.virusres.2020.198168, Virus Research, Nov 2020. The eukaryotic system to uncouple transcription from translation is complex and employs hundreds of genes that act in concert.
A tripartite mechanism catalyzes Mad2-Cdc20 assembly at unattached kinetochores by Pablo Lara-Gonzalez et al., doi:10.1126/science.abc1424, Science, 01 Jan 2021. ...the detailed molecular choreography that allows a single, unattached kinetochore to arrest cell division.
Histone variants in archaea and the evolution of combinatorial chromatin complexity by Kathryn M. Stevens et al., doi:10.1073/pnas.2007056117, PNAS, 29 Dec 2020. ...the ancestor of eukaryotes might have already had complex chromatin.
Polymerization and editing modes of a high-fidelity DNA polymerase are linked by a well-defined path by Thomas Dodd, Margherita Botto et al., Nature Communications, 23 Oct 2020.
Ribosome quality control antagonizes the activation of the integrated stress response on colliding ribosomes by Liewei L. Yan and Hani S. Zaher, doi:10.1016/j.molcel.2020.11.033, Molecular Cell, 17 Dec 2020.
Exo1 recruits Cdc5 polo kinase to MutLγ to ensure efficient meiotic crossover formation by Aurore Sanchez et al, doi:10.1073/pnas.2013012117, PNAS, 16 Nov 2020.
We simply cannot go on being so vague about 'function' by W. Ford Doolittle, Genome Biol, 18 Dec 2018.
Deep conservation of the enhancer regulatory code in animals by Emily S. Wong et al., doi:10.1126/science.aax8137, Science, 06 Nov 2020. Our results suggest the existence of an ancient and conserved, yet flexible, genomic regulatory syntax that has been repeatedly co-opted into cell type-specific gene regulatory networks across the animal kingdom.
90S pre-ribosome transformation into the primordial 40S subunit by Jingdong Cheng et al., doi:10.1126/science.abb4119, Science, 18 Sep 2020.
Bridging of DNA breaks activates PARP2-HPF1 to modify chromatin by Silvija Bilokapic et al., doi:10.1038/s41586-020-2725-7, Nature, 16 Sep 2020.
Massive project reveals complexity of gene regulation by Elizabeth Pennisi, Science, 11 Sep 2020.
Expanded ENCODE delivers invaluable genomic encyclopedia by Chung-Chau Hon and Piero Carninci, Nature, 29 Jul 2020.
Principles of Epigenetic Homeostasis Shared Between Flowering Plants and Mammals by Ben P. Williams and Mary Gehring, doi:10.1016/j.tig.2020.06.019, Trends in Genetics, 2020. Maintaining epigenetic states through mitotic or meiotic cell divisions ...requires continual reestablishment of epigenetic information by enzymatic writers and erasers.
Dynamic human MutSα–MutLα complexes compact mismatched DNA by Kira C. Bradford et al., doi:10.1073/pnas.1918519117, PNAS, 14 Jul 2020; and
Recurrent mismatch binding by MutS mobile clamps on DNA localizes repair complexes nearby by Pengyu Hao et al., doi:10.1073/pnas.1918517117, PNAS, 15 Jul 2020; and commentary:
Genome Guardians Stop and Reel in DNA to Correct Replication Errors by Tracey Peake, NC State News (+Newswise), 16 Jul 2020.
Contact area–dependent cell communication and the morphological invariance of ascidian embryogenesis by Lèo Guignard1, Ulla-Maj Fiúza et al., doi:10.1126/science.aar5663, Science, 10 Jul 2020.
Hybrid Gene Origination Creates Human-Virus Chimeric Proteins during Infection by Jessica Sook Yuin Ho, Matthew Angel, Yixuan Ma, Elizabeth Sloan et al., doi:10.1016/j.cell.2020.05.035, Cell, 25 Jun 2020. ...a mechanism employed by sNSVs [segmented negative strand RNA viruses] to generate chimeric host-virus genes.
Genetic dominance governs the evolution and spread of mobile genetic elements in bacteria by Jerónimo Rodríguez-Beltrán et al., doi:10.1073/pnas.2001240117, PNAS, 22 Jun 2020.
Adaptive evolution among cytoplasmic piRNA proteins leads to decreased genomic auto-immunity by Luyang Wang, Daniel A. Barbash and Erin S. Kelleher, doi:10.1371/journal.pgen.1008861, PLoS Genet, 11 Jun 2020.
Multilayered mechanisms ensure that short chromosomes recombine in meiosis by Murakami, H., Lam, I., Huang, P. et al., doi:10.1038/s41586-020-2248-2, Nature, 04 Jun 2020.
Global fitness landscapes of the Shine-Dalgarno sequence by Syue-Ting Kuo, Ruey-Lin Jahn,Yuan-Ju Cheng et al., doi:10.1101/gr.260182.119, Genome Res., 18 May 2020. A mechanism for "directed mutation?" ...the genotype-fitness correlation of SD promotes its evolvability by steadily supplying beneficial mutations across fitness landscapes....
21 May 2020 and 20 May 2020: projects that observe robust software management.
The TERB1-TERB2-MAJIN complex of mouse meiotic telomeres dates back to the common ancestor of metazoans by Irene da Cruz et al., doi:10.1186/s12862-020-01612-9, BMC Evol Biol, 14 May 2020.
The Ccr4-Not complex monitors the translating ribosome for codon optimality by Robert Buschauer et al., doi:10.1126/science.aay6912, Science, 17 Apr 2020.
Repair, Removal, and Shutdown: It All Hinges on RNA Polymerase II Ubiquitylation by Kook Son and Orlando D. Schärer, doi:10.1016/j.cell.2020.02.053, Cell, 19 Mar 2020.
Caenorhabditis elegansADAR editing and the ERI-6/7/MOV10 RNAi pathway silence endogenous viral elements and LTR retrotransposons by Sylvia E. J. Fischer and Gary Ruvkun, doi:10.1073/pnas.1919028117, PNAS, 02 Mar 2020.
Integrated structural and evolutionary analysis reveals common mechanisms underlying adaptive evolution in mammals by Greg Slodkowicz and Nick Goldman, doi:10.1073/pnas.1916786117, PNAS, 02 Mar 2020.
Silencers, Enhancers, and the Multifunctional Regulatory Genome by Marc S. Halfon et al., doi:10.1016/j.tig.2019.12.005, Trends in Genetics, Mar 2020.
Evolutionary History of GLISGenes Illuminates Their Roles in Cell Reprograming and Ciliogenesis by Yuuri Yasuoka et al., doi:10.1093/molbev/msz205, Molecular Biology and Evolution, 05 Sep 2019.
Widespread Transcriptional Scanning in the Testis Modulates Gene Evolution Rates by Bo Xia et al., doi:10.1016/j.cell.2019.12.015, Cell, 23 Jan 2020; and commentary:
Scanning system in sperm may control rate of human evolution, NYU Langone Health via PhysOrg.com, 23 Jan 2020.
...transcription-coupled repair (TCR)... replaces faulty DNA patches just before transcription....
A kinase-dependent checkpoint prevents escape of immature ribosomes into the translating pool by Melissa D. Parker et al., doi:10.1371/journal.pbio.3000329, PLoS Biol, 13 Dec 2019.
A unified allosteric/torpedo mechanism for transcriptional termination on human protein-coding genes by Joshua D. Eaton et al., doi:10.1101/gad.332833.119, Genes & Dev., 05 Dec 2019.
Origin and Evolution of Two Independently Duplicated Genes ...in Caenorhabditisand Vertebrates by Diego A. Caraballo et al., G3, 03 Dec 2019. In both lineages, the catalytic domain of the duplicated genes was subjected to a strong purifying selective pressure, while the recognition domain was subjected to episodic positive diversifying selection.
Accessibility of promoter DNA is not the primary determinant of chromatin-mediated gene regulation by Răzvan V. Chereji, Peter R. Eriksson, Josefina Ocampo et al., Genome Res., Dec 2019. ...suggesting that transcription factors can penetrate heterochromatin.
Genomic sites hypersensitive to ultraviolet radiation by Sanjay Premi et al., PNAS, 26 Nov 2019. ...over 2,000 such genomic sites that are up to 170-fold more sensitive than the average site. These sites occur at specific locations near genes, so may let UV radiation drive direct changes in cell physiology rather than act through rare mutations.
14 Oct 2019: ...a group of yeasts ...capturing multiple genes from bacteria through horizontal gene transfer (HGT).
The nucleosome core particle remembers its position through DNA replication and RNA transcription by Gavin Schlissel and Jasper Rine, PNAS, 08 Oct 2019.
Cracking How 'Water Bears' Survive the Extremes, UC San Diego via newswise, 27 Sep 2019. ...Dsup protects cells by forming a protective cloud that shields DNA from hydroxyl radicals, which are produced by X-rays.
Widespread cis-regulatory convergence between the extinct Tasmanian tiger and gray wolf by Charles Y. Feigin et al., Genome Res., 18 Sep 2019. Our findings support the hypothesis that ...positive selection on cis-regulatory elements is likely to be an essential driver of adaptive convergent evolution....
05 Sep 2019: ...how a genome can seemingly intentionally respond to stress and pass those favorable adaptations on to its young.
Evolution of intron splicing towards optimized gene expression is based on various Cis- and Trans-molecular mechanisms by Idan Frumkin et al., PLoS Biol, 23 Aug 2019. ...our work reveals various mechanistic pathways toward optimizations of intron splicing to ultimately adapt gene expression patterns to novel demands.
27 Aug 2019: Directed mutation can produce convergent evolution.
Mammalian Mediator as a Functional Link between Enhancers and Promoters by Julie Soutourina, Cell, 22 Aug 2019.
The Unexpected Noncatalytic Roles of Histone Modifiers in Development and Disease by Yann Aubert et al., doi:10.1016/j.tig.2019.06.004, Trends in Genetics, 10 Jul 2019.
10 Jul 2019: ...a large insertion of DNA from the endosymbiont bacteria Wolbachia ...integrated itself directly into the pillbug chromosome....
Building bridges to move recombination complexes by Emeline Dubois et al., doi:10.1073/pnas.1901237116, PNAS, online 30 May 2019. ...the conundrum of how recombination complexes move from on-axis localization at coalignment to between-axis localization on SC central regions....
11 May 2019: beetles acquire and optimize GH45 gene
Homolog Dependent Repair Following Dicentric Chromosome Breakage in Drosophila melanogaster by Jayaram Bhandari et al., Genetics, online 03 May 2019.
Hit and run versus long-term activation of PARP-1 by its different domains fine-tunes nuclear processes by Colin Thomas et al., PNAS, 26 Apr 2019.
Genetic paradox explained by nonsense by Miles F. Wilkinson, Nature, 11 Apr 2019. ...the upregulation of compensatory genes is specifically triggered by mutations that generate short nucleotide sequences known as premature termination codons (PTCs). These sequences – also known as nonsense codons – signal the early cessation of the translation of messenger RNAs into proteins.
18 Apr 2019: the "grammar" of proteins can be investigated using tools borrowed from linguistics — Lijia Yu et al.
08 Apr 2019: Helpful genetic mutations can be induced by environmental stress... (our comments about):
What is mutation? A chapter in the series: How microbes "jeopardize" the modern synthesis by Devon M. Fitzgerald and Susan M. Rosenberg, PLoS Genet., 01 Apr 2019. These mechanisms reveal a picture of highly regulated mutagenesis, up-regulated temporally by stress responses and activated when cells/organisms are maladapted to their environments—when stressed—potentially accelerating adaptation. Mutation is also nonrandom in genomic space, with multiple simultaneous mutations falling in local clusters, which may allow concerted evolution—the multiple changes needed to adapt protein functions and protein machines encoded by linked genes.
Transposable elements drive rapid phenotypic variation in Capsella rubella by Xiao-Min Niu et al., PNAS, online 15 Mar 2019. These results indicate that TE insertions drive rapid phenotypic variation, which could potentially help adapting to novel environments in species with limited genetic variation.
A DNA repair protein and histone methyltransferase interact to promote genome stability in the Caenorhabditis elegans germ line by Bing Yang, Xia Xu, Logan Russell, et al., PLoS Genet., online 22 Feb 2019.
Evolution of resilience in protein interactomes across the tree of life by Marinka Zitnik et al., PNAS, online 14 Feb 2019. ...organisms stave off collapse through all manner of backup and workaround mechanisms....
Immune genes are primed for robust transcription by proximal long noncoding RNAs located in nuclear compartments by Stephanie Fanucchi et al., v 51, Nature Genetics, online 10 Dec 2018.
Nucleosome Positioning by an Evolutionarily Conserved Chromatin Remodeler Prevents Aberrant DNA Methylation in Neurospora by Andrew D. Klocko et al., doi:10.1534/genetics.118.301711, Genetics, online 15 Dec 2018.
A Bacterial Chromosome Structuring Protein Binds Overtwisted DNA to Stimulate Type II Topoisomerases and Enable DNA Replication by Monica S. Guo, Diane L. Haakonsen et al., doi:10.1016/j.cell.2018.08.029, Cell, 04 Oct 2018.
10 Oct 2018: Elegant and precise genetic programs guide the forces that allow seemingly identical starting cells to develop into highly specialized entities....
The NORAD lncRNA assembles a topoisomerase complex critical for genome stability by Mathias Munschauer et al., doi:10.1038/s41586-018-0453-z, Nature, 27 Aug 2018.
The organization of genome duplication is a critical determinant of the landscape of genome maintenance by Blanca Gómez-Escoda and Pei-Yun Jenny Wu, doi:10.1101/gr.224527.117, Genome Res., 22 Jun 2018.
RES complex is associated with intron definition and required for zebrafish early embryogenesis byJuan Pablo Fernandez, Miguel Angel Moreno-Mateos et al., PLoS Genet., 03 Jul 2018. ...long introns surrounding short exons are recognized and spliced through "exon definition" mechanisms....
Uncovering universal rules governing the selectivity of the archetypal DNA glycosylase TDG by Thomas Dodd et al., PNAS, online 21 May 2018. Our results show that DNA sculpting, dynamic glycosylase interactions, and stabilizing contacts collectively provide a powerful mechanism for the detection and discrimination of modified bases and epigenetic marks in DNA.
Dynamic Architecture of DNA Repair Complexes and the Synaptonemal Complex at Sites of Meiotic Recombination by Alexander Woglar and Anne M. Villeneuve, Cell, doi:10.1016/j.cell.2018.03.066, online 10 May 2018. Meiotic double-strand breaks (DSBs) are generated and repaired in a highly regulated manner to ensure formation of crossovers (COs) while also enabling efficient non-CO repair to restore genome integrity.
A Post-Transcriptional Feedback Mechanism for Noise Suppression and Fate Stabilization by Maike M.K. Hansen, Winnie Y. Wen, Elena Ingerman et al., Cell, doi:10.1016/j.cell.2018.04.005, online 10 May 2018.
Widespread and precise reprogramming of yeast protein-genome interactions in response to heat shock by Vinesh Vinayachandran et al., Genome Res., online 14 Feb 2018. Together, these findings reveal protein–genome interactions that are robustly reprogrammed in precise and uniform ways far beyond what is elicited by changes in gene expression.
Stable Intronic Sequence RNAs Engage in Feedback Loops by Jun Wei Pek, Trends in Genetics, online 01 Feb 2018. The use of sisRNAs as mediators for local feedback control may be a general phenomenon.
Widespread and precise reprogramming of yeast protein-genome interactions in response to heat shock by Vinesh Vinayachandran et al., Genome Res., online 14 Feb 2018. Our findings reveal a precise positional organization of proteins bound at most genes, some of which rapidly reorganize within minutes of heat shock.
RNA Interference Pathways Display High Rates of Adaptive Protein Evolution in Multiple Invertebrates by William H. Palmer et al., doi:10.1534/genetics.117.300567, Genetics, 01 Feb 2018.
Protecting and Diversifying the Germline by Ryan J. Gleason et al., doi:10.1534/genetics.117.300208, Genetics, 01 Feb 2018.
Systematic discovery of antiphage defense systems in the microbial pangenome by Shany Doron, Sarah Melamed et al., doi:10.1126/science.aar4120, Science, 25 Jan 2018. Our data also suggest a common, ancient ancestry of innate immunity components shared between animals, plants, and bacteria.
DNA mismatch repair preferentially protects genes from mutation by Eric J. Belfield, Zhong Jie Ding et al., doi:10.1101/gr.219303.116, Genome Res., 12 Dec 2017.
Structural basis for the initiation of eukaryotic transcription-coupled DNA repair by Jun Xu et al., Nature, 30 Nov 2017.
Mismatch repair prefers exons by Dashiell J Massey and Amnon Koren, Nature Genetics, Dec 2017.
Rapid Gene Family Evolution of a Nematode Sperm Protein Despite Sequence Hyper-conservation by Katja R. Kasimatis and Patrick C. Phillips, G3, online 21 Nov 2017.
Structure of the Post-catalytic Spliceosome from Saccharomyces cerevisiae by Rui Bai, Chuangye Yan, Ruixue Wan et al., Cell, 16 Nov 2017.
The Mobile World of Transposable Elements by Caryn Navarro, Trends in Genetics, Nov 2017.
23 Aug 2017: ...a different code embedded in histone marks....
15 Jul 2017: Several studies have suggested that TE [transposable element] insertions have contributed to the rewiring and evolution of regulatory networks by recruiting multiple genes into the same regulatory circuit.
06 Jul 2017: How bacteria remember and defend against harmful viruses.
22 May 2017: ...ERVL LTRs provide molecular mechanisms for stochastically scanning, rewiring, and recycling genetic information on an extraordinary scale.
24 Jul 2016: A cell's deciphering arsenal....
14 Jun 2016: Robust software management systems must effect the assembly, deployment, repair and optimization of acquired genetic programs....
07 Apr 2016: ...molecular-resolution reconstruction of a central assembly of the human spliceosome.
28 Apr 2015: Diversity-generating retroelements (DGRs) use mutagenic reverse transcription and retrohoming to generate myriad variants of a target gene.
30 Jan 2015: I guess we owe the evolution of pregnancy to what are effectively genomic parasites.
19 Jan 2015: ...Deliberate killing of nonimmune cells ...releases DNA and makes it accessible for HGT.
07 July 2014: ...not only may mutations be non-random but horizontal gene transfer too need not be random.
20 Dec 2012: Evolution: A View from the 21st Century by James A. Shapiro
Quantifying the mechanisms of domain gain in animal proteins by Marija Buljan, Adam Frankish and Alex Bateman, doi:10.1186/gb-2010-11-7-r74; and commentary:
How do proteins gain new domains? by Joseph A Marsh and Sarah A Teichmann, doi:10.1186/gb-2010-11-7-126, Genome Biology, 15 Jul 2010.
Enard D, Depaulis F, Crollius HR, "Human and Non-Human Primate Genomes Share Hotspots of Positive Selection" [link], PLoS Genet 6(2): e1000840. doi:10.1371/journal.pgen.1000840, online 5 Feb 2010. "Our results show that positive selection affecting the same genes independently in human and other primates is a common phenomenon and is not restricted to specific functions such as defence against pathogens or reproduction."
6 Aug 2005: Parallel evolution has been observed in fruitflies.
9 May 2006: The structure of a bacterial enzyme that inserts mobile gene cassettes has been resolved by French biochemists and geneticists.
24 Feb 2006: Retroposed genes have contributed to human evolution.
24 Mar 2005: Plants can overwrite unhealthy genes.
28 Feb 2005: Can pre-existing genetic programs be pieced together?
29 Oct 2004: Pack-MULE transposable elements mediate gene evolution in plants.
31 Dec 2003: Stress can increase the rate of horizontal gene transfer.
30 Jun 2003: Introns can cause new stretches of DNA to be precisely inserted into genomes.
03 Nov 1998: Two geneticists find evidence for "a predominating integration mechanism," that inserts acquired foreign genes into genomes in clustered fragments.
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3. Shozo Yokoyama et al., "
Adaptive evolution of color vision of the Comoran coelacanth...", PNAS, 25 May 1999.
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