Inheritance & Evolution
The chemical differences among various species and genera of animals and plants are certainly as significant for the history of their origins as the differences in form. ~ Ray Lankester in 1880
Physically, inheritance from one generation to the next occurs in at least 3 ways: 1) genetically, 2) epigenetically, and 3) commensally (microbiotic transfer, from mother to offspring). While genetic transfer is the nominal inheritance route, many traits are passed on epigenetically. Roundworms inherit longevity without any genetic mutations that could confer that capability.
Genetic Inheritance
Horizontal gene transfer (HGT), a dominant evolutionary process, at least in prokaryotes, appears to be a form of (quasi) Lamarckian inheritance. The rate of HGT and the nature of acquired genes depend on the environment of the recipient organism and, in some cases, the transferred genes confer a selective advantage for growth in that environment, meeting the Lamarckian criteria. ~ Russian-American biologist Eugene Koonin & Russian-American cytologist & geneticist Yuri Wolf
Prokaryotes pick up stray genetic material via transformation (from the environment), horizontal gene transfer, and transduction (viral gift-giving). By contrast, eukaryotes only directly get foreign genes from viruses (transduction).
Eukaryotes do have their own genetic exchange, like the “genetic friends with benefits” of prokaryotic conjugation: intracellular gene transfer from endosymbionts. Eukaryotes arose from fusions of numerous viral and prokaryotic genomes.
The main difference of prokaryotes from eukaryotes is that prokaryotic reproduction is independent of DNA acquisition and recombination. Instead, DNA is obtained from fragmented chromosomes obtained via parasexual means (that is, without reproduction). These mechanisms of DNA exchange are not restricted to gene exchange within species, and therefore traits can and do come from highly divergent organisms. ~ evolutionary microbiologists Thane Papke & Peter Gogarten
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Genes fall into 2 functional classes: informational and operational. Each of these classes have their own evolutionary lineages which are extremely intricate due to regular genetic transfers between organisms.
Informational genes provide the data bank for transcription, translation, and other processes related to conveying genetic information. Operational genes are those involved in cellular housekeeping, such as genes for biosyntheses of amino acids, nucleotides, and lipids, genic regulation, and maintaining cell envelopes.
The 2 gene classes have different inheritance paths. Eukaryotes got almost all of their informational genes from archaeal hyperthermophiles (methanogens), likely one of the earliest life forms. Contrastingly, ~70% of the operational genes of eukaryotes came from bacteria, the ubiquitous prokaryotes. ~40% of those operational genes are from Escherichia: anaerobic, rod-shaped bacteria that now reside in animals’ guts. ~30% are from cyanobacteria, the original photosynthesizers that turned algae into plants.
It is not surprising that nuclear eukaryotic genes are derived from multiple prokaryotic sources. But it is startling that eukaryotic informational genes and operational genes have arisen from different types of prokaryotes.
The coherence of the informational lineage might reflect demanding functional constraints imposed on a tightly integrated set of genes. In contrast, the malleability of the operational lineage might reflect a less demanding functional coupling. ~ American molecular biologist Maria Rivera et al
Complex cell structures result from a genetic stew by copious cooks. The microbiome in a eukaryotic organism take up residence symbiotically and donate genetic bits. Further, viral and bacterial infections also occasionally contribute genetically, albeit with less well-meaning intent.
For macrobes, evolution is invariably a process of coevolution. But then, so it is too for the community of microbes that comprise a microbiome or colony.
Gene Flow
Gene flow can evolve. ~ American botanist Norman Ellstrand
Gene flow is the transfer of genes from one population to another. Thanks to airborne pollen delivery, and from pollinators, gene flow is more frequent in plants than animals. Plants exchange genes at considerable distances: hundreds or thousands of meters. One fig tree was found to have its paternal sire 85 km away.
Physical barriers impact gene flow, as can less tangible hindrances. In animals, female sexual preferences are instrumental in limiting gene flow.
Plants seldom have such inhibitions. Generally, hybridization is less restrictive in plants than animals, as plants are more flexible genetically and cognizant of what may be reproductively viable or not.
Gene flow acts as a cohesive force in uniting species. While gene flow is biodiversity in reverse, it may also provide adaptive opportunities that otherwise might be forgone.
Horizontal gene flow is thus both a homogenizing and a diversifying force. It typically involves groups of organisms that preferentially exchange genetic material. ~ Thane Papke & Peter Gogarten
Whereas proximity engenders gene flow, isolation dims it. Fragmenting forests lessen the prospects for biodiversity by segregating populations.
Genetic exchange groups appear to be the basis of many lineages observed in prokaryotes and are initiated or extinguished by sharing a common spatiotemporal existence with other exchange groups. Many prokaryotes, including pathogens, soil, and marine dwellers, use quorum sensing to regulate gene exchange. ~ Thane Papke & Peter Gogarten
Mutation
A mutation is a change in a gene sequence. The term comes courtesy of Dutch botanist Hugo de Vries, who, unaware of Mendel’s work, reiterated his discoveries.
In 1889 de Vries presented a variant of Darwin’s 1868 pangenesis hypothesis. de Vries postulated that traits were carried in particles he termed pangenes.
To de Vries, different characters had different hereditary carriers. His mutations were plant varieties that suddenly appeared: a product, he supposed, of altered pangenes.
20 years later, Danish botanist Wilhelm Johannsen mutated pangenes into genes. Johannsen’s conceptualization matched the modern notion of genes as carriers of heredity.
Johannsen broke with Darwin in suggesting the evolutionary suddenness of saltation, as contrasted to adamant Darwinian gradualism.
In dropping the idea of epigenetics, which was rejected as Lamarckian woolliness, Johannsen led geneticists into an unrealistically simplistic direction that would hold for well over a half century. The tidiness of Johannsen’s gene concept was compelling.
Genetics is illustrative of a conceptual hypothesis coming well in advance of a supporting fact base: a long-standing mental construct awaiting confirmation. Evidence that did not fit the preconception was considered auxiliary or ignored altogether.
In this case, the concept of genes easily meshed with the model of DNA from Watson & Crick. The fit was so easy that there was no question by geneticists that the puzzle of heredity had been completely solved. This smugness held the discipline back for over half a century.
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Several types of mutation exist, at variable ranges of impact: from a sole nucleotide to an entire chromosome. A point mutation exchanges a single nucleotide for another. Insertions add 1 or more nucleotides. Deletions subtract. Translocations interchange genetic material. Inversions rearrange a gene sequence.
There are numerous provocations that can cause a mutation: from an error or deviation in the complex process whereby DNA is replicated, to mutagenic chemicals, radiation, or viruses. Stress drives evolution.
Proteins that regulate gene expression or DNA sequence let changes occur. These alterations tend to be adaptively responsive. Such coherent teleology is both obvious and empirically inexplicable.
Internally invoked mutations are called spontaneous. Induced mutations are caused by radiation or chemicals, commonly toxins.
A mutation may have no effect, alter a gene’s product, prevent a gene from properly functioning, or render a gene inoperable. In effect, mutations may be neutral (not affecting fitness), harmful (decreasing fitness), or beneficial (improving fitness). Overtly non-damaging mutations are commonly accepted by a cell.
Due to the damage that mutations may have, cells have several DNA repair mechanisms which are able to proofread and mend damaging deviations before they become permanent. If repair is not possible, organisms have techniques for eliminating permanently mutated cells.
Mutations can be immediately adaptive. Somatic hypermutation is the mechanism by which an immune system learns to confront a new foreign element, commonly a pathogenic microbe.
Recombination
Genetic recombination occurs when a molecule of nucleic acid is broken then joined to a different one. Recombination may occur between similar (homologous) or dissimilar molecules, either DNA or RNA.
In homologous recombination (HR) nucleotide sequences are exchanged between similar genes. HR is most widely used by cells trying to repair ruptured DNA sequences after the double-strand breaks.
Non-homologous end joining (NHEJ) repairs breaks when no homologous copy exists. Non-homologous recombination helps immune cells in an adaptive immune system rapidly diversify to recognize and adapt to new pathogens. NHEJ may have evolved to allow bacteria to survive desiccation: being able to repair breaks without a template to gain a soluble rebound.
Recombination is a common technique for both microbes and eukaryotes for various purposes. During meiosis, in which eukaryotes make gamete cells (e.g., sperm and egg cells in animals), a dash of recombination puts some spice in the genome potential for offspring. Chromosomal crossover – exchange of genetic material between homologous chromosomes – is how offspring become a blend of parental genomes.
Transposable elements (TE) are a genetic wildcard: DNA sequences able to self-transpose. These Tinkertoy genes may decide to change relative position with a cell’s genome. Such mobile elements provide powerful pathways to genetic recombination and are mutagens of the highest order.
TEs are ubiquitous among prokaryotes and eukaryotes. There are 2 classes of transposable element: transposons and retrotransposons.
Retrotransposons (aka retroelements) are DNA genetic amplifiers: mobile “copy and paste” elements via an RNA assist. The copy comes in 2 stages: 1) DNA to RNA by transcription; 2) from RNA back to DNA via reverse transcription. The DNA copy is inserted into a different position in the genome.
Large swaths of the genomes of eukaryotes are taken up by retroelements. Retrotransposons are especially abundant in plants: often comprising the principal component of nuclear DNA. 42% of the human genome are retroelements.
Retroviruses, such as HIV, do their business along the retroelement road, hijacking host machinery for production. The disorderly nature of genetic insertion by retroviruses can activate oncogenes: errant DNA with the potential to cause cancer.
Transposons are a “cut and paste” TEs, able to work their magic without an RNA intermediate. Transposons are also able to adopt external DNA sequences as their own.
Gene Conversion
Gene conversion is a recombination transfer between DNA sequences. The converting gene is unaltered, but the gene receiving the DNA transfer may well be mutated by the process.
Gene conversion happens at high frequencies during meiotic division, but also occurs in somatic cells, notably immune system cells. Gene conversion lies outside Mendelian inheritance.
Gene conversion tends to homogenize the DNA in the gene pool of a species. A gene conversion takes 2 similar-but-different DNA because of sequence mismatches and yields 2 identical DNA sequences.
Gene conversion is a cohesive force linking DNA sequences within different organisms of a species. Over time, absent other dynamics, gene conversion would yield a homogenous set of DNA.
Gene conversion is not random. Biased gene conversion (BCG) – where a certain allele is favored – is quite common. BCG can selectively accelerate evolution in certain genes, increasing the rate at which specific mutations spread through a population. BCG is often strongest in genetic regions prone to high recombination rates.
Self-Splicing Elements
Introns – self-splicing gene segments – are another avenue for altering the expression of genetic codes.
Proteins are a cell’s workforce. Genes are merely templates for producing proteins and other bioproducts that work in concert with proteins. Any mechanism that alters protein operation has the potential to alter the genome via feedback.
Inteins are self-splicing protein segments which can excise themselves from larger protein molecules and rejoin a polypeptide chain (extein) via a peptide bond. In prokaryotes, inteins are known to function as genome maintenance proteins.
Inteins have been called protein introns. Both introns and inteins are agents in gene expression and regulation.
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Directly altering DNA is merely the coarsest means to alter genetic expression. Epigenetics takes genetic engineering to a whole new level of subtlety.
Epigenetic Inheritance
Evolution can occur through the epigenetic dimension of heredity even if nothing is happening in the genetic dimension. ~ Israeli geneticist Eva Jablonka & English evolutionary biologist Marion Lamb
The DNA double-helix presents a malleable script. A wide variety of regulatory actions may adjust gene expression. Life experiences are encoded epigenetically and may be passed on to cell offspring, affecting an organism and its progeny without shifting DNA sequences.
Vinegar Flies
Adaptation to different environments may lead to reproductive isolation. ~ American evolutionary biologist Henry Chung et al
The vinegar fly Drosophila serrata speciated from Drosophila birchii via epigenetic regulation of a single gene that affects both mating preference and desiccation resistance.
Cuticular hydrocarbons (CHCs) have various functions in insects, including communication. One class of CHC – methyl-branched CHC (mbCHC) – protects an insect from desiccation by sealing its cuticle.
D. birchii is a niche specialist that lives in the rainforests of Australia and Melanesia. Owing to a low mbCHC level, D. birchii is extremely sensitive to dryness.
In contrast, the generalist D. serrata is found on the fringes of the rainforest on the east coast of Australia. It is relatively desiccation-resistant, thanks to generous manufacture of mbCHCs.
The 2 vinegar flies do not interbreed. mbCHC level is a factor in mating success for male D. serrata, as females won’t mate with a fly that has low mbCHC.
The gene that controls mbCHC production is regulated by RNA interference (RNAi), which mediates mbCHC level. By contributing to both mating success and desiccation resistance, mbCHC level constitutes a dual trait.
