Soma, Germ and Speciation

I want to start from this statement.

Any genetic/genomic alteration occurs on a single chromosome in a single cell of a single organism.  Each genetic/genomic alteration is private and personal to that chromosome.  DNA replication is the only way to reproduce the identical alteration.

In a diploid organism, a genetic/genomic alteration may cause phenotypic changes in a dominant or recessive manner, or cause no phenotypic change, in which case it is called a neutral alteration. This is basic knowledge of Mendelian genetics. 

There are two cell lineages in all diploid animals: somatic and germ lineages. Soon after fertilization, somatic cells and the future germ cells are separated in animals. Then, a species-specific developmental process increases the number and types of cells through cell proliferation and differentiation and allocates them to specific locations through morphogenesis. The period of totipotency is very short in animals and differs from that in plants. Somatic cells cannot become the germ lineage, and vice versa. Recognizing the soma-germ difference is essential to understanding the process of animal evolution. 

Somatic cells are the cell population comprising all our body cells, except for the germ lineage. They are responsible for an individual's phenotypes, including size, shape, colour, and physiology. By contrast, the germ lineage gives rise only to sperm or oocytes. They do not contribute to the individual’s phenotypes but to reproduction. 

Reproduction, sexual mating, is not only an issue for germ cells but also for somatic phenotypes. 

Somatic phenotypes can prevent successful sexual mating due to differences in size, shape, colour, and physiology. Body size and shape, as well as the size and shape of the sexual organs, must be compatible. In addition, various somatic body parts contribute to successful mating, not limited to the sexual organs. Reproductive physiology must also be synchronized, as successful sexual mating requires an encounter between a mature male and female at the right time of ovulation. Importantly, all of these are somatic phenotypes that contribute to reproductive success.

On the other hand, germ cell phenotypes can also contribute to reproductive success. The most obvious example is sperm-oocyte compatibility. Without their fusion, fertilization cannot occur. In addition, because germ cells are the only cell population that undergoes meiosis, defects in meiosis uniquely affect them and, in turn, reproductive success. On many occasions, somatic phenotypes are independent of the germ lineage, and vice versa.  

Returning to the first statement of this essay, each genetic/genomic alteration occurs on a single chromosome in a single cell of a single organism. No exception. The alteration can be phenotypically dominant, recessive, or neutral in the somatic or germline lineage. The terms ‘dominant’ and ‘recessive’ describe the relationship between an allele and a phenotype in genetics. 

Because the diploid organism has a pair of homologous chromosomes, an alteration in one of the two does not always result in a detectable phenotype. Dominant means that an alteration in one copy is sufficient to change the phenotype, whereas recessive means that an alteration in both copies is required to exhibit a phenotype. The phenotype observed in heterozygous individuals is called dominant. By contrast, heterozygotes for recessive alleles show no difference from the WT phenotype. 

Somatic phenotypes arise from somatic cells, while germline phenotypes arise in the germ cells. They are independent. However, reproductive success depends on both somatic and germline phenotypes. Somatic phenotypes alone can prevent reproductive success even with normal, healthy germ cells, and germline phenotypes alone can do so even with normal, healthy somatic phenotypes.  

A genetic/genomic alteration creates a new allele on a single chromosome in a single cell. Then, there are only four phenotypic possibilities: somatic dominant or recessive, or germline dominant or recessive.

If the allele is somatic dominant, the somatic-dominant phenotype appears in the first individual carrying the alteration. In this case, the genotype-phenotype relationship is one-to-one. The concept of heritable ‘fitness’ applies to somatic-dominant phenotypes.

To inherit this alteration from the first individual, the only option is to mate with WT partners. If the somatic-dominant phenotype prevents mating with WT, inheritance is impossible, even if its fitness is higher than that of others. The somatic-dominant phenotype allows direct inheritance of the phenotype by offspring, known as vertical inheritance. However, because it requires crossing with a WT partner, the somatic-dominant phenotype cannot create a reproductive barrier that separates it from the parental WT species.  

On the other hand, if the allele is somatic recessive, there is no phenotype in the first individual because the first individual is heterozygous. Phenotypically, the first individual is indistinguishable from other WTs. It mates with WT partners and produces offspring.

According to Mendelian inheritance, the recessive allele is inherited by 50% of the offspring, but all are still heterozygous. Therefore, there is no chance of the recessive phenotype being expressed. When heterozygous siblings mate, 25% of their offspring will be homozygous for the recessive allele. These homozygotes are the first to exhibit the somatic-recessive phenotype. This differs from the somatic-dominant case. The first individuals exhibiting the somatic-recessive phenotype are not alone. Some of their siblings are also homozygotes with the recessive phenotype. 

The recessive somatic phenotype can create differences in size, shape, colour and physiology. Although WT and heterozygotes are phenotypically identical, homozygotes differ. These differences can prevent successful mating, for example, if homozygotes are twice as small or if the sexual season shifts later. Although they cannot mate with WT and heterozygotes, they can mate with other homozygotes. 

These homozygotes are now reproductively separated from the parental species and thus have the potential to become a new species.

Interestingly, during this process, not only the altered allele but also other alleles on the chromosomes are carried along as a consequence of the founder effect. The newly reproductively separated small group can have the somatic-recessive phenotype of the allele, as well as other genetic variation that is accidentally accompanied on the founder chromosomes.

With the founder effect of sibling mating and a somatic-recessive phenotype, a somatic-recessive allele has the potential to give rise to a new species.

Then, what if a new alteration has a germline-dominant phenotype? I consider only dominant subfertility because if the first individual is dominant-sterile, there is no chance of allele inheritance. Dominant subfertility is problematic but heritable. Heterozygotes exhibit the subfertility phenotype. Then, what would happen if the allele becomes homozygous? Would it be more severe, or would fertility be restored? 

Along this line, you can see that a germline-recessive phenotype is also highly problematic. Reproductive problems arise only in homozygotes. Both germline-dominant and recessive create reproductive problems but do not appear to create a barrier to reproductive separation from the parental species. They simply create reproductive problems.

To build a barrier, a germline-dominant trait can create reproductive problems in heterozygotes, but it should be resolved in homozygotes.  Is there such a convenient genetic/genomic alteration?

I do not know of any example of a gene alteration that suffices for this, but I do know that chromosomal rearrangements can do so. Chromosomal rearrangements include deletion, insertion, inversion and translocation. Although the microscale sequence remains unchanged in chromosomal rearrangements, the macroscale order and orientation within a chromosome change.

Meiosis is a specific process in the germ lineage that reduces the diploid genome to the haploid genome in gametes. During meiosis, two homologous chromosomes must align with each other. Chromosome rearrangements may compromise this alignment. The success rate of alignment could be reduced due to a change in macroscale structural order (e.g., it takes too long to complete within a limited time frame). This could reduce the number of sperm or oocytes, while the quality of the sperm/oocytes produced should remain intact. 

Interestingly, this incompatibility occurs only in heterozygotes. Once homozygotes arise from intercrossing between heterozygotes, the subfertility issue will disappear. Therefore, the chromosome rearrangement can be a barrier to reproductive separation from the parental species. 

Having the germline phenotype does not guarantee the presence of somatic phenotypes. However, chromosomal rearrangements can produce somatic phenotypes. The number of DNA sequence alterations in a single chromosomal event ranges from three to six. In a deletion, two sites are broken, and a new junction forms by rejoining them. For an insertion, one site is broken, and two new junctions are created. For an inversion, two sites are broken, and two new junctions are created. For a translocation, three sites are broken, and three new junctions are created. 

It is possible that a single chromosomal event causes no phenotype at all, but it can also produce massive phenotypic changes. If each break lies within a gene sequence, it is theoretically possible to alter three genes simultaneously via a single translocation, although this view remains gene-centric.

Modern genome research shows that each chromosome forms reproducible 3D structures, called topologically associated domains (TADs), that control the physical proximity of two DNA sequence regions. In addition, gene regulation is carried out by the DNA sequence surrounding the gene body. Those regulatory sequences are not limited to adjacent sequences in 1D order but also include distant ones, a phenomenon known as long-range regulation. Although those sequences appear far away in 1D sequence order, they are physically close in the reproduced 3D structure. In the context of gene regulation, the physical proximity of two or more DNA sequences within the 3D chromosomal structure is important.

For example, one chromosomal translocation destroys three neighbour-proximity and creates new three neighbour-proximity. A single event results in 6 changes to neighbour interactions.

This may result in somatic phenotypes. A chromosomal rearrangement may lead to a somatic-dominant or recessive phenotype, in addition to causing a germline-dominant phenotype and the founder effect.

An interesting case is one in which a chromosomal rearrangement creates somatic-recessive and germline-dominant phenotypes. Meiosis in heterozygotes is compromised, but there is no somatic phenotype. Therefore, heterozygotes can cross with WT or other heterozygotes. Heterozygote sibling crosses can generate homozygotes, which exhibit the first-generation somatic-recessive phenotype. 

They are the first to exhibit the somatic-recessive phenotype. In these homozygotes, there is no incompatibility between the two homologous chromosomes. Therefore, their reproductive ability is restored. Reproductive separation from the parental species is achieved. These homozygotes have the potential to become a new species. 

So far, I have presented two possibilities: First, a somatic-recessive phenotype can create a reproductive barrier. Second, a somatic-recessive phenotype with a germline-dominant phenotype due to chromosomal rearrangement, can also create one. Both scenarios can accompany the accidental founder effect. These processes can generate a small, reproductively separated group from the parental species.

Are they a new species? Not yet. The survival of the new small group depends on the somatic-recessive phenotype. They do not need to be better but should be different to continue as a new species.

All species can live only in a specific area and during specific seasonal/daytime periods. No single species can live everywhere, from the tropics to the Arctic, at any time, 24/7 and all year round. There is always an optimal and an impossible in space and time. Many species move seasonally from one place to another because a certain period in one location is uninhabitable. All species have their unique livable niche in space and time. I call this INSIDE. Therefore, there is always an OUTSIDE of it. 

The parental species does not care about OUTSIDE, because it is unlivable. Only if the somatic-recessive phenotype permits the new small group to live OUTSIDE (i.e., outside is not limited to space but also includes time), does the new small group continue as a new species. The phenotype that permits living OUTSIDE cannot be shared with the parental species because of reproductive separation. The new somatic-recessive phenotype is the necessity to live OUTSIDE. No individual in the parental species cares about or aims to move OUTSIDE, because they have their own INSIDE where they can live. The new somatic-recessive phenotype does not need to be better at living INSIDE at all, but is necessary to live OUTSIDE. This INSIDE/OUTSIDE concept in space and time is essential to understanding animal evolution.  

The necessity creates commonality. A species is a group of individuals that exhibit a stable and consistent range of phenotypic variation, most of which is created by epigenetic regulation. This sets the commonality of species. This commonality permits enough opportunities for a sufficient number of survivors to continue as a species in its local environment. This sets INSIDE. The individual’s survival INSIDE is a matter of luck, simply based on ‘where’ and ‘when’ one exists. In other words, being in the right place at the right time. 

Some people don’t like the idea of luck determining an individual’s survival and reproduction. Then I must ask what the genome or genes determine. The genome determines which species the individual becomes. Some gene mutations determine lethality. All other genes contribute to phenotypic variation to some extent, but most are subtle deviations. Rather than individual genes, epigenetic regulation produces much wider phenotypic variation. Think of development and aging. From a fertilized egg to a newborn baby, to an adult, to aging. A huge range of somatic phenotypic variation. Personal history also affects phenotypes. Past accidents, such as amputations, and past environmental impacts, such as nutrient and temperature conditions, substantially affect an individual’s phenotype beyond their gene set. This is simply ‘where’ and ‘when’ one existed in the past.

Gene-based subtle deviations will be noticeable only after all other variable conditions are eliminated. This can occur only through artificial human interventions. 

How about sexual selection? It is still a matter of luck, based on an encounter at the right time. I do not think that population genetic selection occurs by sexual selection . Importantly, I believe that sexual selection primarily acts on epigenetic phenotypes that reflect past nutrient and temperature conditions, rather than on superior genes.

Life continues as a species. For a species, who survives is not important. Whoever survives can successfully pass their genome to offspring. As a whole, a species continues. Please don’t read intention into this. This is a consequence without intention.

Natural selection, currently interpreted as allelic selection (or populational genetic selection) within an environment, can occur only under highly limited conditions. Importantly, it cannot create new species but only cause population drift within a species. We need to be reminded that all genetic/genomic alteration occurs on a single chromosome in a single cell within a single organism. No alteration can suddenly become a variant or common in a population. Only absolute necessity or an accidental founder effect can enrich the new allele in a local population.

Without necessity, errors will overwrite the alterations because of an erroneous DNA replication system. Importantly, nothing new is required as long as living INSIDE. The commonality of species fully supports living INSIDE. However, this does not guarantee the individual’s survival. No single individual is guaranteed to survive and reproduce.

Conversely, as a group, the species’ commonality provides enough opportunities for a sufficient number of survivors to continue in its local environment. Whoever survives can pass the commonality to their offspring. This is why the species is a stable and consistent entity as a whole.

A species is a group entity. From speciation to extinction, its commonality does not change. Because the commonality is sufficient to live INSIDE, when the environment that provides opportunities for the commonality disappears, the species becomes extinct.

Genetic variation is not necessary to live INSIDE, whilst it is necessary to live OUTSIDE. If any accidental new variation, either dominant or recessive, permits living OUTSIDE, the variation will be necessary to live in this local environment. The variation is not better but necessary to live OUTSIDE. Those without it just need to stay INSIDE. The variation is enriched in a specific local area. Without reproductive separation, it remains a local variation and thus a subspecies. 

As I discussed above, somatic-dominant phenotypes and alleles have little chance of creating a new species (only under very specific conditions) but are highly effective at creating subspecies within a species because of the consistent vertical transmission of the phenotype to direct offspring. Allele frequency in a local population reflects the probabilistic compatibility with its environment. It is not the consequence of competition but shared probabilities with the local environment. Because of shared probabilities, minorities never disappear but just persist as minorities at equilibrium

Studies in human genetics provide many examples of this type of natural selection, or purifying selection. The best example is the relationship between malaria and sickle cell anemia. The dominant phenotype of the sickle cell anemia allele prevents malaria lethality in the tropical zone. Without the allele, individuals are at high risk of dying early from malaria. Heterozygotes with the somatic dominant phenotype are enriched in the local area. As an inevitable consequence, occasionally homozygotes are born with sickle cell anemia, and those individuals die early because of it. However, because malaria lethality is high in the local area, the allele remains in the population at equilibrium.

Effective vertical transmission of the phenotype occurs in somatic-dominant alleles. With a high lethal challenge, the allele is enriched locally in a population, not because of competition. But this can not give rise to a new species. Proportional dominance of an allele indicates its suitability to the local environment, but is irrelevant in speciation

On the other hand, the recessive phenotype is not easily observed in a population without sibling mating that creates the founder effect. The consistency of vertical transmission of the recessive phenotype to offspring is highly conditional. I would say that consistent transmission of recessive phenotypes is highly unlikely without reproductive separation. 

Some readers might have noticed that I am not using the term ‘reproductive isolation’; instead, I am using ‘reproductive separation’. My reasoning is that, as I explained above, when a new species emerges, the new group of individuals only needs to separate from the parental species and does not need to be isolated. The word ‘isolation’ often connotes ‘independence’ from all others. 

Speciation only requires separation from the parental species. This separation can be geographical, somatic-reproductive, or germ-reproductive. The smaller the bottleneck, the stronger the founder effect.

Separation from the parental species does not guarantee separation from sister species. Sister species arise from the same parental species, but their speciation occurs in different places and at different times. At the time of speciation, the two sister species are unlikely to encounter each other. However, spatial and temporal changes in their local environment may permit their physical encounter. This can lead to gene flow or hybridization.

Each species is tightly associated with its local environment. Because each living organism is a physical entity, it can only move to physically adjacent locations. Humans have moved many other species to new locations through our economic activities. For them, those new locations are physically far from their original habitat. Without human help, they have no chance of encountering it.

Then, on some occasions, some human-transferred species found an environment that offers enough opportunities for a sufficient number of survivors to continue. These are the invasive species. They are not intended to invade, but humans provide them with an opportunity to discover.

Invasive species are no better than native species in the habitat. They find a space to insert their layer into a stack of layered local native species. The newly inserted layer only affects its downstream. Invasive species exhaust the opportunities for native species from their upstream. 

Opportunities are accidental encounters in space and time. They are not uniform and consistent, but spontaneous and temporal. Opportunities are temporally layered. Think of fruit. Unripe, ripe, and rotten. When a local native eats ripe fruit, what happens if the invasive one eats unripe or rotten fruit? The invasive one can survive in either case, but the impact on the local native differs. If unripe fruit is taken, and taken in large amounts, the local native has nothing left and no chance of fighting back. If rotten fruit is taken, the local native doesn’t care. Neither unripe nor rotten is an edible resource for the local native. There is no way to change their own edible. 

I hope readers recognize that the process I describe above has no implications for competition, but rather concerns the compatibility of species with their local environment. Species provide probabilistic individual survival within their local environment, based on their commonality. In INSIDE, the probability of an individual’s survival is neither zero nor 100%. But as a whole, a sufficient number of survivors remains to continue. At OUTSIDE, the probability is zero. The boundary of INSIDE/OUTSIDE is not sharp but rather blurred and fructuous. Species do not need to and cannot improve to live INSIDE. However, a new difference is absolutely necessary to survive OUTSIDE. Once the difference is obtained, the previous OUTSIDE becomes a new INSIDE. A new species expands as much as it can until it reaches the local carrying capacity and discovers its new OUTSIDE. Not only speciation but also symbiosis and symbiogenesis must be on the same line.

In addition, the opportunities that a local environment provides are layered for multiple species, similar to water flowing from upstream to downstream in a river.  When opportunities are declined or exhausted upstream, the downstream species disappears from that local environment. If the species cannot find opportunities in the physically connected area, it goes extinct. This is not the consequence of competition but deprivation of opportunities.

Better does not exist in nature, but difference does. Each local environment on Earth is unique. The compatibility of species with a specific environment has always had spatial and temporal limits. Therefore, there is always OUTSIDE. The history of life is a series of accidental discoveries of compatibility with OUTSIDE. OUTSIDE is always inexistence and unnecessary for the original parental species. When, accidentally, a new compatibility that permits living OUTSIDE emerges, a new species with a new INSIDE emerges. This opening of a probability OUTSIDE permits diversity and expansion of living organisms across the entire surface of the Earth.

Humans are the only species that changes our compatibility through tools, clothing, fire, cooking, building, and agriculture. Without changing our own genetic sequence, we overcome the limits of OUTSIDE. This permitted the great human migration that no other organism attempted. Humans are the only species that lives on the entire surface of Earth, except for the tops of Mt. Everest, the North and South Poles, the interiors of volcanoes, etc. Those places I listed are where no one cares to live, because of OUTSIDE for us, still.

Theoretically, each local environment is highly robust and plastic to various perturbations. However, human activities, such as construction and building, fundamentally alter the local environment. Modern artifacts create global uniformity, like concrete buildings, roads, and many plastic materials. All locally unique opportunities that local living organisms rely on are exhausted by our ability to alter the environment. 

Interestingly, personal wealth in modern human societies acts as a heritable dominant trait that supports winning in competition and selection. Highly efficient vertical transmission. The process appears well-suited to Darwinian heredity, variation, and natural selection. This makes sense to me because Darwin derived the concept of competitive natural selection from observations of industrializing modern human society, drawing on Thomas Malthus’s 1798 essay on human population and limited resources. Competition with others for survival is justified and implemented as a process to improve compatibility with one's local environment. As I discussed above, the process in nature is the opposite. Compatibility does not improve through competition; it accidentally emerges. When the new compatibility opens a probability of living OUTSIDE, a new species emerges. There is no improvement in living INSIDE, while new variations are necessary for living OUTSIDE, where no one cares.

The other individuals in the same species are not opponents but fellows, colleagues, companions, or friends. Fundamentally, there is no competition in living INSIDE. Life exists as a species. A species is a populational system of betting on the probability of continuity, as a whole. Sunfish lays millions of eggs, but only a few survive. They do not disappear. They do not improve anything through selection. But they maintain the stable, consistent commonality. Commonality provides enough opportunities for a sufficient number of survivors to continue in its local environment. Whoever survives can pass on the commonality to future generations. 

The desire to increase personal possessions is the driving force behind capitalism. In the natural world, ownership is always physical. The owner must be physically present at the site to claim and defend it. However, cognitive ownership in human societies operates in the owner’s absence. Cognitive ownership is the concept of excluding others’ access in the owner's absence. This is a human-specific ability.

Cognitive ownership is limitless. Historically, it was originally restricted to objects. It then expanded from objects to land and opportunities, from materials to space, and from immediate consumption to storage for the future. The concept of reservation does not exist in nature, nor investment. Cognitive ownership equals the physical exclusion of others. With economic power, the rich can exclude many others from future opportunities. They can even exhaust opportunities from upstream. Through exclusion, elimination, monopolization, and siphoning, inexcusable wealth inequality is created and effectively vertically inherited.  

I admit that capitalism is the best way to encourage steps into the OUTSIDE. Surplus supports curiosity and imagination, which are the only guides towards the OUTSIDE – an investment with no guaranteed return. Aiming OUTSIDE is always crazy and insane. A small number of individuals have been reshaping our perceptions of the natural world and human societies through the arts, philosophy, literature, and the sciences by bravely stepping into uncertainty. They opened a probability OUTSIDE where there had been inexistence.

Consequently, humans expanded our INSIDE. Interestingly, a new INSIDE often expands much larger than the previous INSIDE. Through this, the original exception (or unique variation) becomes common and ubiquitous in a population. Think of electricity during the last couple of centuries and cell phones for the last few decades. A minor unnecessity in the previous INSIDE has shifted to an abundant necessity in the updated INSIDE.

On the other hand, logically supported justifications aim for ‘better’ and ‘faster’ under predictions. This encourages picking low-hanging fruit for a first-mover advantage through exclusion. Populational/proportional dominance can effectively exclude and eliminate minorities for the sake of efficiency, convenience and uniform fairness. All of these are unique to human societies, but not in the way Mother Nature has been working. 

Transparency and high fluidity are closely linked to efficiency and fairness. Uniform, identical environments improve efficiency and predictability but also introduce fragility. No living organisms can survive in such a uniform, identical environment. Sedimentation and many places to hide can create biologically rich environments. ‘Rich’ means many variations and a wide range of uniqueness. Sedimentation is neither deadly stagnation nor constant mixing currents, but rather variation and inconsistency. Slow, steady current movement creates various unique microenvironments. Many different microenvironments permit many different compatibilities. This leads to a high level of biodiversity. Under capitalism and globalization, this is seen as the cause of inefficiency and non-tariff barriers to trade.  Although those variations are the reason that we currently exist, they counteract efficiency. Fairness justifies uniformity, and then uniformity facilitates efficiency, despite not being such a thing as fairness that is globally, uniformly and eternally applicable to all humans.  After all, fairness is context-dependent.

By contrast, the natural world exhibits high variation and complexity. Each organism interacts with others in layers, none in isolation. Each living organism exists in a unique, suitable local microenvironment. Its current existence is due to the first small group of its ancestors having physically identified it at the time of speciation, and that environment has persisted to this day. 

High predictability, based on uniformity and consistency, is efficient but fragile. Chaos is messy and unpredictable, yet it is impossible to perturb. Ironically, transparency, fairness and uniformity only bring fragility as a trade-off to efficiency. When capitalism points to the INSIDE, where it is more predictable, it encourages transparency and uniformity because that is more efficient. However, the uniform, fluidic, transparent and efficient condition facilitates monopoly and the siphoning of all wealth by rare superrich. All sediments are cleared to achieve a uniform, boring consistency, like a concrete river. All diversity will be gone; no life can live. We are killing the richness of diversity and chaotic robustness for the sake of short-sighted fairness and efficiency. We must embrace the uncertainty inherent in diversity and chaos. Weakly chaotic and weakly coherent permit diversity.  Opening a probability OUTSIDE is the best way to increase diversity because it depends on unique differences.