The major ( hypothesized) transitions in evolution

The major ( hypothesized) transitions in evolution

https://reasonandscience.catsboard.com/t3046-the-major-hypothesized-transitions-in-evolution

Different explanatory challenges
There are a number of different ongoing research questions associated with the major transitions, which we can organize into three classes. 
1.How transitions occur:
2.Why transitions occur –
3.How the higher-level organization is maintained

In a general sense, the transition zones are:
Replicating molecules to populations of molecules in compartments
Unlinked replicators to chromosomes
RNA as gene and enzyme to DNA and protein (genetic code)
Prokaryotes to eukaryotes
Asexual clones to sexual populations
Protists to animals, plants and fungi (cell differentiation)
Solitary individuals to colonies (non-reproductive castes)
Primate societies to human societies (language)

What has to be explained, is:
1. Origin of eukaryotes
2. Origin of multicellularity ( animals, fungi, plants )
3. Origin of obligatory social groups of animals ( ex. wasps)
4. Origin of language
5. Origin of different communication systems in the animal world
6. Dominance of tool-using and conscious planning (man).

Origin of eukaryotes
Eukaryotic cells function on different physical principles compared to prokaryotic cells, which is directly due to their (comparatively) enormous size. The diversity of the outcomes of phylogenetic analysis, with the origin of eukaryotes scattered around the archaeal diversity, has led to considerable frustration and suggested that a ‘phylogenomic impasse’ has been reached, owing to the inadequacy of the available phylogenetic methods for disambiguating deep relationships
 
- Actins
- Centrioles
- Cell walls in plant cells
- Centrosome
- Cytoskeleton
- Cyanelles
- Chloroplasts
- DNA replication ( different than in prokaryotes)
- Directing new deliveries of proteins and lipids to the appropriate organelle
- Endosomes
- Eukaryotic flagellum
- Ejectosomes
- Haptonema.
- Histones
- Introns and exons
- Lysosome
- Meiosis
- Mitosis
- Mitochondrion
- Motor proteins ( dynein, kinesin etc.)
- Nucleus
- Nucleolus
- Nucleosomes
- Pseudopods
- Plastids
- Ribosome ( different than in prokaryotes )
- Spliceosome
- Complex distribution systems transport-specific products from one compartment to another.
- Obligate sexuality
- Over 30 different genetic codes
- Organelles ( Rough and smooth endoplasmic reticulum, Golgi apparatus, nucleus, mitochondrion, endosomes, lysosome, and peroxisome )
- Sexual recombination
- Tubulin cytoskeletons,
- The nuclear pores,
- The proteasome
- Ubiquitin signalling systems
- Undulipodia
- Vacuoles
- Vesicle

In plant cells:
- Tonoplast
- Plasmodesmata

Division of labor between nuclear, cytoplasm organelles (flagellates, other protozoa (eukaryotes)).


A current hy pothesis of genealogical relationships among eukary otic organisms, based on molecular sequence comparisons of ten genes. Note the dotted line that connects diplomonads (which include Giardia lamblia) and parabasalids to the remainder of tree. This indicates the uncertainty surrounding the nature and composition of early branches on the tree.


Origin of multicellularity

Six major transitions in animal evolution  

Animal tissue classification
There are four basic types of animal tissues: muscle tissue, nervous tissue, connective tissue, and epithelial tissue

1.  origin of multicellularity;
2.  symmetry, two germ layers, neurons;
3.  bilateral symmetry, three germ layers, axial nerve cord, through gut;
4.  dorsoventral axis inversion;
5.  neural crest, new cell types;
6.  migratory mesoderm paired appendages, jaws. 

- Multicellular organisms with some cellular differentiation (sponges, algae, fungi).
- Differentiated systems of organs and tissues (coelenterates, flatworms, higher plants).
- Organized central nervous system, well-developed sense organs, limbs (arthropods, vertebrates).
- Homeothermic metabolism (warmblood) (mammals, birds).

Major transitions in the evolution of early land plants

Plant tissue classification
Dermal tissue, Vascular tissue, Ground tissue, Meristematic tissue

Deployment of gametophytic structures and mechanisms, as well as a number of major innovations.

1. The last common ancestor of land plants probably was a leafless axial gametophyte bearing morphologically simple unisporangiate sporophytes.
2. Stomata in mosses, hornworts and polysporangiophytes probably are homologous; the monophyletic lineage encompassing these three groups is therefore referred to as the ‘stomatophytes’.
3. Stomata are a sporophyte innovation, possibly with the ancestral functions of producing a controlled transpiration-driven flow of water and solutes from the parental gametophyte and facilitating the separation of maturing spores before release.
4. Stomata/air spaces and sporophyte vascularization, the latter probably by deployment of vascular tissue from the gametophyte, were pivotal to the divergence of the stomatophyte lineage.
5. Determinate sporophyte development based on embryonic meristematic activity is the ancestral condition in land plants, still present in modern liverworts and mosses.
6. An indeterminate sporophyte body (the sporophyte shoot) developing from an apical meristem (SAM) is the fundamental innovation of polysporangiophytes.
7. Poikilohydry is the ancestral condition in land plants; homeohydry evolved in the sporophyte of polysporangiophytes.
8. Symbiotic associations with fungi
9. Hydroids are an imperforate type of WCC evolved in advanced (peristomate) mosses; hydroids are not homologous to xylem vascular cells.
10. Xylem vascular cells evolved in the sporophyte of polysporangiophytes, either from pre-existing perforate vascular cells or de novo, in parallel with the establishment of homoiohydry.
11. Food-conducting cells first evolved in the gametophyte generation at the dawn of land plant evolution.

It is estimated ( claimed ) that the transition to multicellularity would have required to take place at least 25 times – in other words, 25 different cellular lineages would have had to evolve independently making the jump to communally organized life

Explaining organismal form depends on explaining how organs, tissues, and cells form and gain shape. 


On the lowest level of the hierarchy, the formation of cells in a multicellular organism depends on the specification of: 

1. Morphogenesis of various eukaryotic cells, structures, and shapes
2. Cell fate determination and differentiation ( phenotype, or what cell type each one will become )
3. Cell growth and size
4. Development and cell division counting: cells need to be programmed  to stop self-replicating after the right number of cell divisions
5. Mechanisms of pattern formation
6. Hox genes
7. Directing cell position and place in the body. This is crucial. Limbs like legs, fins, eyes, etc. must all be placed at the right place.
8. Set up of cell communication system and channels ( the creation of close to 30 different epigenetic codes and languages )
9. Set up of cell sensory and stimuli functions to interact with its environment and surroundings. 
10. Setting up de novo cell regulatory functions 
11. Timing and regulation for the development program of the organism to express the genes to grow new cells during development
12. Change regulation in the composition of the cell membrane and/or secreted products.
13. Specification of the cell-cell adhesion proteins and which ones will be used in each cell to adhere to the neighbor cells ( there are 4 classes )
14. Apoptosis: programming of the time period the cell keeps alive in the body, the timing of self-destruction, and replacement
15. Set up specific nutrition demands for each cell type.  
16. Programming of cell shape changes for adaptation.
17. Cell proliferation: the process that results in an increase in the number of cells, a balance between cell divisions, and cell loss through cell death or differentiation.
18. Set up Cell layers 
19. Formation of extracellular matrix molecules, 

1. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3310499/



Ádám Kun: The major evolutionary transitions and codes of life December 2021

The Origin of the Eukaryotic Cell
The origin of the eukaryotic cells; suffice it to say that the picture seems more obscure than 20 y ago. Spectacular individual complexity is a feature of the eukaryotes. Indeed, the divide between prokaryotes and eukaryotes is the biggest known evolutionary discontinuity. What allows this increase in complexity? A consensus seems to emerge that the answer lies in energy. It was the acquisition of mitochondria that allowed more energy per gene available for cells , which, in turn, allowed experimentation with a higher number of genes. This change was accompanied by a more K-selected lifestyle relative to the prokaryotes and optimization for lower death rates.

Appearance of Phagocytosis and Mitochondria
I illustrate the situation by two strong competing views: phagocytosis (and associated cellular traits) followed by the acquisition of mitochondria and the opposite, the acquisition of mitochondria, followed by the evolution of phagocytosis. (Phagocytosis is the process by which a cell uses its plasma membrane to engulf a large particle, giving rise to an internal compartment) Phylogeny could in principle tell this difference in order, but the analyses are inconclusive. The major argument against the phagocytosis-early scenario is once again energetic. According to this view, the boost provided by mitochondria not only was necessary for the evolution of very complex eukaryotic genomes but also was essential for the origin of the eukaryotic condition. It is important to realize that these two claims are different, and that the first is often portrayed to imply the latter, which is wrong. The snag is that “archezoan” protists lack mitochondria. Archezoa was once a high taxonomic rank until it became clear that all known examples have or had mitochondria. This development has dethroned Archezoa and at the same time has weakened the position of the phagocytosis-early hypothesis although the latter step is not a logical necessity. The “archezoan niche” admittedly exists. So why cannot one imagine an archezoan-like intermediate? An attempted answer is again related to the energy. The genome sizes of prokaryotes and eukaryotes overlap around 10 Mb and around 10,000 genes. This is the reason why frequent reference to average genome sizes is irrelevant for the discussion of origins. The overlap suggests that a lineage of prokaryotes could have evolved a small but sufficient preeukaryotic genome without mitochondria. If not, why not? Here it is: “the energetic cost for the de novo ‘invention’ of complex traits like phagocytosis must far exceed the costs of simply inheriting a functional system” (it must take many more than the total number of genes that are required in the end. Ten times as many?. If the argument holds, then it should hold in principle for any complex eukaryotic trait (mitosis and meiosis, nucleus, cilia, etc.), and indeed for any complex prokaryotic trait (photosynthesis, multicellularity with fruiting bodies, ribosomes, flagella) as well because both empires experimented with novel gene families and folds relative to what had been there before. There is no theoretical or comparative evidence to support the imagination of such “exuberant evolutionary scaffolding” that would require a transient appearance of a huge number of genes exceeding the final count by up to an order of magnitude. If it is not phagocytosis, then it can only be syntrophy or bacteriovory that allowed the entry of the ancestor of mitochondria. There are comparative concerns with these ideas. Archaea are not known to harbor prokaryotic symbionts; only eubacteria harbor (rarely) other eubacteria so the appropriate cross-domain analogy is missing. The same holds for known cases of syntrophy. Moreover, there is no example of a relevant cross-domain syntrophic endosymbiosis.  (syntrophy, or cross-feeding is the phenomenon of one species living off of the products of another species. In this type of biological interaction, the growth of one partner depends on the nutrients, growth factors, or substrates provided by the other partner.)However, it is logically true that it is not necessary for a prokaryote to get into another prokaryote by phagocytosis, but it is equally true that one does not need mitochondria for phagocytosis. Archaea have a cytoskeleton and can even fuse their cells, and there is the undeniable ecological advantage of the phagotrophic niche.

The Nucleocytoplasm and Meiotic Sex.
The origin of the nucleocytoplasm (The nucleus and cytoplasm of a cell considered together, especially to the exclusion of mitochondria and other distinct cytoplasmic organelles.) cannot be considered in detail here, but there are two novel, important points to mention. One is that the breaking up of the tight prokaryotic genome organization was presumably due to the invasion of self-splicing introns from mitochondria, followed by the emergence of the spliceosome. This transformation would have been impossible unless sexual recombination would have developed rather early: asexual genomes are a challenge to the spread of selfish genetic symbionts. Meiosis is a shared ancestral character state in eukaryotes. As testified by halobacteria, a form of fusion–recombination–fission cycle may have been strictly speaking the first. Rather than a separate major transition, meiosis and syngamy seem to be better regarded as a coevolving form of maintenance or transformation of an emerging higher-level evolutionary unit. The other component of the genetic revolution is the emergence of the nucleus itself, from which the name eukaryote is derived. The origin of introns and eukaryotic gene regulation would have been impossible without the spatial separation of transcription and translation. Without the nucleus the genome expansion allowed by the mitochondrial extra energy could not have been realized. The division of labor between cytoplasm in eukaryotes is as important as that between nucleic acids and proteins in prokaryotes: both are enabling constrains.

Several people have questioned the validity of eukaryotic sex as a separate major transition. Although it is true that, during sex, two individuals are needed instead of one and that they share the benefits equally, giving it an egalitarian flavor, there are two heavy counterarguments: mating pairs do not become parts in the further hierarchy (like cells, for example) and they do not give rise to mating pairs as propagating units. The equal sharing of benefits can be realized through haploid or diploid offspring.

Haploid is the term used when a cell has half the usual number of chromosomes. A normal eukaryote organism is composed of diploid cells, one set of chromosomes from each parent. However, after meiosis, the number of chromosomes in gametes is halved.

Enduring diploidy is an optional consequence of sex that arose in certain lineages independently.

Question: How is this known?

Now, it seems that the origin of sex is coincident with the origin of the eukaryotic cells, and, in a loose form, it may have preceded it as an archaeal legacy. Whether demoting sex from the major transitions remains justified or not time will tell: we need an updated, detailed scenario for the very origin of the eukaryotic cell. It could be that some stages of the origin of meiosis preceded, others were coincident, and the remaining once followed the acquisition of mitochondria—we do not know. However, just as the prokaryotic stage as we know it may not have been established and maintained without horizontal gene transfer, the eukaryotic condition may never have arisen and been maintained without evolving meiosis.

The sub-cellular structures of eukaryotic cells are surrounded by membranes and each carries out particular functions. They have analogies with the specialized functions of o anelles organs and are often referred to as organelles.

The nucleus contains the genetic material (DNA). Unlike the DNA in prokaryotic systems, the genetic material is wrapped up around proteins called histones to form thread-like structures called chromosomes. The number of chromosomes in each nucleus is characteristic of each organism. In prokaryotic cells there is no such packaging of DNA which remains more-or-less naked within the 'jelly' of the cytoplasm. Also embedded in the nucleus may be one-or-more dark staining bodies called nucleoli (singular nucleolus). These are the sites in which ribosomes are assembled. Ribosomes are small particles which are the sites for making proteins. The ribosomes of prokaryotic and eukaryotic cells show some quite fundamental differences although both act as protein synthesis factories. You will learn much more about them later.

Outside of the nucleus are many small, often discoid, organelles called mitochondria. These are the sites where the final oxidation of the nutrients used for energy takes place. In other words these act as the power house of the cell, providing the energy for the cell to carry out its particular functions.

The endoplasmic reticulum is a membrane system which ramifies through the cytoplasm. Ribosomes attach to this membrane system to give the endoplasmic reticulum a rather granular appearance (the so called rough endoplasmic reticulum). The endoplasmic reticulum is responsible for 'processing' the protein products made by the ribosomes.

The formation of cells in a multicellular organism depends on the specification of: 

1. Morphogenesis of various eukaryotic cells, structures, and shapes
2. Cell fate determination and differentiation ( phenotype, or what cell type each one will become )
3. Cell growth and size
4. Development and cell division counting: cells need to be programmed  to stop self-replicating after the right number of cell divisions
5. Mechanisms of pattern formation
6. Hox genes
7. Directing cell position and place in the body. This is crucial. Limbs like legs, fins, eyes, etc. must all be placed at the right place.
8. Set up of cell communication system and channels ( the creation of close to 30 different epigenetic codes and languages )
9. Set up of cell sensory and stimuli functions to interact with its environment and surroundings. 
10. Setting up de novo cell regulatory functions 
11. Timing and regulation for the development program of the organism to express the genes to grow new cells during development
12. Change regulation in the composition of the cell membrane and/or secreted products.
13. Specification of the cell-cell adhesion proteins and which ones will be used in each cell to adhere to the neighbor cells ( there are 4 classes )
14. Apoptosis: programming of the time period the cell keeps alive in the body, the timing of self-destruction, and replacement
15. Set up specific nutrition demands for each cell type.  
16. Programming of cell shape changes for adaptation.
17. Cell proliferation: the process of increasing the number of cells, a balance between cell divisions, and cell loss through cell death or differentiation.
18. Set up Cell layers 
19. Formation of extracellular matrix molecules 

1. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3310499/

2. Prokaryote to Eukaryote Transition:

Delve into the characteristics that distinguish prokaryotic cells (bacteria and archaea) from eukaryotic cells.
Explore the endosymbiotic theory and the role of symbiosis in the evolution of eukaryotic cells.
Discuss the significance of membrane-bound organelles, such as mitochondria and chloroplasts, in eukaryotic cells.

3. Single-Celled to Multicellular Transition:

Explore the factors that might have led to the transition from single-celled organisms to multicellular organisms.
Discuss the advantages and challenges of multicellularity, including cell differentiation, communication, and division of labor.
Provide examples of the diversity of multicellular life, from simple multicellular organisms to complex multicellular structures in plants and animals.

4. Colonization of Land:

Explain the challenges and adaptations that organisms faced when transitioning from aquatic to terrestrial environments.
Discuss the evolution of features such as lungs, limbs, and water conservation mechanisms in terrestrial organisms.
Explore the significance of the colonization of land in shaping Earth's ecosystems and biodiversity.

5. Origin of Complex Animals:

Dive into the Cambrian explosion and the rapid diversification of complex animal life during this period.
Discuss the emergence of key animal body plans and the development of novel features, such as hard shells and exoskeletons.
Explore the ecological interactions and evolutionary pressures that contributed to the explosion of animal diversity.

6. Vertebrate Terrestrialization:

Trace the evolutionary path of vertebrates from aquatic to terrestrial environments.
Discuss the development of limbs and adaptations for movement on land.
Explore the transition of fish to tetrapods and the emergence of amphibians, reptiles, and eventually mammals.

7. Origin of Flight:

Examine the adaptations and anatomical changes that allowed certain groups of animals to evolve flight.
Discuss the convergent evolution of flight in insects, birds, and bats.
Explore the ecological implications of flight and its role in diversification and species success.

8. Origin of Flowers and Angiosperms:

Detail the characteristics of angiosperms (flowering plants) and their significance in modern ecosystems.
Discuss the co-evolution of plants and pollinators, including insects and animals.
Explore the role of flowers in reproduction, seed dispersal, and the formation of complex ecosystems.

9. Evolution of Social Behavior:

Discuss the emergence of social behaviors in various animal species.
Explore the advantages of social behavior, including cooperation, communication, and division of labor.
Examine examples of social structures in insects, mammals, and birds, and the evolutionary drivers behind them.

10. Cultural Evolution in Humans:

Explore the concept of cultural evolution and its role in shaping human societies.
Discuss the development of language, technology, art, and other cultural traits.
Examine the interplay between biological and cultural evolution in the human species.
For each transition, consider including examples, case studies, and recent research findings to provide a well-rounded and up-to-date perspective. Additionally, integrating diagrams, illustrations, and visual aids can help make complex concepts more accessible to your readers.