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Evolution of SPECIES

The first attempt to lay out evolutionary history as a progression based on anatomy was Ernst Haeckel's Biogenetic Law (1866). His tree "Pedigree of Man" had the correct sequence of Primitive - Invertebrate - Vertebrate - Mammals.

We now have much more fossil history, biochemical information and DNA. A tree based on Mitochondrial DNA was recently compiled giving a more detailed view of relationships. The family tree drawing was inspired by a linear diagram of species differentiation in cytochrome C from a biochemistry textbook, Lehninger. Cytochrome C is a genetic protein common in all living things. The organic curved branches is humans centered but not at the top of the tree. Canines evolved with better smell, whales with bigger brains, and eagles with better vision.

https://scitechconnect.elsevier.com/africa-retracing-human-evolution-migration-dna

https://rsscience.com/the-biological-classification-of-paramecium-name-history-and-evolution/

Personal communication from Mark Hom MD

I annotated the evolution tree with the key functions of metabolism, energy distribution, structure and reproduction, that enabled the different branches. Life started with cyanobacteria and plants that use photosynthesis to absorb CO2 fix carbon and produce oxygen, seeding earths atmosphere. Decomposers such as mushrooms then evolved that took plant proteins and produce carbon dioxide and energy. The first oxygen users were the mollusks (insects, crustaceans, octopus) that had copper based blood that flowed through their body cavity. Octopus evolved a closed blood distribution that enabled oxygen to be delivered to key organs. Iron based blood (hemoglobin) in a closed circulation system then became universal in vertebrates from lampreys and fish onwards. Warm blood evolved in dinosaurs on, enabling much faster metabolism. The final step increases the development of their young. Eggs provide a finite amount of energy to the developing fetus. Octopus' actively protect their eggs, sharks let them develop in their bodies for protection, and monotremes suckle their young after hatching. The placental mammals provide unlimited time and access to energy to maximize fetal development.

The key functions that appear as the species evolve can be overlayed on the Mitochondrial tree proving a much more detail of the expansion of functionality.

It starts with a bacteria lipid walled, single cell with a ring of DNA. Cloroplasts evolved that could absorb sunlight. The first big branch is to plants with multiple cellulose walled cells with full DNA functionality in including Mitochondria. Mitochondria provide energy to the eukaryote cell by oxidizing sugars or fats and releasing energy as ATP. These two are responsible for the oxygen atmosphere. Mitochondrial DNA is inherited only from the mother and contains only information needed for the mitochondria to work.

The ancestors of land plants evolved in water. An algal scum formed on the land 1,200 million years ago,

Next up are the Fungi, which are the clean up crew as decomposers of protein and cellulose. The users of oxygen starts with sponges which evolved as fixed growths in the water that filtered nutrients from the flowing water. Then locomotion starts with the Jelly fish.

Around 610 My ago, the Protostomes appeared who developed mouth before anus in the embryo. They split into one branch (Arthropods) with a jointed exoskeleton such as centipedes, millipedes, scorpions, spiders, woodlice, mites, and ticks, 6 legged insects and crustaceans. Another branch led to mollusks and Cephalopods such as Squid and Octopus. The Mollusks appeared with an shell and a whole body circulation of oxygen using "Hemolymph" and copper based blood. The snails evolved into squids and octopus with closed circulation of a copper containing blood, which enables oxygen to be delivered to key organs. The octopus only have one cycle of reproduction in their lives. The female protects their eggs as they develop, one of the hallmarks of higher intelligence. The octopus evolved a genome as complex as humans with "jumping genes". In these, the DNA is 45% transposed (reorganized within the animal) a feature that has been linked to intelligence in humans. The octopus has demonstrated remarkable intelligence in problem solving and ability to self camouflage in color and texture. The octopus seems be a real "alien" intelligence on this planet with completely different design, and biochemistry.

What they found was a brain more complex than that of a rat or a mouse. In fact, its complexity was similar to that of a dog’s brain. Some cephalopods have more than 500 million neurons. In comparison, the resourceful rat has 200 million, and the ordinary mollusk has 20,000. Their brain-to-body-mass ratio falls between that of cold and warm blooded vertebrates.[8]:s.

https://www.medicalnewstoday.com/articles/are-squids-as-smart-as-dogs#Squids-have-more-complex-brains-than-rats

They demonstrate tool use, recognition of humans, the ability to solve abstract problems for instance; captive cephalopods have also been known to climb out of their aquaria, maneuver a distance of the lab floor, enter another aquarium to feed on captive crabs, and return to their own aquarium. They can unscrew the lids of bottles from the inside. These suggest an intelligence superior to dogs, on a par with primates.

Around 450 million years ago, the first land plants appeared. Around 420 million years ago, club mosses, ferns then appear. By the end of the 363 My ago, most of the basic features of plants today were present, including roots, leaves and secondary wood in trees. The 358-298 My ago saw the development of forests in swampy environments dominated by clubmosses and horsetails, including some as large as trees, and the appearance of early gymnosperms, the first seed plants.

There were no land based creatures so a huge niche was empty. The insects evolved from crustations as pollinators of the plants that appeared around 400 M years ago. Insects took over and ruled the land until the amphibians showed up. Today, they probably represent 90% of the species on earth. They show some amazing collective capabilities. Butterfly's evolved around 50 M years ago post KT extinction. Butterflies have the unique migration from Mexico to Alaska, travelling north over 4-5 generations each lasting 2 months using the sun as a guide, following the flowering of milkweed. They then fly south in a single 8 month generation. Bees have developed signals to show each other the direction to food. Ants are herbivores that demonstrate large scale communication and cooperative action.

https://www.nationalgeographic.com/animals/article/monarch-butterfly-migration

Lampreys were the first to evolve a closed circulation system with iron containing blood - hemoglobin. This enables oxygen to be delivered to key organs.

The vertebrates first appeared with fish such as tuna and carp, the sharks evolved keeping their eggs inside their bodies until they hatched to protect their young. The amphibians marked the transition onto land,

The origin of the reptiles lies about 310–320 million years ago, in the steaming swamps of the late Carboniferous period. The major line of reptiles that is around today includes; Lizards, Snakes, Iguanas and Turtles. A second branch leads to the Crocodiles and cold blooded dinosaurs.

The Permo-Triassic extinction event 251 My ago radically changed the structures of communities with a 60% marine extinction. This may have set the scene for the evolution of flowering plants in the Triassic (~200 million years ago), Conifers diversified from the Late Triassic onwards, and became a dominant part of floras in the Jurassic.

It is thought that warm blooded dinosaurs evolved to better survive the volcanic created extinctions 250 and 205 M years ago.

The dinosaur era lasted 200M years and was the cradle of most of todays species. The birds evolved from warm blooded dinosaurs.

The monotremes were the first mammals who laid eggs but suckled their young.

At the time Australia left Africa, the Marsupials must have developed, but the placentals had not. 100-120 My ago

The first placental mammals were shrew - like and small enough to be ignored by the dinosaurs.

To this point all species of animals used eggs for reproduction with a limited energy supply before the fetus had to be viable. The placenta allowed much longer time for the fetus to develop with unlimited energy supply. This enabled much more complex species.

Rodents and primates diverged 80-55 My ago, 53 My ago is the date of the earliest primate fossil. The KT meteor extinction 65 My ago killed off anything over 50 lbs which included all large dinosaurs. The dinosaurs that were left evolved into warm blooded birds and cold blooded reptiles. All the resource niches occupied by large dinosaurs become available such as grasslands and tree tops accessed from land and air. After the KT extinction, the birds and mammals exploded to occupy all these empty niches. Of the birds, the corvids (ravens, crows, jays, magpies, etc.) and psittacines (parrots, macaws, and cockatoos) are often considered the most intelligent. They demonstrate tools use. Cormorants have been shown to count to 7. Kea's also show malicious destruction including letting air out of tires.

The mammals also rapidly evolved with great variety. Compared to rodents, the primates are much larger tree dwellers, with all sorts of enabling adaptations such as grip, strength, and prehensile tails. As large tree dwellers they were safe from most predators. There was little competition for high calorie food. The result was they thrived and developed much larger brains.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8185448/

Size is a very effective protection from predation, at the expense of development time and adaptability. Hence the success of elephants, giraffes etc.

At the time India was still attached to Africa, and South America attached to Africa, so the primates must have developed 57My ago for the primates to have spread into India and Asia. Around 200 K years ago humans appeared and are now for better or worse are the dominant species.

It appears that the recipe for intelligence is a creature with locomotion, a closed circulation oxygen deliver system for key organs, and a complex gene structure that can be locally reorganized.

Cats actually have 90.2% of the DNA in common with us! You read that right! Cats are genetically surprisingly closer to us than dogs, who share about 84% of the genes with us (Pontius et al, 2007).

Match to Human DNA

Plants (18%) 1.5 B years for 82% change 18 My/%

Insects (44%) 500M years 66% 9 My/%

Birds (80%) 200 M years for 20% 10 My/%

Dogs 84%

Cats (90.2%)

Rodents (93%) 80 M years for 7% 11 My/% Apes (99%) 7 M years for 1% 7 My/%

Humans (100%)

It took 1.5 By for plants to evolve to Dinosaurs (80% human DNA), who then lasted for 200My. Insects have 60% human DNA. It took 60My for Shrews (93% human DNA) to evolve to Apes (99.5% human DNA). It took 7M years for Apes to evolve to Humans. The DNA differences represent a "round trip", so the mutation rate is around 20M years for 1% DNA change in gene location.

Intelligence

The most intelligent species seem to track the brain to body weight ratio, but requires a long time to reach maturation.

Primates are large tree dwellers which protects them from predation.

Elephants have great size which protects them.

Octopuses have remarkable camouflage for protection.

Cetaceans (whales & dolphins) are the largest water dwellers.
Crows show remarkable adaptability and the ability to problem solve.

Small mammals, such as rodents, were prey for many larger species. Survival requires mobility with little time for maturation. This would block evolution of greater intelligence.

Function evolution

Metabolism

Metabolism started with bacteria and plants evolving photosynthesis that used light energy to combine carbon dioxide and water to fix carbon produce oxygen and grow the full range of biomolecules, catalyzed by enzymes.

Next digesters such as fungi evolved that use oxygen and enzymes to breakdown carbohydrates into carbon dioxide and energy using the citric acid cycle.

Animals evolved to combine these 2 steps using sugars as the energy source in the citric acid cycle to generate ATP energy and use ATP energy to grow and live.

In bio systems, energy is stored and released in the exchange between ADT "diphosphate" and ATP "triphosphate". Cyanobacteria use photosynthesis as an energy source to support replication leading to stromatolites and oxygen. This includes creating a wide range of molecules in their cells such as DNA, lipids, proteins. In photosynthesis, plants use the energy of sunlight to make ATP and then the Calvin cycle fixes carbon to create glucose, and a full range of biomolecules. There are also nitrogen fixing bacteria.

The Calvin cycle uses CO2 and energy from ATP in a process of taking a 5 carbon bi-phosphate, making two 3 carbon phosphates one of which is used and the other recycled. The key enzyme of the cycle is called RuBisCO, another bi-phosphate. After 5 cycles, the five 3 carbon phosphates are reorganized into three more of the 5 carbon bi phosphates, completing the cycle.

Plants expanded their metabolism to grow cellulose shells for huge multicellular structures, and added more efficient energy generation from chloroplasts to become prolific oxygen generators.

Fungi were the first "digesters" that could breakdown carbohydrates into heat, carbon dioxide and water. Fungi use the citric acid (Krebs) cycle to break down biomolecules and release the energy as heat. The citric acid cycle is found in species as diverse as the unicellular bacterium Escherichia coli, fungi, and huge multicellular organisms like elephants. They breath in oxygen and breath out carbon dioxide.

The citric acid energy cycle starts with citric acid (5 carbon, 3 acid ,1 ketone molecule). It gets oxidized to remove 2 carbons leaving succinic acid, (4 carbon 2 acid molecule) plus energy as ATP. The succinic acid then combines with acetyl (2 carbon 1 acid molecule) to regenerate citric acid. The acetyl molecules are peeled off glucose. Additional byproducts of the cycle are a number of bio precursors.

Fungi also fabricate new biomolecules to grow. The engine for building sequences is the ribosome that uses messenger RNA to provide the template, and the t-RNA bound to amino acids to build a peptide chain.

Animals evolve ways convert the biomolecules in plants and animals in food to glucose using their new specialized organs. They use the glucose in the citric acid (Krebs) cycle to produce usable energy in the form of ATP. Animals expanded their metabolism to include oxygen supply using blood, in using energy to trigger molecular reconfiguration in muscles, and electrical transfer in nerves and neurons, and the growth of biomolecules. These reactions combine monosaccharides to form polysaccharides, fatty acids to form triglycerides, amino acids to form proteins, and nucleotides to form nucleic acids. These processes require energy in the form of ATP molecules generated by catabolic reactions. Anabolic reactions, also called biosynthesis reactions, create new molecules that form new cells and tissues, and revitalize organs.

The first animals were all cold blooded. The evolution of warm blood enables higher metabolic rates with enhanced unloading of oxygen by hemoglobin. This relationship is helpful as metabolically-active peripheral tissues such as exercising skeletal muscle which often display supra-normal temperatures. Because of this increased temperature, oxygen unloading by hemoglobin is enhanced in these metabolically-active tissues, thus improving oxygen transport to areas which require it most.

https://courses.lumenlearning.com/suny-ap2/chapter/energy-and-heat-balance/

https://portlandpress.com/essaysbiochem/article/64/4/607/226177/Metabolism

Transport

The animals use blood to concentrate and deliver oxygen. Copper blood carries 1/4 of the oxygen as iron blood (haemoglobin), but works better at low temperature and may have less tendency to clot.

Copper blood first appeared in mollusks with open circulation throughout their body cavity.

Closed circulation with arteries and veins evolved to better deliver oxygen and nutrients to key organs in vertebrates and cephalopods like octopus.

The vertebrates then evolved with more efficient iron based blood.

Finally amphibians evolved lungs that enabled complex air breathing life.

Structure

Bacteria started with dual lipid based cell walls.

Plants added a cellulose superstructure that enabled large trees.

Exoskeletons appeared with the first mollusks that provided physical protection and a structure for load bearing and locomotion. The big limitation was that the skeleton does not grow, it must be shed and regrow for the animal to grow larger.

The evolution of vertebrates with an internal support structure started with fish and continues today. The basic bone architecture has been retained for hundreds of millions of years. The internal structure allows growth and training changes.

Reproduction

It starts with cell division in bacteria. Plants use seeds usually spread annually.

The first animals reproduced through large numbers of fertilized eggs, that were left to fend for themselves. Eggs provide a limited energy supply and when it is used the fetus must be self supporting.

An improved survival strategy appeared where eggs are protected by parents (octopus) before birth. Warm blooded animals had to keep the eggs warm as well (birds). After birth, the infants are often fed by parents until self-supporting.

Another survival strategy appeared in monotremes. After eggs are hatched, the infants are supported by mothers milk

One way to improve survival appeared when eggs were allowed to develop protected inside the mothers body, for example in sharks.

The final evolution occurred in placental mammals, where the fetus develops with unlimited energy and time, with energy supplied by the placenta inside the mother, and then is supported after birth by mothers milk.

Genes

The Mendelian gene is a basic unit of heredity and the molecular gene is a sequence of nucleotides in DNA that is transcribed to produce a functional RNA. There are two types of molecular genes: protein-coding genes and noncoding genes.[3][4][5][6]

During gene expression, the DNA is first copied into RNA. The RNA can be directly functional or be the intermediate template for a protein that performs a function. Most biological traits are under the influence of polygenes (many different genes) as well as gene–environment interactions. Some genetic traits are instantly visible, such as eye color or the number of limbs, and some are not, such as blood type, the risk for specific diseases, or the thousands of basic biochemical processes that constitute life.

The concept of gene continues to be refined For example, regulatory regions of a gene can be far removed from its coding regions, and coding regions can be split into several exons. Some viruses store their genome in RNA instead of DNA and some gene products are functional non-coding RNAs. Therefore, a broad, modern working definition of a gene is any discrete locus of heritable, genomic sequence which affect an organism's traits by being expressed as a functional product or by regulation of gene expression.[9][10]

The total complement of genes in an organism or cell is known as its genome, which may be stored on one or more chromosomes. A chromosome consists of a single, very long DNA helix on which thousands of genes are encoded.[46]: 4.2 The region of the chromosome at which a particular gene is located is called its locus. The chromosomal or genomic location of a gene or any other genetic element is called a locus (plural: loci) and alternative DNA sequences at a locus are called alleles. Each locus contains one allele of a gene; however, members of a population may have different alleles at the locus, each with a slightly different gene sequence.

Telomeres are long stretches of repetitive sequences that cap the ends of the linear chromosomes and prevent degradation of coding and regulatory regions during DNA replication. The length of the telomeres decreases each time the genome is replicated and has been implicated in the aging process.

All genes are associated with regulatory sequences that are required for their expression. First, genes require a promoter sequence.

Sets of three nucleotides, known as codons, each correspond to a specific amino acid.[46]: 6 The principle that three sequential bases of DNA code for each amino acid was demonstrated in 1961. There are 64 possible codons (four possible nucleotides at each of three positions, hence 43 possible codons) and only 20 standard amino acids; hence the code is redundant and multiple codons can specify the same amino acid. The correspondence between codons and amino acids is nearly universal among all known living organisms.

Alleles at a locus may be dominant or recessive; dominant alleles give rise to their corresponding phenotypes when paired with any other allele for the same trait, whereas recessive alleles give rise to their corresponding phenotype only when paired with another copy of the same allele. If you know the genotypes of the organisms, you can determine which alleles are dominant and which are recessive. For example, if the allele specifying tall stems in pea plants is dominant over the allele specifying short stems, then pea plants that inherit one tall allele from one parent and one short allele from the other parent will also have tall stems.

The error rate in eukaryotic cells can be as low as 10−8 per nucleotide per replication,[83][84] whereas for some RNA viruses it can be as high as 10−3.[85] This means that each generation, each human genome accumulates 1–2 new mutations. If it takes roughly 10 M years for a new species, and a generation lasts 10 years. There are 1-2 M DNA differences between nearest species.

The relationship between genes can be measured by comparing the sequence alignment of their DNA.[46]: 7.6 The degree of sequence similarity between homologous genes is called conserved sequence.

Jumping genes

A transposable element (TE, transposon, or jumping gene) is a nucleic acid sequence in DNA that can change its position within a genome, sometimes creating or reversing mutations and altering the cell's genetic identity and genome size. Transposition is responsible for some diseases such as Hemophilia skipping generations.

Fifty percent of the DNA in each human cell is in the form of mobile jumping genes—strands of DNA called transposable elements (TE) that have the ability to sew themselves in and out of DNA as well as move to different sections and to place copies in different sections. The mobile strands of DNA in the jumping gene can create new types of proteins, disrupt the entire genetic process and provide new sources of regulation of DNA through many kinds of RNA effects. The jumping gene can provide new epigenetic changes, as well. Previous posts noted that these jumping genes and alternative messenger RNA splicing are especially critical for the human brain and its evolution.

mRNA transposition in humans is 98% of the jumping genes, representing almost half of the entire human DNA. Recent dramatic findings show that jumping genes are very active in the brain. These SINEs and LINEs are actively altering and regulating neurons and other cells. Some of the changes have been incorporated into day-to-day functions. There is strong evidence that these jumping genes and their effects on alternative functions have been significant in the development of the human brain. This goes along with the evidence that the human brain uses the most alternative messenger RNA splicing. While these findings are still too complex to fully understand, it does appear to be part of the picture that has developed where jumping genes and cellular defense against them are crucial for evolution in general and especially so for the evolution of the human brain.

https://jonlieffmd.com/blog/jumping-genes-regulation-of-the-brain

Cell components

Bio- phosphates such as lipids, ATP, DNA, RNA, many metabolic cycle components.

Polysaccharides such as cellulose. Cellulose is an organic compound consisting of a linear chain of several hundred to many thousands of β(1→4) linked D-glucose units.

Proteins built from combinations of 12 amino acids. Amino acids are organic compounds that contain both amino and carboxylic acid functional groups.[1] Although hundreds of amino acids exist in nature, by far the most important are the alpha-amino acids, which comprise proteins.[2] Only 22 alpha amino acids appear in the genetic code

Proteins perform a vast array of functions within organisms, including enzymes that catalyse biochemical reactions and are vital to metabolism. Proteins also have structural or mechanical functions, such as actin and myosin in muscle and the proteins in the cytoskeleton, which form a system of scaffolding that maintains cell shape. Other proteins are important in cell signaling, immune responses, cell adhesion, and the cell cycle. In animals, proteins are needed in the diet to provide the essential amino acids that cannot be synthesized. Digestion breaks the proteins down for metabolic use.

Proteins differ from one another primarily in their sequence of amino acids, which is dictated by the nucleotide sequence of their genes, and which usually results in protein folding into a specific 3D structure that determines its activity. The basic folding pattern is thought to be controlled by the grouping of hydrophobic amino acid residues, leaving the hydrophilic on the outside providing the functionality. The folding can be preserved by hydrogen bonds or crosslinks. The outward facing hydrophilic groups will ensure that the protein is water soluble. When the protein "denatures", it unfolds and becomes water insoluble.

Shortly after or even during synthesis, the residues in a protein are often chemically modified by post-translational modification, which alters the physical and chemical properties, folding, stability, activity, and ultimately, the function of the proteins. Some proteins have non-peptide groups attached, which can be called prosthetic groups or cofactors. Proteins can also work together to achieve a particular function, and they often associate to form stable protein complexes.

Once formed, proteins only exist for a certain period and are then degraded and recycled by the cell's machinery through the process of protein turnover. A protein's lifespan is measured in terms of its half-life and covers a wide range. They can exist for minutes or years with an average lifespan of 1–2 days in mammalian cells.