Unraveling the Mysteries of Evolution: A Look into the Past and Present of Biological Diversity

Evolution is the gradual change in the inherited characteristics of living organisms. These characteristics are determined by genes, which are passed on from parent to offspring during reproduction. Variation in a population occurs due to genetic mutation and recombination. Evolution occurs when natural selection, sexual selection, and genetic drift act on this variation, resulting in certain characteristics becoming more or less common in a population.

Charles Darwin and Alfred Russel Wallace independently developed the theory of evolution by natural selection in the mid-19th century, which is supported by the observation that more offspring are produced than can survive, traits vary among individuals, certain traits confer better survival and reproduction, and traits can be inherited. All life on Earth shares a universal common ancestor and the fossil record shows a progression from early single-celled organisms to complex multicellular life forms.

Evolutionary biologists continue to study and understand evolution through research and experimentation. Their discoveries have had a significant impact on various fields including biology, agriculture, medicine and computer science.

Hereditary

Evolution in organisms is the result of changes in heritable traits(genes), which are the inherited characteristics of an organism. For example, in humans, eye color is an inherited trait and an individual may inherit the "brown-eye trait" from one of their parents. These traits are controlled by genes, and the complete set of genes within an organism's genome is called its genotype.

The observable traits that make up an organism's structure and behavior are called its phenotype. These traits come from the interaction of its genotype with the environment, and many aspects of the phenotype are not inherited. Heritable traits are passed down through DNA, a molecule that encodes genetic information. Some changes cannot be explained by changes to the DNA sequence and are known as epigenetic inheritance systems. Additionally, heritability can occur at larger scales, such as through the process of niche construction in the environment and the inheritance of cultural traits.

Source of Variation

Evolution happens when there is variation in the genetic makeup of a population. This variation can come from mutations in the genetic makeup, the mixing of genes through sexual reproduction, and the movement of individuals between populations (gene flow). Despite the constant introduction of new variations, most of the genome of a species is the same in all individuals of that species. However, even small differences in the genotype can result in significant differences in the phenotype. For example, chimpanzees and humans have only about a 5% difference in their genomes.

The characteristics of an organism, known as its phenotype, are determined by a combination of its genetic makeup (genotype) and the environment it has been exposed to. A large portion of the variation in traits observed among a population is due to differences in genotype. Evolution is defined as changes in the frequency of alleles (different versions of a gene) within a population over time. This can result in the emergence of new traits and the disappearance of others as certain alleles become more or less common or even fixed in the population.

Before the understanding of Mendelian genetics, a popular theory was that inherited traits blended together in offspring. However, this theory of blending inheritance would lead to the rapid loss of genetic variation and make evolution through natural selection unlikely. The Hardy-Weinberg principle, however, explains how genetic variation can be maintained in a population through Mendelian inheritance. According to this principle, the frequency of alleles in a population will remain stable in the absence of factors such as natural selection, mutation, migration, and genetic drift.

Mutation

Mutations are changes in the DNA sequence of a cell's genome and are the driving force behind genetic variation in all organisms. These changes can have varying effects such as altering the product of a gene, to preventing it from functioning, to having no effect at all. Studies on the fruit fly Drosophila melanogaster have shown that mutations that alter the protein produced by a gene are likely to be harmful, with approximately 70% having negative effects, while the remaining mutations may be neutral or weakly beneficial.

Mutations can also involve duplication of large sections of a chromosome, which can introduce extra copies of a gene into the genome. These extra copies of genes are a key source of the raw material needed for the evolution of new genes. This is significant because most new genes evolve within gene families, which share a common ancestor. For example, in the human eye, four genes are used to create light-sensing structures, three for color vision and one for night vision, all of which have evolved from a single ancestral gene.

New genes can be created from an existing gene when a duplicate copy undergoes mutations that give it a new function. This process is facilitated when a gene has already been duplicated, as it increases the redundancy of the system and allows one copy to evolve a new function while the other copy continues to perform its original function. Additionally, new genes can also be formed from previously noncoding DNA through mutations, a process known as de novo gene birth.

Another way new genes can arise is through the duplication and recombination of small parts of multiple genes, referred to as exon shuffling. This process allows for the assembly of new genes with new functions by mixing together pre-existing domains with simple, independent functions. An example of this is polyketide synthases, large enzymes that produce antibiotics, which can contain up to 100 domains that each catalyze a different step in the overall process, similar to an assembly line.

A specific example of mutation can be seen in wild boar piglets. They are camouflage-colored and have characteristic patterns of dark and light longitudinal stripes. However, mutations in the melanocortin 1 receptor (MC1R) gene disrupt this pattern. Many pig breeds carry mutations in the MC1R gene that disrupt the wild-type color and can cause dominant black coloration.

Sex and Recombination

Sexual organisms produce offspring with a random mixture of their parents' chromosomes through independent assortment and homologous recombination, a process that exchanges DNA between matching chromosomes. This does not change allele frequencies, but creates new combinations of alleles in the offspring. Sexual reproduction usually increases genetic variation and may accelerate evolution.

John Maynard Smith first proposed the concept of the two-fold cost of sex, which includes the fact that only one sex can bear young in sexually dimorphic species, and that each individual can only pass on 50% of its genes to any individual offspring. This cost does not apply to hermaphroditic species. Despite this cost, sexual reproduction is more common among eukaryotes and multicellular organisms. The Red Queen hypothesis explains that sexual reproduction allows for continual evolution and adaptation to an ever-changing environment. Another hypothesis is that it primarily serves to promote accurate recombinational repair of germline DNA and increased diversity is a byproduct that can be beneficial.

Gene Flow

Gene flow refers to the movement of genes between populations or species, introducing new variations. This can happen when individuals move between separate groups of organisms, such as mice between different areas or pollen (that have a high tolerance for heavy metals) between populations of plants with different tolerances to heavy metals.

Gene transfer between species encompasses the creation of hybrid organisms and horizontal gene transfer. Horizontal gene transfer is the transfer of genetic material from one organism to another organism that is not its offspring. This is most commonly seen among bacteria, and in medicine, it contributes to the spread of antibiotic resistance. Horizontal transfer of genes from bacteria to eukaryotes such as yeast and insects has been observed. Some examples include the eukaryotic bdelloid rotifers, which have received a range of genes from bacteria, fungi, and plants. Viruses can also transfer DNA between organisms, allowing gene transfer across different biological domains.

Large-scale gene transfer has also occurred between the ancestors of eukaryotic cells and bacteria, during the acquisition of chloroplasts and mitochondria. It is also possible that eukaryotes themselves originated from horizontal gene transfers between bacteria and archaea.

Process of Evolution

From a neo-Darwinian point of view, evolution occurs when the frequencies of alleles within a population of interbreeding organisms change. For example, the allele for black color in a population of moths becoming more prevalent. The mechanisms that can cause changes in allele frequencies include natural selection, genetic drift, gene flow, and mutation bias.

Natural Selection

Evolution by natural selection is the process by which traits that improve survival and reproduction become more prevalent in subsequent generations of a population. It is based on three key principles: the existence of variation in traits among individuals within a population; the fact that certain traits result in better survival and reproduction rates; and the heritability of these traits. The result is competition for resources and reproduction, with organisms possessing advantageous traits more likely to pass on their genes to the next generation. This process is known as teleonomy, where natural selection creates and preserves traits that are well suited for their purpose. Natural selection also leads to nonrandom mating and genetic hitchhiking.

The central concept of natural selection is the evolutionary fitness of an organism, which is determined by its ability to survive and reproduce. Fitness is not the same as the number of offspring, but rather the proportion of future generations that carry an organism's genes. For example, an organism that reproduces quickly but has offspring that do not survive would have low fitness.

If an allele increases fitness more than others, it will become more common in the population over time. These traits are said to be "selected for." Conversely, alleles that decrease fitness will become less common and are said to be "selected against." However, the fitness of an allele can change with changes in the environment. Traits that were lost in the past may not re-evolve in the same form, but dormant genes can be reactivated, leading to the reappearance of traits thought to be lost, known as atavisms.

Natural selection for a trait that can vary across a range, such as height, can be divided into three types. The first is directional selection, which is a shift in the average value of a trait over time, for example, organisms gradually getting taller. The second is disruptive selection, which is selection for extreme trait values and often results in two different values becoming most common, with selection against the average value. For example, either short or tall organisms having an advantage, but not those of medium height. The third is stabilizing selection, which is selection against extreme trait values on both ends, which causes a decrease in variance around the average value and less diversity, causing organisms to eventually have a similar height.

Natural selection evaluates individuals and their traits based on their ability to survive in their ecosystem, which includes all of the organisms and physical elements in a specific area and their interactions. Each population within an ecosystem occupies a distinct niche, or position, with distinct relationships to other parts of the system. Selection can act at different levels of organization, such as genes, cells, individual organisms, groups of organisms, and species, and can occur simultaneously at multiple levels. An example of selection occurring below the level of the individual organism are genes called transposons, which can replicate and spread throughout a genome. Selection at a level above the individual, such as group selection, may allow the evolution of cooperation.

Genetic hitchhiking

Recombination is the process by which alleles on the same strand of DNA become separated, but it occurs at a low rate. As a result, genes located close together on a chromosome are often inherited together, a phenomenon known as linkage. This tendency is measured by linkage disequilibrium, which compares the frequency of two alleles occurring together on a single chromosome to expectations. A group of alleles that is typically inherited together is called a haplotype. This can be significant when one allele in a haplotype is highly beneficial, as natural selection can drive a selective sweep that causes the other alleles in the haplotype to also become more common in the population. This effect is called genetic hitchhiking or genetic draft. The impact of genetic draft caused by the linkage of neutral genes to those under selection can be partly captured by an appropriate effective population size.

Sexual selection

Sexual selection is a specific form of natural selection in which traits that increase an organism's attractiveness to potential mates are favored. These traits are often more pronounced in male animals. However, traits like large antlers, mating calls, big body size, and bright colors, which are favored by sexual selection, can also make the males more vulnerable to predation. This trade-off is compensated by the increased reproductive success of males that possess these hard-to-fake, sexually selected traits.

Genetic drift

Genetic drift is a random fluctuation in the frequency of alleles within a population from one generation to the next. When selective pressures are weak or absent, allele frequencies can randomly increase or decrease in each generation due to sampling error. This process stops when an allele becomes fixed in the population, either by disappearing or replacing other alleles. Genetic drift can also cause two populations with the same genetic structure to diverge into different sets of alleles.

The neutral theory of molecular evolution, which is now mostly discredited, suggests that most evolutionary changes are due to the fixation of neutral mutations by genetic drift. A better-supported version of this theory is the nearly neutral theory, which proposes that a mutation that would be effectively neutral in a small population may not be neutral in a large population. Other theories suggest that genetic drift is overshadowed by other random forces in evolution such as genetic hitchhiking. Another concept, constructive neutral evolution (CNE), explains that complex systems can spread through a population via neutral transitions due to excess capacity, presuppression, and ratcheting.

The rate of fixation of a neutral allele by genetic drift depends on the population size, with smaller populations experiencing more rapid fixation. The critical factor is not the total population size, but a measure known as the effective population size, which takes into account factors such as inbreeding and population size at certain stages of the lifecycle. The effective population size may also vary for different genes within the same population.

The relative importance of selection and neutral processes, including genetic drift, in driving evolutionary change is an area of ongoing research and is difficult to measure.

Gene flow

Gene flow refers to the transfer of genes between populations and between species. The presence or absence of gene flow significantly impacts the direction of evolution. Even if two isolated populations remain adaptively identical, genetic incompatibilities will eventually arise through neutral processes, as per the Bateson-Dobzhansky-Muller model.

If genetic differences develop between populations, gene flow can introduce traits or alleles that are detrimental to the local population, which may lead to the evolution of mechanisms that prevent mating with genetically distant populations. This can ultimately result in the formation of new species. Thus, the exchange of genetic information between individuals plays a crucial role in the development of the Biological Species Concept.

During the development of the modern synthesis, Sewall Wright's shifting balance theory emphasized the importance of gene flow between partially isolated populations in adaptive evolution. However, recently, there has been significant criticism of the importance of the shifting balance theory.

Mutation bias

Mutation bias refers to the difference in the expected rates of different types of mutations, such as transition-transversion bias, GC-AT bias, or deletion-insertion bias. Historically, some scientists believed that the influence of mutation biases on evolution was minimal because selection could easily overcome them. However, with the advent of molecular biology, researchers have begun to reconsider the role of mutation biases in shaping the genomes of different species. Mutation biases have been invoked in models of codon usage and have played a role in understanding the evolution of genome composition and size. However, more recent research has shown that GC-biased gene conversion and AT-biased mutation in bacteria have also contributed to genomic composition. Contemporary thinking about mutation biases suggests that they can shape evolution by introducing new alleles, rather than relying on neutral evolution or high mutation rates.

Applications

Evolutionary biology concepts and models, such as natural selection, have a wide range of applications. One such application is artificial selection, which is the intentional selection of certain traits in a population of organisms. This technique has been used for thousands of years in the domestication of plants and animals, and more recently in genetic engineering through the use of selectable markers. Another application is directed evolution, which is the process of repeatedly mutating and selecting proteins with valuable properties, such as modified enzymes and new antibodies.

Evolutionary biology also has applications in medicine, as many human diseases are capable of evolving. For example, viruses, bacteria, fungi, and cancers evolve to be resistant to host immune defenses and pharmaceutical drugs. Evolutionary theory is also used to predict and slow the evolution of pathogens.

In computer science, evolutionary algorithms and artificial life simulations have been used to optimize complex engineering problems and design systems. Genetic algorithms, in particular, have become popular through the work of John Henry Holland. Artificial evolution has been recognized as an efficient optimization method, and evolutionary algorithms are now used to solve multi-dimensional problems more efficiently than software produced by human designers.