Rate of evolution

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The rate of evolution is quantified as the speed of genetic or morphological change in a lineage over a period of time. The speed at which a molecular entity (such as a protein, gene, etc.) evolves is of considerable interest in evolutionary biology since determining the evolutionary rate is the first step in characterizing its evolution. [1] Calculating rates of evolutionary change is also useful when studying phenotypic changes in phylogenetic comparative biology. [2] In either case, it can be beneficial to consider and compare both genomic (such as DNA sequence) data and paleontological (such as fossil record) data, especially in regards to estimating the timing of divergence events and establishing geological time scales. [3]

Contents

At the organism level

In his extensive study of evolution and paleontology, George Gaylord Simpson established evolutionary rates by using the fossil record to count the number of successive genera that occurred within a lineage during a given time period. For example, in studying the evolution of horse (Equus) from Eohippus, he found that eight genera were given rise over the course of approximately 45 million years, which gives a rate of 0.18 genera per million years.

J.B.S. Haldane proposed the first standard unit for morphological evolutionary rate, the darwin (d), which represents a change in measurable trait by a factor of e (the base of natural logarithms) per million years (my). For example, he found that tooth length during the evolution of the horse changed at an average rate of about 4 × 10−8 per year, or 4% per million years. [4] [3]

However, if evolution is dependent upon selection, the generation is a more appropriate unit of time. Therefore, it is more efficient to express rates of evolution in haldane units (H), quantified by standard deviations per generation, indexed by the log of the time interval. [5]

While the generational time scale is considered the time scale of evolution by natural selection, it cannot by itself explain microevolutionary change over multiple generations or macroevolutionary change over geological time. This is due to effects which damp values over longer intervals, as elucidated by morphological rate comparisons which found that there is a negative correlation between rates and measurement interval. Therefore, appropriate temporal scaling is necessary for comparing rates of evolution over different time intervals. [6] [7]

At the molecular level

At the molecular level, the rate of evolution can be characterized by the rate at which new mutations arise within a species or lineage, thus it is typically measured as the number of mutant substitutions over time. [3] These rates vary among both genes and lineages due to gene effects (such as nucleotide composition, among-site variation, etc.), lineage effects (generation time, metabolic rates, etc.), and interactions between the two. [8] Even at the molecular level, population dynamics (such as effective population size) must also be taken into account when considering gene substitution since the rate of fixation of a mutant allele is affected by selective advantage. [3]

Estimating mutation rates

Amino acid substitution

Expanding upon the previous findings of Zuckerkandl and Pauling, [9] Kimura found that the rate of amino acid substitution in several proteins is uniform within lineages, and so it can be used to measure the rate of mutant substitution when the time of divergence is known. [10] [11] [3] This is achieved by comparing the amino acid sequence in homologous proteins of related species. [3] He suggested using pauling as the unit of such measurements, which he defined as the rate of substitution of 10−9 per amino acid site per year. [11]

Nucleotide substitution

Underlying the changes in the amino acid sequence of a given protein are changes in nucleotide sequence. Since this process occurs too slowly for direct observation, statistical methods for comparing multiple sequences derived from the sequence a common ancestor are required. [12] The rate of nucleotide substitution is highly variable among genes and gene regions, and is defined as the number of substitutions per site per year with the calculation for mean rate of substitution given as: r = K / 2T (K is the number of substitutions between two homologous sequences and T is the time of divergence between the sequences). [1]

Factors that influence the nucleotide substitution rates of most genes as well as nongenic genomic regions include random genetic drift, purifying selection, and rarely, positive selection. [1] Whether a substitution is synonymous or nonsynonymous is also important when focusing on protein-coding genes, as it has been shown that synonymous substitution rates are much higher than those of nonsynonymous substitutions in most cases. [1] Functional constraint plays a role in the rate of evolution of genes that encode proteins as well, with an inverse relationship likely present. [1]

Neutral Theory

During his comparative studies of various protein molecules among different groups of organisms, Kimura calculated a nucleotide substitution rate of one nucleotide pair roughly every two years. [10] In reconciling this high rate of nucleotide substitution with the limit set by the substitutional load, he formed the neutral mutation hypothesis. According to this hypothesis, if substitutions are due to the random fixation of selectively neutral or nearly neutral mutations, then the substitution rate is equal to the mutation rate per gamete of the mutants. [10] [3]

Molecular Clock Theory

The existence of a molecular clock was first posited by Zuckerkandl and Pauling who claimed that in regards to proteins, the evolutionary rate is constant among lineages throughout time. [9] Under this assumption, estimates of substitution rates, r, can be used to infer the timing of species divergence events. [1] [8] In its original form, the molecular clock is not entirely valid as evidenced by variation in evolutionary rates among species and within lineages. [8] [1] However, new models and methods which involve calibrations using geological and fossil data and statistical factors are being developed and may prove to be more accurate for determining time scales which are useful for further understanding of evolutionary rates. [8]

The effect of artificial selection

Humans have created a wide range of new species, and varieties within those species, of both domesticated animals and plants. This has been achieved in a very short geological period of time, spanning only a few tens of thousands of years, and sometimes less. Maize, Zea mays, for instance, is estimated to have been created in what is now known as Mexico in only a few thousand years, starting between about 7,000 and 12,000 years ago, from still uncertain origins. [13] In the light of this extraordinarily rapid rate of evolution, through (prehistoric) artificial selection, George C. Williams [14] and others, [15] [16] [17] have remarked that:

The question of evolutionary change in relation to available geological time is indeed a serious theoretical challenge, but the reasons are exactly the opposite of that inspired by most people's intuition. Organisms in general have not done nearly as much evolving as we should reasonably expect. Long term rates of change, even in lineages of unusual rapid evolution, are almost always far slower than they theoretically could be. The basis for such expectation is to be found most clearly in observed rates of evolution under artificial selection, along with the often high rates of change in environmental conditions that must imply rapid change in intensity and direction of selection in nature. [14]

Evolvability

Evolution is imposed on populations. It is not planned or striven for in some Lamarckist way. [18] The mutations on which the process depends are random events, and, except for the "silent mutations" which do not affect the functionality or appearance of the carrier, are thus usually disadvantageous, and their chance of proving to be useful in the future is vanishingly small. Therefore, while a species or group might benefit from being able to adapt to a new environment by accumulating a wide range of genetic variation, this is to the detriment of the individuals who have to carry these mutations until a small, unpredictable minority of them ultimately contributes to such an adaptation. Thus, the capability to evolve is close to the discredited [19] concept of group selection, since it would be selectively disadvantageous to the individual.

Overcoming koinophilia

If sexual creatures avoid mates with strange or unusual characteristics, in the process called koinophilia, [20] [21] [22] [23] then mutations that affect the external appearance of their carriers will seldom be passed on to the next and subsequent generations. They will therefore seldom be tested by natural selection. Evolution is, therefore, effectively halted or slowed down considerably. The only mutations that can accumulate in a population are ones that have no noticeable effect on the outward appearance and functionality of their bearers (i.e., they are "silent" or "neutral mutations", which can be, and are, used to trace the relatedness and age of populations and species. [20] [24] )

This implies that evolution can only occur when mutant mates cannot be avoided, as a result of a severe scarcity of potential mates. This is most likely to occur in small, isolated communities. These occur most commonly on small islands, in remote valleys, lakes, river systems, or caves, [25] or during the aftermath of a mass extinction. [24] Under these circumstances, not only is the choice of mates severely restricted but population bottlenecks, founder effects, genetic drift and inbreeding cause rapid, random changes in the isolated population's genetic composition. [25] Furthermore, hybridization with a related species trapped in the same isolate might introduce additional genetic changes. If an isolated population such as this survives its genetic upheavals, and subsequently expands into an unoccupied niche, or into a niche in which it has an advantage over its competitors, a new species, or subspecies, will have come in being. In geological terms this will be an abrupt event. A resumption of avoiding mutant mates will, thereafter, result, once again, in evolutionary stagnation.

Fossil record

Alternative explanations of the pattern of evolution observed in the fossil record. While apparently instantaneous change may look like macromutation, gradual evolution by natural selection could readily give the same effect, since 10,000 years barely registers in the fossil record. Punctuated Equilibrium.svg
Alternative explanations of the pattern of evolution observed in the fossil record. While apparently instantaneous change may look like macromutation, gradual evolution by natural selection could readily give the same effect, since 10,000 years barely registers in the fossil record.

The fossil record of an evolutionary progression typically consists of punctuated equilibrium, with species that suddenly appear, as if by macromutation, and ultimately disappear, in many cases close to a million years later, without any change in external appearance. This is compatible with evolution by smaller mutational steps because periods of a few tens of thousands of years can barely be distinguished in the fossil record: relatively rapid evolution will always appear as a sudden change in a sequence of fossils. [24] [26] [27] Charles Darwin indeed noted in On the Origin of Species that periods of change would be short compared to the overall existence of a species. [28] In general, morphological changes are too rapid to determine from which cotemporal species a new species originated, as seen in the evolution of modern humans. [27]

Related Research Articles

<span class="mw-page-title-main">Microevolution</span> Change in allele frequencies that occurs over time within a population

Microevolution is the change in allele frequencies that occurs over time within a population. This change is due to four different processes: mutation, selection, gene flow and genetic drift. This change happens over a relatively short amount of time compared to the changes termed macroevolution.

<span class="mw-page-title-main">Mutation</span> Alteration in the nucleotide sequence of a genome

In biology, a mutation is an alteration in the nucleic acid sequence of the genome of an organism, virus, or extrachromosomal DNA. Viral genomes contain either DNA or RNA. Mutations result from errors during DNA or viral replication, mitosis, or meiosis or other types of damage to DNA, which then may undergo error-prone repair, cause an error during other forms of repair, or cause an error during replication. Mutations may also result from insertion or deletion of segments of DNA due to mobile genetic elements.

Molecular phylogenetics is the branch of phylogeny that analyzes genetic, hereditary molecular differences, predominantly in DNA sequences, to gain information on an organism's evolutionary relationships. From these analyses, it is possible to determine the processes by which diversity among species has been achieved. The result of a molecular phylogenetic analysis is expressed in a phylogenetic tree. Molecular phylogenetics is one aspect of molecular systematics, a broader term that also includes the use of molecular data in taxonomy and biogeography.

<span class="mw-page-title-main">Molecular evolution</span> Process of change in the sequence composition of cellular molecules across generations

Molecular evolution is the process of change in the sequence composition of cellular molecules such as DNA, RNA, and proteins across generations. The field of molecular evolution uses principles of evolutionary biology and population genetics to explain patterns in these changes. Major topics in molecular evolution concern the rates and impacts of single nucleotide changes, neutral evolution vs. natural selection, origins of new genes, the genetic nature of complex traits, the genetic basis of speciation, evolution of development, and ways that evolutionary forces influence genomic and phenotypic changes.

<span class="mw-page-title-main">Neutral theory of molecular evolution</span>

The neutral theory of molecular evolution holds that most evolutionary changes occur at the molecular level, and most of the variation within and between species are due to random genetic drift of mutant alleles that are selectively neutral. The theory applies only for evolution at the molecular level, and is compatible with phenotypic evolution being shaped by natural selection as postulated by Charles Darwin. The neutral theory allows for the possibility that most mutations are deleterious, but holds that because these are rapidly removed by natural selection, they do not make significant contributions to variation within and between species at the molecular level. A neutral mutation is one that does not affect an organism's ability to survive and reproduce. The neutral theory assumes that most mutations that are not deleterious are neutral rather than beneficial. Because only a fraction of gametes are sampled in each generation of a species, the neutral theory suggests that a mutant allele can arise within a population and reach fixation by chance, rather than by selective advantage.

<span class="mw-page-title-main">Molecular clock</span> Technique to deduce the time in prehistory when two or more life forms diverged

The molecular clock is a figurative term for a technique that uses the mutation rate of biomolecules to deduce the time in prehistory when two or more life forms diverged. The biomolecular data used for such calculations are usually nucleotide sequences for DNA, RNA, or amino acid sequences for proteins. The benchmarks for determining the mutation rate are often fossil or archaeological dates. The molecular clock was first tested in 1962 on the hemoglobin protein variants of various animals, and is commonly used in molecular evolution to estimate times of speciation or radiation. It is sometimes called a gene clock or an evolutionary clock.

<span class="mw-page-title-main">Nucleic acid sequence</span> Succession of nucleotides in a nucleic acid

A nucleic acid sequence is a succession of bases signified by a series of a set of five different letters that indicate the order of nucleotides forming alleles within a DNA or RNA (GACU) molecule. By convention, sequences are usually presented from the 5' end to the 3' end. For DNA, the sense strand is used. Because nucleic acids are normally linear (unbranched) polymers, specifying the sequence is equivalent to defining the covalent structure of the entire molecule. For this reason, the nucleic acid sequence is also termed the primary structure.

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<span class="mw-page-title-main">Substitution model</span> Description of the process by which states in sequences change into each other and back

In biology, a substitution model, also called models of DNA sequence evolution, are Markov models that describe changes over evolutionary time. These models describe evolutionary changes in macromolecules represented as sequence of symbols. Substitution models are used to calculate the likelihood of phylogenetic trees using multiple sequence alignment data. Thus, substitution models are central to maximum likelihood estimation of phylogeny as well as Bayesian inference in phylogeny. Estimates of evolutionary distances are typically calculated using substitution models. Substitution models are also central to phylogenetic invariants because they are necessary to predict site pattern frequencies given a tree topology. Substitution models are also necessary to simulate sequence data for a group of organisms related by a specific tree.

<span class="mw-page-title-main">Conserved sequence</span> Similar DNA, RNA or protein sequences within genomes or among species

In evolutionary biology, conserved sequences are identical or similar sequences in nucleic acids or proteins across species, or within a genome, or between donor and receptor taxa. Conservation indicates that a sequence has been maintained by natural selection.

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In genetics, the Ka/Ks ratio, also known as ω or dN/dS ratio, is used to estimate the balance between neutral mutations, purifying selection and beneficial mutations acting on a set of homologous protein-coding genes. It is calculated as the ratio of the number of nonsynonymous substitutions per non-synonymous site (Ka), in a given period of time, to the number of synonymous substitutions per synonymous site (Ks), in the same period. The latter are assumed to be neutral, so that the ratio indicates the net balance between deleterious and beneficial mutations. Values of Ka/Ks significantly above 1 are unlikely to occur without at least some of the mutations being advantageous. If beneficial mutations are assumed to make little contribution, then Ka/Ks estimates the degree of evolutionary constraint.

Neutral mutations are changes in DNA sequence that are neither beneficial nor detrimental to the ability of an organism to survive and reproduce. In population genetics, mutations in which natural selection does not affect the spread of the mutation in a species are termed neutral mutations. Neutral mutations that are inheritable and not linked to any genes under selection will be lost or will replace all other alleles of the gene. That loss or fixation of the gene proceeds based on random sampling known as genetic drift. A neutral mutation that is in linkage disequilibrium with other alleles that are under selection may proceed to loss or fixation via genetic hitchhiking and/or background selection.

<span class="mw-page-title-main">Masatoshi Nei</span> American geneticist

Masatoshi Nei is a Japanese-born American evolutionary biologist currently affiliated with the Department of Biology at Temple University as a Carnell Professor. He was, until recently, Evan Pugh Professor of Biology at Pennsylvania State University and Director of the Institute of Molecular Evolutionary Genetics; he was there from 1990 to 2015.

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<span class="mw-page-title-main">History of molecular evolution</span> History of the field of study of molecular evolution

The history of molecular evolution starts in the early 20th century with "comparative biochemistry", but the field of molecular evolution came into its own in the 1960s and 1970s, following the rise of molecular biology. The advent of protein sequencing allowed molecular biologists to create phylogenies based on sequence comparison, and to use the differences between homologous sequences as a molecular clock to estimate the time since the last common ancestor. In the late 1960s, the neutral theory of molecular evolution provided a theoretical basis for the molecular clock, though both the clock and the neutral theory were controversial, since most evolutionary biologists held strongly to panselectionism, with natural selection as the only important cause of evolutionary change. After the 1970s, nucleic acid sequencing allowed molecular evolution to reach beyond proteins to highly conserved ribosomal RNA sequences, the foundation of a reconceptualization of the early history of life.

A nonsynonymous substitution is a nucleotide mutation that alters the amino acid sequence of a protein. Nonsynonymous substitutions differ from synonymous substitutions, which do not alter amino acid sequences and are (sometimes) silent mutations. As nonsynonymous substitutions result in a biological change in the organism, they are subject to natural selection.

The relative rate test is a genetic comparative test between two ingroups and an outgroup or “reference species” to compare mutation and evolutionary rates between the species. Each ingroup species is compared independently to the outgroup to determine how closely related the two species are without knowing the exact time of divergence from their closest common ancestor. If more change has occurred on one lineage relative to another lineage since their shared common ancestor, then the outgroup species will be more different from the faster-evolving lineage's species than it is from the slower-evolving lineage's species. This is because the faster-evolving lineage will, by definition, have accumulated more differences since the common ancestor than the slower-evolving lineage. This method can be applied to averaged data, or individual molecules. It is possible for individual molecules to show evidence of approximately constant rates of change in different lineages even while the rates differ between different molecules. The relative rate test is a direct internal test of the molecular clock, for a given molecule and a given set of species, and shows that the molecular clock does not need to be assumed: It can be directly assessed from the data itself. Note that the logic can also be applied to any kind of data for which a distance measure can be defined.

A neutral network is a set of genes all related by point mutations that have equivalent function or fitness. Each node represents a gene sequence and each line represents the mutation connecting two sequences. Neutral networks can be thought of as high, flat plateaus in a fitness landscape. During neutral evolution, genes can randomly move through neutral networks and traverse regions of sequence space which may have consequences for robustness and evolvability.

Genetic saturation is the result of multiple substitutions at the same site in a sequence, or identical substitutions in different sequences, such that the apparent sequence divergence rate is lower than the actual divergence that has occurred. When comparing two or more genetic sequences consisting of single nucleotides, differences in sequence observed are only differences in the final state of the nucleotide sequence. Single nucleotides that undergoing genetic saturation change multiple times, sometimes back to their original nucleotide or to a nucleotide common to the compared genetic sequence. Without genetic information from intermediate taxa, it is difficult to know how much, or if any saturation has occurred on an observed sequence. Genetic saturation occurs most rapidly on fast-evolving sequences, such as the hypervariable region of mitochondrial DNA, or in short tandem repeats such as on the Y-chromosome.

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