Molecular evolution

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Molecular evolution describes how inherited DNA and/or RNA change over evolutionary time, and the consequences of this for proteins and other components of cells and organisms. Molecular evolution is the basis of phylogenetic approaches to describing the tree of life. Molecular evolution overlaps with population genetics, especially on shorter timescales. Topics in molecular evolution include the origins of new genes, the genetic nature of complex traits, the genetic basis of adaptation and speciation, the evolution of development, and patterns and processes underlying genomic changes during evolution.

Contents

History

The history of molecular evolution starts in the early 20th century with comparative biochemistry, and the use of "fingerprinting" methods such as immune assays, gel electrophoresis, and paper chromatography in the 1950s to explore homologous proteins. [1] [2] 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 most recent common ancestor. [3] [1] The surprisingly large amount of molecular divergence within and between species inspired the neutral theory of molecular evolution in the late 1960s. [4] [5] [6] Neutral theory also provided a theoretical basis for the molecular clock, although this is not needed for the clock's validity. 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. [1] The Society for Molecular Biology and Evolution was founded in 1982.

Molecular phylogenetics

Multiple sequence alignment (in this case DNA sequences) and illustrations of the use of substitution models to make evolutionary inferences. The data in this alignment (in this case a toy example with 18 sites) is converted to a set of site patterns. The site patterns are shown along with the number of times they occur in alignment. These site patterns are used to calculate the likelihood given the substitution model and a phylogenetic tree (in this case an unrooted four-taxon tree). It is also necessary to assume a substitution model to estimate evolutionary distances for pairs of sequences (distances are the number of substitutions that have occurred since sequences had a common ancestor). The evolutionary distance equation (d12) is based on the simple model proposed by Jukes and Cantor in 1969. The equation transforms the proportion of nucleotide differences between taxa 1 and 2 (p12 = 4/18; the four site patterns that differ between taxa 1 and 2 are indicated with asterisks) into an evolutionary distance (in this case d12=0.2635 substitutions per site). Site pattern frequencies models.jpg
Multiple sequence alignment (in this case DNA sequences) and illustrations of the use of substitution models to make evolutionary inferences. The data in this alignment (in this case a toy example with 18 sites) is converted to a set of site patterns. The site patterns are shown along with the number of times they occur in alignment. These site patterns are used to calculate the likelihood given the substitution model and a phylogenetic tree (in this case an unrooted four-taxon tree). It is also necessary to assume a substitution model to estimate evolutionary distances for pairs of sequences (distances are the number of substitutions that have occurred since sequences had a common ancestor). The evolutionary distance equation (d12) is based on the simple model proposed by Jukes and Cantor in 1969. The equation transforms the proportion of nucleotide differences between taxa 1 and 2 (p12 = 4/18; the four site patterns that differ between taxa 1 and 2 are indicated with asterisks) into an evolutionary distance (in this case d12=0.2635 substitutions per site).

Molecular phylogenetics uses DNA, RNA, or protein sequences to resolve questions in systematics, i.e. about their correct scientific classification from the point of view of evolutionary history. The result of a molecular phylogenetic analysis is expressed in a phylogenetic tree. Phylogenetic inference is conducted using data from DNA sequencing. This is aligned to identify which sites are homologous. A substitution model describes what patterns are expected to be common or rare. Sophisticated computational inference is then used to generate one or more plausible trees.

Some phylogenetic methods account for variation among sites and among tree branches. Different genes, e.g. hemoglobin vs. cytochrome c, generally evolve at different rates. [7] These rates are relatively constant over time (e.g., hemoglobin does not evolve at the same rate as cytochrome c, but hemoglobins from humans, mice, etc. do have comparable rates of evolution), although rapid evolution along one branch can indicate increased directional selection on that branch. [8] Purifying selection causes functionally important regions to evolve more slowly, and amino acid substitutions involving similar amino acids occurs more often than dissimilar substitutions. [7]

Five Stages of Molecular Phylogenetic Analysis Five Stages of Molecular Phylogenetic Analysis.png
Five Stages of Molecular Phylogenetic Analysis

Gene family evolution

Gene phylogeny as lines within grey species phylogeny. Top: An ancestral gene duplication produces two paralogs (histone H1.1 and 1.2). A speciation event produces orthologs in the two daughter species (human and chimpanzee). Bottom: in a separate species (E. coli), a gene has a similar function (histone-like nucleoid-structuring protein) but has a separate evolutionary origin and so is an analog. Ortholog paralog analog examples.svg
Gene phylogeny as lines within grey species phylogeny. Top: An ancestral gene duplication produces two paralogs (histone H1.1 and 1.2). A speciation event produces orthologs in the two daughter species (human and chimpanzee). Bottom: in a separate species (E. coli), a gene has a similar function (histone-like nucleoid-structuring protein) but has a separate evolutionary origin and so is an analog.

Gene duplication can produce multiple homologous proteins (paralogs) within the same species. Phylogenetic analysis of proteins has revealed how proteins evolve and change their structure and function over time. [9] [10]

For example, ribonucleotide reductase (RNR) has evolved a multitude of structural and functional variants. Class I RNRs use a ferritin subunit and differ by the metal they use as cofactors. In class II RNRs, the thiyl radical is generated using an adenosylcobalamin cofactor and these enzymes do not require additional subunits (as opposed to class I which do). In class III RNRs, the thiyl radical is generated using S-adenosylmethionine bound to a [ 4Fe-4S] cluster. That is, within a single family of proteins numerous structural and functional mechanisms can evolve. [11]

In a proof-of-concept study, Bhattacharya and colleagues converted myoglobin, a non-enzymatic oxygen storage protein, into a highly efficient Kemp eliminase using only three mutations. This demonstrates that only few mutations are needed to radically change the function of a protein. [12] Directed evolution is the attempt to engineer proteins using methods inspired by molecular evolution.

Molecular evolution at one site

Change at one locus begins with a new mutation, which might become fixed due to some combination of natural selection, genetic drift, and gene conversion.

Mutation

This hedgehog has no pigmentation due to a mutation. Hedgehog with Albinism.jpg
This hedgehog has no pigmentation due to a mutation.

Mutations are permanent, transmissible changes to the genetic material (DNA or RNA) of a cell or virus. Mutations result from errors in DNA replication during cell division and by exposure to radiation, chemicals, other environmental stressors, viruses, or transposable elements. When point mutations to just one base-pair of the DNA fall within a region coding for a protein, they are characterized by whether they are synonymous (do not change the amino acid sequence) or non-synonymous. Other types of mutations modify larger segments of DNA and can cause duplications, insertions, deletions, inversions, and translocations. [13]

The distribution of rates for diverse kinds of mutations is called the "mutation spectrum" (see App. B of [14] ). Mutations of different types occur at widely varying rates. Point mutation rates for most organisms are very low, roughly 10−9 to 10−8 per site per generation, [15] though some viruses have higher mutation rates on the order of 10−6 per site per generation. [16] Transitions (A ↔ G or C ↔ T) are more common than transversions (purine (adenine or guanine)) ↔ pyrimidine (cytosine or thymine, or in RNA, uracil)). [17] Perhaps the most common type of mutation in humans is a change in the length of a short tandem repeat (e.g., the CAG repeats underlying various disease-associated mutations). Such STR mutations may occur at rates on the order of 10−3 per generation. [18]

Different frequencies of different types of mutations can play an important role in evolution via bias in the introduction of variation (arrival bias), contributing to parallelism, trends, and differences in the navigability of adaptive landscapes. [19] [20] Mutation bias makes systematic or predictable contributions to parallel evolution. [14] Since the 1960s, genomic GC content has been thought to reflect mutational tendencies. [21] [22] Mutational biases also contribute to codon usage bias. [23] Although such hypotheses are often associated with neutrality, recent theoretical and empirical results have established that mutational tendencies can influence both neutral and adaptive evolution via bias in the introduction of variation (arrival bias).

Selection

Selection can occur when an allele confers greater fitness, i.e. greater ability to survive or reproduce, on the average individual than carries it. A selectionist approach emphasizes e.g. that biases in codon usage are due at least in part to the ability of even weak selection to shape molecular evolution. [24]

Selection can also operate at the gene level at the expense of organismal fitness, resulting in intragenomic conflict. This is because there can be a selective advantage for selfish genetic elements in spite of a host cost. Examples of such selfish elements include transposable elements, meiotic drivers, and selfish mitochondria.

Selection can be detected using the Ka/Ks ratio, the McDonald–Kreitman test. Rapid adaptive evolution is often found for genes involved in intragenomic conflict, sexual antagonistic coevolution, and the immune system.

Genetic drift

Genetic drift is the change of allele frequencies from one generation to the next due to stochastic effects of random sampling in finite populations. These effects can accumulate until a mutation becomes fixed in a population. For neutral mutations, the rate of fixation per generation is equal to the mutation rate per replication. A relatively constant mutation rate thus produces a constant rate of change per generation (molecular clock).

Slightly deleterious mutations with a selection coefficient less than a threshold value of 1 / the effective population size can also fix. Many genomic features have been ascribed to accumulation of nearly neutral detrimental mutations as a result of small effective population sizes. [25] With a smaller effective population size, a larger variety of mutations will behave as if they are neutral due to inefficiency of selection.

Gene conversion

Gene conversion occurs during recombination, when nucleotide damage is repaired using an homologous genomic region as a template. It can be a biased process, i.e. one allele may have a higher probability of being the donor than the other in a gene conversion event. In particular, GC-biased gene conversion tends to increase the GC-content of genomes, particularly in regions with higher recombination rates. [26] There is also evidence for GC bias in the mismatch repair process. [27] It is thought that this may be an adaptation to the high rate of methyl-cytosine deamination which can lead to C→T transitions.

The dynamics of biased gene conversion resemble those of natural selection, in that a favored allele will tend to increase exponentially in frequency when rare.

Genome architecture

Genome size

Genome size is influenced by the amount of repetitive DNA as well as number of genes in an organism. Some organisms, such as most bacteria, Drosophila, and Arabidopsis have particularly compact genomes with little repetitive content or non-coding DNA. Other organisms, like mammals or maize, have large amounts of repetitive DNA, long introns, and substantial spacing between genes. The C-value paradox refers to the lack of correlation between organism 'complexity' and genome size. Explanations for the so-called paradox are two-fold. First, repetitive genetic elements can comprise large portions of the genome for many organisms, thereby inflating DNA content of the haploid genome. Repetitive genetic elements are often descended from transposable elements.

Secondly, the number of genes is not necessarily indicative of the number of developmental stages or tissue types in an organism. An organism with few developmental stages or tissue types may have large numbers of genes that influence non-developmental phenotypes, inflating gene content relative to developmental gene families.

Neutral explanations for genome size suggest that when population sizes are small, many mutations become nearly neutral. Hence, in small populations repetitive content and other 'junk' DNA can accumulate without placing the organism at a competitive disadvantage. There is little evidence to suggest that genome size is under strong widespread selection in multicellular eukaryotes. Genome size, independent of gene content, correlates poorly with most physiological traits and many eukaryotes, including mammals, harbor very large amounts of repetitive DNA.

However, birds likely have experienced strong selection for reduced genome size, in response to changing energetic needs for flight. Birds, unlike humans, produce nucleated red blood cells, and larger nuclei lead to lower levels of oxygen transport. Bird metabolism is far higher than that of mammals, due largely to flight, and oxygen needs are high. Hence, most birds have small, compact genomes with few repetitive elements. Indirect evidence suggests that non-avian theropod dinosaur ancestors of modern birds [28] also had reduced genome sizes, consistent with endothermy and high energetic needs for running speed. Many bacteria have also experienced selection for small genome size, as time of replication and energy consumption are so tightly correlated with fitness.

Chromosome number and organization

The ant Myrmecia pilosula has only a single pair of chromosomes [29] whereas the Adders-tongue fern Ophioglossum reticulatum has up to 1260 chromosomes. [30] The number of chromosomes in an organism's genome does not necessarily correlate with the amount of DNA in its genome. The genome-wide amount of recombination is directly controlled by the number of chromosomes, with one crossover per chromosome or per chromosome arm, depending on the species. [31]

Changes in chromosome number can play a key role in speciation, as differing chromosome numbers can serve as a barrier to reproduction in hybrids. Human chromosome 2 was created from a fusion of two chimpanzee chromosomes and still contains central telomeres as well as a vestigial second centromere. Polyploidy, especially allopolyploidy, which occurs often in plants, can also result in reproductive incompatibilities with parental species. Agrodiatus blue butterflies have diverse chromosome numbers ranging from n=10 to n=134 and additionally have one of the highest rates of speciation identified to date. [32]

Cilliate genomes house each gene in individual chromosomes.

Organelles

Animal cell showing organelles. Animal cells SwissBioPics DL20221120.svg
Animal cell showing organelles.

In addition to the nuclear genome, endosymbiont organelles contain their own genetic material. Mitochondrial and chloroplast DNA varies across taxa, but membrane-bound proteins, especially electron transport chain constituents are most often encoded in the organelle. Chloroplasts and mitochondria are maternally inherited in most species, as the organelles must pass through the egg. In a rare departure, some species of mussels are known to inherit mitochondria from father to son.

Origins of new genes

New genes arise from several different genetic mechanisms including gene duplication, de novo gene birth, retrotransposition, chimeric gene formation, recruitment of non-coding sequence into an existing gene, and gene truncation.

Gene duplication initially leads to redundancy. However, duplicated gene sequences can mutate to develop new functions or specialize so that the new gene performs a subset of the original ancestral functions. Retrotransposition duplicates genes by copying mRNA to DNA and inserting it into the genome. Retrogenes generally insert into new genomic locations, lack introns. and sometimes develop new expression patterns and functions.

Chimeric genes form when duplication, deletion, or incomplete retrotransposition combine portions of two different coding sequences to produce a novel gene sequence. Chimeras often cause regulatory changes and can shuffle protein domains to produce novel adaptive functions.

De novo gene birth can give rise to protein-coding genes and non-coding genes from previously non-functional DNA. [33] For instance, Levine and colleagues reported the origin of five new genes in the D. melanogaster genome. [34] [35] Similar de novo origin of genes has been also shown in other organisms such as yeast, [36] rice [37] and humans. [38] De novo genes may evolve from spurious transcripts that are already expressed at low levels. [39]

Constructive neutral evolution

Constructive neutral evolution (CNE) explains that complex systems can emerge and spread into a population through neutral transitions with the principles of excess capacity, presuppression, and ratcheting, [40] [41] [42] and it has been applied in areas ranging from the origins of the spliceosome to the complex interdependence of microbial communities. [43] [44] [45]

Journals and societies

The Society for Molecular Biology and Evolution publishes the journals "Molecular Biology and Evolution" and "Genome Biology and Evolution" and holds an annual international meeting. Other journals dedicated to molecular evolution include Journal of Molecular Evolution and Molecular Phylogenetics and Evolution. Research in molecular evolution is also published in journals of genetics, molecular biology, genomics, systematics, and evolutionary biology.

See also

Related Research Articles

<span class="mw-page-title-main">Evolution</span> Change in the heritable characteristics of biological populations

Evolution is the change in the heritable characteristics of biological populations over successive generations. It occurs when evolutionary processes such as natural selection and genetic drift act on genetic variation, resulting in certain characteristics becoming more or less common within a population over successive generations. The process of evolution has given rise to biodiversity at every level of biological organisation.

<span class="mw-page-title-main">Genetics</span> Science of genes, heredity, and variation in living organisms

Genetics is the study of genes, genetic variation, and heredity in organisms. It is an important branch in biology because heredity is vital to organisms' evolution. Gregor Mendel, a Moravian Augustinian friar working in the 19th century in Brno, was the first to study genetics scientifically. Mendel studied "trait inheritance", patterns in the way traits are handed down from parents to offspring over time. He observed that organisms inherit traits by way of discrete "units of inheritance". This term, still used today, is a somewhat ambiguous definition of what is referred to as a gene.

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.

<span class="mw-page-title-main">Human genome</span> Complete set of nucleic acid sequences for humans

The human genome is a complete set of nucleic acid sequences for humans, encoded as DNA within the 23 chromosome pairs in cell nuclei and in a small DNA molecule found within individual mitochondria. These are usually treated separately as the nuclear genome and the mitochondrial genome. Human genomes include both protein-coding DNA sequences and various types of DNA that does not encode proteins. The latter is a diverse category that includes DNA coding for non-translated RNA, such as that for ribosomal RNA, transfer RNA, ribozymes, small nuclear RNAs, and several types of regulatory RNAs. It also includes promoters and their associated gene-regulatory elements, DNA playing structural and replicatory roles, such as scaffolding regions, telomeres, centromeres, and origins of replication, plus large numbers of transposable elements, inserted viral DNA, non-functional pseudogenes and simple, highly repetitive sequences. Introns make up a large percentage of non-coding DNA. Some of this non-coding DNA is non-functional junk DNA, such as pseudogenes, but there is no firm consensus on the total amount of junk DNA.

<span class="mw-page-title-main">Neutral theory of molecular evolution</span> Theory of evolution by changes at the molecular level

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.

Population genetics is a subfield of genetics that deals with genetic differences within and among populations, and is a part of evolutionary biology. Studies in this branch of biology examine such phenomena as adaptation, speciation, and population structure.

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.

<span class="mw-page-title-main">Molecular genetics</span> Scientific study of genes at the molecular level

Molecular genetics is a branch of biology that addresses how differences in the structures or expression of DNA molecules manifests as variation among organisms. Molecular genetics often applies an "investigative approach" to determine the structure and/or function of genes in an organism's genome using genetic screens. 

<span class="mw-page-title-main">Evolutionary biology</span> Study of the processes that produced the diversity of life

Evolutionary biology is the subfield of biology that studies the evolutionary processes that produced the diversity of life on Earth. It is also defined as the study of the history of life forms on Earth. Evolution holds that all species are related and gradually change over generations. In a population, the genetic variations affect the phenotypes of an organism. These changes in the phenotypes will be an advantage to some organisms, which will then be passed on to their offspring. Some examples of evolution in species over many generations are the peppered moth and flightless birds. In the 1930s, the discipline of evolutionary biology emerged through what Julian Huxley called the modern synthesis of understanding, from previously unrelated fields of biological research, such as genetics and ecology, systematics, and paleontology.

Gene duplication is a major mechanism through which new genetic material is generated during molecular evolution. It can be defined as any duplication of a region of DNA that contains a gene. Gene duplications can arise as products of several types of errors in DNA replication and repair machinery as well as through fortuitous capture by selfish genetic elements. Common sources of gene duplications include ectopic recombination, retrotransposition event, aneuploidy, polyploidy, and replication slippage.

<span class="mw-page-title-main">Sequence homology</span> Shared ancestry between DNA, RNA or protein sequences

Sequence homology is the biological homology between DNA, RNA, or protein sequences, defined in terms of shared ancestry in the evolutionary history of life. Two segments of DNA can have shared ancestry because of three phenomena: either a speciation event (orthologs), or a duplication event (paralogs), or else a horizontal gene transfer event (xenologs).

<span class="mw-page-title-main">Mutation rate</span> Rate at which mutations occur during some unit of time

In genetics, the mutation rate is the frequency of new mutations in a single gene, nucleotide sequence, or organism over time. Mutation rates are not constant and are not limited to a single type of mutation; there are many different types of mutations. Mutation rates are given for specific classes of mutations. Point mutations are a class of mutations which are changes to a single base. Missense and Nonsense mutations are two subtypes of point mutations. The rate of these types of substitutions can be further subdivided into a mutation spectrum which describes the influence of the genetic context on the mutation rate.

<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.

<span class="mw-page-title-main">Gene</span> Sequence of DNA or RNA that codes for an RNA or protein product

In biology, the word gene has two meanings. The Mendelian gene is a basic unit of heredity. 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 non-coding genes.

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> Japanese-American geneticist (1931–2023)

Masatoshi Nei was a Japanese-born American evolutionary biologist.

The evolution of biological complexity is one important outcome of the process of evolution. Evolution has produced some remarkably complex organisms – although the actual level of complexity is very hard to define or measure accurately in biology, with properties such as gene content, the number of cell types or morphology all proposed as possible metrics.

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.

<span class="mw-page-title-main">Genome evolution</span> Process by which a genome changes in structure or size over time

Genome evolution is the process by which a genome changes in structure (sequence) or size over time. The study of genome evolution involves multiple fields such as structural analysis of the genome, the study of genomic parasites, gene and ancient genome duplications, polyploidy, and comparative genomics. Genome evolution is a constantly changing and evolving field due to the steadily growing number of sequenced genomes, both prokaryotic and eukaryotic, available to the scientific community and the public at large.

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Category: molecular evolution (kimura 1968)

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