Methods of illustrating evolutionary relationship
- 1. Methods of illustrating evolutionary relationship Different methods of phylogenetic tree construction: • Phylogenetics is the study of genetic relatedness of individuals of the same, or different, species. • Through phylogenetics, evolutionary relationships can be inferred. • A phylogenetic tree may be rooted or unrooted, depending on whether the ancestral root is known or unknown, respectively. • A phylogenetic tree’s root is the origin of evolution of the individuals studied. • Branches between leaves show the evolutionary relationships between sequences, individuals, or species, and branch length represents evolutionary time. • When constructing and analyzing phylogenetic trees, it is important to remember that the resulting tree is simply an estimate and is unlikely to represent the true evolutionary tree of life. • Various methods can be used to construct a phylogenetic tree. • The two most commonly used and most robust approaches are maximum likelihood and Bayesian methods. Distance-matrix methods Distance-matrix methods are rapid approaches that measure the genetic distances between sequences. After having aligned the sequences through multiple sequence alignment, the proportion of mismatched positions is calculated. From this, a matrix is constructed that describes the genetic distance between each sequence pair. In the resulting phylogenetic tree, closely-related sequences are found under the same interior node, and the branch lengths represent the observed genetic distances between sequences. • Neighbor joining (NJ), and Unweighted Pair Group Method (UPGMA) are two distance-matrix methods.
- 2. • NJ and UPGMA produce unrooted and rooted trees, respectively. • NJ is a bottom-up clustering algorithm. • The main advantages of NJ are its rapid speed, regardless of dataset size, and that it does not assume an equal rate of evolution amongst all lineages. • Despite this, NJ only generates one phylogenetic tree, even when there are several possibilities. • UPGMA is an unweighted method, meaning that each genetic distance contributes equally to the overall average. • UPGMA is not a particularly popular method as it makes various assumptions, including the assumption that the evolutionary rate is equal for all lineages. Maximum parsimony • Maximum parsimony attempts to reduce branch length by minimizing the number of evolutionary changes required between sequences. • The optimal tree would be the shortest tree with the fewest mutations. • All potential trees are evaluated, and the tree with the least amount of homoplasy, or convergent evolution, is selected as the most likely tree. • Since the most-parsimonious tree is always the shortest tree, it may not necessarily best represent the evolutionary changes that have occurred. • Also, maximum parsimony is not statistically consistent, leading to issues when drawing conclusions. Maximum likelihood • Despite being slow and computationally expensive, maximum likelihood is the most commonly used phylogenetic method used in research papers, and it is ideal for phylogeny construction from sequence data. • For each nucleotide position in a sequence, the maximum likelihood algorithm estimates the probability of that position being a particular nucleotide, based on whether the ancestral sequences possessed that specific nucleotide.
- 3. • The cumulative probabilities for the entire sequence are calculated for both branches of a bifurcating tree. • The likelihood of the whole tree is provided by the sum of the probabilities of both branches of the tree. • Maximum likelihood is based on the concept that each nucleotide site evolves independently, enabling phylogenetic relationships to be analyzed at each site. • The maximum likelihood method can be carried out in a reasonable amount of time for four sequences. • If more than four sequences are to be analyzed, then basic trees are constructed for the initial four sequences, and further sequences are subsequently added, and maximum likelihood is recalculated. • Bias can be introduced into the calculation as the order in which the sequences are added, and the initial sequence used, play pivotal roles in the outcome of the tree. • Bias can be avoided by repeating the entire process multiple times at random so that the majority rule consensus tree can be selected. Bayesian inference • Bayesian inference methods assume phylogeny by using posterior probabilities of phylogenetic trees. • A posterior probability is generated for each tree by combining its prior probability with the likelihood of the data. • A phylogeny is best represented by the tree with the highest posterior probability. • Not only does Bayesian inference produce results that can be easily interpreted; it can also incorporate prior information and complex models of evolution into the analysis, as well as accounting for phylogenetic uncertainty.
- 4. Determining Evolutionary Relationships • In general, organisms that share similar physical features and genomes tend to be more closely related than those that do not. Such features that overlap both morphologically (in form) and genetically are referred to as homologous structures; they stem from developmental similarities that are based on evolution. For example, the bones in the wings of bats and birds have homologous structures • Bat and bird wings are homologous structures, indicating that bats and birds share a common evolutionary past. • A phylogeny, phylogenetic tree, or evolutionary tree is a diagram showing the evolutionary relationships between a group of organisms. • Closely related species are likely to have similar characteristics, with some differences. Thus, if one species is known to have certain characteristics, such as containing beneficial drugs, it is reasonable to suppose that closely related species may contain similar drugs. The Narcissus (daffodil) genus is one plant family that contains these potentially life-saving drugs. Papers have been published about the search for Alzheimer’s treatments (Rønsted et al., 2010) and anti-viral drugs (Ooi et al., 2010) in the genus Narcissus. There has also been a paper on the evolution of stylar polymorphisms in this genus (Graham and Barrett, 2004). These papers are freely available online. Some DNA and protein sequences have been determined for several species
- 5. of Narcissus and these have been used to try to understand the evolutionary relationships of species within this genus. Misleading Appearances • Some organisms may be very closely related, even though a minor genetic change caused a major morphological difference to make them look quite different. • Similarly, unrelated organisms may be distantly related, but appear very much alike. • This usually happens because both organisms were in common adaptations that evolved within similar environmental conditions. • When similar characteristics occur because of environmental constraints and not due to a close evolutionary relationship, it is called an analogy or homoplasy. • Similar traits can be either homologous or analogous. • Homologous structures share a similar embryonic origin; analogous organs have a similar function. • Two succulent plant genera, Euphorbia and Astrophytum, are only distantly related, but the species within each have converged on a similar body form. • For example, the bones in the front flipper of a whale are homologous to the bones in the human arm. Molecular Comparisons • With the advancement of DNA technology, the area of molecular systematics, which describes the use of information on the molecular level including DNA analysis, has blossomed. • New computer programs not only confirm many earlier classified organisms, but also uncover previously made errors.
- 6. • As with physical characteristics, even the DNA sequence can be tricky to read in some cases. • For some situations, two very closely related organisms can appear unrelated if a mutation occurred that caused a shift in the genetic code. • An insertion or deletion mutation would move each nucleotide base over one place, causing two similar codes to appear unrelated. • Sometimes two segments of DNA code in distantly related organisms randomly share a high percentage of bases in the same locations, causing these organisms to appear closely related when they are not. • For both of these situations, computer technologies have been developed to help identify the actual relationships, and, ultimately, the coupled use of both morphologic and molecular information is more effective in determining phylogeny. Evolution Connection • Evolutionary biologists could list many reasons why understanding phylogeny is important to everyday life in human society. • For botanists, phylogeny acts as a guide to discovering new plants that can be used to benefit people. • Think of all the ways humans use plants—food, medicine, and clothing are a few examples. • If a plant contains a compound that is effective in treating cancer, scientists might want to examine all of the relatives of that plant for other useful drugs. • A research team in China identified a segment of DNA thought to be common to some medicinal plants in the family Fabaceae (the legume family) and worked to identify which species had this segment. After testing plant species in this family, the team found a DNA marker (a known location on a chromosome that enabled them to identify the species) present. Then, using the DNA to uncover phylogenetic relationships, the team could identify
- 7. whether a newly discovered plant was in this family and assess its potential medicinal properties. *Dalbergia sissoo (D. sissoo) is in the Fabaceae, or legume family. Scientists found that D. sissoo shares a DNA marker with species within the Fabaceae family that have antifungal properties. Subsequently, D. sissoo was shown to have fungicidal activity, supporting the idea that DNA markers can be used to screen for plants with potential medicinal properties. Building Phylogenetic Trees • After the homologous and analogous traits are sorted, scientists often organize the homologous traits using a system called cladistics. • This system sorts organisms into clades: groups of organisms that descended from a single ancestor.
- 8. • For example, all of the organisms in the orange region evolved from a single ancestor that had amniotic eggs. • Consequently, all of these organisms also have amniotic eggs and make a single clade, also called a monophyletic group. Art Connection • All the organisms within a clade stem from a single point on the tree. • A clade may contain multiple groups, as in the case of animals, fungi and plants, or a single group, as in the case of flagellates. • Groups that diverge at a different branch point, or that do not include all groups in a single branch point, are not considered clades. Shared Characteristics • Organisms evolve from common ancestors and then diversify. Scientists use the phrase “descent with modification” because even though related organisms have many of the same characteristics and genetic codes,
- 9. changes occur. This pattern repeats over and over as one goes through the phylogenetic tree of life: 1. A change in the genetic makeup of an organism leads to a new trait which becomes prevalent in the group. 2. Many organisms descend from this point and have this trait. 3. New variations continue to arise: some are adaptive and persist, leading to new traits. 4. With new traits, a new branch point is determined (go back to step 1 and repeat). • If a characteristic is found in the ancestor of a group, it is considered a shared ancestral character because all of the organisms in the taxon or clade have that trait. The vertebrate is a shared ancestral character. Now consider the amniotic egg characteristic in the same figure. Only some of the organisms have this trait, and to those that do, it is called a shared derived character because this trait derived at some point but does not include all of the ancestors in the tree. • The tricky aspect to shared ancestral and shared derived characters is the fact that these terms are relative. The same trait can be considered one or the other depending on the particular diagram being used. • These terms help scientists distinguish between clades in the building of phylogenetic trees. Choosing the Right Relationships • Imagine being the person responsible for organizing all of the items in a department store properly—an overwhelming task. • Organizing the evolutionary relationships of all life on Earth proves much more difficult: scientists must span enormous blocks of time and work with information from long-extinct organisms.
- 10. • Trying to decrypt the proper connections, especially given the presence of homologies and analogies, makes the task of building an accurate tree of life extraordinarily difficult. • Add to that the advancement of DNA technology, which now provides large quantities of genetic sequences to be used and analyzed. • Taxonomy is a subjective discipline: many organisms have more than one connection to each other, so each taxonomist will decide the order of connections. • To aid in the tremendous task of describing phylogenies accurately, scientists often use a concept called maximum parsimony, which means that events occurred in the simplest, most obvious way. • For example, if a group of people entered a forest preserve to go hiking, based on the principle of maximum parsimony, one could predict that most of the people would hike on established trails rather than forge new ones. • For scientists deciphering evolutionary pathways, the same idea is used: the pathway of evolution probably includes the fewest major events that coincide with the evidence at hand. • Starting with all of the homologous traits in a group of organisms, scientists look for the most obvious and simple order of evolutionary events that led to the occurrence of those traits.