CS Mukhopadhyay and RK Choudhary
School of Animal Biotechnology, GADVASU, Ludhiana
Phylogenetic analysis indicates the splits and diversions of species within ancestral lines, leading to a procreation of a clade. The term “clade” means a cluster of two or more species related by a common ancestor. The principle of phylogeny is relatedness among various organisms, due to descending from a nearer or remote common ancestor (CA). Thus, phylogeny is the relationship among different organisms due to sharing of a recent common ancestor (Zimmermann, 1931). It is a method by which to obtain an idea of the evolution and origin of an organism. The term “phylogeny” originates from two Greek words: Phylon (Stem) and Genesis (Origin).
This is based on the regularity of the decay process of radioactive elements. Suppose an ancient rock which has been lying undisturbed is tested, using a mass spectrophotometer, for the amount of radioactive uranium (235U) and normal lead (207Pb). The former is decayed into the latter, with a half‐life of 710 million years (MY) (Guttman, 2007). The wider the ratio of uranium to lead, the older the rock is. Thus, the approximate time of fossilization of an individual can be estimated by geological study, and this forms the geological clock. It is thought‐provoking to note that the first fossil evidence for many of the animal phyla is available from the rocks preserved since the Cambrian Period of the Paleozoic era (510–540 MY) (Benton 1993; Graham 1993).
Geological studies have revealed some geological events that are closely related to the evolution of plants and animals. The birds and mammals first appeared during the Jurassic period of the Mesozoic era (208 million years ago (Mya)), which was the time of the dinosaurs. The supercontinent Pangea (whole land areas of the earth lying together) first disintegrated into Gondwanaland (which included India, Australia, Africa, etc.) and Laurasia (North America and Greenland) during the Mesozoic era (i.e., 160–170 Mya). The first primates had appeared on the earth by the Paleocene epoch of the Tertiary period of the Cenozoic era (≈66.4 Mya). The earliest hominids date back to the Pliocene Epoch (5.3 Mya) (Guttman, 2007). Thus, the genealogical clock reflects on the evolutionary perspective of the earth and the origins of different species on it.
Early phylogenetic studies (prior to the 1960s) were based on morphological (morphos (Gr.): form, logos (Gr.): study) similarity and dissimilarities only. Fossil records and anatomical measurements are the prime sources of data for determining ancestral lineages. However, the morphology‐based approach has some inherent limitations, such as the fact that several morphological traits seems to be convergent and seem to overlap with each other. For example, different species of chickadee (Poecile atricapillus), a small North American songbird, have several apparently indistinguishable characters that can bewilder a skilled birder.
Morphological features are more qualitative than quantitative where the underlying inheritance pattern is not well established (http://www.life.umd.edu/classroom/bsci338m/Lectures/Systematics.html), and the limited availability of morphological data and fossil record makes it further challenging. No consistent results with genealogy or family pedigree can be obtained using morphological data but, nevertheless, the phenotypes of microbes hold little promise in depicting the evolutionary relationship among microbes, using morphology as a means.
Now the other side of the morphological systematic is the confounding resemblance between unrelated species, which could be due to convergent evolution (i.e., independent evolution in a similar environment, such as sharks and dolphins, or African euphorbias (Euphorbia spp.) and American cactus) (Ghosh and Mallick, 2008).
Adaptation to different ecological niche could also bring about strikingly different morphology among closely related species. The Hawaiian islands, an archipelago of eight major islands in the North Pacific Ocean, were formed about 0.5 to 0.8 Mya and became detached from the mainland. Hawaiian honeycreepers, which have descended from a common ancestor, exhibit different beak shapes due to their adaptation to varying ecological niches.
The limitations of morphology‐based phylogeny have now been replaced by molecular phylogeny, which uses molecular data (DNA/RNA/amino acid sequences, enzymatic data, etc.) for constructing the phylogenetic tree. Frederick Sanger first did the sequencing of bovine insulin in 1953. Later, the RNA sequencing technique (Min‐Jou et al., 1972) and then DNA sequencing, using mainly Sanger’s method (Sanger et al., 1977), became available, enabling scientists to make use of these sequences in reconstructing molecular phylogeny. FHC Crick suggested (in 1958) using the molecular sequences for phylogenetic tree reconstruction. However, Emile Zuckerkandl and Linus Pauling used aligned amino acid sequence data to build the first ever phylogenetic tree in 1962 (Morgan et al., 1998) and proposed the theory of the molecular clock (Morgan, 1998). The theory of molecular evolution then gained momentum. In 1967, Walter Fitch and Emanuel Margoliash designed the first algorithm (applying least squares) for phylogenetic tree reconstruction using protein sequences (Fitch and Margoliash, 1967; Fitch, 1970, 1971).
The phenotype (expression of a trait) of an individual is the result of its genotype (allelic combination(s) of a locus or multiple loci), modification of the genotypic effect by the environment in which it is raised, and the interaction between genotype and environment. The DNA sequence of the coding region of a gene is, to a great extent, the determinant of its phenotypic uniqueness. Genetic relationship among the close relatives confers similarity among them and discriminating uniqueness from unrelated individuals.
Traits can show homology as synapomorphies or as symplesiomorphies. Synapomorphies are the homologies that are derived from a common ancestor – in other words, ancestral homologies which are first observed in the ancestor of the clade. Thus, synapomorphies define a clade. On the other hand, symplesiomorphies are shared ancestral characters which have already arisen before the common ancestor of the clade. They are also passed on to the downstream taxa through the common ancestor. The phylogenetic tree is constructed on the basis of the evidence obtained from the synapomorphies only (http://biology.unm.edu/ccouncil/Biology_203/Summaries/Phylogeny.htm).
Shared characteristics among related individuals (having a common ancestor(s)) are the cornerstone of the theory of evolutionary phylogeny. The evolutionary process is depicted by the tree of life (TOL), where each species occupies a distinct position on the branch. The phylogeny represents the evolutionary process through the paths descending from the common ancestor(s) (CA), through the intermediate nodes to the ultimate terminal node or leaf, where the species/gene occupies its position. This path is known as the lineage. Molecular phylogeny, thus, uses the sequence data of DNA, RNA or protein. The accuracy of results depends on the types of input sequences (DNA, RNA, amino acid) and the divergence among the taxa incorporated in the study (Ghosh and Mallick, 2008):
The primary mechanism of molecular evolution is nucleotide substitution during the process of DNA replication. Different types of mutations (gross or point mutation) contribute to different types of germ‐line mutations that alter the phenotype. Among the point mutations, InDels (Insertions, Deletions) are frequently encountered. The types of point mutation vis‐à‐vis corresponding changes in the translated amino acid are shown in Figure E1. Besides, transposition, i.e. movement of the entire gene or non‐coding regions, exon shuffling, i.e. duplication of exons, exchange of structural or functional domains between protein‐coding genes (in multiple exons), transitions and transversions are also the underlying mechanisms.
Apart from mutations, natural selection of individual, genetic drift in a small population, bottleneck effects and so on play a significant role in the process of speciation.
This measures the tempo or pace of mutations occurring during one unit of time. The mutation rate varies with the type of gene, or the type of organism whose genome is being studied. It can be measured in terms of mutations per base pair per cell division, or per gene (or per genome) generation. The molecular clock studies a region with predictable mutation rate, to calculate the time of divergence of two species, in geologic history. The estimated mutation rates of different types of organisms are as follows:
A phylogenetic tree is a tree‐like structure. However, this can be rooted or unrooted. Various terms used to specify the components of a tree are given below:
There are some terminologies which are frequently used in phylogeny:
This illustrates the relatedness of the OTUs without making any assumptions about ancestry. No ancestor is determined in this type of tree. Unrooted trees show the differences between the taxa (regarding distance or proportion of residue change). However, no time frame can be deduced from the orientation of taxa in an unrooted tree.
This is a directed tree, characterized by the finally converged node signifying the most recent common ancestor of all the entities. In other words, the tree topology shows a common ancestor to all the involved taxa. The lineages/branches sprouting from the common ancestor determine the evolutionary path (and its direction). A rooted tree can be generated by introducing an outgroup as the root. The outgroup comprises one or more distantly related taxa, known to share a distant common ancestor. A rooted tree is also generated using a molecular clock where the evolutionary process is assumed to happen at a constant rate along the branches of a tree. The topology is rooted at a point where it splits the amount of character evolution in half.
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