In own words, answer a&,b(1,2,3). please ignore C When constructing phytogenies,
ID: 18817 • Letter: I
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In own words, answer a&,b(1,2,3). please ignore C
When constructing phytogenies, is it better to compare orthologous or paralogous genes? Why? In a hypothetical organism, green fur color is dominant over blue, and fur color is determined by a single gene (G-dominant allele, g-recessive allele) For the following crosses: Blue X pure line green Blue x heterozygous green Heterozygous green x heterozygous green What gametes will be produced and what will be the genotypes and phenotypes of the offspring (answer for each section A, B, C)? What is meant by the P, Fl, F2 generations of cross A above? How many different genes, alleles, phenotypes. and genotypes are involved? What are some assumptions and limitations of molecular clocks?Explanation / Answer
Orthologs and paralogs are two fundamentally different types of homologous genes that evolved, respectively, by vertical descent from a single ancestral gene and by duplication. Orthology and paralogy are key concepts of evolutionary genomics
What are orthologous and what are paralogous genes ?
It is said that:
- Two genes are to be orthologous if they diverged after a speciation event,
- Two genes are to be paralogous if they diverged after a duplication event.
The original quotation is by Walter Fitch (1970, Systematic Zoology 19:99-113):
"Where the homology is the result of gene duplication so that both copies have descended side by side during the history of an organism, (for example, alpha and beta hemoglobin) the genes should be called paralogous (para = in parallel). Where the homology is the result of speciation so that the history of the gene reflects the history of the species (for example alpha hemoglobin in man and mouse) the genes should be called orthologous (ortho = exact)."
Orthologous sequences are sequences which belong to different species and have a common homologue exactly in the common ancestor of both species. Paralogous sequences are sequences which were generated by a gene-duplication event without necessarily any speciation. In terms of the following figure, the ellipses represent species and X1, X2 represent genetic sequences. U is the oldest ancestor, which had a single copy of the sequence X1. At some point, between U and its descendant V, a sequence duplication occurred which left two copies of X1. We label the second copy X2. Later, V speciates, that is it has two different descendants, marked A and B. A inherits both sequences X1 and X2 from V. For this example, we have made B inherit only one of the two sequences, in this case X1. X2 was lost or damaged in the evolution from V to B. Now we can say that A[X1] and A[X2] are an example of paralogous sequences.A[X1] and B[X1] are an example of orthologous sequences.More importantly, we consider that A[X2] and B[X1] are not orthologous sequences.
To build phylogenetic trees we need to find orthologous sequences and estimate the amount of evolution between these sequences. Ideally we would like to work on exactly the same protein across all the family that we want to relate. This normally gives better results than using different proteins, as different proteins may be subject to different evolutionary pressures and may give inconsistent estimates of the distances between species. When we can work with the same protein in many species, many inconsistencies disappear.
The most serious danger when evaluating the distance between species through sequences is to use paralogous instead of orthologous sequences. In our picture above, we could have taken B[X1] and A[X2] (which are homologous) and estimate the distance between A and B from them. This would clearly be wrong, as we would be measuring the distance between A, U and B and not A to B alone. Notice, that this mistake could easily happen if A[X1] had not been sequenced (or had been lost in evolution).
The main contribution of this bio-recipe is to explain an algorithm in Darwin which detects orthologous sequences and avoids most of the paralogous ones. Once this is done, we will select a single protein to produce a phylogenetic tree. The selection of a single protein is based on the same ideas used to detect orthology, which is stable pairs
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