How Biological Diversity is Organized: Phylogenetics & Genomics26.2Phylogenies are inferred from morphological and molecular data- Similarities due to shared ancestry are called homologies. - Genes or other DNA sequences are homologous if they are descended from sequences carried by a common ancestor.- Usually, the more related species are, the more similar their DNA and morphologies.- Can have much different phenotype but similar genes and visa versa.- e.g. Hawaiian silversword plant vary dramatically in appearance but still have very similar genes.Evaluating Molecular Homologies- After sequencing the DNA, the first step in comparing the two organisms DNA is to line up equivalent sections of the DNA. - If closely related, only a few mismatches in sequence should occur.- Two sequences that closely resemble each other at many points along their length most likely are homologous.- If not, many different bases and many different sites as well as different lengths due to insertions and deletions over time.- Molecular Systematics: the disciple that uses DNA and other molecular data to determine evolutionary relationships.Cladistics: common ancestry is the primary criterion used to classify organisms.Biologists place species into groups called clades, each of which includes an ancestral species and all of its descendants. - Monophyletic- consisting of an ancestral species and all of its descendants.- Paraphyletic- consists of ancestral species and some its descendants but not all.- Polyphyletic: some of its members have different common ancestors.Shared Ancestral Character: a character that originated in an ancestor of the taxon.! - e.g. backbone in mammalsShared Derived Character: an evolutionary novelty unique to a particular clade.- e.g. Hair is present on all mammals but not found in their ancestors.inferring Phylogenies Using Derived Characters:- It should be possible to determine the clade in which each shared derived character first appeared and to use that information to infer evolutionary relationships.- As a basis of comparison, you must first select an outgroup.- outgroup: a species or group of species from an evolutionary lineage that is known to have diverged before the lineage that includes the species we are studying (the ingroup). BIOL1108: Test 2 Book Notes! Boston- [ Fig. 26.11 pp 543] Make a character table and translate to a phylogenetic tree.Phylogenetic Trees with Proportional Branch Lengths- In some tree diagrams, branch lengths are proportional to the amount of:- evolutionary change- times at which particular events/change occurred.- Maximum Parsimony:- according to this principle, we should first investigate the simplest explanation that is consistent with the facts.- Examine all possible trees and select the tree that requires fewest evolutionary changes.- According to the principle of maximum likelihood, given certain rules about how DNA changes over time, a tree can be found that reflects the most likely sequence of evolutionary events.- e.g. Research experiment pp. 546Phylogenetic Trees as Hypotheses - Represents hypothesis about how various organisms are related to each other.- Using phylogenetic bracketing, we can predict (by parsimony) that features shared by two groups of closely related organisms are present in their common ancestor and all of its descendants.26.4 An organismʼs evolutionary history is documented in its genome- Molecular Approach of Genomics:- helps identify phylogenetic relationships that we could not determine from other methods such as comparative methodology or morphological similarities that might not be apparent.- allows us to construct phylogenetic relationships for prokaryotes and other microorganisms alive today that we do not have a fossil record for.- Genes evolve at different rates:- (even in the same evolutionary lineage)- e.g. DNA that codes for rRNA changes slowly, so comparisons can help us understand relationships between taxa that diverged hundreds of millions of years ago, while mtDNA (mitochondrial DNA) changes quickly relative to evolution and allows us to compare recent evolutionary events.A. Gene Duplications and Gene Families- Duplications of genes lead to gene families, or groups of related genes within an organismʼs genome. These genes have a common ancestor.- We distinguish these types of homologous genes: orthologous or paralogous genes.- Orthologous genes = refers to homologous genes that are found in different species because of speciation. (can only diverge after speciation, so in separate gene pools)- e.g. cytochrome c (codes for an electron transport chain protein) genes of dogs are orthologous- Paralogous genes = result from gene duplication, so more than one copy is found in the same genome. (can diverge within the ʻsameʼ species bc they are present in more than one copy)BIOL1108: Test 2 Book Notes! Boston*Different colored bands mark regions of the genes where diff. in base sequences have accumulated.- Application: The olfactory receptor genes in vertebrates have undergone many gene duplications in vertebrates, so humans and mice both have huge families of more than 1,000 of these paralogous genes.B. Genome Evolution- Because we have the ability to compare entire genomes now, two facts have been established:- 1. Orthologous genes are widespread and can extend over huge evolutionary distances.- 99% of human and mice genes are orthologous, and 50% of our genes are orthologous with yeast. This shows all living organisms share many biochemical pathways.- 2. The number of genes seems not to have increased through duplication at the same rate as perceived phenotypic complexity.- humans have only ~4x the number of genes than do yeast, a single-celled eukaryote, but we have a large complex brain and complex body.Concept Check 26.41. Explain how comparisons between the proteins of two species can yield data about their evolutionary relationship.a. Proteins are gene products. Their amino acid sequences are determined by the nucleotide sequences of the DNA that codes for them. Thus, differences between comparable proteins in two species reflect underlying genetic differences.2. Suppose Gene A is orthologous in species 1 and species 2, and gene B is paralogous to gene A in species 1. Suggest a sequence of two evolutionary events that could result in the following: Gene A differs considerably between species, yet gene A and gene B show little sequence divergence from each other.a. These observations suggest