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Phylogeny

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BIOLOGY 3: Biodiversity
LECTURE 7 PHYLOGENY

Objectives: To recognize the characters used in phylogenies, To define homologous, analogous and homoplastic features, To interpret phylogenetic trees

Phylogeny
 refers to the evolutionary descent of taxa
 refers to the relationship between ancestors and descendants and relationships among descendant taxa
 shows the lineage of taxa and can be summarized in a branching diagram called is phylogenetic tree o Phylogenetic trees illustrate the evolutionary relationships among groups of organisms, or among a family of related nucleic acid or protein sequences Phylogeny Applications
 Tree of life – analyzing changes that have occurred in evolution of different organisms  Phylogenetic relationships among genes can help predict which ones might have similar functions (e.g., ortholog detection)  Follow changes occuring in rapidly changing species (e.g., HIV virus)  Phylogeny Packages o PHYLIP, Phylogenetic inference package  Felsenstein o PAUP, phylogenetic analysis using parsimony  Swofford Characters used in Phylogenies  Ancestral characters o states that are inherited unchanged from the ancestor o The character present in the ancestor which is also observed in the descendant taxon is an ancestral character. o Taxa with numerous ancestral characters are described as primitive.  Eg. Turtles (relic)  Derived characters o states that are inherited from the ancestor but already in modified form. A character present in the descendant taxon but has not been observed in the ancestor is derived character. o Taxa with numerous derived characters are described as advanced Determining whether a character is ancestral or derived:  Time element o this refers to the sequence of appearance of the character state o If the time of appearance among comparable character states can be determined, then the earlier evolved character state will be considered ancestral while that which evolved later is derived. o The presence of fossils facilitate determination of ancestral and derived character states o The character in the older fossil will be ancestral while that in the younger fossil or is absent in a fossil but present in an extant or living taxon will be derived.





scales in fossils dated as early as 400 million years ago and feathers in bird fossils dated 195 million years ago. The complexity of the character state o Simpler structure is considered ancestral while the more complex structure is derived o The lung of frogs is a simple sac-like structure and, hence, is ancestral to the lung of birds which consists of units called airsacs. However, simple structures may also evolve from complex structures- a case of regression or reduction in structure.  eyelessness in cave fishes is derived to presence of eyes in most fishes which is the ancestral state  a corolla tube in flowers is a derived state to free petals which is the ancestral state; fusion of bases of petals into a corolla tube is a case of reduction in number of flower plants Outgroup method o The presence of a character state among some members of lineage and an outgroup (defined as a taxon not closely related to any member of the lineage) indicates that the character is ancestral. o Absence of the character state in the outgroup indicates that the character state is derived.



Basis of Similarities Among Characters  Homology o The resemblance in characters in different tax due to common origin. A character is similar in two or more taxa because they inherited that same character from a common ancestor. Similar ancestral characters present in different taxa are always homologous. o Similar derived characters present in different taxa maybe homologous only if it can be determined that the character came from a common origin, that is a common ancestor. o There are homologous characters, however, that do not necessarily look alike and may have significant differences  Arm of chimpanzee and arm of man  Forelimb of dog and arm of man. There is structural similarity in bone structure of these parts (humerus, radio-ulna, carpals and digits) despite the differences in dog paw and human palm.  Hand and arm of man, flipper of seal, wing of bat and wing of bird. These are morphologically different structures, having different functions but are structurally similar in bone structure.  Swim bladders of fishes and lungs of tetrapod vertebrates- structurally and functionally different but upon tracing the development of these structures, they are derived from a common origin. Swim bladders are simple sac-like structures that are floatation aides of fishes that gave rise to complex sac-like lungs used in respiration of air in amphibians, reptiles, birds and mammals. A difference in structure is due to the increasing complexity of lungs.  Lower jaw of amphibians and reptiles and the middle ears of mammals. Amphibians and reptiles do not have a middle ear bone. They have numerous bones in their lower jaw while the mammalian jaw is a single bone only. It is believed that the reduction in the hind jaw bones of reptiles occurred and these reduced bones became the middle earbones of mammals. o Differences in homologous characters in two related taxa maybe a product of divergent evolution, as in example 1,2,4 and 5.  Divergent evolution – a trend in evolution that results from differences in evolutionary pathways followed by two descendant lineages from their ancestor.  Adaptive radiation, likewise produces differences in homologous characters in several related taxa, as in example 3.

o 

Adaptive radiation is multiple divergent evolution that results in differences in characters/ traits in several related taxa due to exposure to different environment conditions, i.e. land, sea, air



Analogy o the resemblance in structure in unrelated taxa due to similarity in function. Analogous structures are similar in appearance because they are adaptations to similar environmental conditions. Because two unrelated taxa are performing the same or similar functions/ roles in a specific situation, then they evolve similar structures. o Wings are present in insects, birds and bats which have been favored in aerial environments due to the presence of expanded membranes called wings that they use in flight. Insects, birds and bats have unrelated immediate ancestors and hence their wings are analogous structures. Analogous structures are products of convergent evolution, a trend in evolution that produces resemblance in features of unrelated taxa due to exposure to similar environmental conditions. Homoplasy o the resemblance in structure of distantly related taxa because they are same forming. The similarity in the characters is due to having followed similar developmental plans only and not due to inheritance from common ancestor. The two unrelated taxa with the similar character inherited similar developmental plans (that resulted in the character) from a common but very distant ancestor. o Homoplastic characters are products of parallel evolution, a trend in evolution that produces resemblance in features of unrelated or distantly related taxa that have followed the same or similar developmental plans. Given two taxa A and B with different immediate ancestors C and D which have a common distant ancestor, a similar character in A and B is homoplastic.

Monophyly and Polyphyly  Taxa belonging to the same genus or famly (for nay higher category) should belong to a single lineage descending from a single recent ancestor that is, they should be monophyletic. This will reflect.  Monophyly o One class o Usually genes and older taxonomy degree o Named group shares an exclusive common ancestor  Primates (humans, great apes, old world monkeys, new world monkeys, lemurs)  Polyphyly and Paraphyly o “not natural” o Named group is not an exclusive set of closet relatives  Marine mammals (sea lions, sea otters, whales)

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