University of Nizwa, Department of Biological Sciences & Chemistry
BIOL102, Lecture notes #4 by: Dr. Mustafa A. Mansi
The Phylogenetic Systematics
- Phylogeny?
- Systematics?
- Phylogenetic systematics? Connection between phylogeny and classification.
3- Phylogenetic systematics informs the construction of phylogenetic trees based on shared characters
3.1- Cladistics
3.1.1- Shared Primitive and Shared Derived Characters
3.1.2- Outgroups
3.2- Phylogenetic Trees and Timing
3.2.1- Phylograms
3.2.2- Ultrametric Trees
3.3- Maximum Parsimony and Maximum Likelihood
3.4- Phylogenetic Trees as Hypotheses
Cladogram: A diagram depicting patterns of shared characteristics among species (see Figure 25.11b on p. 499).
- If the shared characteristics are due to common ancestry (that is, if they are homologous), then the cladogram forms the basis of a phylogenetic tree.
- A phylogentic tree includes clades.
Clade: A group of species that includes an ancestral species and all its descendants.
Cladistics:
- Cladistics is the analysis of how species may be grouped into clades.
- Clades, like taxonomic ranks, can be nested within larger clades. For example, the cat family represents a clade within a larger clade that also includes the dog family
- Not all groupings of organisms qualify as clades.
A valid clade is monophyletic; it consists of the ancestor species and all its descendants ( Figure 25.10a).
Monophyletic: Pertaining to a grouping of species consisting of an ancestral species and all its descendants; a clade.
- If we lack information about some members of a clade the results would be paraphyletic or polyphyleic groupings of species.
Paraphyletic: Pertaining to a grouping of species that consists of an ancestral species and some, but not all, of its descendants. ( Figure 25.10b).
Polyphyletic: Pertaining to a grouping of species derived from two or more different ancestral forms. (grouping of several species that lack a common ancestor, Figure 25.10c)
Shared Primitive and Shared Derived Characters
- First, separation of homologous from analogous similarities.
(The characters that are relevant to phylogeny are the homologous ones)
- Second, sorting through the homologies to distinguish between shared primitive and shared derived characters.
Shared primitive character
- A character displayed in species outside a particular taxon.
(In other words it is a character that is shared beyond the taxon we are trying to define)
- EXAMPLE: The character of backbone in mammals is a shared primitive character; all mammals share the homologous character of a backbone. But a backbone is also found in nonmammalian vertebrates such as fishes and reptiles; that means the presence of a backbone does not distinguish mammals from other vertebrates.
- The backbone is a homologous structure that predates the branching of the mammalian clade from the other vertebrates; it is a shared primitive character.
Shared derived character:
- The shared derived character is an evolutionary novelty that evolved within a particular clade.
(In other words it is an evolutionary novelty unique to a particular clade)
- EXAMPLE: the hair, a character shared by all mammals but not found in nonmammalian vertebrates,
( hair is an evolutionary novelty unique to a particular clade—in this case, the mammalian clade)
Note that:
- The backbone is a shared derived character in all vertebrates (i.e. at a deeper branch point that distinguishes all vertebrates from other animals)
- The backbone is a shared primitive character Among vertebrates because it evolved in the ancestor common to all vertebrates.
Outgroups
- How Systematists differentiate between shared derived characters and shared primitive characters? (using outgroup comparison)
Ingroup: In a cladistic study of evolutionary relationships among taxa of organisms, the group of taxa that is actually being analyzed.
Outgroup: A species or group of species that is closely related to the group of species being studied, but clearly not as closely related as any study–group members are to each other.
Example (Figure 25.11a and Figure 25.11b):
-The ingroup:are five vertebrates—a leopard, turtle, salamander, tuna, and lamprey (a jawless aquatic vertebrate).
- The outgroup: is a lancelet, a small animal that lives in mudflats and (like vertebrates) is a member of the phylum Chordata, but does not have a backbone.
- Outgroup comparison is based on the assumption that homologies present in both the outgroup and ingroup must be primitive characters that predate the divergence of both groups from a common ancestor.
-The notochord, a flexible rod running the length of the animal, is one homologous structure present in both the outgroup and ingroup.
- The species making up the ingroup display a mixture of shared primitive and shared derived characters.
- The outgroup comparison enables us to focus on just those characters that were derived at the various branch points of vertebrate evolution.
Phylogenetic Trees and Timing
- Any chronology represented by the branching pattern of a phylogenetic tree is relative (earlier versus later) rather than absolute (so many millions of years ago).
- Phylograms present information about the sequence of events relative to one another.
- Ultrametric trees present information about the actual time that given events occurred.
Phylograms:
- In a phylogram, the length of a branch reflects the number of changes that have taken place in a particular DNA sequence in that lineage ( Figure 25.12).
- The total length of the vertical lines leading to the mouse is less than that of the line leading to the fruit fly Drosophila. This implies that more genetic changes have occurred in the Drosophila lineage than in the bird and mammal lineages since they diverged.
- The varying lengths of the branches indicate that the gene has evolved at slightly different rates in the different lineages.
Ultrametric Trees
- ( Figure 25.13).
-All the different lineages that descend from a common ancestor have survived for the same number of years.
- Ultrametric trees do not contain the information about different evolutionary rates that can be found in Phylograms.
- Ultrametric trees can draw on data from the fossil record to place certain branch points in the context of geologic time.
(In other words, ultrametric tree is a phylogenetic tree in which the lengths of the branches reflect measurements of geologic time)
Maximum Parsimony and Maximum Likelihood
- Growing the difficulty of building the phylogenetic tree that best describes evolutionary history.
- What if you are analyzing data for 50 species? There are 3 × 1076 different ways to arrange 50 species into a tree!
- Which tree in this huge forest of evolutionary trees reflects the true phylogeny?
- We can never be sure of finding the single best tree in such a large data set.
- We can narrow the possibilities “of finding the single best tree” by applying the principles of maximum parsimony and maximum likelihood.
Maximum parsimony
- Maximum parsimony is a principle that states that when considering multiple explanations for an observation, one should first investigate the simplest explanation that is consistent with the facts.
- (It is a minimalist problem–solving approach of “shaving away” unnecessary complications.)
- For phylogenetic trees based on morphological characters, the most parsimonious tree is the one that requires the fewest evolutionary events to have occurred in the form of shared derived characters.
- For phylograms based on DNA sequences, the most parsimonious tree requires the fewest base changes.
Maximum Likelihood
- Maximum likelihood: is a principle that states that when considering multiple phylogenetic hypotheses, one should take into account the one that reflects the most likely sequence of evolutionary events, given certain rules about how DNA changes over time.
- (In other words: given certain rules about how DNA changes over time, which tree reflects the most likely sequence of evolutionary events?)
- Figure 25.14 shows two possible, equally parsimonious trees for the phylogenetic relationships between a human, a mushroom, and a tulip.
- In tree 1, the human is more closely related to the mushroom, whereas in tree 2, the human is more closely related to the tulip.
- Assuming that equal rates “of DNA changes have occurred along all the branches of the tree from the common ancestor” are more common than unequal rates, tree 1 is more likely.
Figure 25.15 walks you through the process of identifying the most parsimonious molecular tree for a four–species problem.
Phylogenetic Trees as Hypotheses
- Any phylogenetic tree represents a hypothesis about how the various organisms in the tree are related to one another.
- The best hypothesis is the one that best fits all the available data.
- Many older phylogenetic hypotheses have been changed or rejected since the introduction of molecular methods for comparing species and tracing phylogenies.
- In the absence of conflicting information, the most parsimonious tree is also the most likely.
- Nature does not always take the simplest course, see Figure 25.16.
- Sometimes, based on compelling evidences, the best hypothesis is not the most parsimonious one.
- Perhaps the particular morphological or molecular character we are using to sort taxa actually did evolve multiple times.
- Example: both birds and mammals have hearts with four chambers, whereas lizards, snakes, turtles, and crocodiles have hearts with three chambers.
- The parsimonious assumption would be that the four–chambered heart evolved once and was present in an ancestor common to birds and mammals but not to lizards, snakes, turtles, and crocodiles.
- However, abundant evidence indicates that birds are more closely related to lizards, snakes, turtles, and crocodiles than they are to mammals.
- The four–chambered heart appears to have evolved independently in birds and mammals (the four–chambered hearts of birds and mammals develop differently)
- Parsimony and the analogy–versus–homology problem.
- The problem is not with the principle of parsimony. It is with the analogy–homology issue.
(The four–chambered hearts of birds and mammals turn out to be analogous, not homologous)
- Misjudging an analogous similarity in morphology as a shared derived (homologous) character is less likely to distort a phylogenetic tree if each clade in the tree is defined by several derived characters
- Applying parsimony in molecular systematics is more reliable for a data set of many long DNA sequences than for a smaller data set.
- The strongest phylogenetic hypotheses are those supported by multiple lines of molecular and morphological evidence as well as by fossil evidence.
4- Much of an organism′s evolutionary history is documented in its genome
- Molecular systematics—comparing nucleic acids or other molecules to infer relatedness—is a valuable tool for tracing organisms′ evolutionary history.
- Molecular systematics helps us uncover evolutionary relationships between groups that have little common ground for morphological or anatomical comparison, such as mammals and bacteria.
- Molecular systematics enables scientists to compare genetic divergence within a species.
- The ability of molecular trees to encompass (include) both short and long periods of time is based on the fact that different genes evolve at different rates, even in the same evolutionary lineage.
- For example, the DNA that codes for ribosomal RNA (rRNA) changes relatively slowly, so comparisons of DNA sequences in these genes are useful for investigating relationships between taxa that diverged hundreds of millions of years ago.
- Studies of rRNA sequences, for example, indicate that fungi are more closely related to animals than to green plants (see Figure 25.2).
- In contrast, the DNA in mitochondria (mtDNA) evolves relatively rapidly and can be used to explore recent evolutionary events.
- One research team has traced the relationships among Native American groups through their mtDNA sequences. The molecular findings corroborate other evidence that the Pima of Arizona, the Maya of Mexico, and the Yanomami of Venezuela are closely related, probably descending from the first of three waves of immigrants that crossed the Bering Land Bridge from Asia to the Americas about 13,000 years ago.
Gene Duplications and Gene Families
- Gene duplication is a mutation that increases the number of genes in the genome, providing opportunities for further evolutionary changes.
- The molecular phylogenies of gene duplications must account for repeated duplications that have resulted in gene families, which are groups of related genes within an organism′s genome (see Figure 19.17).
- Like homologous genes in different species, these duplicated genes have a common ancestor.
- We distinguish these types of homologous genes by different names: orthologous genes and paralogous genes.
- Orthologous genes refer to homologous genes that are passed in a straight line from one generation to the next but have ended up in different gene pools because of speciation (Figure 25.17a).
- Orthologous genes can only diverge after speciation has taken place, with the result that the genes are found in separate gene pools.
- For example, the β hemoglobin genes in humans and in mice are orthologous.
(Humans and mice each have one functioning β hemoglobin gene. These genes serve similar functions, but their sequences have diverged since the time that humans and mice had a common ancestor.)
- Paralogous genes result from gene duplication, so they are found in more than one copy in the same genome (Figure 25.17b).
- Paralogous genes can diverge even while they are in the same gene pool, because they are present in more than one copy in the genome.
- For example, the olfactory receptor genes, which have undergone many gene duplications in vertebrate animals.
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