Phylogeny and Systematics Chapter 25 Phylogeny and Systematics

Overview: Investigating the Tree of Life Phylogeny - the evolutionary history of a species or group of related species Systematics - an analytical approach to understanding the diversity and relationships of organisms (current and extinct) uses morphological, biochemical, and molecular comparisons to infer evolutionary relationships

Concept 25.1: Phylogenies are based on common ancestries inferred from fossil, morphological, and molecular evidence To infer phylogenies, systematists gather information about morphologies, development, and biochemistry of living organisms They also examine fossils to help establish past relationships between living organisms

LE 25-4 Leaf fossil, about 40 million years ago Petrified trees in Arizona, about 190 million years old Insects preserved whole in amber Dinosaur bones being excavated from sandstone Casts of ammonites, about 375 million years old Boy standing in a 150-million-year-old dinosaur track in Colorado Tusks of a 23,000-year-old mammoth, frozen whole in Siberian ice

Morphological and Molecular Homologies More similar = more recent common ancestor Need to distinguish whether a similarity is the result of homology or analogy ( due to convergent evolution)

Sorting Homology from Analogy In constructing a phylogeny, systematists need to distinguish whether a similarity is the result of homology or analogy Homology is similarity due to shared ancestry Analogy is similarity due to convergent evolution

Evaluating Molecular Homologies Systematists use computer programs and mathematical tools when analyzing comparable DNA segments from different organisms

LE 25-6 Computer programs and mathematical tools are used when analyzing DNA segments from different organisms 1 2 Deletion 1 2 Insertion 1 2 1 2

Concept 25.2: Connecting classification with evolution Taxonomy is the division of biology that sorts organisms into categories based on similarities and differences Phylogenetic trees - depict evolutionary relationships though branches Each branch point represents the divergence of two species “Deeper” branch points represent progressively greater amounts of divergence

LE 25-9 Panthera pardus (leopard) Mephitis mephitis (striped skunk) Lutra lutra (European otter) Canis familiaris (domestic dog) Canis lupus (wolf) Species Genus Panthera Mephitis Lutra Canis Family Felidae Mustelidae Canidae Order Carnivora

Concept 25.3: Creating Phylogenetic Trees Cladistics studies resemblances among clades Clade is a group of species that includes an ancestral species and all its descendants – 3 types: Monophyletic, paraphyletic, polyphyletic Cladogram depicts patterns of shared characteristics among taxa, shows RELATIVE times of change

A valid clade is monophyletic signifying that it consists of the ancestor species and all its descendants

A paraphyletic grouping consists of an ancestral species and some, but not all, of the descendants

A polyphyletic grouping consists of various species that lack a common ancestor

How the clades are determined: A shared primitive character is a character that is shared beyond the taxon we are trying to define A shared derived character is an evolutionary novelty unique to a particular clade

Outgroups An outgroup is a (monophyletic) group of organisms that serves as a reference group to determine the evolutionary relationship between three or more monophyletic groups of organisms. Conclusion is that the outgroup branched from the parent group before the other two groups branched from each other. Assumes that shared homologies must be primitive characters that predate the divergence of both groups from a common ancestor helps focus on characters derived at various branch points in the evolution of a clade

LE 25-11 TAXA (outgroup) Salamander Lancelet Lamprey Leopard Turtle Tuna Turtle Hair Amniotic (shelled) egg CHARACTERS Four walking legs Hinged jaws Vertebral column (backbone) Character table Leopard Turtle Hair Salamander Amniotic egg Tuna Four walking legs Lamprey Hinged jaws Lancelet (outgroup) Vertebral column Cladogram

Phylograms In a phylogram, the length of a branch reflects the number of genetic changes that have taken place in a particular DNA or RNA sequence in that lineage

Ultrametric Trees Branching in an ultrametric tree is the same as in a phylogram, but all branches traceable from the common ancestor to the present are equal length

Maximum Parsimony and Maximum Likelihood Systematists can never be sure of finding the best tree in a large data set The most parsimonious tree requires the fewest evolutionary events to have occurred in the form of shared derived characters (novelties) The principle of maximum likelihood uses the rules regarding DNA change over time to reflect the most likely sequence of evolutionary events

LE 25-14 Human Mushroom Tulip Human 30% 40% Mushroom 40% Tulip 30% 40% Mushroom 40% Tulip Percentage differences between sequences 25% 15% 15% 20% 15% 10% 5% 5% Tree 1: More likely Tree 2: Less likely Comparison of possible trees

Molecular Changes The most efficient way to study hypotheses is to consider the most parsimonious hypothesis, the one requiring the fewest molecular changes

Phylogenetic Trees as Hypotheses The best hypotheses for phylogenetic trees fit the most data: morphological, molecular, and fossil Sometimes the best hypothesis is not the most parsimonious

Concept 25.4: Much of an organism’s evolutionary history is documented in its genome Comparing nucleic acids or other molecules to infer relatedness is a valuable tool for tracing organisms’ evolutionary history Studies include: Gene Duplications and Gene Families Orthologous genes Paralopgous genes

Gene Duplications and Gene Families Gene duplication increases the number of genes in the genome, providing more opportunities for evolutionary changes

Genes found in a single copy in the genome LE 25-17a Orthologous Genes Genes found in a single copy in the genome They can diverge only after speciation occurs Ancestral gene Speciation Orthologous genes

Genome Evolution Orthologous genes are widespread and extend across many widely varied species The widespread consistency in total gene number in organisms indicates genes in complex organisms are very versatile and that each gene can perform many functions

Paralogous genes result from gene duplication, so are found in more than one copy in the genome They can diverge within the clade that carries them, often adding new functions Ancestral gene Gene duplication Paralogous genes

Molecular Clocks – have to extend what we know to fill in gaps Provides a way to measure absolute time of evolutionary change based on the observation that some genes and other regions of genomes seem to evolve at constant rates

Neutral Theory States that a lot of evolutionary change in genes and proteins has no effect on fitness, therefore is not influenced by Darwinian selection It states that the rate of molecular change in these genes and proteins should be regular like a clock

However….. The molecular clock does not run as smoothly as neutral theory predicts Irregularities DO result from natural selection in which some DNA changes are favored over others Estimates of evolutionary divergences older than the fossil record have a high degree of uncertainty

Applying a Molecular Clock: The Origin of HIV Phylogenetic analysis shows that HIV is descended from viruses that infect chimpanzees and other primates Comparison of HIV samples throughout the epidemic shows that the virus evolved in a very clocklike way