Phylogeny and Systematics

Phylogeny and Systematics

• Phylogeny represents the evolutionary history of a species or a group of related species.
• Systematics is a discipline that classifies organisms and determines their evolutionary relationships.
• Systematists utilize fossil, molecular, and genetic data to infer evolutionary relationships.

Evolutionary Relationships and Taxonomy

• Phylogenies illustrate evolutionary relationships among organisms.
• Taxonomy involves the ordered division and naming of organisms.

Binomial Nomenclature

• In the 18th century, Carolus Linnaeus introduced a system of taxonomy based on resemblances.
• Two key features of Linnaeus's system are still used today: two-part names for species and hierarchical classification.
• The two-part scientific name of a species is called a binomial.
• The first part of the binomial is the genus.
• The second part of the binomial, or specific epithet, is unique for each species within the genus.
• The first letter of the genus is capitalized, and the entire species name is italicized.
• Both parts together name the species, not the specific epithet alone.

Hierarchical Classification

• Linnaeus introduced a system for grouping species into increasingly broad categories.
• From broad to narrow, the taxonomic groups are: domain, kingdom, phylum, class, order, family, genus, and species.
• A taxonomic unit at any level of hierarchy is called a taxon.
• Broader taxa are not comparable between lineages.
• An order of snails has less genetic diversity than an order of mammals.

Linking Classification and Phylogeny

• Systematists demonstrate evolutionary relationships in branching phylogenetic trees.

PhyloCode

• Linnaean classification and phylogeny can differ from each other.
• Systematists proposed the PhyloCode, which recognizes only groups that include a common ancestor and all its descendants.

Phyogenetic Trees

• A phylogenetic tree represents a hypothesis about evolutionary relationships.
• Each branch point signifies the divergence of two species.
• Sister taxa are groups sharing an immediate common ancestor.
• A rooted tree includes a branch to represent the last common ancestor of all taxa.
• A basal taxon diverges early in the history of a group.
• A polytomy is a branch from which more than two groups emerge.
• Phylogenetic trees show patterns of descent, and not phenotypic similarity.
• Phylogenetic trees do not indicate when species evolved or the amount of change in a lineage.
• An assumption that a taxon evolved from the taxon next to it is wrong.

Inferring Phylogenies

• Systematists gather information about morphologies, genes, and biochemistry of living organisms to infer phylogenies.

Morphological and Molecular Homologies

• Homologies are phenotypic and genetic similarities due to shared ancestry.
• Organisms with similar morphologies or DNA sequences are likely to be more closely related compared to organisms with different structures or sequences.
• Systematists distinguish homology from analogy when constructing a phylogeny.
• Homology refers to similarity due to shared ancestry.
• Analogy refers to similarity due to convergent evolution.
• Convergent evolution occurs when similar environmental pressures and natural selection produce similar (analogous) adaptations.
• Systematists use computer programs and mathematical tools when analyzing comparable DNA segments.
• Mathematical tools help identify molecular homoplasies or coincidences.
• Molecular systematics uses DNA and other molecular data to determine evolutionary relationships.
• Once homologous characters have been identified, they can be used to infer a phylogeny.

Cladistics

• Cladistics groups organisms by common descent.
• A clade is a group of species that includes an ancestral species and all its descendants.
• Clades can be nested in larger clades.
• A valid clade is monophyletic, consisting of an 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 with different ancestors.
• An organism can have shared and different characteristics in comparison with its ancestor.
• A shared ancestral character originated in an ancestor of the taxon.
• A shared derived character is an evolutionary novelty unique to a particular clade.
• A character can be both ancestral and derived, depending on the context.
• It is useful to know in which clade a shared derived character first appeared when inferring evolutionary relationships.
• An outgroup is a related species or group of species to the ingroup being studied.
• The outgroup diverged before the ingroup.
• Systematists compare each ingroup species with the outgroup to differentiate between shared derived and shared ancestral characteristics.
• Characters shared by the outgroup and ingroup are ancestral characters that predate the divergence of both groups from a common ancestor.

Maximum Parsimony and Maximum Likelihood

• Systematists can never be sure of finding the best tree in a large data set.
• They narrow possibilities by applying the principles of maximum parsimony and maximum likelihood.
• Maximum parsimony assumes that the tree that requires the fewest evolutionary events is the most likely.
• Maximum likelihood states that a tree can be found that reflects the most likely sequence of evolutionary events, given certain rules about how DNA changes over time.

Evidence of Evolution

• Evidence of evolution is found in: biogeography, the fossil record, DNA/protein sequences, homology, and embryology.
• Homologous structures have underlying similarity arising from being derived from a common ancestral structure.
• Analogous structures have similarity from similar function rather than a common ancestor.
• Comparative embryology reveals anatomical homologies not visible in adult organisms.
• Vestigial structures are remnants of features that served important functions in an organisms ancestors.
• The fossil record depicts the extinction of species, the origin of new groups, and changes within groups over time.
• Fossils can document important transitions.
• Biogeography, the geographic distribution of species, provides evidence of evolution.
• Earth's continents were formerly united in a single large continent called Pangaea, but have since separated by continental drift.

Evolution of Population

• The smallest unit of evolution is a population.
• The evolutionary impact of natural selection becomes apparent in population changes over time, not in individual organisms.
• During a drought, finches with larger beaks were better able to crack and eat larger, harder seeds, surviving at a higher rate than those with smaller beaks.
• Population can be defined in its smallest scales as a microevolution that is a change in allele frequencies in a population over generations.
• Mechanisms that can alter allele frequencies in a population: natural selection (adaptation), genetic drift (chance events that alter allele frequencies), gene flow (the transfer of alleles between populations).
• Genetic variation makes evolution possible.
• Darwin proposed natural selection as the mechanism for evolutionary change.
• Individuals differ in inherited traits and that selection acts on such differences, leading to evolutionary change.
• Individuals within a species vary in characteristics.
• Phenotypic variations often reflect genetic variation, the differences among individuals in the composition of their genes or other DNA sequences.
• The genetic variation on which evolution depends originates when mutation, gene duplication, or other process produce new alleles and new genes.
• New alleles are formed in a series or steps starting with mutation that is a change in the nucleotide sequence of an organism's DNA.
• The gene pool consists of all copies of every type of allele at every locus in all members of a population.

Hardy-Weinberg Equation

• Hardy-Weinberg equation is often used as an initial test of whether evolution is occurring in a population.
• The equation also has medical applications, estimating the percentage of a population carrying the allele for an inherited disease.
• With random mating, a large population with frequencies p and q for two alleles at a locus, e.g. A and a, will attain in one generation the frequencies p², 2pq, and q² for the three genotypes formed, i.e., AA, Aa, aa, respectively.
• Assumptions for Hardy-Weinberg Law, there is no selection with equal rates of survival and equal reproductive success for all genotypes, no new alleles are created or converted from one allele into another by mutation, individuals do not migrate into or out of the population, the population is infinitely large to a point where sampling errors and other random effects are negligible and individuals in the population mate randomly.
• Frequencies of alleles in a gene pool do not change over time.
• Two alleles at a locus, A and a, are considered, after one generation of random mating, the frequencies of the genotypes AA:Aa:aa in the population can be calculated as p² + 2pq + q² = 1.
• p is the frequency of the "A" allele in the population and q is the frequency of the “a” allele in the population.
• The frequency of the homozygous genotype AA is represented by p², q² represents the the homozygous genotype aa and 2pq represents the heterozygous genotype Aa.
• The sum of the allele frequencies for all the alleles at the locus must be one, so p + q = 1.
• If the p and q allele frequencies are known, then the frequencies of the three genotypes may be calculated using the Hardy-Weinberg equation.
• Hardy-Weinberg Equilibrium is reached in a population that meets certain criteria, such in which the frequencies of p and q, two alleles at a given locus result in the predicted genotype frequencies.

Regulating Internal Environment

• Animals manage their internal environment by regulating or conforming to the external environment.
• A regulator uses internal control mechanisms to moderate internal change in the face of external, environmental fluctuation.
• A conformer allows its internal condition to vary with certain external changes.
• Animals may regulate some environmental variables while conforming to others.
• Organisms use homeostasis to maintain a "steady state" or internal balance regardless of external environment.
• Body temperature, blood pH, and glucose concentration are each maintained at a constant level in humans.
• Mechanisms of homeostasis moderate changes in the internal environment.
• For a given variable, fluctuations above or below a set point serve as a stimulus, that are detected by a sensor that trigger a response.
• The response returns the variable to the set point.
• The dynamic equilibrium of homeostasis is maintained by negative feedback, which helps to return a variable to a normal range.
• Most homeostatic control systems function by negative feedback.
• Positive feedback amplifies a stimulus and does not usually contribute to homeostasis in animals.