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Classification and Systematics

• Classification is a system of grouping species into a hierarchical structure.
• Groups are nested within larger groups.
• A Taxon is a group of organisms assigned to any level of the Linnean system.
• Taxonomy involves the naming of Taxa.
• Nomenclature includes the rules used when naming taxa.

Evolution Concepts

• Evolution represents change over time, occurring in populations over generations.
• Central ideas of evolution include: life having a history, change over time, and shared common ancestors among different species.
• A phylogenetic tree is a hypothesis of the evolution of taxa.
• Phylogenetic trees support biological classification.
• Tips are the things that are observed, typically where names are assigned on a phylogenetic tree.
• Anagenesis involves changes occurring within a species.
• Cladogenesis is the branching of a lineage into two or more descendant lineages
• Cladogenesis needs to include a split
• Cladogenesis is the branching of evolutionary lineages, while anagenesis is gradual change within a lineage.
• Cladograms represents topology
• A cladogram depicts relationships
• The axis of a cladogram has no meaning
• A cladogram uses lines that branch off in different directions.
• A cladogram represents a group of organisms with a last common ancestor, that ends at a clade.
• Model-based/additive trees show changes between common ancestor organisms.
• Branch length indicates evolutionary distance.
• On a cladogram the y axis means something
• Branches from node to tip have different lengths.
• Branch lengths represent time change
• Short branch lengths indicate the organisms are very similar
• A scale bar indicates distance in the time/amount of change
• Branch length indicates time of divergence in a dated tree.
• Polytomy is when information on who are sisters & unrelated is unknown/partially resolved- cannot tell who is separated from each other.
• Polyphyly is when independent multiple ancestors from different lineages.
• Monophyly includes clades that has all descendants that share the most recent common ancestor
• Paraphyly does not include all descendants that share a most recent common ancestor, but does include ones that share certain traits.
• Homology is when a trait is present in an ancestor and its descendants.
• Homoplasy is when similarities arise via independent evolution.

Building Trees

• A homologue is the same organ in different animals under every variety of form and function
• Taxic homology focuses on the similarity of physical structures or traits across different species.
• Molecular homology examines the similarity of molecules; in particular, DNA and protein sequences.
• Sequence alignment is needed
• Insert gaps to get the same size in alignment
• Molecular data that can be aligned includes DNA, RNA, and proteins/amino acids.
• Morphology involves studying the organism.
• Molecules uses the same gene to get the same sequence alignment
• OTUs (Operational Taxonomical Units) are terminals
• HTUs (Hypothetical Taxonomical Units) are nodes and speciation events.
• Hard polytomy involves simultaneous divergence
• Soft polytomy represents uncertainty of when divergence occurred.
• Parsimony only gives one cladogram.
  • The simplest explanation is that the best hypotheses are that is requires the fewest evolutionary changes
  • Uses the lowest number of changes because less explanation is needed
• Maximum likelihood is the best probability of being true to evolution.
• Bayesian needs to finds a tree with higher exterior probability made by evolution

Additional probabilities

• Pr (Data | Tree ) represents Likelihood
• Likelihood is calculated as before, but integrating the prior probability of all parameters
• Pr ( Tree) is the probability that our tree is the correct among all trees.
• Pr ( Data ) is summation of over all trees.

Molecular Data: Homology

• Orthology: copies of the same gene across different animals.
• Paralogy: copies that exist within the same organisms/ different families.
• Paralogy can give incorrect phylogeny.

Molecular Evolution

• Sequence evolution represents changes in the nucleotides / amino acids at a particular position in that sequence.
• Substitution involves one base change into a different base at the same position.
• Insertion means one base appeared in the sequence without a locally homologous position
• Deletion is when one base disappeared in the sequence.

Multiple Sequence Alignment

• Progressive alignment calculates distance from sequences that decreases distance by making trees and new alignments.
• Iterative alignment subdivides alignments based on distance, then calculates the distance between subgroups, and then you merge and repeat until there is a good tree.
• Transition involves A-G and C-T
• Transversions include A-C, A-T, G-c, and G-T

Population Genetics

• Microevolution involves small-scale changes within a population or species over relatively short periods.
• Microevolution includes changes in allele frequencies, adaptation to local environments, and the emergence of new traits.
• Macroevolution involves large-scale evolutionary change over long periods.
• Macroevolution occurs leading to the formation of new species, genera, or higher taxonomic groups.
• Species, extinction, and life diversity are encompassed by macroevolution
• Microevolution = anagenesis because it represents gradual changes within a single lineage over time, driven by the same microevolutionary processes that affect population
• Macroevolution = cladogenesis
• Cladogenesis, or branching evolution, is a fundamental mechanism driving macroevolutionary patterns and processes
• Cladogenesis is the process where one ancestral species splits into two or more descendant species, which leads to increased biodiversity and the creation of new lineages on the tree of life.
• Population genetics is the study of the distribution of alleles in populations and causes of allele frequency changes.
• Evolution is seen as a change in allele frequencies across generations.
• Allele frequencies are the proportion of gene copies in a population that are a given allele.
• Gene pool is the totality of genes of a population
• Genotype freq: Number of AA, Aa, aa/ total number of organism
• Allele freq: number of A or a / totl number of genotpes
• P = freq of dominant allele (one letter)
• Q = freq of recessive allele (one letter)
• P2 = freq of homozygous genotype (AA)
• Q2 = freq of homozygous recessive genotype (aa)
• Frequency of an allele (one letter) = square root

Microevolutionary mechanisms

• Natural selection: environment puts pressure on certain alleles and removes genetic variation.
• Selection happens when individuals with different genotypes survive or make gametes at different rates.
• Mutation: increases genetic variation VERY SLOWLY in a population
• Mutation occurs when mistakes during meiosis turn copies of one allele into copies of another, by substitution in nucleotides.
• Migration: increases genetic variation VERY FAST in a population .
• Migration occurs when individuals move into or out of the population.
• Drift involves random events that remove genetic variation.
• Drift is FASTER than natural selection
• Drift occurs when blind chance allows gametes with some genotypes to participate in more fertilizations than gametes with other genotypes
• In Hardy-Weinberg equilibrium (HWE) allele frequencies do not change
• HWE has no mutation, gene flow, natural selection, as well as random mating, infinite size population, which represents essentially no evolution.
• Evolution results from chance events (survival, reproduction, inheritance)
• Chance plays a key role in evolution for example meiosis
• Random fluctuations in allele frequencies are larger in smaller populations
• Genetic variation is caused to be lost
• Populations that are initially identical to become different are caused.
• An allele can become fixed without natural selection
• Gene trees helps reconstruct the evolutionary history of genes
• Coalescence happens when lineages of two gene copies merge.
• The bottleneck effect is when a population is reduced to a small size for a small number of generations.

Founder effects

• A new population is started from a small number of individuals.
• Specific genes are carried into a new population.
• The Zera finch in the lesser sundas islands was founded by 9 individuals.
• Gene flow is the exchange of genes between two populations, which mixes of alleles with different populations.
• Two roles of gene flow are that it equalizes allele frequencies and introduces new alleles into a population.
• Gene flow results from dispersal by movement of individuals and gametes (migration).

Mutations

• Central dogma
  • DNA replicates by DNA → DNA
  • DNA transcribes by DNA RNA
  • RNA translates by RNA PROTEIN
• Genes expression regulation
• Genes are not expressed all the time or in the same cells
• Splicing involves Removal of introns
• Alternative splicing removes exons too
• Exon shuffling is the interchange of the exon position at the mRNA strand
• Genetic mixing results from genetic recombination, a process that combines in a gamete a gene copy at one locus from the maternal lineage.
• The copy is combined with a gene copy at a second locus inherited from the paternal lineage
• Recombination rate (r) is the probability that recombination occurs between a given pair of loci.
• When an allele at one locus is found together in a population more often than expected by chance with an allele at a second locus, we say these loci are in linkage disequilibrium.
• Meiosis happens during diplonema and crossing over
• Mutations are the ultimate source of variation
• Point mutations involve changes in single nucleotides
• Structural mutations – insertion of nucleotides
• JC69 (Jukes and Cantor 1969) assumes every nucleotide has the same rate of changing into another nucleotide.
• K80 (Kimura 1980) accounts for different rates for transitions and transversions.
• HKY85 (Hasegawa et al. 1985) involves unequal base compositions and asymmetrical substitution rates
• GTR (General reversible model) claims each possible substitutions has its own probability
• Synonymous mutation is change in nucleotide from original but codes for the sam amino acid
• Nonsynonymous mutation is change in nucleotides codes for a different amino acid
• Nonsense mutation uses 3 stop codons
• Darwinian selection can be positive or negative/purifying
• Mutation is favored with > 1 because it is positive or Darwinian selection
• Mutation is not favored with <1 because it is negative or Purifying selection
• Mutation involves the use of ~1 or =1 Neutral Evolution because Mutations are no a results of selection
• Can calculate this ratio on "phylogenetic branches” or at specific sites
• Evolving faster = positive selection
• Evolving slowly = negative selection
• Evolving neutral = neutral

Chromosomic structural mutations

• Deletion involves removal of parts of chromosome
• Duplication is when part of the chromosome is duplicated
• Inversion – rearranged chromosome
• Fission involves splitting chromosomes
• Fusion is when chromosomes join together

Genetic effects

• Genetic effects are unrelated to mutations
• Epistasis happens when the effect on one allele at one locus depends on the allele at a second locus.
• Linkage disequilibrium can exist between these alleles if there are under the pressure of Natural selection.
• Epigenetic inheritance affects organisms by altering how genes are expressed, but not their sequences.
• Maternal effects occur when the genotype or phenotype of the mother directly influences the phenotype or genotype of the offspring
• Mutation rates is the probability that an offspring carries a new mutation, that is represented by the letter μ
• Smaller organisms = more mutations
• The environment puts pressure on organisms which is natural selection
• Adaptation enhances the survival or reproduction of organisms that bear it and evolves under natural selection.
• Adaptation has no goal.
• Natural selection interacts with mutation.
• Genetic drift interacts with mutation.
• Natural selection does not cause evolution.
• Positive selection causes the allele with higher fitness to increase in frequency.