Evolution Final Exam

• Shared derived characteristics


  A characteristic that is derived from a common ancestor but is not present in all descendants
• Shared primitive characters

  are present in all species of a clade.
• Synapomorphy

  is a character that is shared by all members of a clade
• Sympleisiomorphy

  1. Has a broader group share a trait, indicating more than two groups or species.
  2. Shared traits among a larger, more diverse group
• Convergent character

  1. is a trait that arises independently in different groups due to similar environmental presence or functional requirement
  2. Not because of a common ancestor
• Monophyletic group

  1. Has a single common ancestor and all of its descendants
  2. Characterized by synapomorphy
• Paraphyletic group

  1. This is a common ancestor and some of its descendants.

  This is similar to sympleisiomorphy

  It excludes some descendants that has evolved significant changes
• Polyphyletic group 


  This is a group composed of organisms that do not share a common ancestor

  1. Due to convergent evolution
  2. Assembled due to convergent characters & traits
• Parallel and Convergent Evolution leads to what?

  Homoplasy
• What is homology? 


  It is similarity in structure, physiology, or development of different species of organisms.

  1. Due to Common Ancestor
• What is Homoplasy? 


  This is a similarity between organisms not due to a Common ancestor.

  1. Due to convergent evolution.
• What is congruence?

  When multiple sources of data (diff. genes, morphological traits) agree on the same evolutionary relationships or phylogeny

  1. Consistency
• What is Incongruence


  This is when different sources of data suggest different evolutionary relationships.

  1. It is inconsistent
  2. Needs reanalysis and reevaluation
• What is parsimony? 


  Aims to find the simplest explanation for evolutionary relationships. It is typically the one with the fewest evolutionary changes.
• Most parsimonious ancestral reconstruction

  1. This is like a family tree (phylogenetic tree).
  2. You need to find out what the oldest traits are.
  3. Then you have to find the simplest path that explains how things changed over time.
• How to perform the most parsimonious ancestral reconstruction?

  1. Start with observed traits across various species. (Physical and molecular traits)
  2. When data (traits) are collected, possible phylogenetic trees are built to show evolutionary relationships among species.
  3. Calculate the # of changes required to explain observed character data.
  4. The tree that requires the fewest changes is considered the most parsimonious.
• For example, what happens when one single evolutionary trait is present in both hypotheses of a phylogenetic tree?


  The character doesn't help distinguish between different phylogenetic hypotheses.
• The most parsimonious tree would have one change while the rest won't be parsimonious because?

  They have more than the least amount of evolutionary changes
• What is an outgroup method?

  When making a phylogenetic tree, you need a point of reference.

  1. Outgroup is like a cousin who isn't part of your immediate family.
  2. However, you still need a starting point to understand the direction of change.
• What is character polarity?

  The order in which different variants of a trait evolved over evolutionary time

  1. For example, it there is an outgroup and you were to guess the character polarity. You would start from the root and go up and follow the trend
• What is characters?


  Things that define you

  1. Eye color
  2. Hair type
• What is character states?

  Specific version of a character

  1. Eye is blue
  2. Eye is brown
• What is Morphological Characters

  Morphological characters are physical traits

  1. Shapes of leaves
  2. Size of bones
• What is molecular characters:

  DNA and proteins
• What is a DNA matrix

  It's basically like a giant spreadsheet where the rows are different species and columns are different traits.

  1. Keeps everything organized.
• Distance methods is what?

  You're just measuring the distance between DNA. Measuring how far apart different species are through genetic makeup.
• Multiple sequence Alignment


  A tool to identify evolutionary relationships and common patterns between genes.

  1. Usually, you need to align the sequences of three or more biological sequences such as protein, DNA, RNA
  2. Find the best way to line them up and identify similarities and differences
• Homologous Nucleotide and Amino acid sequence

  Basically, you find common ancestors in the family tree.

  1. When positions are significantly homologous, they share a common origin.
  2. Kind of like distant cousins who share a great-grandparent.
• Insertions mutation 


  Definition: You add pieces to a DNA sequence

  1. Can affect genetic information
• Deletion mutation: 


  Definition: Deleting pieces from DNA sequence.

  1. Can affect genetic information
• Progressive Alignment Methods: 


  This method aligns sequences step-by-step. You start with a basic alignment and keep adding sequences to see how they fit.
• UPGMA 


  Basically arranging family members by similar traits
• Neighbor-Joining 


  Connecting people based on who is closest.
• Why do people use UPGMA and Neighbor Joining Methods?

  A technique to create phylogenetic trees.
• Weighted Least Square Methods

  Definition: Giving more importance to certain data points to get a better estimate

  ** IF some information is more reliable = weigh it more heavily in calculations **
• Genetic Distances


  p distance: You just count how many spots are different between two DNA or protein sequences. It's the proportion of sites that don't match.

  d distance: When the same location may have changed more than once, so it adjusts the distance to reflect those repeated changes, giving a more accurate measurement.
• Transition Rate Matrix: 


  A chart that shows how often one letter in a DNA changes to another
• Jukes-Cantor Model 


  Definition: A simple way to understand DNA changes, considering each nucleotide has an equal chance of changing.

  1. This is a way to calculate the genetic distance
• Bootstrapping: 


  Definition: The way to test how reliable your phylogenetic tree is. You shuffle the data and create new trees to see if they come out the same.

  1. Kinda like re-running an experiment multiple times to confirm the results.
• Max. Likelihood 


  Definition: Looking for the most probable tree given the data.

  1. Guessing which scenario is most likely based on data.