Lecture 2: Phylogeny & the Tree of Life

Question 1

How do biologists distinguish and categorize the millions of species on Earth?

Answer 1

• Genetic Sequences
• Morphology

Question 2

Phylogeny Def

Answer 2

• Examine the evolutionary history of a species or group of species
• serve as hypothesis

Question 3

Systematics Def

Answer 3

• Discipline focused on classifying organisms and determining evolutionary relationships

Question 4

Common Ancestry def

Answer 4

Organisms share many characteristics

Question 5

Taxonomy def

Answer 5

The study of naming & classifying organisms

Question 6

Who developed the classification scheme we use today?

Answer 6

Carolus Linnaeus

Question 7

How to properly format a scientific name?

Answer 7

First part= Genus (capitilized)
Second part= species (lowercase)

Written => underline
type =>italized

Question 8

Levels of Hierarchical Classification

Answer 8

Dear => Domain Broadest
King => Kingdom
Philip => Phylum
Came => Class
Over => Order
For => Family
Grape => Genus
Soda => Species Most specific

Question 9

Taxon def

Answer 9

named taxonomic unit at any level of the hierarchy

Question 10

How did taxonomists determine how “different” organisms are from each other?

Answer 10

Genetics, evolution, biological species, etc.

Question 11

Phylogenetic tree def

Answer 11

Branching pattern often matches how taxonomists have classified groups of organism nested within more inclusive groups

• Represents a Hypothesis about evolutionary relationships

Question 12

Sister Taxa def

Answer 12

Share immediate common ancestor

Question 13

Basal Taxa def

Answer 13

Diverges early in history of group
- originate common ancestor of all groups

Question 14

Polytomy def

Answer 14

More than 2 descendant groups emerge

Question 15

What we learn from Phylogenetic Trees?

Answer 15

• They show patterns of descent, NOT phenotypic similarity
• Sequence of branching in a tree does not necessarily indicate actual AGES of the particular species

IF AGES => MOLECULAR CLOCK

• We shouldn’t assume that a taxon on a phylogenetic tree evolved from the taxon next to it

Question 16

What happens during long branch lengths?

Answer 16

more genetic differences/ changes

Question 17

Divergence dates/time

Answer 17

impose molecular clock

Question 18

Application of Phylogenetics

Answer 18

• Examine evolutionary relationships
• Medical applications
• Forensics
• Infer species identities

Question 19

What types of data can be used to infer/ build phylogenies?

Answer 19

• Morphological characters
• DNA sequences
• Microsatellites (repeats)
• Mobile elements

Question 20

Homologous Characters

Answer 20

Phenotypic & genetic similarities due to shared ancestry

Question 21

Result of Homologous Characters

Answer 21

Environmental Pressure

Question 22

Analogous Characters

Answer 22

Similarities due to Convergent evolution

convergent= not share common ancestor

Question 23

Result of Analogous Characters

Answer 23

Similar environmental pressure and natural selection produce similar adaptations in organisms from different evolutionary lineages

Question 24

Could different datasets result in different phylogenies?

Answer 24

Morphology- physical characteristics

Question 25

Homologous vs Analogous Characters

Answer 25

Corroborative similarities - number and intensity of similarities increases the more closely related two species are

Question 26

Cladistics def

Answer 26

an approach in systematics in which organisms are placed into groups based primarily on common descent

Question 27

Clades def

Answer 27

Monophyletic Group - Biologists attempt to place species into groups

Question 28

Monophyletic Group def

Answer 28

consists of an ancestral species and ALL of its descendants

Question 29

Paraphyletic Group def

Answer 29

consists of an ancestral species and SOME, but NOT all, of its descendants

Question 30

Polyphyletic Group def

Answer 30

includes distantly related species but DOES NOT include their most recent common ancestor

Question 31

Maximum Parsimony def

Answer 31

SIMPLEST explanation that is consistent w/ facts

Question 32

Maximum Likelihood def

Answer 32

Tree most likely to have produced a given set of data, based on PROBABILITY RULES

Question 33

Max Likelihood vs Max Parsimony

Answer 33

Max Parsimony-> Recovers the most parsimonious tree, require fewest evolutionary events BAYESIAN Max Likelihood-> - Simple: all nucleotide substitutions are equally likely - Complex: accounts for different rates of change

Question 34

Molecular Clock def

Answer 34

An approach based on observation that some genes and other regions of genomes appear to evolve at CONSTANT RATES

Question 35

What two Domains are closely related to each other?

Answer 35

Eukaryotes and Archaea

Question 36

Horizontal gene transfer def

Answer 36

process which genes are transferred from one genome to another

Question 37

What makes it difficult to resolve relationships at higher taxonomic levels in the tree of life?

Answer 37

Two factors - Events are closely spaced in time, so phylogenetic species are often small which lead short internal tree branches to resolve -If species are ancient, branches tend to be long with multiple substitutions occuring at a same position.