week 1

Question 1

what is a phylogeny

Answer 1

• representation of the evolutionary relationships between different taxa
  -always hypothetical
  -sometimes phylogenies inferred using different methods or data types depict conflicting relationships
  -composed of tips, branches and nodes

Question 2

what are cladograms

Answer 2

a type of phylogeny with no branch lengths

Question 3

what do nodes represent

Answer 3

common ancestry

Question 4

what is a clade

Answer 4

• a monophyletic group formed by a common ancestor and all of its descendants
• they can be nested within eachother

Question 5

what is monophyly

Answer 5

• based of the taxa and the ancestor of those taxa having synapomorphies (shared derived features)
• all taxa in the monophyletic group share an ancestor
  -phylogenetic relationships are inferred through these shared characteristics

Question 6

what is paraphyly

Answer 6

• a grouping where a clade/lineage/taxon is excluded
• taxa in paraphyletic groups share a common ancestor but not all descendants of the ancestor are included in the paraphyletic group
• usually based on some autapomorphic difference

Question 7

what is polyphyly

Answer 7

• grouping not based on common ancestry
• not useful in evolutionary biology
  -usually grouped based on homoplasy (same trait evolved in different lineages independently: convergent evolution)

Question 8

how do we infer phylogenetic trees

Answer 8

comparing shared derived features among taxa (synapomorphies)

Question 9

what is synapomorphy

Answer 9

• synapomorphies help us reconstruct evolutionary relationships
• synapomorphic features are homologous (they come from common ancestry)

Question 10

what is homology

Answer 10

same evolutionary origin (though not necessarily still same function)

Question 11

what is autapomorphy

Answer 11

• autapomorphies are derived features only present in one taxon
• these are important for providing a ‘diagnosis’ of a species

Question 12

what is plesiomorphy

Answer 12

• plesiomorphies are shared ancestral features

Question 13

what is homoplasy

Answer 13

• the same derived trait independently evolved in different lineages
  or
• multiple independent reversals back to the ancestral (plesiomorphic trait)

Question 14

how to infer trees

Answer 14

• parsimony and bayesian approaches are the main ones
• parsimony is used to infer relationships based on the number of evolutionary changes
• the most parsimonious hypothesis of relationships is the one with the fewest number of steps
• bayesian approaches are probability-based
• we use character matrices to encode variation among tips (e.g. morphology, DNA bases, amino acids)

Question 15

what are crown groups

Answer 15

the last common ancestor of the living memebers of a clade and all its descendants
they include extant and extinct taxa

Question 16

what are stem groups

Answer 16

all the extinct taxa that are more closely related to the crown group than any other living taxa
they can only be extinct never extant

Question 17

what are exoskeletons

Answer 17

• outside the body
• most commonly mentioned for invertebrates e.g. beetle
• exoskeletal-like elements are found in vertebrates

Question 18

what are endoskeletons

Answer 18

• inside the body
• only found in vertebrates

Question 19

basic terms of anatomy

Answer 19

dorsal view - from above
posterior view - from behind
anterior view - from in front
ventral view - from underneath
lateral view - from the side

Question 20

what are the 3 basic skeletal structures in the vertebrate skull

Answer 20

chondrocranium
splanchnocranium
dermatocranium

Question 21

what is the chondrocranium

Answer 21

• envelops and protects the brain
• initially composed of cartilage in early
  development
• usually relegated inside the skull except for sharks
• secondary bone (forming neurocranium) replaces chondrocranium in most vertebrates, other than sharks, during development

Question 22

what is the splanchnocranium

Answer 22

• supporting structure of jaws
• initially composed of cartilage and bone, but cartilage replaced in most vertebrates
  -forms jaws and gills in fish and part of facial skeleton and ears in more derived vertebrates

Question 23

what is the dermatocranium

Answer 23

• skull surface, facial skeleton and operculum
• composed of bone
• not developed in sharks