Evolution - 5.4 Cladistics

Question 1

what is a clade (understanding)

Answer 1

A clade is a group of organisms that have evolved from a common ancestor

• each clade consists of an ancestral organism and ALL of its evolutionary descendants
• most members of a clade will posses common characteristics (due to their shared evolutionary lineage)

Question 2

What is a Cladograms (understanding)

Answer 2

Cladograms are tree diagrams that show the most probable sequence of divergence in clades

Question 3

Evidence for a clade/species (understanding)

Answer 3

Evidence for which species are part of a clade can be obtained from the base sequence of a gene or the corresponding amino acid sequence of a protein

• also includes biomolecules (eg DNA/RNA/protein/cytochromes)
• also includes structural characteristics (eg wings, egg laying)

Question 4

differences in species and divergence (understanding)

Answer 4

Sequence differences accumulate gradually so there is a positive correlation between the number of differences between two species and the time since they diverged from a common ancestor

Question 5

traits throughout species (changes in them) (understanding)

Answer 5

Traits can be analogous or homologous
Evidence from cladistics has shown that classification of some groups based on structure did not correspond with the evolutionary origins of a group or species

Question 6

cladistics definition

Answer 6

it is a new branch of taxonomy that classifies organisms in terms of their place in the evolutionary tree based on chated characteristic with a common ancestor

Question 7

what organism will have the DNA most SIMILAR to a bird (question from page 24)

Answer 7

= crocodiles because they are very close (= THE DIVERGE AT THE CLOSEST POINT) and have many similar characteristics

Question 8

what organism will have the DNA most DIFFERENT to a bird (question from page 24)

Answer 8

= sharks because they are very close (= THE DIVERGE AT THE FUREREST POINT) and do not have many similar characteristics

Question 9

main groups of primates

Answer 9

1. prosimians
2. New world monkeys
3. old world monkeys
4. hominoids
   1) apes
   2) hominids

Question 10

examples of hominoids (primate species make closely related to humans)

Answer 10

1) apes
eg. chimpanzees, gorillas, orangutans, gibbons
2) hominids
eg. humans, neanderthal, Australopithecus

Question 11

relation between number of differences between 2 species and time

Answer 11

sequence differences accumulate gradually so there is a positive correlation between the number of differences between two species and the time since they diverged from a common ancestor

Question 12

Phylogeny

==> information from this can be used to construct a phylogenetic tree (or clades) based on the genetic difference (%) between different species

Answer 12

” can be described as the relationship between all the organisms on Earth that have descended from a common ancestor, whether they are extinct or extant.”

= it has added to cladistics by using genetic analysis of the genomes to determine the genetic difference between species

Question 13

significance of Mitochondrial (DNA (mt DNA)) in determining the genetic distance/difference of species

Answer 13

mitochondrial DNA (aka the Y chromosome DNA) can be used to determine the genetic distance between species

= as: all cells in our body began from the egg cell, then the mitochondrial DNA in our cells came from our MOTHER, our GRANDMOTHER etc - ie its passed down throughout the maternal ancestral line

• the mitochondrial DNA is not affected by the sperm = it mutates at a constant rate

Question 14

Mitochondrial (DNA (mt DNA)) is not in bacteria and viruses so for evidence we use:

Answer 14

their main DNA strand

Question 15

details on Cladograms (NODES)

Answer 15

Nodes – Each node corresponds to a hypothetical common ancestor that speciated to give rise to two (or more) daughter taxa

Question 16

details on cladograms (ROOT)

Answer 16

Root – The initial ancestor common to all organisms within the cladogram (incoming line shows it originates from a larger clade)

Question 17

details on cladograms (OUTGROUP)

Answer 17

Outgroup – The most distantly related species in the cladogram which functions as a point of comparison and reference group

Question 18

details on cladograms (CLADES)

Answer 18

Clades – A common ancestor and all of its descendants (i.e. a node and all of its connected branches)

Question 19

steps to constructing a cladogram (Using Structural Evidence)

Answer 19

https://ib.bioninja.com.au/standard-level/topic-5-evolution-and-biodi/54-cladistics/cladograms.html

1. Organise selected organisms according to defined characteristics
2. Sequentially order organisms according to shared characteristics to construct a cladogram

Question 20

steps to constructing a cladogram ( Using Molecular Evidence)

Answer 20

https://ib.bioninja.com.au/standard-level/topic-5-evolution-and-biodi/54-cladistics/cladograms.html

1. Select a gene or protein common to a range of selected organisms
2. Copy the molecular sequence (DNA or amino acid) for each of the selected organisms
3. Run a multiple alignments to compare molecular sequences (DNA or amino acid)
4. Generate a phylogeny tree (cladogram) from multiple alignment data

Question 21

molecular clock (concept)

Answer 21

Some genes or protein sequences may accumulate mutations at a relatively constant rate (e.g. 1 change per million years)

If this rate of change is reliable, scientists can calculate the time of divergence according to the number of differences

Question 22

molecular clock limiting factors (3)

Answer 22

Different genes or proteins may change at different rates (e.g. haemoglobin mutates more rapidly than cytochrome c)

The rate of change for a particular gene may differ between different groups of organisms

Over long periods, earlier changes may be reversed by later changes, potentially confounding the accuracy of predictions

Question 23

The number of differences between comparable base sequences demonstrates the DEGREE of evolutionary DIVERGENCE …. therefore

Answer 23

more difference = more divergence = less related

less difference = less divergence = closely related

Question 24

reasons for using non-coding DNA in evidence for divergence

Answer 24

Non-coding DNA provides the best means of comparison as mutations will occur more readily in these sequences

Question 25

reasons for using gene sequences in evidence for divergence

Answer 25

Gene sequences mutate at a slower rate, as changes to base sequence may potentially affect protein structure and function

Question 26

reasons for using Amino acid sequences in evidence for divergence

Answer 26

Amino acid sequences may also be used for comparison, but will have the slowest rate of change due to codon degeneracy

Question 27

However, there are 2 key limitations to using morphological (STRUCTURAL) differences as a basis for classification:

Answer 27

1. Closely related organisms can exhibit very different structural features due to adaptive radiation (e.g. pentadactyl limb) 2. Distantly related organisms can display very similar structural features due to convergent evolution

Question 28

Convergent evolution =

Answer 28

is the independent evolution of similar features in species with distinct lineages

Question 29

reasons for convergent evolution (eg the black and white moths)

Answer 29

1. It may occur when different species occupy the same habitat and are thus subjected to the same selection pressures 2. The shared conditions cause common adaptations to be selected in different species, resulting in structural similarity

Question 30

homologous structures (in divergences) =

Answer 30

Traits that are SIMILAR because they are derived from COMMON ancestry

Question 31

analogous structures (in divergence) =

Answer 31

Traits that are superficially SIMILAR but were derived through SEPARATE evolutionary pathways

Question 32

mDNA

Answer 32

- Female line only - Easy to find mutations (constant mutation rate) - short - cheap

Question 33

nuclear DNA - divergence and cladistics

Answer 33

= it is found in the nucleus of cells, contains 3000 million bases, not usually used for evolutionary studies as it contains a mix of the male and female chromosomes. Can be used to understand the evolutionary relationships between populations

Question 34

Y chromosome DNA - divergence and cladistics

Answer 34

Y chromosome contains 59 million base pairs and also accumulates more mutations than other chromosomes. Passed from father to son, therefore, the genetic difference for different species can be determined by analysing the y chromosomes of each species = the ancestry of the male line can be determined

Question 35

Amino acid analysis - divergence and cladistics

Answer 35

the slowest rate of change due to codon degeneracy = mutations change at a constant rate

Question 36

Homologous structure

Answer 36

features that are common in difference organisms because of common ancestry - different function - common structure - common ancestor

Question 37

Analogous structure

Answer 37

features in different organisms that have a similar function due to similar selection factors, but are structurally different as they do not have a common ancestry - similar function - differing structure - different ancestor!

Question 38

Historically - classification was based primarily on morphological differences EXPECTATIONS:

Answer 38

closely related species were expected to show similar structural features, indicating common ancestry

Question 39

Reclassification (UNDERSTANDING)

Answer 39

Evidence from cladistics has shown that classifications of some groups based on structure did not correspond with the evolutionary origins of a group or species

Question 40

species more closely related than thought

Answer 40

using molecular evidence, scientists have discovered that many species thought to be closely related based on shared structural characteristics actually demonstrate distinct evolutionary origins eg. crocodiles = more closely related to birds than lizards red panda = more closely related to raccoons than padas

Question 41

Figworts!!!!

Answer 41

plants were placed into their own figwort family based on similarity of features BUT recent DNA analysis of the CHLOROPLAST GENE has move some "figworts-like" plants into the Lopseed and PLantain families. now less than 1/2 o the species remain in the figwort family

Question 42

base sequence (definition)

Answer 42

order of bases on a DNA molecule that is used to determine a gene (and therefore similarities between gene of different organisms)

Question 43

amino acid sequence

Answer 43

sequence that codes for proteins - that can then be compared to determine difference between organisms

Question 44

morphology

Answer 44

study of the form of things

Question 45

phylogeny

Answer 45

branch of biology that deals with phylogensis

Question 46

phylogensis

Answer 46

the evolutionary development and diversification of a species or group of organisms or of a particular feature of an organism

Question 47

molecular clock

Answer 47

hypothesis that states: DNA and protein sequences evolve at a rate that is relatively constant over time and among different organisms term for a technique that uses the mutation rule of biomolecules to deduce the time in prehistory when 2 or more life forms diverged

Question 48

reclassification

Answer 48

reclassification is when a species has been reinvestigated and concluded that the once believed ancestor is actually different - thus linking it instead to a different species and ancester from which it has diverged