topic 2 Flashcards

1
Q

how can phylogenies ve developed

A

• Not only organisms have phylogenies
• Phylogeny can be developed using genetic info
• Gene tree or gene genealogy
○ A branching diagram portraying history of DNA sequences of a gene (= haplotypes)

• Ex. Mitochondrial cytochrome b gene in McGillivray's warbler 
	○ Haplotypes are more closely related within a region than between regions
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2
Q

example of parsimony analysis - new world vs old world monkeys, look at this in notes

A

ok

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3
Q

what is traditional evolutionary taxonomy

A

c Evolutionary taxonomy utilizes common descent and amount of adaptive evolutionary change to rank higher taxa.
Sometimes includes
paraphyletic groupings.

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4
Q

fate of pongidae

A

• No! it doesn’t
• It is a paraphyletic group, not a monophyletic group
Chimpanzee & human share a common ancestry
and must be classified together in a group
The most parsimonious tree we just saw has EIGHT
fewer evolutionary changes than the tree that separates
chimpanzee & human
Family pongidae is no longer recognized!

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5
Q

describe molecular clock. ex in notes

A

• Estimating time of divergence - molecular clock
• Does DNA evolve at a constant rate?
• More DNA similarities = more closely related, more recent divergence
• Much of a DNA molecule is non-coding, not
expressed in the phenotype, and therefore
not subject to selection
• Evolving in large part by drift, it may have an
approximately clock-like rate of change
• Molecular clock used to estimate time of divergence

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6
Q

why should rates of DNA change be constaNT?

A

• Why should rates be approx. constant?
• Most DNA consists of non-coding parts of the molecule
• Even within coding regions, changes at 3rd base positions
of each codon are mostly silent substitutions (they don’t
change the amino acid)
• If non-coding and silent changes predominate, then most
mutations are not expressed in the phenotype
• Not being expressed, they are not subject to selection
They, thus, may accumulate at a stochastic (=non-
deterministic) rate

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7
Q

why arent DNA change rates constant

A

They are known to differ from one taxonomic
group to another, on average
-Use of the molecular clock to date lineages is thus approximate at best
Many estimates of the ages of groups obtained by molecular clocks are absurdly wrong by paleontological
standards (estimates of group origins are usually far too
ancient). This situation is improving with new methods.

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8
Q

classification of organisms b4 and after darwin

A
  • Before darwin
    • Kinds, types, ideals
    • Similarity, characteristic features
    • After darwin
    • Shared ancestry, phylogeny (genealogical relationships)
    • Adaptations
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9
Q

darwins theory on common ancestor

A

tree of life with 3 domains (eucarya, bacteria, archaea) and root (CA)
modern studies based on DNA molecules say there is one ancestor

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10
Q

when did darwins phylogeny appear

A
  • The first such diagram ever published, in 1859

* But darwin had been thinking along these lines since at least 1837, as his notebook sketch shows

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11
Q

5 building blocks of taxonomy

A
• Descries species 
	• Identification 
	• Classification 
	• Collections 
	• Conservation 
	• The 5 building blocks of taxonomy 
`
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12
Q

describe linnean taxonomy

A
  • First to give us this hierarchical system
    • Find key features of groups (shared adaptations/ancestry under darwin’s tree concept)
    • Discern God’s plan
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13
Q

linnean taxonomy rules

A
• Italicized or underlined: 
		○ Genus and species only 
	• Capitalization: 
		○ All except specific epithet 
	• Singular or plural names: 
		○ Family and up: plural 
		○ Genus and species: singular
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14
Q

what did wilsons editorial say (1st 5 points)

A

wilson, father of biology

1.
Systematics is the study of biological diversity
2. At present, we do not even know, to the nearest order of
magnitude, how many species there are in the world
3. Approx. 1.7 million have been described, but this number
is far below the actual biodiversity
4. approx10,000 new species across all groups described every
year
5. Recent studies in rainforests and other major habitats
indicate as many as 30 million kinds of insects alone

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15
Q

what did wilsons editorial say (last 3 points)

A

6
Because of largely unknown nature of biodiversity,
systematics remains a tremendous source of discoveries
& new ideas in biology
7 Much of the research in taxonomy & systematics has
economic & medical importance
8 world supply of trained taxonomists is no where near
the number required to research even a small part of
unknown/poorly-known aspects of biodiversity

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16
Q

who uses knowledge gathered from systematic research

A
All disciplines within biology 
Conservationists & resource managers 
Forestry, fisheries, wildlife, & agriculture 
researchers 
Biotechnology researchers 
Human & animal health & medical 
researchers
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17
Q

what is systematics

A

• Study of biological diversity
• Reconstruction of patterns of relationships
• Building classifications based on these patterns
• Working definition: field of biology that studies and tries to establish phylogenies (=evolutionary histories)
W

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18
Q

systematics purpose

A

identify and document earth’s biodiversity and organize this in a form that can be utilized by others
• Systematic patterns are hypotheses of the history of life and form the basis of modern classifications
• Patterns, resulting from systematic study, have predictive value

19
Q

willi hennig contribution

A

Best known for developing the idea of phylogenetic systematics (1950) ○
Wasn’t popular until translated into english

20
Q

hennings principles

A

○ Genealogical relationship
○ Synapomorphy
\taxonomy must be logically consistent with inferred pattern of historical relationship

21
Q

describe plesiomorphic

A

○ Earliest

○ Original character state that gave rise to derived state

22
Q

symplesiomorphy

A

Symplesiomorphy = shared among multiple organisms/groups

23
Q

apomorphy

A

• Apomorphic (derived/advanced)
○ Descended
○ Character state derived from primitive state
○ Synapomorphy

24
Q

what are phylogenetic systematics based on

A

• Based on characters that most clearly reveal evolutionary relationships = based on shared derived character states (synapomorphies)
• Many characters can be measured but not all are useful
Phylogeny is directly related to classification = can only identify monophyletic groups

25
Q

what data is used for inferring phylogenies

A

• Characters
○ Characteristics of an organism - an observable feature; a trait
○ Variable features eg. Bill size
§ External and internal morphological/behavioral/physiological/cell structure/ biochemistry/ chromosome structure
• Character states
○ Alternate conditions of feature e.g. large or small
○ Ancestral (plesiomorphic) vs derived (apomorphic)
• Monophyletic group
○ The set of species derived from any one ancestor
Recognized by synapomorphies

26
Q

what is homology

A

• Similarities due to shared ancestry
• Do not necessarily have the same function
The sharing of homologies among species indicates that they have evolved from a common ancestor that possessed the same feature

27
Q

what is analogy

A
  • Similarity between structures that is NOT the result of a common evolutionary origin / ancestry
    • Phenotypic similarity due to similarity of function - analogous
    • Similarity due to convergent evolution that led to a analogous character
    • Ex. Fusiform body shape
28
Q

what is convergence

A

• Convergence:
○ Similar appearance not due to common ancestry
○ Could be analogous but not homologous

29
Q

what is parallelism

A

• Parallelism
• Independent evolution of similar structure from common ancestor
Ex. Raptorial feet from perching feet in owls and falcons - appeared independently as their shared ancestor did not have this trait

30
Q

basic rules and goals of claudistics

A
  • All species in a natural group (clade) share the most recent common ancestor
    • All species that share this ancestor must be included in the group
    • Goal: monophyletic tree
31
Q

what is the OTU

A

Oper..a.tionaLT.aXQ.nQ.mic-Unit-(OTU): Taxonomic level of sampling selected by the user to
be used in a study, such as individuals, populations, species, genera, or bacterial strains.

32
Q

what is a clade

A

Clade: A group of two or more taxa or DNA sequences that includes both their most recent
common ancestor and all their descendents.

33
Q

what are nodes and branches

A

Node: A branch-point in a tree (a presumed ancestral OTU).
Branch: Defines the relationship between the taxa in terms of descent and ancestry.

34
Q

branch length, topology, sister groups

A

Topology: The branching patterns of the tree.
branchlength-(scaled trees only): Represents the number of changes that have occurred in
the branch.
Root: The common ancestor of all taxa.
Sister-group: TWO clades resulting from the splitting of a single lineage.

35
Q

homologies definition

A

shared features that are inherited from that species ancestor

36
Q

what are homoplasties. two kinds

A

shared features that are not homologies
reversals (to ancestral state)
covergences (indepdent origin of apomorhies in 2 or more taxa

37
Q

who came up with parsimony. why is it used

A

• Parsimony:
○ Used since the 14th century
○ Ockham’s razor:
§ Attributed to william of ockham, a friar from the village of ockham, surrey, england
§ A methodological principle tending toward simpler theories
• When faced with competing hypotheses that are equal in other respects, select the one with the fewest new assumptions
• Simplest explanation preferable over more complicated hypotheses that need more assumptions

38
Q

preferred phylogenetic tree

A

• The preferred tree is the one with the least homoplasty (fewest reversals and convergences)
• i.e., the one that postulates the fewest evolutionary
changes
— Because it minimizes the hypotheses required to explain it
Often called the shortest tree: it is the tree with the
fewest changes of character state
— Often there are multiple short trees from which to choose
— We might prefer the one with 293 postulated changes
over those with 294 or more

39
Q

outgroup vs ingroups

A

• Outgroups are close relatives of the ingroup used to help root the tree of the ingroup (group being studied)
○ By rooting the tree they indicate the direction of evolution, including which character states are primative and which are derived
• The most closely related outgroup, and thus the most useful for this purpose, is the sister group

40
Q

what are outgroups

A

• A taxon outside the group of interest
• Members of the ingroup are more closely related to each other than they are to outgroup
Hence outgroup may represent ancestral features

41
Q

rooted vs unrooted trees

A
  • Rooted tree represents the most basal ancestor of the tree in question
    • Unrooted trees do not imply a known ancestral root
42
Q

how to root a tree

A
  • Three strategies:
    • No rooting: leave tree unrooted
    • Mid-point rooting: rooting the tree in its middle point
    • Outgroup rooting: placing the root in the right place
43
Q

• Steps in max parsimony analysis

A
  1. Select ingroup species
    1. Select one or more outgroup species
    2. Determine the polarity of each of many characters in each species based on the polarity of states in the outgroup
    3. Draw an un-rooted tree with all species, plotting state changes of all characters
    4. If there is more than a few species, there will be a huge # of possible trees generated
    5. Choose the tree with the fewest changes
      Root the tree between outgroup and ingroup to represent time directed evolutionary history
44
Q

why root

A

without outgroup, we usually dont know direction of evolution