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BIO3A: Processes 2 Patterns > S2: W5 (Dr. Hanlie) > Flashcards

S2: W5 (Dr. Hanlie) Flashcards

1
Q

S1 vs S2?

A

● S1
= processes that cause variation.

● S2
= organisation of variation.

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2
Q

Biosystematics?

A

= study of the variability & diversity of organisms, and any and all relationships among them.

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3
Q

Type specimen definitions? (2)

A

¹= species used to identify the species original (golden).

²= specimen on which you’ve defined a species from.

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4
Q

How would you document your observations? (3)

A

• Collections (of samples).
• Preserve.
• Identify & catalogue.

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5
Q

Egs of samples you would collect? (2)

A

• Plants.
• Animals.

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6
Q

Egs of Preserve? (2)

A

• Press plants.
• Preserve animals in alcohol/dried/skinned.

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7
Q

How would you identify and catalogue?

A

By creating lists, guides & books.

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8
Q

Approaches to study variation/Investigate relationships among & origins of organisms on the island? (3)

A

• Morphological similarity.
• Genetic similarity.
• Phylogeny.

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9
Q

Morphological similarity?

A

= infer relationship.

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10
Q

Genetic similarity?

A

= DNA sequencing to compare the degree of similarity.

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11
Q

Phylogeny?

A

= construct a phylogeny/”tree” to depict relationships.

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12
Q

Systematics?

A

=

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13
Q

What does systematics involve? (3)

A

• Taxonomy.
• Processes resulting in genetic variability & new species.
• Phylogeny reconstruction.

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14
Q

Taxonomy?

A

= who is related to who based on what.

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15
Q

Taxonomy attributes? (2)

A

• Grouping & ordering.
• Involves nomenclature & describing.

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16
Q

Phylogeny reconstruction attributes? (3)

A

• Evolutionary history of a group.
• Discovering relationship among organisms.
• Tool to get us to classify organisms.

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17
Q

Sub-terms of Classification? (3)

A

• Taxonomy.
• Nomenclature.
• Phylogeny.

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18
Q

Evolution?

A

= change by modification.

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19
Q

At what level does evolution take place?

A

Populations.

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20
Q

How does evolution occur? (6)

A

• Genetic drift.
• Natural selection.
• Gene flow.
• Non-random mating (SS).
• Founder effect.
• Bottleneck effect.

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21
Q

Genetic drift?

A

= random change of allele frequency in a population.

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22
Q

NS attribute?

A

• Results in adaptation & increased fitness.

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23
Q

NS?

A

= directed & non-random change.

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24
Q

Result of evolution?

A

Speciation.

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25
Q

Speciation?

A

= formation of a new species from existing species by lineage splitting (cladogenesis).

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26
Q

Lineage?

A

= a chain of ancestors & their descendants.

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27
Q

Taxon?

A

= a category into which related organisms are placed.

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28
Q

Species complex?

A

= a group of closely related organisms that are so similar in appearance & other features that the boundaries between them are often unclear.

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29
Q

Sensu lato?

A

= in a broader sense, ie., in a broader sense this species is this.

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30
Q

Sensu stricto?

A

= this species is strictly this species.

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31
Q

What kinds of questions do systematicists address? (8)

A

Questions on:

• Biodiversity.
• Species Concepts.
• Nomenclature.
• Classification.

• Are the species that are recognized today truly “unique entities”?

• How closely related are species or populations in a species?

• Are some species rarer than others? Why?

• What are the implications of species identification for biocontrol of invasive aliens?

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32
Q

Question on Biodiversity that systematicists address?

A

How many species are in a region?

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33
Q

Question on Species Concepts that systematicists address?

A

How are species recognized?/How do we distinguish one species from another?

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34
Q

Question on Nomenclature that systematicists address?

A

How are species named?

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35
Q

Question on Classification that systematicists address?

A

How many species are recognized in a group?

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36
Q

Importance of knowing a species & everything about it?

A
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37
Q

Eg of Systematicist question 5?

A

Polar bear.

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38
Q

Eg of Systematicist question 8?

A

Tamarix species.

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39
Q

Importance of knowing a species & everything about it?

A

Conservation purposes.

Eg. Is the species endangered, threatened, vulnerable, etc?

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40
Q

Eg of rare species?

A

Tuatara (sphenodon).

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41
Q

Why study biosystematics? (3)

A

• Conservation.
• Engineering & Economics.
• Medicine.

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42
Q

Conservation reason for studying biosystematics?

A

= knowledge of species, their distributions, endemicity, rarity, relationships & interactions in the ecosystem.

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43
Q

Engineering & Economics reason for biosystematics?

A

= food sources, chemicals, materials for industry, etc.

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44
Q

Medicine reason for biosystematics?

A

= new drugs for new & old diseases.

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45
Q

Important & useful tools for biosystematics? (4)

A

• DNA sequencing.
• Phylogenetic methods & software.
• Computers.
• Historical information & materials.

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46
Q

DNA sequencing tool for biosystematics?

A

= includes barcoding & whole gene sequencing.

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47
Q

Phylogenetic methods & software tool for Biosystematics?

A

= analysis of evolutionary relationships.

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48
Q

Computers tool for biosystematics?

A

= storage & analysis of large datasets.

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49
Q

Artificial classification trait?

A

=

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50
Q

Natural classification trait?

A

=

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51
Q

Eg of Classification?

A

Periodic table.

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52
Q

Criteria for a good classification system? (3)

A

• Unambiguous.
• Stable.
• Highly predictive (informative).

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53
Q

What do we mean by saying that a good classification system must be Unambiguous?

A

We mean that it must be very useful/utilitarian.

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54
Q

Why should a good classification system be Highly predictive (informative)?

A
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55
Q

Why classify information? (3)

A

• Store knowledge.
• Recall it later.
• Have predictive (informative) value.

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56
Q

Paradigms of classification/How classification evolved? (3)

A

Observation
|
Descriptions
|
Ordering

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57
Q

Observation under Paradigms of classification?

A

= done by classical Greek scholars (Aristotle).

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58
Q

Descriptions under Paradigms of classification?

A

= done during the Age of Herbalists.

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59
Q

Ordering under Paradigms of classification?

A

= done by early classifiers (John Ray).

60
Q

Artificial classification vs Natural classification?

A

●Artificial classification

61
Q

What are the 2 things that a natural classification should reflect?

A

• Evolutionary relationship.
• Similarity.

62
Q

Evolutionary relationship?

A

= relationship due to a common ancestor.

63
Q

Ranking?

A

= assigning the groups to taxonomic ranks.

64
Q

Grouping?

A

= assigning organisms to groups.

65
Q

Ranking vs Grouping?

A

● Ranking
= assign groups to taxonomic ranks.

● Grouping
= assign organisms to groups.

66
Q

Eg of ranking?

A

Carl Linnaeus’s system.

67
Q

Eg of grouping?

A
68
Q

Genus?

A

= group.of related species.

69
Q

Carl Linnaeus attributes? (2)

A

• Influential in taxonomy.
• Initiated/Invented classification systems.

70
Q

Nomenclature?

A

= the naming of species.

71
Q

Voucher specimen?

A

= specimen linked to a particular study.

72
Q

How to memorize Linnaeus’s classification system? (8)

A

Dear
King
Philip,
Come
Out
For
Goodness
Sake!

73
Q

Type specimen vs Voucher specimen?

A

● Type specimen
= used to identify species original.

● Voucher specimen
= linked to a particular study.

74
Q

Species Plantanim document attributes? (3)

A

• By Linnaeus.
• Documented all known species of plants.
• Described species with binomial system.•

75
Q

How did the binomial naming system come about?

A

At first, a species was given many names (polynomial), trivial names were then done by Linnaeus & this was the beginning of binomial naming, it was not too descriptive.

76
Q

Polynomial?

A

= many names.

77
Q

Why Polynomial?

A

For a detailed description of that particular species.

78
Q

Nomenclature rules? (3)

A

• Species names are binomial.
• Suffix of “dae” = family.
• Suffix of “nae” = subfamily.

79
Q

What do you mean by binomial in Nomenclature rules?

A

Genus + species/specific epithet (italicized) + species authority.

80
Q

Importance of a scientific name? (3)

A

• To eliminate ambiguity from the system.
• To eliminate assumptions (differentiate species with common name).
• For universal communication.

81
Q

Synonyms in Taxonomy?

A
82
Q

Eg of synonyms in Taxonomy?

A

Reptile database keeps a record of history of the species names.

83
Q

Conditions for a name to be published/valid? (3)

A

• Must be published.
• New species name must be linked to a detailed description.
• Must include a reference to a specimen (the type specimen).

84
Q

Explain Must be published?

A

Name must be published in a journal/book with minimum number of copies & offered for sale to the public.

85
Q

Type specimen (TS) attributes? (3)

A

May physically be:

• A specimen.
• A culture collection.
• An illustration.

86
Q

In what cases may you not access a TS? (2)

A

• If TS is extinct.
• If TS is endangered.

87
Q

Types of TS? (7) [PHLI²NS]

A

• Paratype.
• Holotype.
• Lectotype.
• Isotype.
• Iconotype.
• Neotype.
• Syntype.

88
Q

Paratype?

A

= additional specimen collected at the same time & location as the holotype.

89
Q

Holotype?

A

= original specimen linked to a name.

90
Q

Lectotype?

A

= chosen type (usually from a list of specimens cited in the original description).

91
Q

Isotype?

A

= duplicate of the original specimen.

92
Q

Iconotype?

A

= illustration of the original specimen.

93
Q

Neotype?

A

= new type designated if the holotype & all isotopes are destroyed.

94
Q

Syntype?

A

= cited in the original description when no holotype was designated by another.

95
Q

Syntype vs Neotype?

A

● Syntype

96
Q

Principle of Priority (PoP)?

A

= principle that says that the oldest (first) legitimate name applies.

97
Q

PoP =…?

A

Valid name.

98
Q

Eg of PoP?

A

Kaleniczenko described Limacus maculatus, but Boettger named the same slug Limax ecarinatus.

99
Q

ICN kinds? (2)

A

• ICN for algae, fungi & protists.
• ICN for zoological species (animals).

100
Q

ICN stands for?

A

International Code of Nomenclature.

101
Q

Outgroup?

A

= closely related to the ingroup but not part of the ingroup.

102
Q

Outgroup attributes? (2)

A

• Polarizes the ingroup/shows direction of evolution for the ingroup.
• Diverges first than the others.

103
Q

Ways to polarize characters? (3)

A

• Ontogeny.
• Fossil record.
• Outgroup method.

104
Q

Ontogeny?

A

= morphological changes that occur as an organism develops.

105
Q

Ontogeny attributes as way to polarize characters? (2)

A

• Recapitulates phylogeny.
• Initiated by Ernst Haeckel.

106
Q

Fossil record as a way to polarize characters?

A

= evidence for progression.

107
Q

Superphylogeny/Superphylogenetic tree?

A

= amalgamation of Phylogenetic trees.

108
Q

Outgroup criteria/Criteria you need to be an outgroup? (6)

A

• Not a member of the ingroup.
• Closely related to the ingroup.
• Need a higher level phylogenetic study to reveal the outgroup for a study group.
• Roots the tree (roots the ingroup).
• Provides polarity (direction).
• The outgroup is older.

109
Q

Why must the outgroup be older?

A

It’s because you want to study the derived older state.

110
Q

Assumption of outgroups?

A

The outgroup reflects the ancestral (plesiomorphic) condition.

111
Q

Monophyletic?

A

= common ancestor + all its descendants.

112
Q

Paraphyletic?

A

= common ancestor + some of its descendants.

113
Q

Topology of tree?

A

= how the tree looks.

114
Q

When creating a Phylogenetic tree, do the following? (3)

A

• Choose the correct outgroup.
• Place the root at the correct place of the tree.
• Go find the branch that contains all taxa representing the outgroup.

115
Q

Boodstrapping method in phylogeny attributes? (5)

A

• One statistical method you can apply to phylogenetic trees.
• Representated by a number of the branch.
• Pay attention to the node support.
• Phylogenetic term.
• RULE.

116
Q

Rule of the Bootstrapping method?

A

If you get >= 70%, it means you can trust the relationship.

117
Q

Phylogenetic phrase in Bootstrapping method?

A

“Relationship is unresolved.”

118
Q

“Relationship is unresolved”?

A

= when you have a low number on the branch and are unable to conclude on the level of relatedness between two organisms (insufficient data).

119
Q

Can we completely trust phylogenies?

A

No.

120
Q

Why can’t we completely trust phylogenies? (3)

A

• Phylogenies are hypotheses.
• Missing data influences the topology of the tree.
• Genes depend on the gene types & the number of genes you’re analyzing.

121
Q

Best approach to establish relationships on?

A

Use as much evidence as possible.

122
Q

Cladogram?

A

= branching diagram tracing evolutionary history.

123
Q

Branch point/Node?

A

= common ancestor of species above it.

124
Q

Terminal taxa?

A

= extant/living.

125
Q

Why draw trees? (3)

A

• To trace evolutionary relationships.
• To trace ancestor to descendant relationships.
• To test hypotheses of evolutionary relationships.

126
Q

Explain eg of Phylogeny of impalas & Gnus and hartebeests? (2)

A

● Gnus & hartebeests diverged into various kinds of variation due to them having available niches to occupy as they may be specialists.

● Impalas didn’t diverge into much variation possibly due to them being generalists and occupying any space available.

127
Q

How to build a tree?

A

Use synapomorphies.

128
Q

Synapomorphy?

A

= shared derived characters.

129
Q

Summary diagram of speciation event?

A

It’s a simpler version with only mutations mapped (apomorphies).

130
Q

Apomorphy?

A

= derived features.

131
Q

How do you identify synapomorphies? (2)

A

• Must be homologous features.
• Must have similar origin (common ancestor).

132
Q

Homology?

A

= similar in position/structure but not in function due to common ancestry.

133
Q

Why is there similarity in position/structure in homologous features?

A

Indicates common ancestry.

134
Q

Analogy?

A

= similarity in function but different ancestors.

135
Q

Tests for homology? (3)

A

• Similarity.
• Conjunction.
• Congruence.

136
Q

Similarity homology test?

A

= includes structure, position & ontogeny.

137
Q

Conjunction homology test attributes? (2)

A

• No two homologues in the same individual.
• Never will you find homologues within the same lineages.

138
Q

Eg of Conjunction homology test?

A

Human arms & wings of birds would not be homologous if both found in angel.

139
Q

Congruence homology test attributes? (2)

A

• Weight of evidence (phylogenetic trees using molecular data vs morphological data).

• Similar but not identical.

140
Q

NB? (4)

A

● Write a summary paragraph on Phylogenetic tree on Treehoppers slide provided on Ulwazi discussion.

● Might be in an exam.

● Use evolutionary terms.

● You can practice & give Dr. Hanlie for review.

141
Q

What do you mean that a good biosystematics classification system must be Unambiguous?

A
142
Q

What do you mean that a good biosystematics classification system must be Highly predictive (informative)?

A
143
Q

What do you mean that a good biosystematics classification system must be Stable?

A
144
Q

Eg of a Stable attribute of a good classification system?

A

Stable gases on the periodic table indicating that they are not easily reactive.

145
Q

Eg of an Unambiguous attribute of a good classification system?

A

Scientific names being useful.

146
Q

Eg of a Highly predictive (informative) attribute of a good classification system?

A

Car brands/logos.

BIO3A: Processes 2 Patterns (12 decks)

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