S2: W5 (Dr. Hanlie) Flashcards
S1 vs S2?
● S1
= processes that cause variation.
● S2
= organisation of variation.
Biosystematics?
= study of the variability & diversity of organisms, and any and all relationships among them.
Type specimen definitions? (2)
¹= species used to identify the species original (golden).
²= specimen on which you’ve defined a species from.
How would you document your observations? (3)
• Collections (of samples).
• Preserve.
• Identify & catalogue.
Egs of samples you would collect? (2)
• Plants.
• Animals.
Egs of Preserve? (2)
• Press plants.
• Preserve animals in alcohol/dried/skinned.
How would you identify and catalogue?
By creating lists, guides & books.
Approaches to study variation/Investigate relationships among & origins of organisms on the island? (3)
• Morphological similarity.
• Genetic similarity.
• Phylogeny.
Morphological similarity?
= infer relationship.
Genetic similarity?
= DNA sequencing to compare the degree of similarity.
Phylogeny?
= construct a phylogeny/”tree” to depict relationships.
Systematics?
=
What does systematics involve? (3)
• Taxonomy.
• Processes resulting in genetic variability & new species.
• Phylogeny reconstruction.
Taxonomy?
= who is related to who based on what.
Taxonomy attributes? (2)
• Grouping & ordering.
• Involves nomenclature & describing.
Phylogeny reconstruction attributes? (3)
• Evolutionary history of a group.
• Discovering relationship among organisms.
• Tool to get us to classify organisms.
Sub-terms of Classification? (3)
• Taxonomy.
• Nomenclature.
• Phylogeny.
Evolution?
= change by modification.
At what level does evolution take place?
Populations.
How does evolution occur? (6)
• Genetic drift.
• Natural selection.
• Gene flow.
• Non-random mating (SS).
• Founder effect.
• Bottleneck effect.
Genetic drift?
= random change of allele frequency in a population.
NS attribute?
• Results in adaptation & increased fitness.
NS?
= directed & non-random change.
Result of evolution?
Speciation.
Speciation?
= formation of a new species from existing species by lineage splitting (cladogenesis).
Lineage?
= a chain of ancestors & their descendants.
Taxon?
= a category into which related organisms are placed.
Species complex?
= a group of closely related organisms that are so similar in appearance & other features that the boundaries between them are often unclear.
Sensu lato?
= in a broader sense, ie., in a broader sense this species is this.
Sensu stricto?
= this species is strictly this species.
What kinds of questions do systematicists address? (8)
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?
Question on Biodiversity that systematicists address?
How many species are in a region?
Question on Species Concepts that systematicists address?
How are species recognized?/How do we distinguish one species from another?
Question on Nomenclature that systematicists address?
How are species named?
Question on Classification that systematicists address?
How many species are recognized in a group?
Importance of knowing a species & everything about it?
Eg of Systematicist question 5?
Polar bear.
Eg of Systematicist question 8?
Tamarix species.
Importance of knowing a species & everything about it?
Conservation purposes.
Eg. Is the species endangered, threatened, vulnerable, etc?
Eg of rare species?
Tuatara (sphenodon).
Why study biosystematics? (3)
• Conservation.
• Engineering & Economics.
• Medicine.
Conservation reason for studying biosystematics?
= knowledge of species, their distributions, endemicity, rarity, relationships & interactions in the ecosystem.
Engineering & Economics reason for biosystematics?
= food sources, chemicals, materials for industry, etc.
Medicine reason for biosystematics?
= new drugs for new & old diseases.
Important & useful tools for biosystematics? (4)
• DNA sequencing.
• Phylogenetic methods & software.
• Computers.
• Historical information & materials.
DNA sequencing tool for biosystematics?
= includes barcoding & whole gene sequencing.
Phylogenetic methods & software tool for Biosystematics?
= analysis of evolutionary relationships.
Computers tool for biosystematics?
= storage & analysis of large datasets.
Artificial classification trait?
=
Natural classification trait?
=
Eg of Classification?
Periodic table.
Criteria for a good classification system? (3)
• Unambiguous.
• Stable.
• Highly predictive (informative).
What do we mean by saying that a good classification system must be Unambiguous?
We mean that it must be very useful/utilitarian.
Why should a good classification system be Highly predictive (informative)?
Why classify information? (3)
• Store knowledge.
• Recall it later.
• Have predictive (informative) value.
Paradigms of classification/How classification evolved? (3)
Observation
|
Descriptions
|
Ordering
Observation under Paradigms of classification?
= done by classical Greek scholars (Aristotle).
Descriptions under Paradigms of classification?
= done during the Age of Herbalists.
Ordering under Paradigms of classification?
= done by early classifiers (John Ray).
Artificial classification vs Natural classification?
●Artificial classification
What are the 2 things that a natural classification should reflect?
• Evolutionary relationship.
• Similarity.
Evolutionary relationship?
= relationship due to a common ancestor.
Ranking?
= assigning the groups to taxonomic ranks.
Grouping?
= assigning organisms to groups.
Ranking vs Grouping?
● Ranking
= assign groups to taxonomic ranks.
● Grouping
= assign organisms to groups.
Eg of ranking?
Carl Linnaeus’s system.
Eg of grouping?
Genus?
= group.of related species.
Carl Linnaeus attributes? (2)
• Influential in taxonomy.
• Initiated/Invented classification systems.
Nomenclature?
= the naming of species.
Voucher specimen?
= specimen linked to a particular study.
How to memorize Linnaeus’s classification system? (8)
Dear
King
Philip,
Come
Out
For
Goodness
Sake!
Type specimen vs Voucher specimen?
● Type specimen
= used to identify species original.
● Voucher specimen
= linked to a particular study.
Species Plantanim document attributes? (3)
• By Linnaeus.
• Documented all known species of plants.
• Described species with binomial system.•
How did the binomial naming system come about?
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.
Polynomial?
= many names.
Why Polynomial?
For a detailed description of that particular species.
Nomenclature rules? (3)
• Species names are binomial.
• Suffix of “dae” = family.
• Suffix of “nae” = subfamily.
What do you mean by binomial in Nomenclature rules?
Genus + species/specific epithet (italicized) + species authority.
Importance of a scientific name? (3)
• To eliminate ambiguity from the system.
• To eliminate assumptions (differentiate species with common name).
• For universal communication.
Synonyms in Taxonomy?
Eg of synonyms in Taxonomy?
Reptile database keeps a record of history of the species names.
Conditions for a name to be published/valid? (3)
• Must be published.
• New species name must be linked to a detailed description.
• Must include a reference to a specimen (the type specimen).
Explain Must be published?
Name must be published in a journal/book with minimum number of copies & offered for sale to the public.
Type specimen (TS) attributes? (3)
May physically be:
• A specimen.
• A culture collection.
• An illustration.
In what cases may you not access a TS? (2)
• If TS is extinct.
• If TS is endangered.
Types of TS? (7) [PHLI²NS]
• Paratype.
• Holotype.
• Lectotype.
• Isotype.
• Iconotype.
• Neotype.
• Syntype.
Paratype?
= additional specimen collected at the same time & location as the holotype.
Holotype?
= original specimen linked to a name.
Lectotype?
= chosen type (usually from a list of specimens cited in the original description).
Isotype?
= duplicate of the original specimen.
Iconotype?
= illustration of the original specimen.
Neotype?
= new type designated if the holotype & all isotopes are destroyed.
Syntype?
= cited in the original description when no holotype was designated by another.
Syntype vs Neotype?
● Syntype
Principle of Priority (PoP)?
= principle that says that the oldest (first) legitimate name applies.
PoP =…?
Valid name.
Eg of PoP?
Kaleniczenko described Limacus maculatus, but Boettger named the same slug Limax ecarinatus.
ICN kinds? (2)
• ICN for algae, fungi & protists.
• ICN for zoological species (animals).
ICN stands for?
International Code of Nomenclature.
Outgroup?
= closely related to the ingroup but not part of the ingroup.
Outgroup attributes? (2)
• Polarizes the ingroup/shows direction of evolution for the ingroup.
• Diverges first than the others.
Ways to polarize characters? (3)
• Ontogeny.
• Fossil record.
• Outgroup method.
Ontogeny?
= morphological changes that occur as an organism develops.
Ontogeny attributes as way to polarize characters? (2)
• Recapitulates phylogeny.
• Initiated by Ernst Haeckel.
Fossil record as a way to polarize characters?
= evidence for progression.
Superphylogeny/Superphylogenetic tree?
= amalgamation of Phylogenetic trees.
Outgroup criteria/Criteria you need to be an outgroup? (6)
• 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.
Why must the outgroup be older?
It’s because you want to study the derived older state.
Assumption of outgroups?
The outgroup reflects the ancestral (plesiomorphic) condition.
Monophyletic?
= common ancestor + all its descendants.
Paraphyletic?
= common ancestor + some of its descendants.
Topology of tree?
= how the tree looks.
When creating a Phylogenetic tree, do the following? (3)
• 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.
Boodstrapping method in phylogeny attributes? (5)
• 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.
Rule of the Bootstrapping method?
If you get >= 70%, it means you can trust the relationship.
Phylogenetic phrase in Bootstrapping method?
“Relationship is unresolved.”
“Relationship is unresolved”?
= when you have a low number on the branch and are unable to conclude on the level of relatedness between two organisms (insufficient data).
Can we completely trust phylogenies?
No.
Why can’t we completely trust phylogenies? (3)
• Phylogenies are hypotheses.
• Missing data influences the topology of the tree.
• Genes depend on the gene types & the number of genes you’re analyzing.
Best approach to establish relationships on?
Use as much evidence as possible.
Cladogram?
= branching diagram tracing evolutionary history.
Branch point/Node?
= common ancestor of species above it.
Terminal taxa?
= extant/living.
Why draw trees? (3)
• To trace evolutionary relationships.
• To trace ancestor to descendant relationships.
• To test hypotheses of evolutionary relationships.
Explain eg of Phylogeny of impalas & Gnus and hartebeests? (2)
● 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.
How to build a tree?
Use synapomorphies.
Synapomorphy?
= shared derived characters.
Summary diagram of speciation event?
It’s a simpler version with only mutations mapped (apomorphies).
Apomorphy?
= derived features.
How do you identify synapomorphies? (2)
• Must be homologous features.
• Must have similar origin (common ancestor).
Homology?
= similar in position/structure but not in function due to common ancestry.
Why is there similarity in position/structure in homologous features?
Indicates common ancestry.
Analogy?
= similarity in function but different ancestors.
Tests for homology? (3)
• Similarity.
• Conjunction.
• Congruence.
Similarity homology test?
= includes structure, position & ontogeny.
Conjunction homology test attributes? (2)
• No two homologues in the same individual.
• Never will you find homologues within the same lineages.
Eg of Conjunction homology test?
Human arms & wings of birds would not be homologous if both found in angel.
Congruence homology test attributes? (2)
• Weight of evidence (phylogenetic trees using molecular data vs morphological data).
• Similar but not identical.
NB? (4)
● 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.
What do you mean that a good biosystematics classification system must be Unambiguous?
What do you mean that a good biosystematics classification system must be Highly predictive (informative)?
What do you mean that a good biosystematics classification system must be Stable?
Eg of a Stable attribute of a good classification system?
Stable gases on the periodic table indicating that they are not easily reactive.
Eg of an Unambiguous attribute of a good classification system?
Scientific names being useful.
Eg of a Highly predictive (informative) attribute of a good classification system?
Car brands/logos.
