Ch.19

Question 1

Systematics

Answer 1

The study and classification of the division of the diversity of life based in the evolutionary history and relationships (I.e., phylogeny) of organisms.

Question 2

Taxonomy

Answer 2

Science of naming and classifying organisms based on similarity.
-taxo = to arrange (Greek)
-nomos = knowledge/science of… (Greek)

Question 3

Nomenclature

Answer 3

A system of rules for naming organisms

Question 4

Classification

Answer 4

An arrangement of organisms into a hierarchical groups that reflect their relatedness

Question 5

Binomial (binomen)

Answer 5

Linnaeus created this in which each species is given unique 2 part name. (Binomen or binomial)

•1st part of name identifies the genus.
•2nd part is the specific epithet, which is not the same as species name.

•species name includes both genus + species epithet.
-species are given Latinized binomial names.

•binomial (scientific names) avoid confusion of common names b/c every species has a unique binomial.

Rules:
•Binomial must always be italicized- both genus and species epithets
•when handwritten both under lined
•genus epithet must start in capital letter, specie epithet is all small numbers.
•Genera have 1-word names
•species have 2-word names. 1st part same as genus name
•species names can be abbreviated using only first letter of genus followed by a period.

In traditional Linnaean taxonomy rules:
•primary unit is the species
-each species has a type specimen accessioned in an appropriate institution (museum, zoological or botanical garden collections)
-whoever describes type specimen of new species has right to name new species.
•next huger unit, the genus is composed of 1 or more species.
-each had a type species: all other species are assigned to genus based on their similarity to the type species.

2 important aspects:
•naming a species
-dedicated set of rules
-Latin grammar for names

•authorship
-another set of rules
-authors can’t name a species after themselves or can’t use same genus and higher rank names (only species epithet can be used multiple times)
-no brackets when originally named and not changed.
-name of species and genus can be same.

Question 6

Genus

Answer 6

A group of species that share similar characteristics.

Question 7

Species epithet

Answer 7

•is not the same as species name.

Question 8

Taxon (pl. taxa)

Answer 8

Linnaean system involves nested subsets called taxonomic levels or ranks, containing groups of organisms called taxa (singular taxon)

•Indicate the grouping of organisms at each level in the Hierarchy.

•a taxon can be a species, class, family, etc.

Question 9

Taxonomic hierarchy

Answer 9

Species are organized into a Taxonomic hierarchy, comprising a nested series of formal categories.

Question 10

Taxonomic categories:

Answer 10

Broad

•domain
Multiple kingdoms In ^
•kingdom
Multiple phyl in ^
•phylum
Multiple classes In ^
•class
Multiple orderies in ^
•order
Multiple families in ^
•family
Multiple genera in ^
•genus
Multiple species in ^
•species

Specific

Question 11

Traditional systematics

Answer 11

Uses phenotypic similarities and differences.
-based on distinct body plans and way of life.
-may not include all ancestors
-not always reflective of patterns of evolution history and relationships

Question 12

Phylogeny

Answer 12

•show evolutionary history of a group of organisms.
•most phylogenetic trees have implicit or explicit timeline that indicates the relative times for cladogenesis.

Question 13

Cladistics

Answer 13

Classification based solely on evolutionary relationships
-produced phylogenetic hypotheses and classifications that reflect only the branching pattern of evolution, ignoring morphological divergence.
-evolutionary relationships are analyzed by comparing orgnismal (morphological) and genetic characteristics

•clade = morphological lineage
•cladogram • tree made of clades(branded diagram)
•phylocode = strictly cadistics system that identifies identifies and names clade no stead of placing a organism into the familiar taxonomic groups.
•some linnaesns classifications not walkways consistent with clasistics

Question 14

Phylogenic character

Answer 14

Similarity of structure or function due to phylogeny (common ancestry) or Similarity of structure or function due to convergence.
-A systematic category that includes an ancestor and all of its descendants. 

Question 15

Character state

Answer 15

Character- Type of structure, behaviour, DNA sequence, etc

State- manifestations/forms of that character.

Character states: one or more forms of a character used in a phylogenic analysis.

Ancestral character state: a trade that was present in a distant common ancestor.

Derived character state: a new version of a trait found in the most recent common ancestor of a group. 

Question 16

Clade and sister clades

Answer 16

•branch points described as nodes and monophyletic lineages as called clades.

•2 lineages that share a node are called sister clades.

Question 17

Phylogenetic tree

Answer 17

Show the evolutionary relationships between organisms (past and present), and more generally between common ancestors and descendants.

•Phylogenetic tree are hypotheses of the evolutionary relationships among taxa.
•portray the branching pattern of evolution.

•relationships among taxa are interpreted from order in which the branches split, not from how names of taxa are arranged at the tips of branches.
-can be rotated around it’s nodes without altering the relationships.

Question 18

Cladogram

Question 19

Nodes and branches

Answer 19

Node: The point on a system where one or more leaves are attached. I know with all the branches, branchleyts, Twigs that emerge from is called a clade.

Branches: When they first emerge, the two branches may represent new species. But as cladogenesis continues repeatedly through evolution every time with branches giving rise to branchlet and branchlet to twigs each of those new species may become the common ancestor of its own many descendants.

Question 20

Polytomy

Answer 20

A term for an internal node of a cladogram that has more than two immediate descendants, in which the evolutionary relationships cannot be fully resolved to dichotomies. 

Question 21

Terminal taxon/taxa

Answer 21

A clade, species, or lineage that appears at the tip of a phylogenic tree. Terminal taxa may be an extant or extinct.

Question 22

In group and out group

Answer 22

•in-group: the study group; taxa whose relationships we are interested in untangling.

•outgroup: 1 or more taxa that are related to our in group, but that have diverged form it at an earlier time. Serves to polarize the character states and root the tree.

Question 23

Principle of parsimony (Occam’s razor)

Answer 23

•a philosophical concept stating that the simplest plausible explanation of any phenomenon is the best explanation.

•used in cladistics to identify the optimal phylogenetic tree(s)

•principal suggests that the best tree is the one that hypothesizes the smallest # of evolutionary changes needed to to explain the distribution of character states in a clade.

•If one must postulate a number of a unknowable events (changes in character states), the best hypothesis is the one requiring the fewest postulates (I.e., the fewest number of events) = Occam’s razor 

•Choosing the phylogeny that requires the fewest number of evolutionary events = b/c it’s more probable.

•event = change From ancestral state to another state (Gaining or losing) 

Question 24

Homoplasy (homoplastic) 

Answer 24

Analogies = homoplasies (homoplastic characters)
-similar traits that evolved independently in different lineages (no commons ancestry)
-such characters are phenotypically similar b/C They have similar functions.

•Homoplastic traits: structures in different species that are due to separate ancestries.

Question 25

Convergent evolution

Answer 25

The evolution of similar adaptations in distantly related oranisms that occupy similar environments.

-Independent evolution of similar traits in different lineages.

Question 26

monophyletic, paraphyletic, polyphyletic

Answer 26

Mono:
-contains a common ancestor and all of its descendants and no other unrelated taxa (mono = one) —> clade
-goal organize species into groups with common ancestry that reflect ancestor-descendant relationships—> only mono taxa
-ideal taxon = mono group.
-only mono can be called clades.
-must use traits that are similar b/c of common ancestry.
-structures in diff species that are acquired from common ancestry are homologous traits.
-Shared drive characteristics, called Synapomorphies.

Poly:
-taxa get lumped together even though they do not share recent ancestors.
-more than 1 common ancestor (possessing different ancestors) OR
-Lacking a single common ancestor that unites all members in a group
-incorrectly grouped by superficial similarities and not due to common ancestry. (I.e., analogy or homoplastic)

Para:
-Groups do not contain all descendants of a common ancestor.
-often the result of the removal of taxa that are highly divergent from the rest of the clade.
-Usually, the mistake is due to the fact that some descendants appear quite different from other members of the clade and we miss the intermediate forms. 

Class Aves Is a monophyletic group = clades. 

Question 27

Apomorphy, Synapomorphy

Answer 27

Apo = ‘away from’
-away from Ancestry
-Derived character state

Syn = ‘with’ or ‘together’
-Shared (together) derived characteristics
-Only Synapomorphies Are useful for reconstructing phylogenic relationships (with the cladistics method)
-Derived character state found in two or more species.


Question 28

Plesiomorphy, symplesiomorphy

Answer 28

Plesio = ‘near’
-Near ancestral type
-(Ancestral trait) an evolutionary trait that is homologous within a particular group of organisms but is not unique to members of that group and therefore cannot be used as a diagnostic or defining character for the group.

Sym = ‘with’ or ‘together’
-Shared ancestral type
-Shared ancestral state
-An ancestry a trait that is shared by two or more modern groups. Are not usually helpful in assisting more recent evolutionary relationships within a larger group.

-Both are synonyms for an ancestral character shared by all members of the clade, which does not distinguished clade from other clades. 

Question 29

Probability methods for phylogenetics

Answer 29

1. Maximum likelihood method
2. Bayesian likelihood method
3. A statistical technique that compares alternative phylogenetic trees with specific models of evolutionary change.
4. a model is defined by a likelihood function and a prior. represents the data-generating process; more specifically, it is the density of the data conditional on the structure of the model and conditional on the model parameters.
   •These methods are based on probability theory; they are mathematical models with defined parameters that accounts for our knowledge about the evolution underlining the data set (hence, about our study group). Parameters are set in advance and then applied to the data set of characters to calculate the most probable phylogenic tree.
   •They have been applied only two molecular data for a long time, but now we are also able to set parameters for morphological data. 

Why are using different phylogenic message to reconstruct phylogenies:
•Because of the DNA structure, genetic mutations that change an A base to a G base are much more common than mutations that change an A base to a T or C base.
•Maximum likelihood and the Bayesian likelihood can take this into account and generate trees that are more likely to be accurate based on bio chemical information about which bases are likely to mutate into one another. 
•Parsimony cannot account for this! It just provides the most parsimonious trees.

Molecular phylogenetics
•Most systematists conduct phylogenic analysis using molecular characters, such as nucleotide bases sequence of DNA and RNA. 
•Because DNA is inherited, shared changes in molecular sequences insertions, deletions, or substitutions, provide clues to the evolutionarily relationships of organisms.

Question 30

Molecular clock

Answer 30

•Because mutations that arise in non-coding regions of DNA do not affect protein structure, they are probably not often eliminated by natural selection.
•If mutations accumulate in these segments at a reasonably consistent rate, differences in their DNA sequences can serve as a molecular clock, indexing the time with two species diverged. 

Question 31

Punctuated equilibrium (pl. equilibria)

Answer 31

•In the early 1970s, Stephen J. Gould and Niles Eldredge challenged the strictly gradualistic view saying that there is sufficient fossil evidence to show that some species remain essentially the same for millions of years (stasis$ and then and then underwent short periods of very rapid, major change (associated with speciation events).
•They suggested essentially that a more accurate model in such species evolutionary history would be a punctuated equilibrium rather than a gradual change. 

Misconceptions (does not)
•Suggest that Darwins theory of evolution by natural selection is wrong.
•Mean that the central conclusion for evolutionary theory, which is that organisms share a common ancestor, no longer holds. 
•Negate previous work on how evolution by natural selection works.
•Imply that evolution only happens in rapid bursts.

•It just emphasizes that Mac revolutionary changes sometimes a peer relatively fast after longer periods of stasis during which micro evolution and mechanisms were accumulating genetic differences.
•It often tends to match better with the evolutionary changes found in the fossil record, because the fossil record is incomplete ( = when we find fossils with different anatomical characteristics, we defined them as different species—morphological species concept)

Question 32

Phyletic gradualism

Answer 32

•A model of long-term gradual change is usually referred to as gradualism or phyletic gradualism.
•It is essentially Darwins idea that species evolve slowly add a more or less steady rate.
•A natural consequence of this sort of macroevolution would be the slow progressive change of one species into the next in line (along a branch or lineage in a phylogeny)

Question 33

How do we begin to categorize, classify and name organisms?

Answer 33

•form, colour, size, chemical structure, genetic makeup… are some ways to create categories (I.e., classify)

• the key is “similarity” of some sort

•earliest attempts used general appearance:
-anatomy
-physiological similarities (things that aren’t that apparent).

•today: more focus on molecular similarities, protein, DNA, etc.

Question 34

Problems with common names

Answer 34

•different names for same species
-common names differ among countries and languages.
-ex: horse = pferd (german) = cavallo (Italian)
-Problem can occur within same language and country.
-ex: northern pike = jackfish

•same name for different species
-ex magpie.
-north American species is pica hudsonia (corvidae), Australian is Gymnorhina tibicen (cracticidae)

•common may have imply relationships that don’t exist
-ex: northern wasterthrush is actually a warbler(Parulidae) and not a thrush (Turdidae)