Final Lecture Exam Flashcards
1
Q
Nomenclature
A
Assigning names to objects. Plants, categories used in classification
2
Q
Classification
A
Arrangement into groups that have similar characteristics.
3
Q
Describe the Linnaean Classification System
A
- God created, Linnaeus arranges
- 1753: invention of the binomial system
- Hierarchical groups but pre-darwin, so hierarchy os not the same
- Characters chosen to define groups are useful for identification, but does not define “natural, related” groups
4
Q
Describe the Hennigian Classification System + the two criteria for it
A
- Phylogenetic classification
- Modifications of the Linnean systems to take into account phylogenetic relationships
Criteria:
1. Recognize monophyletic groups
2. Sister taxa have the same rank (regardless of differences in appearance or number in the two clades).
5
Q
Phylogeny
A
Relative order of appearance of taxa forming a monophyletic group.
6
Q
Taxa
A
An taxonomic group (that possess a name), no matter what the rank.
7
Q
Sister Group
A
Two lineages that share an immediate exclusive common ancestor.
8
Q
Monophyletic
A
Includes a group’s ancestor and all its descendants.
- Based at least on one synapomorphy.
9
Q
Paraphyletic
A
Group that has a shared common ancestor, but does not include all the descendants.
- Based on the possession of symplesiomorphies.
10
Q
Polyphyletic
A
Includes organisms with mixed evolutionary origin, but does not include their most recent common ancestor.
- Based on the possession of similar characters. (converging or plesiomorphic characters).
11
Q
Synapomorphy
A
A character state shared by taxa and derived rather than representing the ancestral state.
12
Q
Symplesiomorphy
A
Character state shared by taxa, inherited unchanged from common ancestor.
13
Q
What is the goal of nomenclature and what does the code specify?
A
Goal: Obtain a single correct name for each taxon
Code specifies:
1. Rank
2. Scientific name
14
Q
What are the 3 Units of a Scientific Name?
A
Names are in Latin italiques
- Name of the genera: Capital
- Specific epithet: lower case, conjugated
- Author: 1st person to describe the species
15
Q
What is the purpose of type specimens?
A
They stabilize the application of names to taxa
16
Q
Type specimens with Rank higher than the species
A
- Select a taxon of immediately lower rank
- The name of the type taxon serves as the basis for the higher-ranking taxon
17
Q
Principal of Priority - Publication Priority
A
Only the oldest name applicable to a given taxon after comparative examination of types is valid.
- It takes precedence over any more recent name of the species rank
18
Q
What is the exception to publication priority
A
Conserved names
19
Q
Legitimate Plant Species Name
A
Oldest validly published name for a taxon
20
Q
Synonym (Plant Name)
A
Name published after a legitimate name.
21
Q
Systematics and its 3 objectives
A
The study of phylogenetic relationships between species or groups of species.
- The aim is to produce a natural classification = taxonomy
Objectives:
1. Species inventory - discovering and describing biodiversity
2. Phylogenetic analysis - understanding biodiversity
3. Classification - Managing biodiversity
22
Q
Taxonomy
A
The science of classifying organisms, including the identification, description, naming, and grouping of species
- Concerned with the organization and classification of organisms into hierarchal groups
23
Q
What is the difference between Taxonomy and Systematics?
A
- Taxonomy focuses on the identification, description, and classification of plants - - - Systematics is the study of diversity and evolutionary relationships of organisms through time. Determining evolutionary relationships of organisms
24
Q
What are some uses for herbaria in taxonomic and evolutionary studies
A
- Herbra provides a permanent record of botanical diversity
- Herbaria are a massive opportunity in the era of Big Data
- Importance for nomenclature: Repositories of type specimens
- Herbaria important for species discovery
- Important for floristic revisions
- Importance for conservation assessments of wild species
- Herbaria provide data through space and time
- Less biased data with herbarium specimens rather than just online//community based collections (such as inaturalist)
- Digitization of herbaria stimulates research
25
Describe Herbaria Data
Physical material from a species that has been collected and prepared for long term storage (dried, pressed, mounted)
- Specimens are accompanied by data from collection and taxonomic identification
26
Describe Inaturalist Observations
Digital records or species presence in a location. Observations are photos or recoding and species identity is verified ny the community. Can be considered research grade on occasion at which point the observation is added to online repositories such a GBIF.
- Can sometimes be biased towards species in highly populated areas
27
Name the major clades of land plant evolution that we have seen in class (7)
1. Ferns and Allies
2. Gymnosperms
3. Early Diverging Angiosperms
4. Monocots
5. Early Diverging Eudicots
6. Eudicots - EuRosids
7. Eudicots - EuAsterids
28
Describe the Moss Life Cycle
...
29
Describe the Lycopodium Life Cycle
...
30
Describe the Fern Life Cycle
...
31
Describe the Gymnosperm Life Cycle
...
32
What are the four major angiosperm groups?
1. ANA -
2. Magnoliid
3. Monocots
4. Eudicots
33
What is the ANA-Dicot group?
Amborella - One of the oldest flowering plant lineages, which separated from the common ancestor firsts.
- Worlds oldest living lineage of flowering plants
- First branch of the phylogenetic tree
Nymphaeaceae - Water lilies
Austrobaileyales - Woody plants growing as shrubs and lianas
34
Describe the Magnoliid-Dicot Group
Magnoliaceae
Perianth parts are undifferentiated called tepals rather than sepals and petals
35
Describe the Monocots
- Monocopalte pollen
- Trimerous floral parts
- Cambium rarely present
- Roots are typically adventitious, fibrous and fleshy
- Usually leaf veins parallels
- Predominantly herbaceous
36
Describe the Eudicots
- Monophyletic on the basis of tricolpate or triaperture pollen
- Early diverging - ranunculaceae, caryophylaceae, papaveraceae
- Rosids
- Euasterids - mostly united by flowers with epipetalous stamens that equal the number of corolla lobes and a gynoecium of two fused carpels
37
What is APG and how has it changes our understanding of modern plant classification
Angiosperm Phylogeny Group (APG)
The major outcome of the APG system is the disappearance of the traditional division of the flowering plants into two groups, monocots and dicots
38
What is ELC; and what is it's purpose in Canada
Ecological Land Classification
ELCs aim to classify ecologically distinct areas, providing a consistent national spatial context for better monitoring, reporting, and management of Canada's ecosystems.
- Canada is broken into 18 terrestrial ecozones
39
What are the ELC units from largest to smallest
1. Ecozones
2. Ecoregions
3. Ecodistricts
4. Ecosections
5. Ecosites
6. Ecoelements
40
What Defines an Ecozone?
The largest unit
Defined by:
- Broad climate patterns
- Bedrock which influence ecosystem processes
41
What defines an Ecoregion?
Each ecozone is composed of many ecoregions
Defined by:
- Defined by patterns in temperature, precipitation, humidity and other climate variables
42
What defines an Ecodistrict?
Ecoregions divided into ecodistricts
Defined by:
- Defined based on bedrock and topography that determines local vegetation and habitats in each ecodistrict
43
What defines an Ecosection?
Smaller than ecodistricts
Defined by:
- Defined based on patterns in slope, landforms, soil texture and soil moisture
44
What defines an Ecosite?
Smaller than ecosections
Defined by:
- Moisture, slope, soils, vegetation
45
What defines an Ecoelement?
Smallest units
Defined by:
- Substrate + vegetation
46
What are the four major wetland types in Canada?
1. Swamp
2. Bog
3. Marsh
4. Fen
47
Swamp
Wetland characterized by standing or gently moving water that supports woody plants, nutrient rich, waterlogged soils, pH about 4.5-7.0
48
Bog
Acidic, nutrient poor wetland containing peat, primarily fed by rain, fog and snow. Thick carpet of moss. pH levels as low as 3.0
49
Marsh
Nutrient rich wetland characterized by non-woody plants like cattails, reeds, rushes, and sedges (grasses). Typically found near rivers or lakes and drains very slowly. Neutral to slightly alkaline from 7 to or 8
50
Fen
Less acidic than bogs and have higher nutrient levels. Fed by ground water or springs and the water moves. They are typically alkaline or basic. Contains peat.
51
Parsimony
The simplest explanation that can explain data is preferred
- hypothesis of evolution that requires the smallest number of character changes is most likely to be correct.
52
How does statistics test if groups differ significantly (two means are significantly different)
T-test
- Calculates the ratio of the 'signal' to the noise'
53
What does log likelihood show (-lnl)
How good is each model at predicting the character states at the tips of the phylogeny?
- Higher log likelihood means a better fitting model
54
Asymmetric Model of Evolution
Unconstrained
- 2 transitions are free to vary (default assumption)
55
Symmetric Model of Evolution
Constrained
- 1 transition rate for both directions
56
Likelihood ratio = ...
2 x (the absolute value of the difference in likelihood values for the two models)
57
If log likelihood is > df...
The models are significantly different and the model with the higher log likelihood is the one you accept
58
Short branch lengths on a maximum likelihood tree suggests...
Few mutations between ancestors and descendants, indicating change in character state is less likely
59
Long branches of ML tree suggest...
Many mutations between ancestors and descendants, indicating change in character state is likely
60
Convergent Evolution
Repeated evolution of longer spur length in different clades
61
What would a ancestral reconstruction for a quantitative trait look like?
Continuous trait map with tips and nodes painted with a gradient of colours
62
What is a phenogram?
Trait values at tips and nodes graphed on a bivariate plot
63
What does PGLS stand for?
Phylogenetic generalized least squares
64
What is lambda in PGLS
Lambda = The amount of phylogenetic dependence
0 = no dependence on phylo
1 = Complete dependence on phylo
65
What is the slope in PGLS
The direction of the difference
- P value used to determine statistical significance
66
Correlated/dependent evolution
Does the evolution of one character state facilitate the evolution of another character state
67
how do you test whether evolutionary change in one trait depends on the state of another trait?
1. Fit independent model of evolution to the data
2. fit dependent model
3. compare the two models to see which is better fit to the data
68
What models can you use to map discrete traits?
1. Maximum Likelihood
2. Parsimony
69
How can you tell if a trait is reversible
when the rate at which a trait changes is greater than zero this implies there is always a non zero chance of cleistogamy being lost again
70
if likelihood ratio < df...
Unconstrained model and constrained models fit equally well, the rate at which a trait is lost and gained is the same
71
Can a t-test tell you if a continuous trait evolves in response to the evolution of an independent trait?
No
72
What can t-test tell us when we have one continuous and one independent trait?
1. Effect size between means
2. We can determine if the continuous trait differs significantly between the independents using p-value
73
What can create a discrepancy between likelihood test and an ancestral reconstruction?
Rarity of a trait can make it more difficult to precisely estimate how it evolves.
74
What approach should you use when visualizing ancestral states of quantitative traits?
Maximum likelihood
1. "paint the tree tips and nodes with colour code that responds to the trait value
2. Phenogram
75
When does a phenogram appear to be asymmetric and what does this imply?
When the values spread in unequal direction
Shows a trend in the data
76
When does a phenogram appear to be symmetric and what does this imply?
When evolution spreads in equal directions
Shows no trend
77
How would you test whether evolution of carnivory is correlated to with evolution of low RGR
PGLS
78
How would you determine if shared ancestry influences the relationship between carnivory and RGR
By looking at the lambda value in PGLS
- close to 1 = shared ancestry has the potential to bias the hypothesis
- Close to 0 = Relationships of traits is independent of shared ancestry
79
How would we conclude if RGR significantly differs between carnivorous and non-carnivorous plants?
Using p-value
>0.05 cannot reject the null that RGR differs significantly when accounting for shared ancestry
<0.05 reject the null - RGR differs significantly even when accounting for shared ancestry
80
How would you test for correlated evolution between 1 categorical trait and 1 continuous trait?
PGLS
81
Pagel's test
Where an independent model of trait evolution is compared against a dependent model of evolution
Compares a model where the evolution of two traits is independent to a model where the evolution of two traits is dependent
82
What test would you use when asked "is the evolution of growth forms more likely to occur in one direction, or is evolution equally likely in both directions?"
Likelihood ratio test
83
How would you test correlation between two independent variable
Pagel's test
84
In Pagel's test the lower the AIC...
The better the fit
85
In Pagel's test, when p-value is less than 0.05 log-likelihood ratio is...
Statistically Significant
86
When both dependent and independent variables are quantitative, the analysis is more like a ____ than a t-test
regression
87
What test do you use when testing correlated evolution between two quantitative variables
PGLS
88
When asked about phylogenetic dependence you look at...
Lambda
89
MAP in PGLS test is...
Slope
90
Effect Size
The magnitude and direction of the difference between means, stated using percentage or ratio
