envs lecture 3 Flashcards
1
Q
taxonomy
A
science of describing, naming, classifying organisms
2
Q
taxon
A
unit of taxonomic classification
3
Q
plural of taxon
A
taxa
4
Q
systematics
A
study of biological diversity and evolutionary relationships among organisms
5
Q
extinct
A
no longer present
6
Q
extant
A
taxa that exist today
7
Q
phylogeny
A
history of descent of a group of taxa from their common ancestors
8
Q
phylogenetics
A
study of phylogenies
9
Q
phylogenetic trees
A
diagrams taht depict phylogenies
10
Q
what is taxonomy
A
used to organize groups of species into progressively smaller hierarchical groups
11
Q
originally what was the most inclusive taxonomic group
A
kingdom
12
Q
what system was used for many years
A
5 kingdom system
13
Q
what are the 5 kingdoms
A
monera, protista, fungi, plantae, animalia
14
Q
monera
A
single celled prokaryotic organisms (cells don’t have nucleus) w/ no true nuclear membrane
15
Q
example of monera
A
bacteria
16
Q
protists
A
mostly single celled eukaryotic organisms (meaning cell has a nucleus),
17
Q
examples of protists
A
amoebas
17
Q
multicellular protists
A
kelp, red algae, slime molds
18
Q
fungi
A
eukaryotic organisms with chitin in cell wallys
19
Q
examples of fungi
A
yeasts, molds, mushrooms
20
Q
what are fungi
A
heterotrophs (liike animals)
21
Q
how do heterotrophs take in food
A
take in food, don’t make food; do this by secreting digestive enzymes and absorbing nutrients
22
Q
plantae
A
multicellular eukaryotes
23
Q
how do plantae make their living
A
photosynthesis
24
do plantae make their own food
yuh
25
animalia
multicellular eukaryotes
26
how do animalia make their living
consuming organic material
27
how do animalia reproduce
sexually (unique development)
28
3 domain system
eukarya, prokarya/bacteria, archaea
29
eukarya
multicellular eukaryotes
30
bacteria
prokaryotes
31
archaea
single celled prokaryotes
32
another name for archaea
extremophiles
33
one purpose of taxonomy
to name species
34
who did modern species taxonomy start with
Carl Linnaeus
35
what did Linnaeus do
introduced binomial nomenclature in 1753 'species plantarum' and 'systema naturae'
36
describe binomial nomenclature
each species has two parts, a genus and a species
37
how is studying systematics interesting
relatedness
38
describe relatedness
who is most closely related to who; are dogs more closely related to cats or pigs, etc.
39
eagles and falcons
due to molecular phylogenetic data, falcons are more closely related to parrots and songbirds than hawks
40
shrews
elephant shrews are more closely related to elephants than shrews
41
why else is studying systematics interesting
trait evolution and comparative biology
42
trait evolution and comparative biology
phylogenetic trees provide a foundation for understanding many aspects of evolutionary history, like pathways thru which various characters evolved [how many times did wings evolve? etc.]
43
another reason why studying systematics is interesting
cutting edge technology
44
cutting edge technology
use of molecular data, including whole genome sequences
45
yet another reason why its interesting
detective work
46
detectie work
we can't observe evolutionary history, must infer it by phylogenetic methods [use characters on living organisms, fossils, DNA to give clues]
47
tree of life metaphor
200 yrs before darwin they used tree as a representation of the history of life
48
what is tree of life/universal tree of life used for
metaphor, model, research tool used to explore evolution of life and describe relationships b/w organisms, living and extinct
49
basically what do trees show
ancestor, descendant relationships; history of evolutionary lineages that have branched over time
50
root
common ancestor of all taxa
51
node
a branchpoint in a tree
52
clade
a group of two or more taxa that includes both their common ancestor and all their descendents
53
what do phylogenetic trees do
depict lines of descent from common ancestors; hierarchical in pattern
54
monophyletic group
includes ALL the descendants of a common ancestor
55
another way to describe monophyletic group
a taxon that is a clade
56
what is in monophyletic group
most recent common ancestor of a group of organisms and all its descendants
57
basically what does monophyletic mean
the group of descendants in question share a common ancestor
58
what are trees formed from
nested monophyletic groups
59
are phylogenetic trees hierarchical
yeah
60
how do we know if a group is monophyletic
rotate the node, see if highlighted box will fit the same taxa inside
61
what is a clade
monophyletic group; includes ALL and ONLY the descendants of a particular ancestor
62
what are groups that are non-monophyletic?
paraphyletic
63
paraphyletic group
group that includes some but not all of the descendants of a common ancestor
64
polyphyletic group
members of multiple evolutionary lineages, but don't include the most recent common ancestor + descendants
65
does length of branches matter
no; don't tell us anything about evolutionary descent
66
does order of letters matter
no; rotating the branches doesn't change relationships
67
why are phylogenies important
provide objective criterion for organizing biodiversity, framework for posing and testing biological questions, predictive power
68
synapomorphies
shared derived traits
69
what diagnoses monophyletic groups
synapomorphies
70
how do we infer phylogeny
synapomorphies
71
what are newly evolved characters that are shared
synapomorphies
72
apomorphy
newly evolved character that ISNT shared
73
do apomorphies tell us about evolution
nope
74
homologous characters
characters that a given set of organisms have inherited from their common ancestor
75
character
particular trait of interest (number of digits on the forelimb)
76
character state
a given character can have many different character states (5 digits on forelimb, one digit on forelimb, etc.)
77
ingroup
the group on interest, assumed to be monophyletic w/r to outgroup
78
what is ingroup w/r to outgroup
assumed to be monophyletic
79
what is outgroup
group of taxon related to ingroup
80
steps
number of inferred changes in character state on a tree
81
most parsimonious tree
tree w/ shortest number of steps or changes
82
plesiomorphy
ancestral character state
83
symplesiomorphy
shared ancestral characters, not phylogenetically informative
84
apomorphy
derived character state
85
synapomorphy
shared derived character, most useful for inferring phylogenetic relatedness
86
autapomorphy
unique derived character state, not useful for inferring relationships, but helpful for identification of species
87
what does cladistics use
parsimony/occam's razor
88
what is occam's razor
among competing hypotheses, the one w/ fewest assumptions should be selected
89
homoplasy
convergence
90
what happens when there's a lot of homoplasy/convergence in characters
parsimony does a poor job of reconstructing phylogenetic relationships; model based statistical approaches are better
91
convergent evolution
homoplasy
92
what is best option for dealing w/ long branches
model based methods able to take into account probability of reversals in character states
93
maximum likelihood (ML)
given a specific model of evolution and a possible tree, this method calculates the likelihood of observing the data, and the algorithms used in analysis calculate this likelihood score across many trees and optimize that likelihood to determine which tree is best
94
bayesian
maximized the probability of observing a particular tree, given the model and the data, unlike the ML method, Bayesian analysis provides the probability of a set of different trees so that they can be compared and summarized
95
what else can we use phylogenies for besides species
to shed light on the history among individuals and populations wihtin a single species
96
what else can phylogenies use to make (what kinda trees)
gene trees, gene geneologies
97
what are gene trees
shows which haplotypes are more closely related within a region
98
what is gene duplication followed by
speciation
99
orthologous genes
loci in diff species descended from same locus in most recent ancestor
100
paralogous genes
loci in same/diff species descended from diff duplicate genes in ancestral species
101
are orthologs homologous loci
yes
102
who is more closely related orthologs or paralogous loci
orthologs/ homologous loci
103
what does each branching event in a tree denote
gene duplication event
104
what does gene phylogeny tell us
about relative timing of these events, helps us infer when duplications occur (creating alpha and beta hemoglobin families and within these gene subfamilies)
105
what else can we use phylogenies to do
to make inferences about evolution of physical traits (ex. evolution of opposable toes in hominids)
106
what else can molecular phylogenetic studies do
study timing of diversification and events
107
what do differences in sequences in concert w/ estimates of timing of splits do
serve as molecular clock, used to calibrate evolutionary trees to absolute time
108
homoplasy
independent evolution of a character/character state on a phylogenetic tree
109
three classes of homoplasy
convergent evolution, parallel evolution, evolutionary reversal
110
what else can we use evolutionary trees to do
help tease apart evolution of similarities among species due to independent evolution of similar characters over evolutionary time
111
convergent evolution
ex. hummingbirds and sunbirds independently evolving long, slender bills for feeding
112
what do phylogenies describe
patterns of diversification
113
what can phylogenies be used to reconstruct
history of adaptive radiations
