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evolution > envs lecture 3 > Flashcards

envs lecture 3 Flashcards

1
Q

taxonomy

A

science of describing, naming, classifying organisms

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2
Q

taxon

A

unit of taxonomic classification

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3
Q

plural of taxon

A

taxa

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4
Q

systematics

A

study of biological diversity and evolutionary relationships among organisms

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5
Q

extinct

A

no longer present

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6
Q

extant

A

taxa that exist today

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7
Q

phylogeny

A

history of descent of a group of taxa from their common ancestors

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8
Q

phylogenetics

A

study of phylogenies

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9
Q

phylogenetic trees

A

diagrams taht depict phylogenies

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10
Q

what is taxonomy

A

used to organize groups of species into progressively smaller hierarchical groups

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11
Q

originally what was the most inclusive taxonomic group

A

kingdom

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12
Q

what system was used for many years

A

5 kingdom system

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13
Q

what are the 5 kingdoms

A

monera, protista, fungi, plantae, animalia

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14
Q

monera

A

single celled prokaryotic organisms (cells don’t have nucleus) w/ no true nuclear membrane

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15
Q

example of monera

A

bacteria

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16
Q

protists

A

mostly single celled eukaryotic organisms (meaning cell has a nucleus),

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17
Q

examples of protists

A

amoebas

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17
Q

multicellular protists

A

kelp, red algae, slime molds

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18
Q

fungi

A

eukaryotic organisms with chitin in cell wallys

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19
Q

examples of fungi

A

yeasts, molds, mushrooms

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20
Q

what are fungi

A

heterotrophs (liike animals)

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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

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22
Q

plantae

A

multicellular eukaryotes

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23
Q

how do plantae make their living

A

photosynthesis

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24
Q

do plantae make their own food

A

yuh

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25
Q

animalia

A

multicellular eukaryotes

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26
Q

how do animalia make their living

A

consuming organic material

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27
Q

how do animalia reproduce

A

sexually (unique development)

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28
Q

3 domain system

A

eukarya, prokarya/bacteria, archaea

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29
Q

eukarya

A

multicellular eukaryotes

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30
Q

bacteria

A

prokaryotes

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31
Q

archaea

A

single celled prokaryotes

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32
Q

another name for archaea

A

extremophiles

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33
Q

one purpose of taxonomy

A

to name species

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34
Q

who did modern species taxonomy start with

A

Carl Linnaeus

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35
Q

what did Linnaeus do

A

introduced binomial nomenclature in 1753 ‘species plantarum’ and ‘systema naturae’

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36
Q

describe binomial nomenclature

A

each species has two parts, a genus and a species

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37
Q

how is studying systematics interesting

A

relatedness

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38
Q

describe relatedness

A

who is most closely related to who; are dogs more closely related to cats or pigs, etc.

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39
Q

eagles and falcons

A

due to molecular phylogenetic data, falcons are more closely related to parrots and songbirds than hawks

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40
Q

shrews

A

elephant shrews are more closely related to elephants than shrews

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41
Q

why else is studying systematics interesting

A

trait evolution and comparative biology

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42
Q

trait evolution and comparative biology

A

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.]

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43
Q

another reason why studying systematics is interesting

A

cutting edge technology

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44
Q

cutting edge technology

A

use of molecular data, including whole genome sequences

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45
Q

yet another reason why its interesting

A

detective work

46
Q

detectie work

A

we can’t observe evolutionary history, must infer it by phylogenetic methods [use characters on living organisms, fossils, DNA to give clues]

47
Q

tree of life metaphor

A

200 yrs before darwin they used tree as a representation of the history of life

48
Q

what is tree of life/universal tree of life used for

A

metaphor, model, research tool used to explore evolution of life and describe relationships b/w organisms, living and extinct

49
Q

basically what do trees show

A

ancestor, descendant relationships; history of evolutionary lineages that have branched over time

50
Q

root

A

common ancestor of all taxa

51
Q

node

A

a branchpoint in a tree

52
Q

clade

A

a group of two or more taxa that includes both their common ancestor and all their descendents

53
Q

what do phylogenetic trees do

A

depict lines of descent from common ancestors; hierarchical in pattern

54
Q

monophyletic group

A

includes ALL the descendants of a common ancestor

55
Q

another way to describe monophyletic group

A

a taxon that is a clade

56
Q

what is in monophyletic group

A

most recent common ancestor of a group of organisms and all its descendants

57
Q

basically what does monophyletic mean

A

the group of descendants in question share a common ancestor

58
Q

what are trees formed from

A

nested monophyletic groups

59
Q

are phylogenetic trees hierarchical

A

yeah

60
Q

how do we know if a group is monophyletic

A

rotate the node, see if highlighted box will fit the same taxa inside

61
Q

what is a clade

A

monophyletic group; includes ALL and ONLY the descendants of a particular ancestor

62
Q

what are groups that are non-monophyletic?

A

paraphyletic

63
Q

paraphyletic group

A

group that includes some but not all of the descendants of a common ancestor

64
Q

polyphyletic group

A

members of multiple evolutionary lineages, but don’t include the most recent common ancestor + descendants

65
Q

does length of branches matter

A

no; don’t tell us anything about evolutionary descent

66
Q

does order of letters matter

A

no; rotating the branches doesn’t change relationships

67
Q

why are phylogenies important

A

provide objective criterion for organizing biodiversity, framework for posing and testing biological questions, predictive power

68
Q

synapomorphies

A

shared derived traits

69
Q

what diagnoses monophyletic groups

A

synapomorphies

70
Q

how do we infer phylogeny

A

synapomorphies

71
Q

what are newly evolved characters that are shared

A

synapomorphies

72
Q

apomorphy

A

newly evolved character that ISNT shared

73
Q

do apomorphies tell us about evolution

A

nope

74
Q

homologous characters

A

characters that a given set of organisms have inherited from their common ancestor

75
Q

character

A

particular trait of interest (number of digits on the forelimb)

76
Q

character state

A

a given character can have many different character states (5 digits on forelimb, one digit on forelimb, etc.)

77
Q

ingroup

A

the group on interest, assumed to be monophyletic w/r to outgroup

78
Q

what is ingroup w/r to outgroup

A

assumed to be monophyletic

79
Q

what is outgroup

A

group of taxon related to ingroup

80
Q

steps

A

number of inferred changes in character state on a tree

81
Q

most parsimonious tree

A

tree w/ shortest number of steps or changes

82
Q

plesiomorphy

A

ancestral character state

83
Q

symplesiomorphy

A

shared ancestral characters, not phylogenetically informative

84
Q

apomorphy

A

derived character state

85
Q

synapomorphy

A

shared derived character, most useful for inferring phylogenetic relatedness

86
Q

autapomorphy

A

unique derived character state, not useful for inferring relationships, but helpful for identification of species

87
Q

what does cladistics use

A

parsimony/occam’s razor

88
Q

what is occam’s razor

A

among competing hypotheses, the one w/ fewest assumptions should be selected

89
Q

homoplasy

A

convergence

90
Q

what happens when there’s a lot of homoplasy/convergence in characters

A

parsimony does a poor job of reconstructing phylogenetic relationships; model based statistical approaches are better

91
Q

convergent evolution

A

homoplasy

92
Q

what is best option for dealing w/ long branches

A

model based methods able to take into account probability of reversals in character states

93
Q

maximum likelihood (ML)

A

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
Q

bayesian

A

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
Q

what else can we use phylogenies for besides species

A

to shed light on the history among individuals and populations wihtin a single species

96
Q

what else can phylogenies use to make (what kinda trees)

A

gene trees, gene geneologies

97
Q

what are gene trees

A

shows which haplotypes are more closely related within a region

98
Q

what is gene duplication followed by

A

speciation

99
Q

orthologous genes

A

loci in diff species descended from same locus in most recent ancestor

100
Q

paralogous genes

A

loci in same/diff species descended from diff duplicate genes in ancestral species

101
Q

are orthologs homologous loci

A

yes

102
Q

who is more closely related orthologs or paralogous loci

A

orthologs/ homologous loci

103
Q

what does each branching event in a tree denote

A

gene duplication event

104
Q

what does gene phylogeny tell us

A

about relative timing of these events, helps us infer when duplications occur (creating alpha and beta hemoglobin families and within these gene subfamilies)

105
Q

what else can we use phylogenies to do

A

to make inferences about evolution of physical traits (ex. evolution of opposable toes in hominids)

106
Q

what else can molecular phylogenetic studies do

A

study timing of diversification and events

107
Q

what do differences in sequences in concert w/ estimates of timing of splits do

A

serve as molecular clock, used to calibrate evolutionary trees to absolute time

108
Q

homoplasy

A

independent evolution of a character/character state on a phylogenetic tree

109
Q

three classes of homoplasy

A

convergent evolution, parallel evolution, evolutionary reversal

110
Q

what else can we use evolutionary trees to do

A

help tease apart evolution of similarities among species due to independent evolution of similar characters over evolutionary time

111
Q

convergent evolution

A

ex. hummingbirds and sunbirds independently evolving long, slender bills for feeding

112
Q

what do phylogenies describe

A

patterns of diversification

113
Q

what can phylogenies be used to reconstruct

A

history of adaptive radiations

evolution (13 decks)

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