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1
Q

phylogeny

A

(phylon - tribe, genesis - origin)

the evolutionary history of a species or group of species

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2
Q

systematics

A

an analytical approach to understanding the diversity and relationships of organisms, both present-day and extinct

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3
Q

systematists have traditionally studied __ and __ among organisms as a basis for inferring evolutionary relationships. in recent decades, systematists have gained a powerful new tool, __

A

morphological, biochemical resemblances;

molecular systematics

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4
Q

molecular systematics

A

uses comparisons of DNA, RNA, and other molecules to infer evolutionary relationships between individual genes and even btwn entire genomes

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5
Q

fossils can help establish relationships between living organisms b/c

A

they reveal ancestral characteristics that may have been lost over time in certain lineages

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6
Q

in order to infer phylogenies, we must study the __, __, and __ of living organisms, as well as __

A

morphologies, development, biochemistry, fossils

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7
Q

formation of sedimentary rocks

A

sand and silt eroded from the land are carried by rivers to seas and swamps, where the minerals settle to the bottom along w/ remains of organisms. over millions of years, deposits pile up and compress the older sediments below into layers called strata

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8
Q

fossil record

A

is based on the sequence in which fossils have accumulated in such strata

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9
Q

fossils inform phylogeny only if ________, clarifying _______

A

we can determine their ages,

the order in which various characteristics appeared and disappeared

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10
Q

the fossil record is biased

A

in favor of species that existed for a long time, were abundant and widespread, and had hard shells, skeletons, or other parts that facilitated their fossilization

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11
Q

homologies

A

similarities due to shared ancestry

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12
Q

if the morphological divergence btwn related species is great and their genetic divergence is small, then we can infer that

A

the morphological diversity of the species is controlled by relatively few genetic differences

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13
Q

analogy

A

similarity due to convergent evolution rather than to shared ancestry

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14
Q

a potential red herring in constructing a phylogeny is

A

analogy

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15
Q

convergent evolution occurs when

A

similar environmental pressures and natural selection produce similar (analogous) adaptations in organisms from diff evolutionary lineages

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16
Q

homoplasy

A

similar (analogous) structure or molecular sequence that has evolved independently in 2 species

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17
Q

another clue to distinguishing btwn homology and analogy is to consider

A

the complexity of the characters being compared

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18
Q

_____________, the less likely it is that the structures evolved independently.

A

the more points of resemblance that 2 complex structures have

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19
Q

scientists have so far sequenced _____ bases’ worth of nucleic acid data from thousands of species

A

more than 20 billion

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20
Q

the fact that molecules have diverged btwn species

A

doesnt in itself tell us how long ago their common ancestor lived

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21
Q

just as w/ morhpological characters, it’s necessary to distinguish homology from analogy to determine

A

the usefulnes sof molecular similarities for evolutionary studies

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22
Q

the discipline of systematics dates to ___ when ____

A

1748; linnaeus published systema naturae “system of nature”

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23
Q

systema naturae

A

linnaeu’s taxonomic classification of all plants and animals known at the time

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24
Q

taxonomy

A

an ordered division of organisms into categories based on a set of characteristics used to assess similarities and differences

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25
linnaeus' classification was based simply on ____ rather than on ____
resemblances; evolutionary relationships
26
2 useful features of linnaeus' ystem
1. binomial designations for species | 2. hierarchical classification
27
binomial
2-part format of the scientific name, instituted by linnaeus
28
genus
1st part of species' binomial name
29
specific epithet
2nd part of species' binomial name; is unique for each species within the genus
30
format of binomial nomenclature
first letter of genus is capitalized, entire bionomial is italicized
31
hierarchical classification from most general to most specific?
kids playing catch on freeways get smashed domain, kingdom, phylum, class, order, family, genus, species
32
taxon
the named taxonomic unit at any level
33
format of writing taxa?
taxa broader than the genus level aren't italicized, although they're capitalized
34
phylogenetic trees
branching diagrams used by systematists to depict their hypotheses about evolutionary relationships
35
a phylogenetic tree is often constructed from
a series of dichotomies, or 2-way branch points; each branch point represents the divergence of 2 species from a common ancestor
36
vintages
actual ages
37
cladogram
diagram that depicts patterns of shared characteristics
38
a cladogram by itself ______
doesn't imply evolutionary history
39
if ______, then the cladogram forms the basis of a phylogenetic tree
the shared characteristics are due to common ancestry (that is, if theyre homologous)
40
clade
within the phylogenetic tree -- a clade is defined as a group of species that includes an ancestral species and all its descendants
41
cladistics
the analysis of how species may be grouped into clades
42
monophyletic
a valid clade; pertaining to a grouping of species consisting of an ancestral species and all its descendants
43
paraphyletic
consists of an ancestral species and some, but not all, of the descendants
44
a paraphyletic grouping results when
we lack information about some members of a clade
45
after systematists have separated homologous from analogous similarties, they must sort thru the homologies to distinguish btwn __ and __
shared primitive characters and shared derived characters
46
what does "character" refer to
any feature that a particular taxon possesses
47
the characters that are relevant to phylogeny are
the homologous ones
48
shared primitive charaacter
a character that's shared beyond the taxon we're trying to define
49
shared derived character
an evolutionary novelty unique to a particular clade
50
systematists use ____ to differentiate btwn shared derived and shared primitive ccharacters
outgroup comparison
51
outgroup
speices/group that's closely related to the group of species being studied, but clearly not as closely as any study-group members are to each other
52
ingroup
the various species that are being studied
53
outgroup comparison is based on the assumption that
homologies present in both the outgroup and ingroup must be primitive characters that predate the divergence of both groups from a common ancestor
54
the species making up the ingroup display
a mixture of shared primitive and shared derived characters
55
any chronology represented by the branching pattern of a phylogenetic tree is __ rather than __
relative; absolute
56
phylogram
diagram in which the length of a branch reflects the number of changes that have taken place in a particular DNA sequence in that lineage
57
humans and bacteria had a common ancestor that lived ____ years ago, and it was a ____
over 3 billion years ago; single called prokaryote
58
ultrametric tree
same branching pattern as in a phylogram, but all the branches that can be traced from the common ancestor to the present are of equal length
59
ultrametric trees don't contain the info about ___ that can be found in phylograms
diff evolutionary rates
60
ultrametric trees can draw on data from ____ to ____
the fossil record; place certain branch points in the context of geologic time
61
maximum parsimony
principle that states that we should first investigate the simplest explanation that's consistent w/ the facts
62
the most parsimonious tree is the one that
requires the fewest evolutionary events to have occurred in the form of shared derived characters
63
for phylograms based on DNA sequences, the most parimonious tree
requires the fewest base chages
64
maximum nlikelihood
given certain rules about how DNA changes over time, a tree can be found that reflects the most likely sequence of evolutionary events
65
computer programs that search for trees that are parsimonious and likely are
1. "distance" methods minimize the total of all the percentage differences among all the sequences 2. more complex "character-state" methods minimize the total number of base changes or search for the most likely pattern of base changes among all the sequecnes
66
any phylogenetic tree represents
a hypothesis about how the various organisms in the tree are related to one another
67
applying parsimony in molecular systematics is more reliable for
a data set of many long DNA sequences than for a smaller set
68
occassionally misjudging an analogous similarity in morphology as a homologous character is less likely to distort a phylogenetic tree if
each clade in the tree is defined by several derived characters
69
molecular systematics
comparing nucleic acids or other molecules to infer relatedness
70
the ability of molecular trees to encompass both short and long periods of time is based on the fact that
diff genes evolve at diff rates, even in the same evolutionary lineage
71
since the DNA that codes for ribosomal RNA _____, _____
changes relatively slowly, comparisons of DNA sequences in these genes are useful for investigating relationships btwn taxa that diverged hundreds of millions of years ago
72
gene dulication is 1 of the most important types of mutation in evolution b/c
it increases the number of genes in the genome, providing opportnities for further evolutionary changes
73
orthologous genes
refers to homologous genes that are paassed in a straight line from one generation to the next but have ended up in diff genes pools b/c of speciation
74
paralogous genes
result from gene duplication, so they'e found in more than one copy in the same genome
75
orthologous genes can only diverge ____, w/ the result that
after speciation has taken place; the genes are found in separate gene pools
76
paralogous genes can diverge ___, b/c ____
even while they're in the same gene pool; they're present in more than one copy in the genome
77
remarkable fact about orthologous genes
they're widespread and can extend over huge evolutionary distances
78
remarkable fact about the number of genes
the number of genes seems not to have increased thru duplication at the same rate as phenotypic complexity m
79
molecular clock
yardstick for measuring the absolute time of evolutionary change based on the observation that some genes and other regions of genomes appear to evolve at constant rates
80
the assumption underlying the molecular clock is that
the number of nucleotide substitutions in orthologous genes is proportional to the time that has elapsed since the species branched from their common ancestor
81
in the case of paralogous genes, the number of substitutions is
proportional to the time since the genes became duplicated
82
we can calibrate the molecular clock of a gene that has a reliable avg rate of evolution by
graphing the number of nucleotide diffferences against the times of a series of evolutionary branch points that are known from the fossil record
83
the graph line representing the evolution rate of the molecular clock can then be used to estimate
the date of evolutionary episodes that can't be discerned from the fossil record
84
the regularity of genetic change that enables us to use some genes as molecular clocks raises the possibility that
many of the changes in these sequecnes result from genetic drift, and the changes are mostly neutral
85
neutral theory
theory that much evolutionary change in genes and proteins has no effect on fitness and therefore isn't influcned by darwinian selection
86
differences in the rate of the molecular clock in diff genes are a function of
how important each gene is
87
if the exact sequence of amino acids a gene specifies is essential to survival, ______ rate of change of genes:
most mutational changes will be harmful and only a few will be neutral slow
88
if the exact sequence of amino acids is less critical, rate of change of genes:
fewer of the new mutations will be harmful and more will be neutral. more quickly
89
in reality, the molecular clock
doesnt run as smoothly as neutral theory predicts
90
many irregularities in molecular clocks are likely to be the result of
natural selection in which some DNA changes are favored over others
91
an abundant fossil record extends back about
550 million years
92
investigators use 2 creteria to identify regions of DNA molecules that can demonstrate the branchin pattern of the tree of life:
1. regions must be able to be sequenced | 2. they must've evolved so slowly that homologies btwn even distantly related organisms can still be detected
93
b/c rRNA genes are fundamental to the workings of the cell,
their molecular clock runs so slowly that they can serve as the basis for a universal tree of life
94
tree of life has 3 domains:
bacteria archaea eukarya
95
the domain bacteria contains
most of the currently known prokarytes
96
archaea consists of
a diverse group of prokaryotic organisms that inhabit a wide variety of environments
97
eukarya conssts of
all the organisms that have cells containing true nuclei
98
comparisons of complete genomes from the 3 domains show that, esp during the early hsitory of life, there have been
substantial interchanges of genes btwn organisms in the diff domains
99
horizontal gene transfer
in which genes are transferred from one genome to another thru mechanisms such as transposable elements, and perhaps thru fusions of diff organisms
100
the 1st eukaryote may have arisen thru
a fusion btwn an ancestran bacterium and an ancestran archaean

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