Download Chapter 2: The Chemical Context of Life

Chapter 25:
Phylogeny and Systematics
phylogeny – evolutionary history of a
species or group of species
systematics – analytical approach
to understanding the diversity and
relationships of present and past
organisms
Phylogenies based on common
ancestors using fossil, morphological
and molecular evidence
the fossil record – based mostly on the
sequence in which fossils have
accumulate in sedimentary rock strata
(layers)
Sedimentary rock forms when silt
builds up on bottom of waterway.
More deposited on top, compress
older sediments into rock.
morphological and molecular
homologies
• organisms with similar morphology or similar
DNA closely related
analogy is not homology; analogy is a
similarity due to convergent evolution
(organisms adapting to similar
environment/niche but no common
ancestor)
• distinguishing analogy from homology critical
to constructing phylogenies
homoplasies – analogous structures
that have evolved independently
Marsupial
mole
(Australia)
No recent common ancestor
eutherian
mole
(North
America)
molecular homologies
• compare nucleic acids of two species; if very
similar, organisms closely related
• a hard to tell how long ago they shared a
common ancestor; must also look at fossil
record
• mathematical tools can distinguish between
distant homologies from coincidental matches
Systematics connects classification
with evolutionary history
taxonomy
– ordered
division of
organisms
into
categories
bionomial nomenclature – scientific
name
• binomial – 2- part scientific name developed
by Linnaeus “Linnean system”
• genus – first part of name
• specific epithet – second part of name
Homo sapiens = humans, means “wise man”
Heirarchical classification
•
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Domain
Kingdom
Phylum
Class
Order
Family
Genus
Species
mnemonic to help you remember:
“Dreadful King Phillip Came
Over From Great Spain”
Linking classification with phylogeny
phylogenetic trees – branching
diagrams that depict hypotheses about
evolutionary relationships.
• uses groups nested within more inclusive groups
• constructed from series of dichotomies
(2-way branch points)
• each branch point represents a divergence of two
species from a common ancestor
cladogram – shows patterns of shared
characteristics
clade – group of species that includes
an ancestral species and all of its
descendants
cladistics – analysis of how species
grouped into clades
• clades can be nested
inside larger clades
– ex. cat family
within a larger clade
that includes dog
family
monophyletic group – ancestral
species and all of its descendants
paraphyletic group– when we lack
information about some members of
the clade
polyphyletic group– several species
that lack a common ancestor (need
more work to uncover species that tie
them together into a monophyletic
clade)
Shared Characteristics – types of
homologous similarities
Chordate characteristics
Shared primitive character –
shared beyond the taxon.
Shared derived character –
evolutionary novelty unique to that
clade.
Ex. hair only found in mammals
Why morphology alone does not
show evolutionary relationship:
• Closely related organisms not always similar in
appearance (rapid environmental change leads to
rapid evolution; also, small changes in genes can
lead to large morphological differences)
• Organisms that appear similar not always closely
related (convergent evolution)
• Just because 2 groups share primitive characters
does not mean they are closely related
outgroups – species or group of
species closely related to the ingroup
• less closely related than members of the
ingroup
• have a shared primitive character that
predates both ingroup and outgroup members
phylogenetic trees – show estimated
time since divergence
• chronology of a phylogenetic tree is relative;
not absolute
phylograms – length of a branch reflects
number of changes in a DNA sequence
ultrametric trees
– length of branch
reflects amounts
of time
maximum parsimony “Occam’s Razor”
– first investigate the simplest explanation
that is consistent with the facts
• Aim is to find the shortest tree that has the
smallest number of changes
The top tree
has the
most
parsimony
maximum
likelihood – given
certain rules of
how DNA changes
over time, a tree
can be found that
reflects the most
likely sequence of
evolutionary
events
Often the most parsimonious tree is
also the most likely
phylogenic trees are hypotheses of
how the organisms are related to each
other
• Best hypothesis is one that fits all the
available data
• May be modified when new evidence
introduced
• Sometimes there is compelling evidence that
the best hypothesis is not the most
parsimonious
Organisms’ genomes document their
evolutionary history
• importance of studying rRNA and
mitochondrial DNA (mtDNA)
rRNA changes very slowly; used to
study divergences that happened a
very long time ago
mtDNA changes very rapidly; used to
study divergences that happened
recently
• – useful for studying relationships between
groups of humans
ex. how Native
Americans
descend from
Asian population
that crossed the
Bering Land Bridge
13,000 years ago
Gene duplication one of most
important types of mutation in
evolution because it increases # of
genes in genome.
• can lead to further evolutionary changes
gene families – groups of related
genes in an organism’s genome
• result of repeated duplications
• have a common ancestor
orthologous genes – homologous
genes passed in a straight line from
one generation to the next.
• can diverge only after speciation
• can be found in separate gene pools due to
speciation
paralogous genes – result of gene
duplication. Found in more than one
copy of the same genome
• can diverge in the same gene pool
Genome evolution
• Orthologous genes are widespread and can
extend over huge evolutionary distances
• 99% of genes in humans and mice are
orthologous; 50% of genes in humans and
yeast are orthologous
– demonstrates that all living organisms share
many biochemical and developmental
pathways
Molecular clocks – way of measuring
absolute time of evolutionary change
• based on some genes seem to evolve at a
constant rate
• # of nucleotide substitutions in orthologous
genes is proportional to time elapsed since
the species branched from common ancestor
neutral theory – for genes that
change regularly enough to use as a
molecular clock, these changes are
probably a result of genetic drift and
are mostly neutral (neither adaptive
nor detrimental)
• conclusion: much
evolutionary change
has no effect on
fitness; therefore,
not influenced by
selection.
• most new mutations
are harmful and
therefore removed
quickly
The universal tree of life
• Genetic code universal to all forms of life so
all life must share a common ancestor
• Researchers trying to link all organisms in a
“tree of life”
• use rRNA genes for this; as they evolve most
slowly
The Tree of Life has three domains:
bacteria, archae and eukarya
The early history of these domains is
not yet clear
• due to horizontal gene transfer, substantial
interchanges of genes between organisms of
different domains
• horizontal gene transfer due to transposable
elements and fusion of different organisms
(first eukaryote fusion of ancient bacteria with
ancient archae)