CHAPTER 25 PHYLOGENY AND SYSTEMATICS

Lecture Outline
The fossil record and geological time
The fossil record
Phylogeny and continental drift
The history of life is punctuated by mass extinction
Systematics: connecting classification to phylogeny
Taxonomy is a hierarchical system
Modern phylogeny is based on cladistics
Phylogenetic trees are hypotheses
Molecular clocks and modern systematics

Systematics & Phylogeny
Systematics: study of biological diversity in an evolutionary context

Phylogeny: the evolutionary history of a species or group of related species

The Fossil Record
Fossils: preserved remnants or impressions left by organisms that lived in the past
Sedimentary rock: layered deposits from the bottom of ancient seas and swamps; rich source of fossils
Fossil record: ordered array of fossils in sedimentary rock; frozen in time
- palaeontologists collect, date and interpret fossils

Fossilization
organic material in dead organisms is replaced with minerals from groundwater
- cast in the shape of the organism
-
Complete skeletons, parts or fragments
Mineralized fossils & fossils with organic material

Trace fossils: footprints, burrows, or other impressions left by activities of animals
-

complete fossils in resin or ice

Methods to date fossils 1
Relative dating:
younger sediments are
superimposed upon
older ones
strata at one location
can be correlated in
time to those at another
through index fossils
-

Table 25.1

Methods to date fossils 2
Radiometric dating: measurement of certain radioactive isotopes in fossils or rocks
most common method to determine absolute ages
measure ratio of ‘parent isotope’ and ‘daughter isotopes’
e.g. carbon 14 ? decays to nitrogen 14
half life 5730 years
-
e.g. uranium 238 ? ? ? lead 206
half life 4.5 billion years
-

Ratio of carbon 14 : carbon 12
proportions in atmosphere known = proportions in live organisms
in dead organisms, carbon 14 decays to nitrogen 14
- ratio carbon 14 to carbon 12 changes
- losses of carbon 14 can be translated into absolute time

The fossil record is an incomplete chronicle of evolutionary history
discovery of fossils depends
on improbable events:
organism must die at the right place and time
rock layer with fossils must escape destruction
fossil must be exposed, found and recognized
-
-

Phylogeny and continental drift
continents are not fixed
drift on Earth’s surface as plates of crust floating on the hot mantle

Figure 25.3x1 Crustal plate boundaries

Fig. 25.3b Events at plate boundaries

continents today:

about 180 million yearsago, Pangaea began to breakup into separate continents

about 250 million years ago, all the land masses were joined into one supercontinent, Pangaea
- shoreline reduced
- harsh climate
- overall diversity reduced

Table 25.1 & Fig 25.4

Diversity of life and periods of mass extinction
fossil record shows five to seven severe mass extinctions
but overall increase in species diversity

Permian mass extinction (250 million years ago)
claimed about 90% of all marine species & many terrestrial species
causes: formation of Pangaea, volcanic eruptions

Cretaceous mass extinction (65 million years ago)
claimed half of the marine species & many families of terrestrial plants and animals (most dinosaurs)
causes: climate change (cooler) & drop in sea level, volcanic eruptions in India, impact of large asteroid

Evidence for impact of asteroid:
Chicxulub crater (65-million-year-old)
widespread layer of clay with iridium
Figure 25.6 Chicxulub crater

Pros and cons of mass extinction
-loss of species, but tremendous opportunities for survivors
-adaptive radiation to fill ecological niches crested or vacated by extinction

CHAPTER 25 PHYLOGENY AND SYSTEMATICS
Lecture Outline
The fossil record and geological time
The fossil record
Phylogeny and continental drift
The history of life is punctuated by mass extinction
Systematics: connecting classification to phylogeny
Taxonomy is a hierarchical system
Modern phylogeny is based on cladistics
Phylogenetic trees are hypotheses
Molecular clocks and modern systematics

Taxonomy is hierarchical
Linnean system: proposed by Carl Linneaus in Systema naturae in 1740
binomial system : each species has a two-part name
e.g. Panthera tigris
genus species
-

Genera are grouped into progressively broader categories:
each taxonomic level is more comprehensive than the previous one
taxon = taxonomic unit
e.g. mammalia = taxon at the class level

Phylogenetic trees: taxonomic groups are nested within more inclusive groups.

Modern phylogenetic systematics is based on cladistic analysis
phylogeny =
determined by fossil, molecular & anatomical evidence
phylogenetic systematists use cladistic analysis to analyze the data
cladogram = phylogenetic diagram constructed from a series of dichotomous relationships
clade = cladogram branch
- ancestor B lived longer ago than ancestor A

Constructing a cladogram
the more homologous parts that two species share, the more closely related they are
e.g. forelimbs of tetrapods
are homolog
the more complex two structures are, the less likely that they evolved independently
e.g. skulls of human and chimpanzee

Homolog or analog?
homologous structures: similarity in form attributed to shared ancestor
e.g. all tetrapods share a common four-legged ancestor

analogous adaptations result from convergent evolution
e.g. succulent desert plants

Homolog or analog?
depends on the level of the examined clade:
forelimbs are homologous at the level of tetrapods

but wings of bats and birds
are analogous, because flight
was developed independently

Derived and primitive characters
shared derived character: unique to a particular clade
e.g. hair of mammals - not found in other tetrapods
shared primitive character: found in the clade being analyzed, but also in older clades
e.g. backbone - found in mammals and all tetrapods
-

Constructing a cladogram
Outgroup comparison: used to differentiate shared primitive characters from shared derived ones
Outgroup:
group of species that is closely related to studied species
but less closely related than any of the study-group members to each other
homologies shared by ingroup and outgroup must be primitive characters
homologies present in ingroup must have evolved after divergence of ingroup and outgroup

ingroup / outgroup relationship:
vertebral column shared by members of ingroup, but not by outgroup - shared derived character
notochord shared by all - shared primitive character
--

Molecular systematists
comparing genes and proteins among organisms to reveal homologies
- the more recently two species have branched from a common ancestor, the more similar their DNA and amino acid sequences should be

allows to assess phylogenetic relationships that cannot be measured by comparative anatomy and other non-molecular methods
e.g. morphologically similar species

DNA comparisons: align homologous DNA sequences of the two species
Ancestral homologous
DNA sequences

Deletion or insertion may
shift DNA sequences

Homologous DNA sequences
do not always align

Align DNA sequences using
computer program

rates of change in DNA sequences vary:
DNA coding for ribosomal RNA (rRNA) changes relatively slowly
- useful in investigating relationships between taxa that diverged hundreds of millions of years ago.
mitochondrial DNA (mtDNA) changes relatively rapidly
- can be used to assess the phylogeny of species that are closely related

Molecular clocks
some regions of genomes evolve at constant rates
number of nucleotide and amino acid substitutions between two lineages is proportional to the time that has elapsed since they branched
e.g. homologous proteins of bats and dolphins are more alike than those of sharks and tuna
-sharks and tuna have been on separate evolutionary paths much longer than bats and dolphins

e.g. dating the origin of a HIV strain:

calibrate molecular clock by comparing DNA sequences in a specific HIV gene sampled at different times

project data back in time: HIV-1M strain invaded humans in the 1930s

Modern systematics
cladistic analysis takes into account the fossil record, morphological and molecular characters
e.g. relationship of crocodiles,birds, lizards and snakes:
fossil record, comparative anatomy, and molecular comparisons agree

Key terms 25
phylogeny
fossil record
geological time sclae
radiometric dating
half life
Pangaea
systematics
binomial
species
genus
family
order
class
phylum/phyla
kingdoms
domain
taxon/taxa
phylogenetic tree
cladogram
clade
monophyletic
homology
convergent evolution
analogy
shared primitive character
shared derived character
outgroup
ingroup
molecular clocks