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Page 1: Phylogeny [phylo = tribe, family; gen = creation, birth] taxonomy: classifying and naming organisms taxon, taxa (pl.): classification unit (e.g. genus,

Phylogeny [phylo = tribe, family; gen = creation, birth]

taxonomy: classifying and naming organisms

taxon, taxa (pl.): classification unit (e.g. genus, order)

systematics: taxonomy based on phylogeny

cladistics: modern approach to systematics

clade: group of spp. with common ancestor

Biological diversity and classification

Biol 121, Fall 2010, Tom Buckley 01 Sep 10

Page 2: Phylogeny [phylo = tribe, family; gen = creation, birth] taxonomy: classifying and naming organisms taxon, taxa (pl.): classification unit (e.g. genus,

Biological diversity and classification

Reminders:

1. print out the lab handout from WebCT

and bring it to lab

2. bring your textbook to lab

Page 3: Phylogeny [phylo = tribe, family; gen = creation, birth] taxonomy: classifying and naming organisms taxon, taxa (pl.): classification unit (e.g. genus,

Hierarchy of classification

Species:Pantherapardus

Genus: Panthera

Family: Felidae

Order: Carnivora

Class: Mammalia

Phylum: Chordata

Kingdom: Animalia

ArchaeaDomain: EukaryaBacteria

Domain

Kingdom

Phylum/Division

Class

Order

Family

Genus

Species

Kids Prefer Cheese Over Fried Green Spinach King Phillip came over for great spaghetti.Keeping Precious Creatures Organized

For Grumpy Scientists

Page 4: Phylogeny [phylo = tribe, family; gen = creation, birth] taxonomy: classifying and naming organisms taxon, taxa (pl.): classification unit (e.g. genus,

Phylogenetic trees

concepts:

common ancestors

sister taxa

trees show sequence,not time

what is sister taxon

of Panthera pardus?

Page 5: Phylogeny [phylo = tribe, family; gen = creation, birth] taxonomy: classifying and naming organisms taxon, taxa (pl.): classification unit (e.g. genus,

monophyletic group: last common ancestor and all of its descendants(a.k.a. clade)

polyphyletic group: does not include last common ancestor

paraphyletic group: includes last common ancestor, but not all descendants

Phylogenetic trees

Page 6: Phylogeny [phylo = tribe, family; gen = creation, birth] taxonomy: classifying and naming organisms taxon, taxa (pl.): classification unit (e.g. genus,

Classification

Carolus Linnaeus (1707-1778)

binomial nomenclature

Homo sapiens L.

genus(always capitalised)

(abbreviated after first use)specific epithet

(never capitalised)

authority

species name (italics or underlined){

Page 7: Phylogeny [phylo = tribe, family; gen = creation, birth] taxonomy: classifying and naming organisms taxon, taxa (pl.): classification unit (e.g. genus,

Nomenclature... which is valid?

Humans are members of the species sapiens.

Humans are members of the species Homo sapiens.

Humans are members of the species Homo sapiens.

Humans are members of the species H. sapiens.

Humans are members of the species Homo Sapiens.

Page 8: Phylogeny [phylo = tribe, family; gen = creation, birth] taxonomy: classifying and naming organisms taxon, taxa (pl.): classification unit (e.g. genus,

Bison bison

Page 9: Phylogeny [phylo = tribe, family; gen = creation, birth] taxonomy: classifying and naming organisms taxon, taxa (pl.): classification unit (e.g. genus,

Marmota marmotahttp://en.wikipedia.org/wiki/List_of_tautonyms

Page 10: Phylogeny [phylo = tribe, family; gen = creation, birth] taxonomy: classifying and naming organisms taxon, taxa (pl.): classification unit (e.g. genus,

How phylogenies are inferred

homology: similarity due to shared ancestry

cf. analogy: similarity due to something else

either coincidenceor convergent evolution

e.g. opposable thumbs in orangutans and humans

e.g. wings in bats and birds

Page 11: Phylogeny [phylo = tribe, family; gen = creation, birth] taxonomy: classifying and naming organisms taxon, taxa (pl.): classification unit (e.g. genus,

Convergence: cacti vs euphorbs

Page 12: Phylogeny [phylo = tribe, family; gen = creation, birth] taxonomy: classifying and naming organisms taxon, taxa (pl.): classification unit (e.g. genus,

Convergence: cacti vs euphorbs

Page 13: Phylogeny [phylo = tribe, family; gen = creation, birth] taxonomy: classifying and naming organisms taxon, taxa (pl.): classification unit (e.g. genus,

Convergence: Equisetum vs Casuarina (diverged 400 MYA)

Page 14: Phylogeny [phylo = tribe, family; gen = creation, birth] taxonomy: classifying and naming organisms taxon, taxa (pl.): classification unit (e.g. genus,

examples: http://evolution.berkeley.edu/evolibrary/search/topicbrowse2.php?topic_id=55

How phylogenies are inferred

homology: similarity due to shared ancestry

cf. analogy: similarity due to something else

analogies are also called homoplasies

Page 15: Phylogeny [phylo = tribe, family; gen = creation, birth] taxonomy: classifying and naming organisms taxon, taxa (pl.): classification unit (e.g. genus,

How phylogenies are inferred

homology: similarity due to shared ancestry

phenotypic: based on anatomy, morphology, physiology

molecular: based on DNA sequences

Page 16: Phylogeny [phylo = tribe, family; gen = creation, birth] taxonomy: classifying and naming organisms taxon, taxa (pl.): classification unit (e.g. genus,

How phylogenies are inferred

shared ancestral characters

shared derived characters

= homologies

conifers

flowering plants

vascularseedless plant

Q: is vascular tissue homologous or analogous in conifers & flowering plants?

vascular seed plant

= analogies

Page 17: Phylogeny [phylo = tribe, family; gen = creation, birth] taxonomy: classifying and naming organisms taxon, taxa (pl.): classification unit (e.g. genus,

How phylogenies are inferred

outgroup vs ingroup

(e.g. ferns are an outgroup of seed plants)

conifers

flowering plants

seed plants

vascularseedless plant

vascular seed plant

seedsevolved

here

ferns

Page 18: Phylogeny [phylo = tribe, family; gen = creation, birth] taxonomy: classifying and naming organisms taxon, taxa (pl.): classification unit (e.g. genus,

Deducing phylogenies by parsimony

somegene

Ancestor

"ancestral sequence" = A outgroup?

ingroup?

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fewest assumptions, simplest story

AA

C

C

AC

A

C

AC

C

AAC A

# of mutations: 1 2 2

somegene

Ancestor

"ancestral sequence" = A

Deducing phylogenies by parsimony

Page 20: Phylogeny [phylo = tribe, family; gen = creation, birth] taxonomy: classifying and naming organisms taxon, taxa (pl.): classification unit (e.g. genus,

tree based on genetic data:

Induction or deduction?

birds & crocs share traits:

e.g., 4-chamber heart

shared trait:

more likely ancestral

than derived

Q: where is common ancestor of birds and crocs?

1

2

3

4

Q: when did 4-chambered heart likely evolve?

did dinosaurs have

4-chambered hearts?

YES, PROBABLY

Page 21: Phylogeny [phylo = tribe, family; gen = creation, birth] taxonomy: classifying and naming organisms taxon, taxa (pl.): classification unit (e.g. genus,

element

number of protons (atomic #)

electronic structure

chemical behaviour

Fossil dating

Page 22: Phylogeny [phylo = tribe, family; gen = creation, birth] taxonomy: classifying and naming organisms taxon, taxa (pl.): classification unit (e.g. genus,

Isotopes: different # of neutrons

Carbon-12 (12C)Carbon-14 (14C)

6 protons6 neutrons

6 protons8 neutrons

element

chemical behaviour

Page 23: Phylogeny [phylo = tribe, family; gen = creation, birth] taxonomy: classifying and naming organisms taxon, taxa (pl.): classification unit (e.g. genus,

Radiometriccosmic rays(neutrons)

14N

14CO2

12CO2 12C

14N

14C12C

14N

14C12C

14N

14C

14C

12C

isotopes

Dating fossils

Page 24: Phylogeny [phylo = tribe, family; gen = creation, birth] taxonomy: classifying and naming organisms taxon, taxa (pl.): classification unit (e.g. genus,

2 Kingdoms: animals

plants (incl. protists, prokaryotes, fungi)

Phylogenies keep changing

5 Kingdoms: prokaryotes

protists

fungi

animals

plants

3 Domains: Archaea

Bacteria

Eukarya

Many Kingdoms...

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Domains

Q: are multicellular organisms monophyletic?

red boxes:non-colonial,multicellularorganisms

monophyletic group: last common ancestor and all of its descendants

Page 26: Phylogeny [phylo = tribe, family; gen = creation, birth] taxonomy: classifying and naming organisms taxon, taxa (pl.): classification unit (e.g. genus,

Mastering Biology

http://www.masteringbiology.com/


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