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Phylogeny and the Tree of Life
Chapter 26
Systematics: Discipline focused on classification of organisms
Taxonomy: naming organisms.
Linnaeus - hierarchy of increasingly inclusive categories.
Taxon: Taxonomic unit at any level of hierarchy
Species
Pantherapardus
PantheraGenus
FamilyFelidae
CarnivoraOrder
MammaliaClass
PhylumChordata
KingdomAnimalia
EukaryaDomain
Binomial nomenclature: genus & specific epithet.
Homo sapiens
Phylogeny: evolutionary history of a group of species.
Phylogenetic tree: evolutionary relationship between species represented in a branching diagram.
Drosophila
Lanc
elet
Fish
Amph
ibia
nBird
Human
Rat
Mou
se
Phylogenetic tree
represents a hypothesis about evolutionary relationships
relationships are represented by a series of dichotomies (branch points)
sister taxa: group of organisms that share an immediate common ancestor (branch point)
branch points within the tree represents the last common ancestor of all taxa in the tree
Polytomy: branch point with more than 2 descendant groups.
Limitations of phylogenetic tree:
Does not tell us when a species arose How much genetic change occurred in each
evolutionary step May not tell us the exact ancestral species
Application of phylogeny:
Agriculture and plant breeding Investigation of poaching Forensic and bioterrorism
Homology: similarities due to shared ancestry
Analogy: similarity due to convergent evolution Homoplasies: Analogous structures; similarities
arose independently
What is the relationship between wings of birds, wings of bats and forelimbs of cats?
Morphological and molecular homologies:
Organisms that share very similar morphologies or similar DNA sequences are likely to be more closely related than organisms with vastly different structures or sequences.
Molecular systematics: Using molecular data to determine evolutionary relationships.
Genes: sequences of thousands of nucleotides.
If genes in two organisms share many portions of their nucleotide sequences, it is highly likely that the genes are homologous.
1
2
1
2
Deletion
Insertion
1
2
1
2
Cladistics: Systematics using common ancestry as the primary criterion.
Clades: groups of species that have been sorted according to common ancestry. Like taxa clades reside within larger clades.
Shared ancestral character: character that originated in an ancestor of the group
Shared derived character: evolutionary novelty unique to a particular group.
Outgroup: species or a group of species from an evolutionary lineage that is known to have diverged before the lineage that is being studied.
Ingroup: species included in the group being studied.
Outgroups and ingroups are determined on the basis of morphology, paleontology, embryonic development, gene sequences
To determine various branch points in a phylogenetic tree we compare members of ingroups to each other and to members of outgroups as well.
Using derived character to infer phylogeny
Hair
Amniotic (shelled) egg
Four walking legs
Hinged jaws
Vertebral column(backbone)
Character table
CH
AR
AC
TE
RS
TAXA
La
nc
ele
t(o
utg
rou
p)
La
mp
rey
Tu
na
Sa
lam
an
de
r
Tu
rtle
Le
op
ard
Turtle Leopard
Hair
Amniotic egg
Four walking legs
Hinged jaws
Vertebral column
Salamander
Tuna
Lamprey
Lancelet (outgroup)
Cladogram
Principle of maximum parsimony: first investigate the simplest explanation that is consistent with the facts Occam’s razor: shaving away unnecessary
complications – minimalist problem solving approach.
Maximum likelihood: the phylogenetic tree that reflects the simplest explanation of DNA change
Gene families and gene duplication:
Gene families: groups of related genes within an organisms genome resulting from repeated duplication.
Orthologous genes: homologous genes found in different species due to speciation.
Paralogous genes: more than one copy of a gene in the same genome
Ancestral gene
Speciation
Orthologous genes
Ancestral gene
Gene duplication
Paralogous genes
Three domain system: All organisms are classified into three domains –
Bacteria: currently known prokaryotes Archaea: very diverse group of prokaryotes,
variety of habitats including extreme ones Eukarya: All organisms that have cells with true
nuclei (single-celled or multicellular)
Eukarya
Characteristics Bacteria Archea Eukarya
Nuclear envelope absent absent present
Membrane bound organelles
absent absent present
Circular chromosomes
present present absent
Peptidoglycans in cell walls
present absent absent
Sensitivity to antibiotics like streptomycin,
chloramphenicol
yes no no
Growth at exterme conditions
(temperature, salt)
nomost species
no
Horizontal gene transfer: genes are transferred through transposable elements, viral infection, plasmids.
According to some scientists – to represent extensive horizontal gene transfer in early organisms, a ring is a better representation than a dichotomous tree
ArchaeaBacteria
Eukarya
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