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Chapter 25. Phylogeny and Systematics. Overview: Investigating the Tree of Life. Phylogeny is the evolutionary history of a species or group of related species. Systematics is an analytical approach to understanding the diversity and relationships of organisms, both present-day and extinct

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chapter 25

Chapter 25

Phylogeny and Systematics

overview investigating the tree of life
Overview: Investigating the Tree of Life
  • Phylogeny is the evolutionary history of a species or group of related species
  • Systematics is an analytical approach to understanding the diversity and relationships of organisms, both present-day and extinct
  • Uses morphological
  • Biochemical
  • and molecular comparisons to infer evolutionary relationships
sorting homology from analogy
Sorting Homology from Analogy
  • Homology is similarity due to shared ancestry
  • Analogy is similarity due to convergent evolution
  • Convergent evolution occurs when similar environmental pressures and natural selection produce similar (analogous) adaptations in organisms from different evolutionary lineages
slide4

These organisms have analogous structures from

Living in similar environments, but do not share a

Recent common ancestor

evaluating molecular homologies
Evaluating Molecular Homologies
  • Not as simple as you would think
  • Systematists use computer software to find and realign similar sequence in DNA between two species
concept 25 2 phylogenetic systematics connects classification with evolutionary history
Concept 25.2: Phylogenetic systematics connects classification with evolutionary history
  • Taxonomy is the ordered division of organisms into categories based on characteristics used to assess similarities and differences
  • In 1748, Carolus Linnaeus published a system of taxonomy based on resemblances.
        • two-part names for species
          • (binomial nomenclature)
        • hierarchical classification
binomial nomenclature
Binomial Nomenclature
  • Genus species
  • G. species
le 25 8

LE 25-8

Panthera

pardus

Species

Panthera

Genus

Felidae

Family

Carnivora

Order

Mammalia

Class

Chordata

Phylum

Animalia

Kingdom

Eukarya

Domain

le 25 9

LE 25-9

Panthera

pardus

(leopard)

Mephitis

mephitis

(striped skunk)

Lutra lutra

(European

otter)

Canis

familiaris

(domestic dog)

Canis

lupus

(wolf)

Species

Genus

Panthera

Mephitis

Lutra

Canis

Family

Felidae

Mustelidae

Canidae

Each branch point represents the divergence of two species

Systematists depict evolutionary relationships in branching phylogenetic trees

Carnivora

Order

le 25 un497

LE 25-UN497

Leopard

Domestic cat

Common ancestor

“Deeper” branch points represent progressively greater amounts of divergence

Wolf

Leopard

Domestic cat

Common ancestor

slide11
Concept 25.3: Phylogenetic systematics informs the construction of phylogenetic trees based on shared characteristics
  • A cladogram depicts patterns of shared characteristics among taxa
  • A clade is a group of species that includes an ancestral species and all its descendants
  • Cladistics studies resemblances among clades
cladistics
Cladistics
  • Clades can be nested in larger clades, but not all groupings or organisms qualify as clades
le 25 10a

LE 25-10a

Grouping 1

A valid clade is monophyletic, signifying that it consists of the ancestor species and all its descendants

Monophyletic

le 25 10b

LE 25-10b

Grouping 2

A paraphyletic grouping consists of an ancestral species and some, but not all, of the descendants

Paraphyletic

le 25 10c

LE 25-10c

Grouping 3

A polyphyletic grouping consists of various species that lack a common ancestor

Polyphyletic

shared primitive and shared derived characteristics
Shared Primitive and Shared Derived Characteristics
  • In cladistic analysis, clades are defined by their evolutionary novelties
  • A shared primitive character is a character that is shared beyond the taxon we are trying to define
  • A shared derived character is an evolutionary novelty unique to a particular clade
outgroups
Outgroups
  • An outgroup is a species or group of species that is closely related to the ingroup, the various species being studied
  • Systematists compare each ingroup species with the outgroup to differentiate between shared derived and shared primitive characteristics
slide18
Outgroup comparison assumes that homologies shared by the outgroup and ingroup must be primitive characters that predate the divergence of both groups from a common ancestor
  • It enables us to focus on characters derived at various branch points in the evolution of a clade
le 25 11

LE 25-11

TAXA

Lancelet

(outgroup)

Salamander

Lamprey

Leopard

Turtle

Tuna

Hair

Amniotic (shelled) egg

CHARACTERS

Four walking legs

Hinged jaws

Vertebral column

(backbone)

Character table

Leopard

Turtle

Hair

Salamander

Amniotic egg

Tuna

Four walking legs

Lamprey

Hinged jaws

Lancelet (outgroup)

Vertebral column

Cladogram

phylogenetic trees and timing
Phylogenetic Trees and Timing
  • Phylogenetic trees depict RELATIVE TIMING –
    • Four walking legs appeared after vertebral columns but before hair
le 25 12

Drosophila

Fish

Lancelet

Amphibian

Rat

Bird

Human

Mouse

LE 25-12

In a phylogram, the length of a branch in a cladogram reflects the number of genetic changes that have taken place in a particular DNA or RNA sequence in that lineage

maximum parsimony and maximum likelihood
Maximum Parsimony and Maximum Likelihood
  • Systematists can never be sure of finding the best tree in a large data set
  • They narrow possibilities by applying the principles of maximum parsimony and maximum likelihood
  • The simplest explanation is the best explanation and therefore most likely
le 25 14

LE 25-14

Human

Mushroom

Tulip

Human

0

30%

40%

Mushroom

0

40%

Tulip

0

Percentage differences between sequences

Tree 2 – Mushrooms must have slowed DNA mutation rates and plants sped up

25%

15%

15%

20%

15%

10%

5%

5%

Tree 1: More likely

Tree 2: Less likely

Comparison of possible trees

phylogenetic trees as hypotheses
Phylogenetic Trees as Hypotheses
  • The best hypotheses for phylogenetic trees fit the most data: morphological, molecular, and fossil
  • Sometimes the best hypothesis is not the most parsimonious
le 25 16

LE 25-16

Lizard

Bird

Mammal

You cannot just use one characteristic as a basis for phylogeny

Four-chambered

heart

Mammal-bird clade

Lizard

Bird

Mammal

Four-chambered

heart

Four-chambered

heart

Lizard-bird clade

concept 25 4 much of an organism s evolutionary history is documented in its genome
Concept 25.4: Much of an organism’s evolutionary history is documented in its genome
  • Comparing nucleic acids or other molecules to infer relatedness is a valuable tool for tracing organisms’ evolutionary history
  • Really useful for organisms that have diverged a long time – like humans and monerans
  • “Seven Daughters of Eve” uses mDNA
gene duplications and gene families
Gene Duplications and Gene Families
  • Gene duplication increases the number of genes in the genome, providing more opportunities for evolutionary changes
  • Orthologous genes are genes found in a single copy in the genome
      • They can diverge only after speciation occurs
  • Paralogous genes result from gene duplication, so are found in more than one copy in the genome
      • They can diverge within the clade that carries them, often adding new functions
le 25 17a

LE 25-17a

Ancestral gene

Speciation

Orthologous genes

Genes are found in separate gene pools

- Human & mice b hemoglobin genes

le 25 17b

LE 25-17b

Ancestral gene

Gene duplication

Paralogous genes

genome evolution
Genome Evolution
  • The widespread consistency in total gene number in organisms indicates genes in complex organisms are very versatile and that each gene can perform many functions
  • Humans have five times as many genes as yeast – so our genes must be more versatile
molecular clocks
Molecular Clocks
  • The molecular clock is a yardstick for measuring absolute time of evolutionary change based on the observation that some genes and other regions of genomes seem to evolve at constant rates
neutral theory
Neutral Theory
  • Neutral theory states that much evolutionary change in genes and proteins has no effect on fitness and therefore is not influenced by Darwinian selection
  • It states that the rate of molecular change in these genes and proteins should be regular like a clock
difficulties with molecular clocks
Difficulties with Molecular Clocks
  • The molecular clock does not run as smoothly as neutral theory predicts
  • Irregularities result from natural selection in which some DNA changes are favored over others
  • Estimates of evolutionary divergences older than the fossil record have a high degree of uncertainty
applying a molecular clock the origin of hiv
Applying a Molecular Clock: The Origin of HIV
  • Phylogenetic analysis shows that HIV is descended from viruses that infect chimpanzees and other primates
  • Comparison of HIV samples throughout the epidemic shows that the virus evolved in a very clocklike way
the universal tree of life
The Universal Tree of Life
  • The tree of life is divided into three great clades called domains: Bacteria, Archaea, and Eukarya
  • The early history of these domains is not yet clear