Classification of Organisms

Professor Andrea Garrison

Biology 3A Illustrations ©2014, 2011 BROOKS/COLE, CENGAGE Learning

Terms

• Systematics: the science of classification (merriam-webster.com); grouping entities based on specific criteria

– Phylogenetics: study of evolutionary relationships between organisms

• Taxonomy: science of naming and describing organisms and placing into classification groups

• Traditional taxonomy classified organisms based on presumed relationships

Classification of Organisms 2

Classification of organisms

• Facilitates study of organisms

– Group them into categories based on similarities

– Study one organism as an example of the group

• Aristotle first to develop classification system

– Unnatural, based on whether organism lived in air, water or on land

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Traditional classification

• Established by Swede Carolus Linnaeus in 1750’s:

– Three kingdoms: plants, animals, minerals (incl fossils)

• Broken down into hierarchical categories

– Binomial nomenclature

• Scientific name for each organism has two parts (genus and species)

• Modified over time

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Traditional classification as used today

Domain Kingdom

Phylum Class

Order Family

Genus Species

• Organisms within any one of these groups make up a taxon

• Some taxa (ex: classes) more inclusive than others (ex: genera)

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Traditional classification as used today

• 3 domains

– Bacteria

– Archaea

– Eukarya

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Traditional classification as used today

• 3 domains

– Bacteria • Prokaryotes

• Typically unicellular

• Cell wall

• Autotrophic or heterotrophic (producers, consumers, decomposers)

• Autotrophs have unique P/S mechanism

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Helicobacter pylori (human gut)

Traditional classification as used today

• 3 domains – Archaea

• Prokaryotes

• Typically unicellular

• Cell wall

• Autotrophic or heterotrophic (producers or decomposers)

• Not more primitive than bacteria (as name implies)

• Often extremophiles

• Unique mechanisms of P/S;

• Some molecular & biochemical characteristics similar to eukaryotes

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Pyrococcus furiosus (ocean sediments near active volcano)

Traditional classification as used today

• 3 domains

– Eukarya • Eukaryotes

• Unicellular or multicellular

• May have cell wall

• Autotrophic or heterotrophic (producers, consumers, decomposers)

• 4 kingdoms

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How do Bacteria and Archaea differ from Eukarya?

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Traditional classification as used today

• Domain Eukarya

– “Kingdom” Protista

– Kingdom Plantae

– Kingdom Fungi

– Kingdom Animalia

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Traditional classification as used today

• Domain Eukarya – “Kingdom” Protista

• Assemblage of eukaryotes that don’t belong in one of other 3 kingdoms

• No phylogenetic relationships

– Unicellular eukaryotes

– Typically cell wall or something similar

– Autotrophic or heterotrophic

– Varied metabolism, etc.

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Traditional classification as used today

• Domain Eukarya

– Kingdom Plantae • Multicellular

• Autotrophic

– Photosynthesis

• Cell wall

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Traditional classification as used today

• Domain Eukarya

– Kingdom Fungi • Unicellular or multicellular

• Heterotrophic

– Typically decomposers

• Cell wall

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Traditional classification as used today

• Domain Eukarya

– Kingdom Animalia • Multicellular

• Heterotrophic (consumers, decomposers)

• No cell wall

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How does kingdom Plantae differ from kingdom Fungi?

How does kingdom Plantae differ from kingdom Animalia?

How does kingdom Fungi differ from kingdom Animalia?

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Traditional classification as used today

Domain

Kingdom

Phylum

Class

Order

Family

Genus

Species

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Domain: Eukarya

Kingdom: Animalia

Phylum: Chordata

Class: Mammalia

Order: Carnivora

Family: Ursidae

Genus: Ursus

Species: Ursus americanus

Figure 1-10 p9

What is a species?

• Species: most specific category of hierarchy

– Traditional definition: group of similar organisms capable of breeding and producing fertile offspring

– Different species sometimes interbreed to form hybrids, but offspring rarely fertile and viable

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Binomial nomenclature

• Scientific name is based on classification – Genus and species name

• Ursus americanus

• Ursus americanus

– Names are latin • Red oak is Quercus (=oak) rubra (=red)

• Species may be named after a person

– Universal use • Rules guiding how applied

– oldest name has precedence

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Domain: Eukarya

Kingdom: Animalia

Phylum: Chordata

Class: Mammalia

Order: Carnivora

Family: Ursidae

Genus: Ursus

Species: Ursus americanus

Figure 1-10 p9

How does the system of binomial nomenclature minimize ambiguity in naming and identifying

species?

How does the taxonomic hierarchy help biologists organize information about different

species?

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Phylogeny

• Field of science that studies taxonomy based on evolutionary relationships

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Phylogenetic trees

• Show hypothesized evolutionary relationships of organisms

– Example: Darwin’s initial ideas on adaptive radiation

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Phylogenetic trees

• Show hypothesized evolutionary relationships of organisms – Initially based on similarities

and differences in structures

– Later based on similarities and differences in DNA, proteins

– Y-axis represents time, generally not to scale

– X-axis generally doesn’t indicate how many differences exist between groups (degree of differentness)

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Figure 1-11 p10

BACTERIA ARCHAEA EUKARYA

(Present) * * * Plantae * Fungi * Animalia

Common ancestor of Fungi and Animalia

Common ancestor of Plantae, Fungi, and Animalia

Tim

e

Common ancestor of all Eukarya

Common ancestor of Archaea and Eukarya

Common ancestor of all living organisms

(Long ago)

* Represent groups lumped into Protista

Phylogenetic trees

• Range of organisms included may vary

• Phylogenetic trees share a specific structure and depict key relationships in similar ways

• Common ancestor of all species in the tree is described as the root of the tree

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Phylogenetic trees

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• Anagenesis: Gradual phyletic change in a species as the environment changes • Does not increase biodiversity –gradual transformation

of one “species” into another • Anagenesis is often illustrated by a straight line in a

phylogenetic tree

Phylogenetic trees

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• Cladogenesis: change of an ancestral species into two descendant species, morphologically different from the ancestor • Does increase biodiversity • Depicted by branching points (nodes) in a phylogenetic

tree • Over time, branches give rise to branchlets, and twigs –

each new species becomes the common ancestor of its own descendants

Phylogenetic trees

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Root = common ancestor

Nodes = common ancestors that underwent cladogenesis

Taxon of reptiles & birds • Crocodilians more closely

related birds than to lizard and snakes

• Taxon of lizards and snakes and Taxon of crocodilians and birds are sister taxa

Taxon = node and all branches emerging from it

Text uses term “clade” for “taxon” here

A monophyletic taxon includes an ancestral species and all of its descendants.

Monophyletic taxon

An ancestor and all of its descendants are included in the monophyletic taxon.

A polyphyletic taxon includes species from different evolutionary lineages.

Polyphyletic taxon

The most recent common ancestor is not included in the polyphyletic taxon.

A paraphyletic taxon includes an ancestral species and only some of its descendants.

Paraphyletic taxon

Some descendants of the common ancestor are excluded from the polyphyletic taxon.

Figure 24-5, p. 533

Phylogenetic trees

Figure 1-11 p10

BACTERIA ARCHAEA EUKARYA

(Present)

* * * Plantae * Fungi * Animalia

Common ancestor of Fungi and Animalia

Common ancestor of Plantae, Fungi, and Animalia

Tim

e

Common ancestor of all Eukarya

Common ancestor of Archaea and Eukarya

Common ancestor of all living organisms

(Long ago)

* Represent groups lumped into Protista

Eukarya is monophyletic Protista is polyphyletic

What is the difference between a phylogenetic tree and a classification?

What is a node?

What is a taxon? A clade?

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How do monophyletic, polyphyletic and paraphyletic taxa differ?

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Phylogenetic analysis

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• Types of traits used for phylogenetic analyses • Traditional traits were morphological similarities and

differences • Sometimes incl. behavioral or physiological

similarities and differences • Molecular sequences (DNA, RNA) provide better

understanding • Eliminate effects of environment that might be

similar on different groups • Ex: fish and marine mammals have similar

body structure

Phylogenetic analysis

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• Types of traits used for phylogenetic analyses • Morphological similarities and differences

• Often reflect genetic differences • Found in fossils, can be compared with extant

species • Homologous vs. analogous structures

Phylogenetic analysis

Homologous vs. analogous structures

• Homologous structures – Derived from common ancestor – Similar in structure and

relationship with surrounding structures

– Develop from same embryonic tissues in similar manner

• Analogous (homoplastic) structures – Not seen in common ancestor – Derived from environmental

influence in different lineages – Different structures – Serve similar function

Wing skeletal structures are homologous

Wing flesh and surfaces are analogous

-different tissues, fly with different parts of wing

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Phylogenetic analysis

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• Types of traits used for phylogenetic analyses • Morphological similarities and differences • Behavior or physiological similarities and differences

• Very similar species may have behavioral or physiological traits that can be used to distinguish species • Different breeding calls or rituals • Chemical cues for fertilization of eggs

• Often these traits prevent interbreeding and keep species distinct

Phylogenetic analysis

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• Types of traits used for phylogenetic analyses • Morphological similarities and differences • Behavior or physiological similarities and differences • Molecular sequences more accurate indication of

similarities • DNA is inherited • Shared changes in molecular sequences (insertions, deletions,

or substitutions) provide clues to evolutionary relationships • Publication of complete genome sequences allows broad

comparative studies • Can compare distantly related species with very few

morphological similarities • Can compare closely related species with almost

undetectable morphological differences

Why do systematists use homologous characters in their phylogenetic analyses,

but not analogous characters?

What are three advantages of using molecular characters in phylogenetic analyses?

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Phylogenetic analysis & classification

• Traditional systematics

– organisms classified based on outward (phenotypic) characteristics

– classifications did not always strictly reflect the patterns of branching evolution

• Ex: Crocodilians outwardly resemble lizards, but share a more recent common ancestor with birds

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Phylogenetic analysis & classification

• Traditional classification recognizes four classes of tetrapod vertebrates: Amphibia, Mammalia, Reptilia, and Aves – Classes given equal ranking

because each represents a distinctive body plan and way of life

• Phylogenetic analysis shows 6 taxa, however – traditional taxon Reptilia is

paraphyletic because, even though birds share a common ancestor with reptiles, they are placed in a separate taxon

– Crocodilians closer to birds than reptiles

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Phylogenetic analysis & classification

Why does a classification produced by traditional systematics sometimes include

paraphyletic groups?

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Phylogenetic analysis & classification

• Traditional systematics leads to some groupings that don’t stand up to evidence based on molecular sequence

• Relatively new field of cladistics attempts to classify organisms based only on evolutionary relationships

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Cladistic analyses

• Taxa are called clades (text uses this term even within the discussion of traditional phylogeny)

• Phylogenetic trees built in same way as traditional phylogeny, but clades only include truly monophyletic taxon

• Two types of traits considered in cladistic phylogeny

– Ancestral vs. derived characters

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Cladistic analyses

Ancestral vs. derived characters • Ancestral character (state)

– Found in ancestral species of a clade

– May change via natural selection over time

– Give rise to derived character (state)

– Ex: fins found in early vertebrates

• Derived character (state) – New in a descendent species

– Ex: limbs found in later vertebrates

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Cladistics analyses

Ancestral vs. derived characters • Fossil record often helps distinguish ancestral and derived characters

– Oldest fossils have ancestral characters – Characters that show up in younger fossils are derived

• If no fossil record, compare “ingroups” with “outgroups” – Ingroup is the clade being studied – Outgroup is the closely related species not part of the clade

• Determined using morphology, fossil record, embryology, gene sequencing

– Characters found in outgroup are ancestral, characters found in ingroup and not outgroup are derived

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Outgroup Comparison C. Monarch butterfly (Danaus plexippus)

B. Orange palm dart butterfly (Cephrenes auglades)

A. Caddis fly (Limnephilidae)

Most insects have six legs.

Most butterfly species have six legs.

Monarch butterflies have four legs.

Figure 24-10, p. 539

Cladistics analyses • Phylogenetic trees group together species that share derived

characters • Phylogenetic tree illustrates the hypothesized sequence of

evolutionary branching that produced the organisms under study • A common ancestor is hypothesized at each node

– every branch is a strictly monophyletic group – shared derived characters that define each clade sometimes listed on the

branches

• Molecular research provides huge database – Maximum parsimony (Occam’s razor)

• Use simplest plausible explanation – Statistical approach (maximum likelihood)

• Use what we know about frequency of certain genetic mutations, etc.

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Cladistic analyses

• Phylogenetic tree shows 6 clades

– Crocodilians shown to be more closely related to birds than reptiles

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