Tree of Life

Tree of LifeTree of Life

Planet Earth is about 4.6 billion years old.Planet Earth is about 4.6 billion years old. Oldest known rocks are about 3.8 billion Oldest known rocks are about 3.8 billion

years old.years old. Oldest fossils (prokaryotes) are about 3.5 Oldest fossils (prokaryotes) are about 3.5

billion years old.billion years old.


All living organisms on this planet share a All living organisms on this planet share a common ancestor.common ancestor.

The tree of life reflects the branching The tree of life reflects the branching pattern of speciation (phylogenetic history pattern of speciation (phylogenetic history of life) that has occurred since the origin of of life) that has occurred since the origin of life.life.


There is an excellent Tree of Life website There is an excellent Tree of Life website in which you can trace the branching in which you can trace the branching pattern of the history of life and explore pattern of the history of life and explore classification.classification.

http://tolweb.org/tree/http://tolweb.org/tree/


There is a hierarchichal classification of There is a hierarchichal classification of life in which organisms are progressively life in which organisms are progressively nested within larger and larger categories nested within larger and larger categories as more distant relatives are included in as more distant relatives are included in the classification (we will explore the classification (we will explore classification shortly).classification shortly).

The highest level of classification is the The highest level of classification is the Domain of which there are three.Domain of which there are three.

26.22

““Bacterial” DomainsBacterial” Domains Domain BacteriaDomain Bacteria Domain ArchaeaDomain Archaea

The domains Bacteria and Archaea are The domains Bacteria and Archaea are both prokaryotes (they have no nucleus both prokaryotes (they have no nucleus and the DNA is not arranged in and the DNA is not arranged in chromosomes). Prokaryote derived from chromosomes). Prokaryote derived from the Greek the Greek ProPro meaning before and meaning before and karyon karyon meaning a kernel [i.e. a nucleus]meaning a kernel [i.e. a nucleus]

Domain BacteriaDomain Bacteria

Bacteria play a major role in Bacteria play a major role in decomposition and many live symbiotically decomposition and many live symbiotically with other organisms including humans with other organisms including humans helping to break down or synthesize foods helping to break down or synthesize foods needed by the host.needed by the host.

Domain BacteriaDomain Bacteria

Includes most of the bacteria people are Includes most of the bacteria people are familiar with including disease-causing familiar with including disease-causing species (species (SalmonellaSalmonella; ; VibrioVibrio cholerae cholerae whichwhich causes cholera), nitrogen-fixing causes cholera), nitrogen-fixing ((NitrosomonasNitrosomonas) and parasites () and parasites (BorreliaBorrelia burgdorferiburgdorferi which causes Lyme disease). which causes Lyme disease).

Domain ArchaeaDomain Archaea The Archaea include many extremophiles, The Archaea include many extremophiles,

organisms that live in extreme environments.organisms that live in extreme environments.

Includes thermophiles which tolerate extreme Includes thermophiles which tolerate extreme heat (e.g. live in geysers and hot springs where heat (e.g. live in geysers and hot springs where temps may reach 90 degrees celsius) and temps may reach 90 degrees celsius) and halophiles (salt lovers, which live in very saline halophiles (salt lovers, which live in very saline environments (e.g. Great Salt Lake, Dead Sea)environments (e.g. Great Salt Lake, Dead Sea)

Archaea in hot springs

Bacteria and ArchaeaBacteria and Archaea

Bacteria and Archaea are both Bacteria and Archaea are both prokaryotes and their DNA is arranged in prokaryotes and their DNA is arranged in circular structures called plasmids. circular structures called plasmids.

However, they have substantial However, they have substantial differences in their biochemistry, cell wall differences in their biochemistry, cell wall structure and other molecular details.structure and other molecular details.

Domain EukaryaDomain Eukarya Domain Eukarya contains the eukaryotic Domain Eukarya contains the eukaryotic

organisms (from Greek organisms (from Greek eueu true and true and karyon karyon aa kernal) which have a true nucleus and kernal) which have a true nucleus and DNA arranged in chromosomes.DNA arranged in chromosomes.

Eukaryotic cells are much larger and Eukaryotic cells are much larger and complex than prokaryotic cells and contain complex than prokaryotic cells and contain organelles such as mitochondria, organelles such as mitochondria, chloroplasts, and lysosomes. chloroplasts, and lysosomes.

Domain EukaryaDomain Eukarya

Domain Eukarya includes three kingdoms Domain Eukarya includes three kingdoms the Plantae, Fungi and Animalia. the Plantae, Fungi and Animalia.

There are also a number of unicellular There are also a number of unicellular eukaryotes that may form as many as five eukaryotes that may form as many as five other kingdoms. These were formerly other kingdoms. These were formerly grouped in the paraphyletic group the grouped in the paraphyletic group the Protista.Protista.

Domain EukaryaDomain Eukarya

Plantae, Fungi and Animalia are mostly Plantae, Fungi and Animalia are mostly multicellular, but plants are autotrophic multicellular, but plants are autotrophic (produce their own food by (produce their own food by photosynthesis) whereas the fungi and photosynthesis) whereas the fungi and animals are heterotrophic (consume other animals are heterotrophic (consume other organisms).organisms).

AnimaliaAnimalia

Zoology is the study of animals and Zoology is the study of animals and multicellular organisms of the kingdom multicellular organisms of the kingdom Animalia are the focus of this semester, Animalia are the focus of this semester, although we will briefly discuss some although we will briefly discuss some single-celled protozoans (“Protistans” single-celled protozoans (“Protistans” when discussing a variety of parasitic when discussing a variety of parasitic diseases).diseases).

AnimaliaAnimalia Traditionally, zoologists divide the Animalia into Traditionally, zoologists divide the Animalia into

vertebrates and invertebrates.vertebrates and invertebrates. Vertebrates are those that possess a vertebral Vertebrates are those that possess a vertebral

column and a suite of other unique derived column and a suite of other unique derived features.features.

Vertebrates are a subphylum of the phylum Vertebrates are a subphylum of the phylum Chordata.Chordata.

The Chordata includes all the vertebrates: fish The Chordata includes all the vertebrates: fish and tetrapods (amphibians, reptiles, birds and and tetrapods (amphibians, reptiles, birds and mammals) and two non-vertebrate chordates the mammals) and two non-vertebrate chordates the Urochordates (sea squirts) and the Urochordates (sea squirts) and the Cephalochordates (lancelets).Cephalochordates (lancelets).

Animalia: InvertebratesAnimalia: Invertebrates The non-chordate animals are the traditional The non-chordate animals are the traditional

Invertebrates and include all the other phyla in Invertebrates and include all the other phyla in the Animalia. These are the groups we will the Animalia. These are the groups we will focus on this semester.focus on this semester.

Major phyla include the Porifera (sponges), Major phyla include the Porifera (sponges), Annelida (earthworms and relatives), Mollusca Annelida (earthworms and relatives), Mollusca (molluscs), Arthropoda (crustaceans, insects (molluscs), Arthropoda (crustaceans, insects and relatives) and Echinodermata (seastars and and relatives) and Echinodermata (seastars and relatives).relatives).

AnimaliaAnimalia Animals are heterotrophic eukaryotes. Most are Animals are heterotrophic eukaryotes. Most are

multicellular. multicellular.

Except for sponges, all animals have tissues Except for sponges, all animals have tissues which are specialized collections of cells that work which are specialized collections of cells that work together to carry out tasks and are separated from together to carry out tasks and are separated from other tissues by membranes. other tissues by membranes.

Tissues are arranged together to produce organs Tissues are arranged together to produce organs and organs are organized into organ systems (e.g. and organs are organized into organ systems (e.g. digestive system).digestive system).

AnimaliaAnimalia Most animals are bilaterally symmetrical Most animals are bilaterally symmetrical

and form a large clade called the Bilateria.and form a large clade called the Bilateria.

Bilateral animals have a left and right side, Bilateral animals have a left and right side, top and bottom, as well as front and rear top and bottom, as well as front and rear ends.ends.

A smaller number are radially symmetrical A smaller number are radially symmetrical (e.g. jellyfish).(e.g. jellyfish).

ClassificationClassification

Before exploring the many groups of Before exploring the many groups of invertebrate animals we need to review invertebrate animals we need to review the general topic of classification or how the general topic of classification or how we group organisms into a manageable we group organisms into a manageable framework.framework.


Science of Systematics dates to Linnaeus Science of Systematics dates to Linnaeus in the 18in the 18thth century who devised the basic century who devised the basic systems of systems of binomial nomenclaturebinomial nomenclature and and hierarchical classificationhierarchical classification in use today. in use today.

All organisms have a unique binomial (2 All organisms have a unique binomial (2 name) namename) name

E.g. Humans are E.g. Humans are Homo sapiensHomo sapiens


Organisms are classified into a Organisms are classified into a hierarchical classification that groups hierarchical classification that groups closely related organisms and closely related organisms and progressively includes more and more progressively includes more and more organisms.organisms.

Phylogenetic treesPhylogenetic trees

Systematists aim to figure out the Systematists aim to figure out the evolutionary relationshipsevolutionary relationships among among species. species.

Branching diagrams called Branching diagrams called phylogenetic phylogenetic trees trees summarize the evolutionary summarize the evolutionary relationships among organisms. relationships among organisms.

Phylogenetic treesPhylogenetic trees

In a phylogenetic tree the tips of the In a phylogenetic tree the tips of the branches specify particular species and branches specify particular species and the branching points represent their the branching points represent their common ancestors.common ancestors.

Common ancestor of wolfand domestic dog

Common ancestor of wolf,domestic dog, otter and skunk

Phylogenetic treesPhylogenetic trees Phylogenetic trees are constructed by Phylogenetic trees are constructed by

studying features of organisms formally studying features of organisms formally called called characterscharacters..

Characters may be morphological or Characters may be morphological or molecular.molecular.

Character similarity resulting from Character similarity resulting from sharedshared ancestryancestry is called is called homologyhomology..

Cladistics and the construction Cladistics and the construction of phylogenetic treesof phylogenetic trees

Cladograms are diagrams that display Cladograms are diagrams that display patterns of shared characteristics.patterns of shared characteristics.

If shared characteristics are due to If shared characteristics are due to common ancestry (i.e., they are common ancestry (i.e., they are homologous) the cladogram forms the homologous) the cladogram forms the basis of a phylogenetic tree.basis of a phylogenetic tree.

CladogramsCladograms

Within a tree a Within a tree a cladeclade is defined as a group is defined as a group that includes an ancestral species and all that includes an ancestral species and all of its descendants.of its descendants.

CladisticsCladistics is the science of how species is the science of how species may be grouped into clades.may be grouped into clades.

Shared derived charactersShared derived characters Cladograms are largely constructed using Cladograms are largely constructed using

synapomorphiessynapomorphies or or shared derived shared derived characterscharacters..

These are characteristics that are evolutionary These are characteristics that are evolutionary novelties or new developments that are unique to novelties or new developments that are unique to a particular clade.a particular clade.

For example, for birds possession of feathers is a For example, for birds possession of feathers is a shared derived character and for arthropods shared derived character and for arthropods possession of a jointed limbs and an exoskeleton possession of a jointed limbs and an exoskeleton are.are.

Shared primitive charactersShared primitive characters Shared primitive characters are characters that are Shared primitive characters are characters that are

shared beyond the taxon we are interested in. shared beyond the taxon we are interested in. AmongAmong groups of vertebrates the backbone is an groups of vertebrates the backbone is an example because it evolved in the ancestor of all example because it evolved in the ancestor of all vertebrates.vertebrates.

If you go back far enough in time a shared primitive If you go back far enough in time a shared primitive character will become a shared derived character. character will become a shared derived character. Thus, the backbone is a shared derived character Thus, the backbone is a shared derived character that distinguishes vertebrates from all other animals.that distinguishes vertebrates from all other animals.

Constructing a cladogramConstructing a cladogram

OutgroupOutgroup comparison is used to begin comparison is used to begin building a cladogram.building a cladogram.

An An outgroupoutgroup is a close relative of the is a close relative of the members of the members of the ingroup ingroup (the various (the various species being studied) that provides a species being studied) that provides a basis for comparison with the others. basis for comparison with the others.


The outgroup lets us know if a character The outgroup lets us know if a character state within the ingroup is ancestral or not.state within the ingroup is ancestral or not.

If the outgroup and some of the ingroup If the outgroup and some of the ingroup possess a character state then that possess a character state then that character state is considered ancestral. character state is considered ancestral.


For example, birds, mammals and reptiles are all For example, birds, mammals and reptiles are all amniotes (produce hard-shelled or amniotic amniotes (produce hard-shelled or amniotic eggs). Birds have no teeth, but mammals and eggs). Birds have no teeth, but mammals and reptiles do. reptiles do.

An outgroup to the amniotes, fish, possesses An outgroup to the amniotes, fish, possesses teeth. Therefore, the ancestral state among the teeth. Therefore, the ancestral state among the amniotes is to possess teeth and birds have amniotes is to possess teeth and birds have secondarily lost them.secondarily lost them.


Having the outgroup for comparison Having the outgroup for comparison enables researchers to focus on those enables researchers to focus on those characters derived after the separation characters derived after the separation from the outgroup to figure out from the outgroup to figure out relationships among species in the relationships among species in the ingroup.ingroup.


Cladogram of various vertebrates: Cladogram of various vertebrates: monkey, horse, lizard, bass and monkey, horse, lizard, bass and amphioxus.amphioxus.

Use amphioxus as outgroup (is a Use amphioxus as outgroup (is a chordate, but has no backbone).chordate, but has no backbone).

Cladogram

Constructing a cladogramConstructing a cladogram In the cladogram new characters are marked on In the cladogram new characters are marked on

the tree where they originate and these the tree where they originate and these characters are possessed by all subsequent characters are possessed by all subsequent groups.groups.

Cladograms and Phylogenetic Cladograms and Phylogenetic TreesTrees

A cladogram and a phylogenetic tree are similar, A cladogram and a phylogenetic tree are similar, but not identical. but not identical.

A phylogentic tree’s branches represent real A phylogentic tree’s branches represent real evolutionary lineages and branch lengths evolutionary lineages and branch lengths represent time or amounts of evolutionary represent time or amounts of evolutionary change. change.

Cladogram branches contain no such Cladogram branches contain no such information. Branching order of cladogram information. Branching order of cladogram should, however, match that of phylogenetic should, however, match that of phylogenetic tree.tree.

Early phylogenetic tree of amniotes based on cytochrome c gene by Fitch and Margoliash (1967).Note numbers on branches.These represent estimated numbers of mutational changes in gene.

Theories of taxonomyTheories of taxonomy

There are two current major theories of There are two current major theories of taxonomy:taxonomy: Traditional Evolutionary TaxonomyTraditional Evolutionary Taxonomy Phylogenetic Systematics (Cladistics)Phylogenetic Systematics (Cladistics)

Both based on evolutionary principles, but Both based on evolutionary principles, but differ in the application of those principles differ in the application of those principles to formulate taxonomic groups.to formulate taxonomic groups.


There are three different ways a taxon There are three different ways a taxon may be related to a phylogentic tree.may be related to a phylogentic tree.

The taxon may be a The taxon may be a monophyleticmonophyletic, , paraphyleticparaphyletic or or polyphyleticpolyphyletic grouping grouping

Monophyletic GroupMonophyletic Group

A monophyletic taxon includes the most A monophyletic taxon includes the most recent common ancestor of a group and recent common ancestor of a group and allall of its descendents. of its descendents.

Paraphyletic groupParaphyletic group

A taxon is paraphyletic if it includes the A taxon is paraphyletic if it includes the most recent common ancestor of a group most recent common ancestor of a group and some but not alland some but not all of its descendents. of its descendents.

Polyphyletic groupingPolyphyletic grouping A taxon is polyphyletic if it does not contain the A taxon is polyphyletic if it does not contain the

most recent common ancestor of all members of most recent common ancestor of all members of the group. the group.

This situation requires the group to have had This situation requires the group to have had independent evolutionary origin of some independent evolutionary origin of some diagnostic feature. E.g. If you grouped birds, diagnostic feature. E.g. If you grouped birds, butterflies and bats into a group you called butterflies and bats into a group you called “WingedThings” it would be a polyphyletic group “WingedThings” it would be a polyphyletic group because each group evolved wings separately.because each group evolved wings separately.


Both traditional evolutionary taxonomy and Both traditional evolutionary taxonomy and cladistics reject polyphyletic groups.cladistics reject polyphyletic groups.

They both accept monophyletic groups, They both accept monophyletic groups, but differ in their treatment of paraphyletic but differ in their treatment of paraphyletic groupings.groupings.

Traditional Evolutionary TaxonomyTraditional Evolutionary Taxonomy

TET uses two principles for designating taxa.TET uses two principles for designating taxa. Common descentCommon descent Amount of adaptive evolutionary changeAmount of adaptive evolutionary change

The second criterion leads to the idea that The second criterion leads to the idea that groups may be designated as higher level taxa groups may be designated as higher level taxa because they represent a distinct “adaptive because they represent a distinct “adaptive zone” (Simpson) because they have undergone zone” (Simpson) because they have undergone adaptive change that fits them to a unique role adaptive change that fits them to a unique role (e.g. penguins, humans).(e.g. penguins, humans).


Classification of anthropoid primates.Classification of anthropoid primates.

The genera Gorilla, Pan (chimpanzee) and The genera Gorilla, Pan (chimpanzee) and Pongo (orang utan) are paraphyletically Pongo (orang utan) are paraphyletically grouped into family Pongidae and humans grouped into family Pongidae and humans (genus Homo) into family Hominidae even (genus Homo) into family Hominidae even though humans are phylogenetically closer though humans are phylogenetically closer to Gorilla and Pan than either of those is to to Gorilla and Pan than either of those is to Pongo.Pongo.


Under TET designation of family Under TET designation of family Hominidae is because humans represent Hominidae is because humans represent a different a different gradegrade of organization. of organization.

Humans are terrestrial, intelligent, Humans are terrestrial, intelligent, omnivores with advanced cultures.omnivores with advanced cultures.

Members of Pongidae are arboreal, less Members of Pongidae are arboreal, less intelligent, herbivores.intelligent, herbivores.

Traditional Evolutionary Traditional Evolutionary TaxonomyTaxonomy

In a similar fashion “vertebrates” have In a similar fashion “vertebrates” have been historically distinguished from been historically distinguished from “invertebrates” because the backbone, “invertebrates” because the backbone, development of the skull and other development of the skull and other features such as much greater size are features such as much greater size are considered as making them substantially considered as making them substantially different.different.

CladisticsCladistics

Cladistics emphasizes the criterion of Cladistics emphasizes the criterion of common descent. The cladistic approach common descent. The cladistic approach proposed by Willi Hennig in 1950.proposed by Willi Hennig in 1950.

Under cladistic rules all groups must be Under cladistic rules all groups must be monophyletic. Thus, cladists would group monophyletic. Thus, cladists would group the Pongidae and Hominidae into one the Pongidae and Hominidae into one group the Hominidae.group the Hominidae.

Current taxonomyCurrent taxonomy Current taxonomy was developed using Current taxonomy was developed using

evolutionary systematic approaches, but evolutionary systematic approaches, but has been extensively revised in part using has been extensively revised in part using cladistic approaches.cladistic approaches.

How classification may finally be resolved How classification may finally be resolved is unclear, but the issues of paraphyletic is unclear, but the issues of paraphyletic groups and grades remain to be sorted groups and grades remain to be sorted out. out.

Taxonomy for this semesterTaxonomy for this semester For this course we will base our organization For this course we will base our organization

on the cladistic phylogeny of Guillaume on the cladistic phylogeny of Guillaume Lecointre and Herve Le Guyader (2006) from Lecointre and Herve Le Guyader (2006) from their book “The Tree of Life.”their book “The Tree of Life.”

Bear in mind that their classification is a Bear in mind that their classification is a hypothesis about the evolutionary hypothesis about the evolutionary relationships of groups and will be revised in relationships of groups and will be revised in the future.the future.

Metazoa

Placozoa

Demospongiae

Hexactinellida

Calcarea

Cnidaria

Ctenophora

Protostomia

Deuterostomia

Ecdysozoa: Onychophora, Tardigrada, Arthropoda, Nematoda, Nematomorpha,Kinorhyncha, Loricifera, Priapulida

Gastrotricha

Cuticulata

Protostomia

Lophotrochozoa

Eutrochozoa: Rotifera, Acanthocephala, Entoprocta,Platyhelminthes, Nemertea, Mollusca, Sipuncula, Annelida

Lophophorata: Ectoprocta, Brachiopoda, Phoronida

Echinodermata

HemichordataDeuterostomia

Chordata

Urochordata

Cephalochordata

Craniata (includes the Vertebrata)

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Tree of Life

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