Phylogeny and
Systematics
Chapter 10

Taxonomy

Taxonomy produces a formal system for naming and classifying species to illustrate their evolutionary relationship.

Taxonomy & Systematics

Taxonomy
 Formal system for naming and classifying species.

Systematics

Broader science of classifying organisms based on similarity, biogeography, etc.
 Systematic zoologists have three goals:
 To discover all species of animals.
 To reconstruct their evolutionary relationships.
 To classify animals according to their evolutionary relationships.


Introduction of evolutionary theory into animal taxonomy changed taxonomist ’ s role from one of classification to systematization.

Classification denotes the construction of classes.

Grouping of organisms that possess a common feature called an essence used to define the class.


Systematization places groups of species into units of common evolutionary descent.

Character variation is used to diagnose systems of common descent.

No requirement that an essential character be maintained throughout the system for its recognition as a taxon.

Taxonomy

In classification

Taxonomist asks whether a species being classified contains the defining feature of a particular taxonomic class.

In systematization

Taxonomist asks whether the characteristics of a species confirm or reject the hypothesis that it descends from the most recent common ancestor of a particular taxon.

Linnaeus and Classification
 Carolus Linnaeus designed our hierarchical classification scheme.

Kingdom

Phylum

Class

Order

Family

Genus

Species

Linnaeus and Classification

All animals are placed in Kingdom Animalia.

Names of animal groups at each rank in the hierarchy are called taxa (taxon).

Each rank can be subdivided into additional levels of taxa.
 Superclass, suborder, etc.

Linnaeus and Classification

Linnaeus and Classification

Binomial nomenclature is the system
Linnaeus used for naming species.

Genus and species

Names are latinized and italicized, only the genus is capatilized.

Sitta carolinensis

Linnaeus and Classification

A trinomial name includes a subspecies epithet.
 Ensatina escholtzii escholtzii
 E. e. klauberi

Species
 Defining a species can be difficult.
 Criteria:

Common descent

The smallest distinct groupings of organisms sharing a pattern of descent.
 Morphological & molecular techniques

Members of a species must form a reproductive community that excludes other species.

Species

The geographic range of a species is its distribution in space.

Evolutionary duration of a species is its distribution in time.
 A worldwide species is cosmopolitan .

One with a very localized range is called endemic .

Typological Species Concept

The typological or morphological species concept relies on type specimens that represent the ideal form for the species. When trying to name a specimen, the type specimens were compared.
 Scientists still name species by designating a type specimen.

The Biological Species
Concept

The biological species concept emerged during the evolutionary synthesis.
 “ A species is a reproductive community of populations (reproductively isolated from others) that occupies a specific niche in nature.
” Mayr 1982
 Sibling species fit this category, but can only be differentiated with molecular techniques.

Lacks a temporal dimension.

Degree of reproductive isolation necessary?

Species that reproduce asexually?

Evolutionary Species Concept

The evolutionary species concept states that a single lineage of ancestor-descendant populations that maintains its identity from other such lineages and that has its own evolutionary tendencies and historical fate.

Definition accommodates both sexual and asexual forms as well as fossils.

Phylogenetic Species
Concept

The phylogenetic species concept is defined as an irreducible (basal) grouping of organisms diagnosably distinct from other such groupings and within which there is a parental pattern of ancestry and descent.

Both asexual and sexual groups are covered.

Phylogenetic Species
Concept

Main difference in practice between the evolutionary and phylogenetic species concepts:

The latter emphasizes recognizing as separate species the smallest groupings of organisms that have undergone independent evolutionary change.

Discerns the greatest number of species but may be impractical.

Disregards details of evolutionary process.

Investigating the Tree of Life

A major goal of systematics is to infer the evolutionary tree or phylogeny – the evolutionary history of a species or group of related species.

Phylogeny

Phylogenies are inferred by identifying organismal features, characters , that vary among species.

Morphological

Chromosomal

Molecular

Behavioral or ecological

Phylogeny

Shared characters that result from common ancestry are homologous .

Independent evolution of similar characters that are
NOT homologous is called homoplasy .

Sorting Homology from
Analogy

A potential misconception in constructing a phylogeny is similarity due to convergent evolution , called analogy , rather than shared ancestry.

Sorting Homology from
Analogy

Convergent evolution occurs when similar environmental pressures and natural selection produce similar (analogous) adaptations in organisms from different evolutionary lineages.

Sorting Homology from
Analogy

Analogous structures or molecular sequences that evolved independently are also called homoplasies .


A shared primitive (ancestral) character :

Is a homologous structure that predates the branching of a particular clade from other members of that clade.

Is shared beyond the taxon we are trying to define.

Example – mammals all have a backbone, but so do other vertebrates.


A shared derived character is an evolutionary novelty unique to a particular clade.

All mammals have hair, and no other animals have hair.

Phylogeny
 The form of the character that was present in the common ancestor of the entire group is called ancestral .

Variant forms of the character arose later and are called derived character states .

Determining polarity of a character involves determining which state is ancestral.

Phylogeny

Polarity is determined by using outgroup comparison .

An outgroup is closely related, but not part of the group being examined (the ingroup ).

If a character is found in both the study group and the outgroup, it is considered ancestral for the study group.

Character groups found in the study groups but not the outgroups are derived .

Phylogeny
 Clades are organisms or species that share derived character states and form a subset within a larger group.

A synapomorphy is a derived character shared by the members of the clade.

A clade corresponds to a unit of evolutionary common descent.

A nested hierarchy is formed by the derived states of all characters in a study group.

Phylogeny

Ancestral character states for a taxon are called plesiomorphic .

Sharing these ancestral characters is called symplesiomorphy .

Symplesiomorphies, unlike synapomorphies, do not provide information on nesting of clades – groups with derived characters get left out.

Phylogeny

The nested hierarchy of clades can be represented as a cladogram that is based on shared synapomorphies.

Phylogeny

A phylogenetic tree is another way of representing evolutionary relationships.

Branches represent real lineages that occurred in the evolutionary past.

Includes information about ancestors, duration of evolutionary lineages, amounts of evolutionary change that has occurred.


Characters used to construct cladograms can be found using:

Comparative morphology – examine shapes and sizes of organismal structures, including developmental origins.
 Comparative biochemistry – examine sequences of amino acids and nucleotides to identify variable characters.

Comparative cytology – uses variation in numbers, shapes, and sizes of chromosomes and their parts.

Taxonomy

A theory of taxonomy allows us to rank taxonomic groups.
 Two popular theories
 Evolutionary taxonomy

Phylogenetic systematics

Both based on evolutionary principles, sometimes results conflict.

Cladistics

A valid clade is monophyletic .
 Signifying that it consists of the ancestor species and all its descendants.

Cladistics

A paraphyletic clade is a grouping that consists of an ancestral species and some, but not all, of the descendants.

Cladistics

A polyphyletic grouping includes numerous types of organisms that lack a common ancestor.


Evolutionary taxonomy utilizes common descent and the amount of adaptive evolutionary change to rank higher taxa.
 Sometimes this type of classification includes paraphyletic groupings.

Phylogenetic Systematics

Phylogenetic systematics , or cladistics , emphasizes common descent and is based on cladograms.

All taxa must be monophyletic.
 Cladistic taxonomists have moved chimpanzees, gorillas, and orangutans into the family Hominidae with humans.

Humans and chimps form a sister group , as do the human/chimp group and gorillas.

Theories of Taxonomy
 Both evolutionary and cladistic taxonomy:

Accept monophyletic groups.

Reject polyphyletic groups.

Differ on accepting paraphyletic groups.
 Traditional evolutionary taxonomy does.

Phylogenetic systematics does not.

Difference has important evolutionary implications.

Theories of Taxonomy

Current State of Animal Taxonomy:

Modern animal taxonomy was established using evolutionary systematics and recent cladistic revisions.
 PhyloCode

New taxonomic system
 Being developed as an alternative to Linnean taxonomy.
 Replaces Linnean ranks with codes that denote the nested hierarchy of monophyletic groups conveyed by cladograms.

The terms “ primitive, ” “ advanced, ” “ specialized ” and “ generalized ” are used for specific characteristics and not for groups as a whole.


Systematists can never be sure of finding the single best tree in a large data set.

Narrow the possibilities by applying the principles of maximum parsimony and maximum likelihood .

Parsimony

Among phylogenetic hypotheses the most parsimonious tree is the one that requires the fewest evolutionary events to have occurred in the form of shared derived characters.

Occam ’ s Razor

Parsimony

The principle of maximum likelihood states that, given certain rules about how DNA changes over time, a tree can be found that reflects the most likely sequence of evolutionary events.


The best hypotheses for phylogenetic trees are those that fit the most data: morphological, molecular, and fossil.

Molecular Systematics

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.

Major Divisions of Life

Aristotle ’s two kingdom system included plants and animals.

One-celled organisms became a problem

Haeckel (1866) proposed Protista for singlecelled organisms.

R.H. Whittaker (1969) proposed a five-kingdom system to distinguish prokaryotes and fungi.

Major Divisions of
Life

Woese, Kandler and Wheelis
(1990) proposed three monophyletic domains above kingdom level —Eucarya,
Bacteria and Archaea —based on ribosomal RNA sequences.

Major Divisions of Life

More revisions are necessary to clarify taxonomic kingdoms based on monophyly.
 “ Protozoa ”

Neither animals nor a valid monophyletic taxon.
 “ Protista ”

Not a monophyletic kingdom.

Most likely composed of seven or more kingdoms.



Branch A ( Mesozoa ): phylum Mesozoa, the mesozoa

Branch B ( Parazoa ): phylum Porifera, the sponges and phylum Placozoa

Branch C ( Eumetazoa ): all other phyla


Branch C ( Eumetazoa ): all other phyla

Grade I ( Radiata ): phyla Cnidaria, Ctenophora

Grade II ( Bilateria ): all other phyla

Division A ( Protostomia ): Protostome characteristics

Acoelomates : phyla Platyhelminthes,
Gnathostomulida, Nemertea

Pseudocoelomates : phyla Rotifera, Gastrotricha,
Kinorhyncha, Nematoda, Nematomorpha,
Acanthocephala, Entoprocta, Priapulida, Loricifera

Eucoelomates : phyla Mollusca, Annelida,
Arthropoda, Echiurida, Sipunculida, Tardigrada,
Onychophora.


Division B ( Deuterostomia ): Deuterostome characteristics
 phyla Phoronida, Ectoprocta, Chaetognatha,
Brachiopoda, Echinodermata, Hemichordata,
Chordata


Recent molecular phylogenetic studies have challenged traditional classification of Bilateria.

Grade II: Bilateria

Division A: ( Protostomia ):
 Lophotrochozoa : phyla platyhelminthes, Nemertea,
Rotifera, Gastrotricha, Acanthocephala, Mollusca,
Annelida, Echiurida, Sipunculida, Phoronida, Ectoprocta,
Entoprocta, Gnathostomulida, Chaetognatha, Brachiopoda

Ecdysozoa : phyla Kinorhyncha, Nematoda,
Nematomorpha, Priapulida, Arthropoda, Tardigrada,
Onychophora, Loricifera
 Division B ( Deuterostomia ):
 phyla Chordata, Hemichordata, Echinodermata