Phylogeny and Systematics

Chapter 10

TaxonomyTaxonomy produces

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

Taxonomy & SystematicsTaxonomy

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.

TaxonomyIntroduction 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.

TaxonomySystematization 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.

TaxonomyIn classification

Taxonomist asks whether a species being classified contains the defining feature of a particular taxonomic class.

In systematizationTaxonomist 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 ClassificationCarolus Linnaeus designed our hierarchical

classification scheme.KingdomPhylumClassOrderFamilyGenusSpecies

Linnaeus and ClassificationAll 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 ClassificationBinomial nomenclature is the system

Linnaeus used for naming species.Genus and speciesNames 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

SpeciesDefining a species can be difficult.

Criteria:Common descentThe 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.

SpeciesThe 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 ConceptThe 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 ConceptThe 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 LifeA major goal of systematics is to infer the evolutionary

tree or phylogeny – the evolutionary history of a species or group of related species.

PhylogenyPhylogenies are inferred by identifying organismal

features, characters, that vary among species.MorphologicalChromosomalMolecularBehavioral or ecological

PhylogenyShared 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.

Shared Primitive and Shared Derived Characteristics

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.

Shared Primitive and Shared Derived Characteristics

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

PhylogenyThe 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.

PhylogenyPolarity 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.

PhylogenyClades 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.

PhylogenyAncestral 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.

Sources of Phylogenetic InformationCharacters 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.

TaxonomyA theory of taxonomy allows us to rank taxonomic

groups.Two popular theories

Evolutionary taxonomyPhylogenetic 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.

Traditional Evolutionary Taxonomy

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 SystematicsPhylogenetic 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 TaxonomyBoth 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 TaxonomyCurrent State of Animal Taxonomy:

Modern animal taxonomy was established using evolutionary systematics and recent cladistic revisions.

PhyloCodeNew 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.

Maximum Parsimony and Maximum Likelihood

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.

ParsimonyAmong 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.

Phylogenetic Trees as HypothesesThe best hypotheses for phylogenetic trees are those

that fit the most data: morphological, molecular, and fossil.

Molecular SystematicsMuch 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 LifeAristotle’s two kingdom system included plants

and animals.One-celled organisms became a problem

Haeckel (1866) proposed Protista for single-celled 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 LifeMore 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.

Major Subdivisions of the Animal Kingdom

Traditional groupings based on embryological and anatomical characters:

Branch A (Mesozoa): phylum Mesozoa, the mesozoa

Branch B (Parazoa): phylum Porifera, the sponges and phylum Placozoa

Branch C (Eumetazoa): all other phyla

Major Subdivisions of the Animal Kingdom

Branch C (Eumetazoa): all other phylaGrade I (Radiata): phyla Cnidaria, CtenophoraGrade II (Bilateria): all other phyla

Division A (Protostomia): Protostome characteristicsAcoelomates: phyla Platyhelminthes,

Gnathostomulida, NemerteaPseudocoelomates: phyla Rotifera, Gastrotricha,

Kinorhyncha, Nematoda, Nematomorpha, Acanthocephala, Entoprocta, Priapulida, Loricifera

Eucoelomates: phyla Mollusca, Annelida, Arthropoda, Echiurida, Sipunculida, Tardigrada, Onychophora.

Major Subdivisions of the Animal Kingdom

Division B (Deuterostomia): Deuterostome characteristicsphyla Phoronida, Ectoprocta, Chaetognatha,

Brachiopoda, Echinodermata, Hemichordata, Chordata

Major Subdivisions of the Animal Kingdom

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