lecture v how to determine evolutionary relationships: concepts in phylogeny and systematics

Lecture V

How to Determine Evolutionary Relationships: Concepts in Phylogeny and Systematics

Textbook Reading: pp 425-433, 435-437 in chapter 23: Reconstructing and using Phylogenies

Nature 413, 277 - 281 (2001) Skeletons of terrestrial cetaceans and the relationship of whales to artiodactyls. J. G. M. Thewissen, E. M. Williams, L. J. Roe & S. T. Hussain. See webpage for link to pdf of this paper, and summary/persptive of this paper

•Taxonomy is the science of the classification (=naming) of organisms

•Linnean classification called binomial nomenclature, in reference to genus and specific epithet

•Taxon is a generic term for any taxonomic unit (level)

•Most inclusive taxon, not shown here, is Domain

Taxonomic classification is hierarchical and nested

Bass Frog Snake Bird

“Basal” lineage

Phylogeny history of descent of a group of organisms from their common ancestor

Phylogenetic Tree or Cladogram. Depiction of a phylogeny. Carries information only on branching relationships; no information about passage of time or amount of phenotypic change. Each branching point (node) reflects a divergence (ie, speciation, cladogenesis) event that took place in the species that is the most recent common ancestor to the descendents of that cladogenesis event

Lineage Organisms in an ancestor-descendent relationship

Vertebrata (fish, amphibians,reptiles, birds)

Tetrapoda (frog, snake, bird)

Amniota (snake, bird)

Bass Frog Snake BirdTunicate

The nested polygons here show taxonomic groupings, but with no regard for “inclusion” or “exclusion” of ancestors common to the groupings

Tunicate Bass Frog Snake Bird

AmniotaTetrapoda

Vertebrata

The nested polygons here do show taxonomic groupings, but with regard for “inclusion” or “exclusion” of ancestors common to the groupings

•Monophyletic taxon is one in which a single ancestor gives rise to all species, and which includes all descendents of that single ancestor

•Paraphyletic taxon excludes one or more species descended from the most recent common ancestor of the taxon

•Polyphyletic taxon excludes the most recent common ancestor of all members of the taxon

Determining monophyletic taxa is key to classifying organisms according to their evolutionary history:

A taxon that includes only A and B would be paraphyletic

A taxon that includes B, C and D would be polyphyletic

A taxon that includes D, E and F would be monophyletic

“SCHOOLS” OF SYSTEMATICS

TRADITIONAL EVOLUTIONARY TAXONOMY [Simpson and others]

•Establish taxa based on common ancestry (clades) and or extent of adaptive evolutionary change:

•evolutionary groups that represent adaptive zone constitute legitimate higher taxa -- a grade

•adaptive zone; “…characteristic reaction and mutual relationship between environment and organism, a way of life and not a place where life is led.”

•paraphyletic taxa may be acceptable

PHYLOGENETIC SYSTEMATICS (CLADISTICS) [Hennig]

•Establish taxa based on clades; monophyletic taxa only •Powerful methodological and analytic tool for determining relationships

•The tools of cladistics now represent the prevailing approach to determining relationships; the philosophy of strict monophyly wrt classification is still under debate --

bears on definition - concept- of species

George Gaylord Simpson (1902-1984). Mammalian Paleontologist, regarded as one of the architects of the modern synthesis. Formulated the principles of evolutionary taxonomy

Willi Hennig (1913-1976). Hennig is best known for developing phylogenetic systematics, a coherent theory of the investigation and presentation of the relations that exist among species.

http://www.cladistics.org/about/hennig.html

Systematists classify organisms and determine evolutionary relationships based on analysis of homologous characters (traits)

•Systematic investigation is based on analysis of homologous characters (traits); characters may be morphological, molecular, behavioral, physiological..

•Homologous character; character that is shared by two or more taxa because those taxa inherited the character from a common ancestor

Divergent Evolution of Homologous Characters Homologous characters may “evolve away” from each other in structure

•Expect shared character to be quite similar, perhaps, but not identical among taxa, as a result of descent with modification

•Homology indicates common ancestry, which is information with which one can determine evolutionary history

Convergent Evolution of Analogous Characters. Three distantly related mammals have structural similarities (analogous characters, homoplasious characters) due to convergent evolution. Each taxon independently evolved morphological traits for feeding on ants and termites.

Aardvark, native to central, southern and eastern Africa

Giant Anteater (at a termite mound), native to Latin America from Southern Mexico to Northern Argentina

Pangolin, native to Africa and southern and southeastern Asia

•Analagous character; character occurring in two or more lineages because it evolved independently in each of those lineages,

•Analagies may arise through convergent evolution: lineages occupy similar ecological

roles and similar selective forces

•Misinterpretation of analagous characters for homologus ones may lead to erroneous conclusions regarding phylogenetic relationships and unintended taxanomic groupings

The supporting structures of bird and bat wings are homologous structures; derived from a common ancestor

The supporting structures of insect wings are analogous to the structures of bird and bat wings; evolved independently.

Spine develops from midrib of leaf

Analagous traits, or homoplasies, in two distantly related plant taxa

Spine of Japanese barberry is a modified leaf

Thorn of downy hawthorn is a modified stem

Thorn develops from axillary bud

Shoot develops from axillary bud

Phylogenetic Systematics Dr. Willi Hennig (1913-1976)

•The history of diversification is recorded through descent with modification

•Modification exists in the form of evolutionary transformation of characters from one state to another state.

•Plesiomorphy: Ancestral character state

•Apomorphy: Derived character state

•Synapomorphy Derived character state that is exclusively shared by a subset of taxa under investigation.

•A synapomorphy is evidence that taxa bearing it are descended from the same common ancestor -- the ancestor in which the derived character arose.

“Cladistic” or “Phylogenetic” Analysis: Procedural Outline

SELECT ORGANISMS

•Identify the ingroup •Select an appropriate outgroup

BUILD TRANSFORMATION MATIX •Select characters for analysis •Assign character states•Determine polarity of character states

ANALYZE AND INTERPRET DATA •Subject data to optimization algorithm

(usually parsimony criteria) to produce an optimal tree, perhaps a concensus tree•Seek congruence•Product: Phylogenetic Hypothesis

Phylogenetic Systematics Dr. Willi Hennig (1913-1976)

•The history of diversification is recorded through descent with modification

•Modification exists in the form of evolutionary transformation of characters from one state to another state.

•Plesiomorphy: Ancestral character state

•Apomorphy: Derived character state

•Synapomorphy Derived character state that is exclusively shared by a subset of taxa under investigation.

•A synapomorphy is evidence that taxa bearing it are descended from the same common ancestor -- the ancestor in which the derived character arose.

“Cladistic” or “Phylogenetic” Analysis: Procedural Outline

SELECT ORGANISMS

•Identify the ingroup •Select an appropriate outgroup

BUILD TRANSFORMATION MATIX •Select characters for analysis •Assign character states•Determine polarity of character states

ANALYZE AND INTERPRET DATA •Subject data to optimization algorithm

(usually parsimony criteria) to produce an optimal tree, perhaps a concensus tree•Seek congruence•Product: Phylogenetic Hypothesis

Determine characters to use for analysis

•bill shape (derived character state: hooked; ancestral= not hooked)

•head feathers (derived = crest; ancestral = no crest)

•toe condition (derived = webbed; ancestral = no webbing)

Species A Species B Species C

Reconstruct the phylogeny of three closely related bird species

Species A Species B Species C

Hooked Bill Hooked Bill No Hooked Bill

Crested Head No Crested Head Crested Head

Webbed Toes Webbed Toes No Webbed Toes

•Character states variously arise in lineages.

•Character states variously accumulate in lineages, in descendents of the ancestor in which the character states arose

?

A B C

Outgroup Closely related species that we know diverged from ancestral lineage before our three species of interest diverged

Ingroup

?

Closely related species that diverged from ancestral lineage before our three species of interest diverged (outgroup)

(ingroup)

Bill Shape Head Plumage Toe Condition

Outgroup H- C- W-

Species A H+ C+ W+

Species B H+ C- W+

Species C H- C+ W-

Outgroup Species A Species B Species C

Transformation Series

H=hooked billC=crestW=webbed toes

+=species has trait -=species lacks trait

Assume character state seen in outgroup is ancestral character state.

?

Closely related species that diverged from ancestral lineage before our three species of interest diverged (outgroup)

(ingroup)

Bill Shape Head Plumage Toe Condition

Outgroup H- C- W-

Species A H+ C+ W+

Species B H+ C- W+

Species C H- C+ W-

Outgroup Species A Species B Species C

Transformation Series

Assume character state seen in outgroup is ancestral.

W-C-

H-

H+

W+

C+

C+

This phylogenetic hypothesis requires four evolutionary transformations to explain the distribution of character states among taxa under investigation

OG B A C

H- C- W- H+ C- W+ H+ C+ W+ H- C+ W-

W-C-

H-

H+

W+

W+

H+

C+

This phylogenetic hypothesis requires five evolutionary transformations to explain the distribution of character states among taxa under investigation

Choosing Among Competing Hypotheses: The Parsimony Principle

•The Parsimony Principle holds that, all other things being equal, the hypothesis requiring the fewest number of evolutionary transformations has the highest likelihood of being the correct hypothesis

Evolutionary relationships may be determined through analysis of molecular characters; DNA, RNA and proteins

•Molecular biology provides powerful tools for systematics

•Nucleotide sequences and therefore amino acid sequences, are inherited; both undergo descent with modification following divergence of one lineage into two

•Extent of sequence differences between taxa is an indicator, an estimator, of time since divergence from a common ancestor

•DNA , RNA and proteins are used to classify organisms and determine evolutionary relationships

Normal RBC’s and normal hemoglobin

Sickled RBC’s and sickle-cell hemoglobin

Phenotypic consequence of a point mutation - a substitution

Molecules evolve at different rates, some, at constant rates

Raven and Johnson 1999)

Hemoglobin Evolution

•Gene duplication Multigene Families

•Evolution of molecular function

Tetrameric Human hemoglobin

•Gene family

-two or more genes in a genome, identical or highly similar in nucleotide sequence

-descended from the same ancestral gene

•Origin of gene families

-Repeated gene duplication from errors during DNA replication and recombination

•Globin gene families are well-studied across taxa for sequence, structure and function

•Hemoglobin multigene families in humans

•Alpha globin family (on chr. 16)

•Beta globin family (on chr. 13)

•Hemoglobin families probably descended from a myoglobin-like ancestral gene

Evo

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Evolution of the Globin Gene

•Genes encoding proteins have undergone continual evolution, accumulating increasing numbers of changes over time

•Length of lines corresponds to number of nucleotide substitutions in the gene

Raven and Johnson 1999