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

Taxonomic classification is hierarchical and nested 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

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

Bass Frog Snake Bird Tunicate Vertebrata (fish, amphibians,reptiles, birds) Tetrapoda (frog, snake, bird) Amniota (snake, bird) Bass Frog Snake Bird Tunicate 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 Amniota Tetrapoda Vertebrata The nested polygons here do show taxonomic groupings, but with regard for “inclusion” or “exclusion” of ancestors common to the groupings

Determining monophyletic taxa is key to classifying organisms according to their evolutionary history: 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 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 the 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 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 Divergent Evolution of Homologous Characters Homologous characters may “evolve away” from each other in structure

Aardvark, native to central, southern and eastern Africa 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 Giant Anteater (at a termite mound), native to Latin America from Southern Mexico to Northern Argentina Aardvark, native to central, southern and eastern Africa Pangolin, native to Africa and southern and southeastern Asia 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.

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.

Thorn of downy hawthorn is a modified stem Spine develops from midrib of leaf Shoot develops from axillary bud Thorn develops from axillary bud Thorn of downy hawthorn is a modified stem Spine of Japanese barberry is a modified leaf Analagous traits, or homoplasies, in two distantly related plant taxa

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

Species A Species B Species C Reconstruct the phylogeny of three closely related bird species Species A Species B Species C 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 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

? (ingroup) Outgroup Species A Species B Species C Transformation Series Closely related species that diverged from ancestral lineage before our three species of interest diverged (outgroup) 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- ? (ingroup) H=hooked bill C=crest W=webbed toes +=species has trait -=species lacks trait Assume character state seen in outgroup is ancestral character state.

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

? (ingroup) Outgroup Species A Species B Species C 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+ 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- This phylogenetic hypothesis requires five evolutionary transformations to explain the distribution of character states among taxa under investigation

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

Phenotypic consequence of a point mutation - a substitution Normal RBC’s and normal hemoglobin Normal rbcs are disk shaped (light micrograph), each with millions of hB molecules that function in O2 transport. hB molecule consists of four polypeptides; first seven amino acids of one of the four are shown; this polypeptide has 146 amino acids. Left; sligh change in the primary structure of hemogloonin, an inherited substitution of one amino acid, causes sickle-cell disease. The substitution occurs in the number 6 position of the polypeptide. The abnormal hb molecules tend to crystalize, deforming some of the cells into a sickle shape. People with sickle cell have periodic sickle-cell crises, which occur when the angular cells clog tiny blood vessesls, impeding blood flow. Sickled RBC’s and sickle-cell hemoglobin Phenotypic consequence of a point mutation - a substitution

Molecules evolve at different rates, some, at constant rates The constant rate at which cytochrome c has evolved raiseds the interesting question of whether other proteins also evolve at constant rates. As a rule of thumb, highly conserved proteins like hemoglobin or cyctochrome c provide the best molecular clocks, but all proteins for which data are available appear to accumulate changes over time. However, different proteins evolve at very different ra5ts, as can be seen in here. This graph presents estimates of the number of “accceptable” point mutations (that is, changes successfully incorporated into the protein) per 100 amino acids per million years. The fastest rate of change appears to be in fibrinopeptides, while the most highly conserved protein is histone H4. Even faster rates of change are seen for pseudogenes, which are not transcribed, suggesting that molecular evolution proceeds more quickly when less constraind by selection. 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

Evolutionary Time

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 Some genes such as the one coding for the protein hemoglobin, have been well studied and the entire time course of their evolution can be laid out with confidence by tracing the origin of particulr substittuions in their nucleotide sequencs The pattern of descent obtained is called a phylogenetic tree. It represents tehe evoltuinary history of the gene. The successive changes in the hemoglobin molecule produce a tree that closely reflects the evolutionary relationships predicted by morphlogical charactrers. Whales, dolphins and porpoises cluster together, as do the primates and the hoofed animals. The patttern of accumulating changes seen in the moecular record consititutes strong direct evidence for macroevoltion