PHYLOGENY AND CLASSIFICATION Module 2 Session 2

Evolution ACCOUNTS FOR LIFE’S diversity AND UNITY

TERMINOLOGY : Classification is a very broad term which simply means putting things in classes Taxonomy means giving names to organisms. It tends to go hand in hand with classification Phylogeny traces the evolutionary history of species Systematics is the process of trying to classify animals (or plants) according to their phylogeny.

Cladistics, also known as phylogenetic systematics. It works by analyzing different taxa to find objective similarities and differences between them, and using those similarities and differences to derive a hierarchical structure showing which taxa are most similar to others Cladistics groups organisms by common descent A clade is a group of species that includes an ancestral species and all its descendants

TAXON: Each level of hierarchy represents a taxon.

LINKING CLASSIFICATION AND PHYLOGENY . Classification and phylogeny do not always match New features may have emerged since last classified. DNA is a valuable tool used for classification. Classification does not reveal evolutionary history Homo sapiens classification

exclusive inclusive Binomial Nomenclature: Use of Genus species names. eg. Panthera pardus – leopard exclusive inclusive Fig. 20.3 Taxonomic hierarchy

Phylum Chordata Invertebrate chordates and vertebrate chordates including fish, sharks, amphibians, reptiles and mammals. Derived characteristics

By studying inherited species' characteristics and other historical evidence, we can reconstruct evolutionary relationships and represent them on a "family tree," called a phylogeny. The phylogeny you see below represents the basic relationships that tie all life on Earth together.

ISSUES WITH classification (proposed by carolus linneaus) DOES NOT REFLECT EVOLUTIONARY HISTORY DOES NOT SHOW EVOLUTIONARY RELATIONSHIP BETWEEN GROUPS PHYLOGENETIC TREES REFLECT EVOLUTIONARY RELATIONSHIPS

UNDERSTANDING PHYLOGENETIC TREES

where lineages diverge Taxon A Branch point: where lineages diverge Taxon A Taxon B Sister taxa Taxon C ROOTED Taxon D POLYTOMY Taxon E ANCESTRAL LINEAGE Taxon F Figure 26.5 How to read a phylogenetic tree. Basal taxon Taxon G This branch point represents the common ancestor of taxa A–G. This branch point forms a polytomy: an unresolved pattern of divergence. DIVERGED EARLIER THAN OTHERS

CREATING A PHYLOGENETIC TREE-ACTIVITY- Molecular Phylogeny of Primates

What CAN WE and Cannot Learn from Phylogenetic Trees? Phylogenetic trees show patterns of descent, not phenotypic similarity Phylogenetic trees do not indicate when species evolved or how much change occurred in a lineage It should not be assumed that a taxon evolved from thE taxon next to it, only that they shared a common ancestor © 2011 Pearson Education, Inc.

MORPHOLOGY AND MOLECULAR DATA ARE USED TO CONSTRUCT PHYLOGENETIC TREES

Sorting Homology from Analogy When constructing a phylogeny, systematists need to distinguish whether a similarity is the result of homology or analogy Homology is similarity due to shared ancestry Analogy is similarity due to convergent evolution Convergent Evolution occurs when environmental conditions and natural selection produce similar adaptations in different species Marsupial ,Mole Eutheriam Mole © 2011 Pearson Education, Inc.

1 1 2 Deletion 2 1 2 Insertion 3 1 2 4 1 2 DNA ALIGNMENT USING Figure 26.8-4 1 1 DNA ALIGNMENT USING SOFTWARE HELPS CONSTRUCT PHYLOGENETIC TREES 2 Deletion 2 1 2 Insertion 3 1 Figure 26.8 Aligning segments of DNA. 2 4 1 2

HOMOLOGOUS GENES

CONSTRUCTING PHYLOGENETIC TREES

HOMOLOGOUS CHARACTERISTICS ARE USEFUL IN CONSTRUCTING PHYLOGENETIC TREES AS THEY SHOW SHARED ANCESTRY

Cladistics is method of hypothesizing relationships among organisms; it is a method of inferring phylogeny from homologous characters Cladogram: diagram showing evolutionary relationship with respect to shared characters. Cladogram

CLADE: INCLUDE ANCESTRAL SPECIES AND ALL OF ITS DESCENDANTS

CLADES MONOPHYLETIC: ANCESTRAL SPECIES AND DESCENDANTS POLYPHYLETIC GROUP: INCLUDES TAXA WITH WITH DIFFERENT ANCESTORS PARAPHYLETIC GROUP: ANCESTRAL GROUP WITH SOME BUT NOT ALL OF ITS DESCENDANTS

SHARED ANCESTRAL VS SHARED DERIVED CHARACTERS CHARACTERS THAT ARE SHARED BY ORGANISMS AND RELATED TO AN ANCESTOR ARE SHARED ANCESTRAL CHARACTERISTICS CHARCTERS THAT ARE SHARED BY SOME ORGANISMS BUT NOT WITH THE ANCESTOR ARE REFERRED TO AS SHARED DERIVED CHARACTERS For eg Backbone in mammals and vertebrates is shared ancestral whereas hair is a derived character unique to mammals

PHYLOGENETIC TREES WITH PROPORTIONAL BRANCH LENGTHS Figure 26.13 PHYLOGENETIC TREES WITH PROPORTIONAL BRANCH LENGTHS MORE GENETIC CHANGES In other trees, branch length can represent chronological time, and branching points can be determined from the fossil record Drosophila Lancelet Zebrafish Frog Chicken Human Mouse PALEOZOIC MESOZOIC CENOZOIC 542 251 65.5 Present Millions of years ago © 2011 Pearson Education, Inc.

From Two Kingdoms to Three Domains Early taxonomists classified all species as either plants or animals Later, five kingdoms were recognized: (Monera) (prokaryotes), (Protista), Plantae, Fungi, and Animalia More recently, the three-domain system has been adopted: Bacteria, Archaea, and Eukarya © 2011 Pearson Education, Inc.

Eukarya Bacteria Archaea Figure 26.21 Land plants Dinoflagellates Green algae Forams Ciliates Diatoms Red algae Amoebas Cellular slime molds Euglena Trypanosomes Animals Leishmania Fungi Sulfolobus Green nonsulfur bacteria Thermophiles (Mitochondrion) Figure 26.21 The three domains of life. Spirochetes Halophiles Chlamydia COMMON ANCESTOR OF ALL LIFE Green sulfur bacteria Bacteria Methanobacterium Cyanobacteria Archaea (Plastids, including chloroplasts)

Why are there some similar genes in the three domains? There have been substantial interchanges of genes between organisms in different domains Horizontal gene transfer is the movement of genes from one genome to another Horizontal gene transfer occurs by exchange of transposable elements and plasmids, viral infection, and fusion of organisms Horizontal gene transfer complicates efforts to build a tree of life

An Organism’s Evolution History is Documented in its Genome Ancestral gene Ancestral species Speciation with divergence of gene Species A Species B Orthologous genes Orthologous Gene Families. The colored bands indicate regions of the gene where a mutation in the DNA sequence occurred. (figure not in textbook)

Orthologous genes refer to homologous genes found in two different species that were inherited from a common ancestor. Similarity or divergence in the DNA sequence between orthologous genes found in two species can be used to reveal phylogenetic relationships. In the time since two species diverged from a common ancestor, random mutations create slight difference in DNA sequence. The longer the time period since divergence from a common ancestor, the greater the variation in the DNA sequence of the orthologous genes. http://evolution.berkeley.edu/evolibrary/article/molecclocks_01

Orthologous genes can extend over long evolutionary distances. A comparison of the human and mice genomes reveals that > 90% of human genes are detectably orthologous to mice genes. Comparing human genes to yeast (single-celled eukaryote) reveals that a large percentage of human genes are detectably orthologous to yeast genes, even though a billion years of evolution separate humans from yeast. Examples of orthologous gene families include: Hox genes – found in all animals, regulates embryonic development. FOXP2 genes – found in all vertebrate animals, regulates the development of vocalization.