CHAPTER 20 PHYLOGENY & HISTORY OF LIFE LEARNING OUTCOMES 20.1 Organization of Life on Earth Exam 1.
20.2 Phylogenetic Trees: Determining Evolutionary Relationships Understand what a phylogeny represents. Describe the difference between shared primitive and derived characters. Differentiate among monophyletic, paraphyletic, and polyphyletic groups. Interpret or construct a phylogenetic tree, including cladogenetic or anagenetic events. 20.3 Perspectives on the Phylogenetic Tree Explain why only shared, derived characters indicate close evolutionary relationship. Demonstrate how a cladogram is constructed. Discuss how a phylogenetic tree can indicate the timing of species diversification. Discuss the differences in approaches to phylogenetic analysis. Molecular Clocks Explain how DNA sequence data can be used to establish the timing of evolutionary divergence of species. Horizontal Gene Transfer Explain why horizontal gene transfer can complicate evolutionary hypotheses. Explain why the "tree of life" is being replaced by the "web of life." 20.1 Organizing Life on Earth A phylogenetic tree depicts the evolutionary relationships among species Copyright 2014 by John Wiley & Sons, Inc.
20.2. Taxonomy and systematics Taxonomy Science of describing, naming, and classifying living and extinct organisms and viruses Systematics Study of biological diversity and the evolutionary relationships among organisms, both extinct and modern Taxonomic groups are now based on hypotheses regarding evolutionary relationships derived from systematics Phylogeny evolutionary history of a species or group of species 4 Taxonomy Hierarchical system involving successive levels
Each group at any level is called a taxon Domains: Eukaryotic supergroups: Large eukaryotic kingdoms: Bacteria Excavata Archaea Eukarya Land plants and algal relatives Alveolata Stramenopila Rhizaria
Plantae Domain Highest level All of life belongs to one of 3 domains Bacteria, Archaea, and Eukarya Amoebozoa Opisthokonta Fungi Animalia 5 Binomial nomenclature: Genus name and species epithet: Genus name always capitalized, Species epithet never capitalized Taxonomic group Gray wolf found in Number of species
~ 4 10 million Domain Eukarya Supergroup Opisthokonta >1 million Kingdom Animalia >1 million Phylum Chordata ~50,000 Class Mammalia
~5,000 Order Carnivora ~270 Family Canidae Genus Canis 7 Species lupus 1
34 Canis lupus Both names either italicized or underlined Rules for naming established and regulated by international 6 Phylogeny evolutionary history of a species or group of species To propose a phylogeny, biologists use the tools of systematics Trees are usually based on morphological or genetic data Phylogenetic Tree: Diagram that describes phylogeny A hypothesis of evolutionary relationships among various species
Based on available information New species can be formed by Anagenesis single species evolves into a different species Cladogenesis a species diverges into 2 or more species 7 Phylogenetic trees Phylogeny evolutionary history of a species or group of species Millions of years ago (mya) Time Present F I G J B
5 H K E C D B 10 A To propose a phylogeny, biologists use the tools of systematics Trees are usually based on morphological or genetic data 8
Phylogenetic Tree: Diagram that describes phylogeny A hypothesis of evolutionary relationships among various species Based on available information New species can be formed by Anagenesis single species evolves into a different species Cladogenesis a species diverges into 2 or more species 9 Monophyletic group or clade Group of species, taxon, consisting of the most recent common ancestor and all of its ancestors
Smaller and more recent clades are nested within larger clades that have older common ancestors H I J D K L E M N F B O
G C H I J D K E M N F B A
(a) Monophyletic L O G C H I J D K E M N F
B A (b) Paraphyletic L G C A (c) Polyphyletic Paraphyletic group O Contains a common ancestor and some, but not all, of its descendents 10 KEY Reptiles (a) Reptiles as a
paraphyletic taxon Birds Crocodiles Lizards and snakes Turtles Birds Crocodiles Orders Classes Lizards and snakes Over time, taxonomic groups will be reorganized so only monophyletic groups are recognized
Reptiles were a paraphyletic groups because birds were excluded Turtles Reptiles (b) Reptiles as a monophyletic taxon 11 20.2 Determining Evolutionary Relationships Homologous structures may not be the result of a close evolutionary relationship Copyright 2014 by John Wiley & Sons, Inc. Homology
Similarities among various species that occur because they are derived from a common ancestor Bat wing, human arm and cat front leg Genes can also be homologous if they are derived from the same ancestral gene 13 20.2 Determining Evolutionary Relationships Analogous structures have the same function but come from different ancestors Copyright 2014 by John Wiley & Sons, Inc. Morphological analysis: First systematic studies focused on morphological features of extinct and modern species Convergent
evolution (traits arise independently due to adaptations 15 to similar environments) can cause problems Molecular systematics Analysis of genetic data, such as DNA and amino acid sequences, to identify and study genetic homologies and propose phylogenetic trees DNA and amino acid sequences from closely related species are more similar to each other than to sequences from more distantly related species 16 Cladistics
Study and classification of species based on evolutionary relationships Cladistic approach discriminates among possible phylogenetic trees by considering the various possible pathways of evolutionary changes and then choosing the tree that requires the least complex explanation for all of the available data Phylogenetic trees or cladograms Cladistic approach compares homologous traits, also called characters, which may exist in two or more character states Shared primitive character or symplesiomorphy Shared by two or more different taxa and inherited from ancestors older than their last common ancestor Shared derived character or synapomorphy Shared by two or more species or taxa and has originated in their 17 most recent common ancestor D
E B F G C A 18 Branch point 2 species differ in shared derived characters Ingroup
group we are interested in Notochord Vertebrae Hinged jaw Tetrapod Mammary glands Lancelet Lamprey Salmon Lizard Rabbit Yes No No No No Yes
Yes No No No Yes Yes Yes No No Yes Yes Yes Yes No Yes Yes Yes Yes Yes (a) Characteristics among species Lancelet Lamprey
Salmon Lizard Rabbit Mammary glands Tetrapod Hinged jaw Vertebrae Notochord (b) Cladogram based on morphological traits Outgroup species or group of species that is assumed to have diverged before the species in the
ingroup An outgroup will lack one or more shared derived characters that are found in 19 the ingroup Cladogram can also be constructed with gene sequences 7 species called A-G A mutation that changes the DNA sequence is analogous to a modification of a characteristic 20 Constructing a cladogram 1. 2. 3.
Choose species Choose characters Determine polarity of character states Primitive or derived? 21 4. Analyze cladogram based on 5. 6. All species (or higher taxa) are placed on tips in the phylogenetic tree, not at branch points Each cladogram branch point should have a list of one or more shared derived characters that are common to all species above the branch point unless the character is later modified All shared derived characters appear together only once in a cladogram unless they arose independently during evolution more than once
Choose the most likely cladogram among possible options Choose a noncontroversial outgroup as root 22 Principle of parsimony Preferred hypothesis is the one that is the simplest for all the characters and their states Challenge in a cladistic approach is to determine the correct polarity of events It may not always be obvious which traits are primitive and came earlier and which are derived and came later in evolution Fossils may be analyzed
4 taxa (A-D) Example A is the outgroup Has all the primitive states 3 potential trees Tree 3 requires fewest number of mutations so is the most parsimonous 23 According to the principle of parsimony, tree number 3 is the more likely choice because it requires only five mutations. 24 Molecular clocks Favorable mutations rare and detrimental mutations eliminated
Most mutations are neutral If neutral mutations occur at a constant rate they can be used to measure evolutionary time Longer periods of time since divergence allows for a greater accumulation of mutations Not perfectly linear over long periods of time Not all organisms evolve at the same rate Differences in generations times Nucleotide differences in a homologous gene between different pairs of species 0 Evolutionary time since divergence of pairs of species 25 (millions of years) Primate evolution example
Evolutionary relationships derived by comparing DNA sequences for cytochrome oxidase subunit II Tends to change fairly rapidly on an evolutionary timescale 3 branch points to examine (A, D, E) Ancestor A Ancestor D This ancestor diverged into two species that ultimately gave rise to siamangs and the other five species 23 million years for siamang genome to accumulate changes different from other 5 species This ancestor diverged into two species that eventually gave rise to humans and chimpanzees Differences in gene sequences between humans and chimpanzees are relatively
moderate Ancestor E This ancestor diverged into two species of chimpanzees Two modern species of chimpanzees have fewer differences in their gene sequences 26 E: This ancestor diverged into two species of chimpanzees Two modern species of chimpanzees have fewer differences in their gene sequences D: This ancestor diverged into two species that eventually gave rise to humans and chimpanzees Differences in gene sequences between humans and chimpanzees are relatively moderate A: This ancestor diverged into two species that ultimately gave rise to siamangs and the other five species 23 million years for siamang genome to accumulate changes
different from other 5 species\ 27 20.3 Perspectives on the Phylogenetic Tree Horizontal gene transfer is the movement of genetic material from one species to another Copyright 2014 by John Wiley & Sons, Inc. Wiley & c. 20.3 Perspectives on the Phylogenetic Tree Genome fusion by endosymbiosis may be the source of a variety of cellular features 20.3 Perspectives on the Phylogenetic Tree There are several different hypotheses for prokaryotic
and eukaryotic evolution Copyright 2014 by John Wiley & Sons, Inc. Horizontal gene transfer Any process in which an organism incorporates genetic material from another organism without being the offspring of that organism Vertical evolution Changes in groups due to descent from a common ancestor 31 20.3 Perspectives on the Phylogenetic Tree The ring of life model describes all three domains arising from the same pool of primitive prokaryotes Copyright 2014 by John Wiley & Sons, Inc.
Systematics Hagfish Tuna _______ Rattlesnake ______ Seagull Human _______ _______ _______ _______ _______ _______ Place the letter in the appropriate
blank a. Tetrapod b. 4 chambered heart c. Amniotic egg d. Wolf e. Hair and mammary glands f. Bullfrog g. Jaws h. Bipedal 34 Humerus Radius Ulna Carpals Metacarpals Phalanges Human Cat Whale Bat
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