Prepared by

Brenda Leady, University of Toledo

1 Copyright (c) The McGraw-Hill Companies, Inc. Permission required for reprod

Taxonomy and systematics

 Field

of biology concerned with the theory, practice, and rules of classifying living and extinct organisms and viruses of biological diversity and the evolutionary relationships among organisms, both extinct and modern

 Study

Taxonomic groups are now based on hypotheses regarding evolutionary relationships derived from systematics

Hierarchical system involving successive levels  Each group called a taxon  Domain

 Highest

level  All of life belongs to one of 3 domains  Bacteria, Archaea, and Eukarya



Binomial nomenclature
Genus name and species epithet  Genus name always capitalized  Species epithet never capitalized  Both names either italicized or underlined  Rules for naming established and regulated by international associations


Domains similar but different
Scientists think all life originated from primordial prokaryotic cells between 4.0 and 3.5 bya  Soon after, 2 prokaryotic domains, Bacteria and Archaea, diverged  2.5-2.0 bya first unicellular eukaryotic species  Multicellular eukaryotes arose about 1.5 bya


   

 

DNA is used as the genetic material All species use the same genetic code (with only a few rare codon exceptions) Messenger RNA encodes the information to produce proteins Transfer RNA and ribosomes are needed to synthesize proteins, using mRNA as a source of genetic information All living cells are surrounded by a plasma membrane Certain metabolic pathways, such as glycolysis, are found in all three domains 8

These traits are universal because all 3 domains evolved from a common ancestor  Dissimilarities exist because major evolutionary changes have occurred since the time that the three domains diverged



Domain Bacteria
 Diverse

collection of many species  So widespread only generalizations about their ecology  Key to success is metabolic diversity  Come in a myriad of shapes and sizes

Domain Archaea
 Less

diverse than Bacteria  Discovered in 1970s  Many found in extreme environments  Most are extreme halophiles, methanogens or hyperthermophiles  Not entirely restricted to extreme environments 11


Domain Eukarya

4 traditional kingdoms
 Protista  Fungi  Plantae  Animalia



Kingdom Protista
Simplest eukaryotes  Most unicellular but some are colonial or simple multicellular  Some photosynthesize while others eat bacterial or other protists  Most live in aquatic habitats  Leftover organisms not put in other 3 kingdoms



Kingdom Fungi
Yeasts, molds, mushrooms  Present worldwide in aquatic and terrestrial environments  Many symbiotic with plants  Cell walls contain chitin  Most multicellular  Mass of hyphae combine to make mycelium



Kingdom Plantae
Multicellular  Almost all capable of photosynthesis  Mosses, ferns, conifers, flowering plants  Cell wall made primarily of cellulose



Kingdom Animalia
 

Multicellular and eat others for food More than 1 million species
 Sponges,

worms, insects, mollusks, fish, amphibians, birds, reptiles, mammals

    

Most ingest food and digest it in an internal cavity Bodies composed of cells organized into tissues (except sponges) Capable of complex and rapid movement Nervous system Lack a rigid cell wall



Phylogeny – evolutionary history of a species or group of species  Gather morphological or molecular data  Use mathematical strategies to analyze data  Construct evolutionary trees  Molecular data has caused many revisions


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


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 subsets of larger clades  For larger taxa, common ancestor existed a long time ago (kingdom)  For smaller taxa, common ancestor more recent (family or genus)



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


Morphological analysis
First systematic studies focused on morphological features of extinct and modern species  Convergent evolution (traits arise independently due to adaptations to similar environments) can cause problems



Molecular systematics/clocks
Analyzing genetic data to identify and study genetic homology and reconstruct phylogenetic trees  DNA sequences from closely related species are more similar to each other than to sequences from more distantly related species


Molecular clock
  

 

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 Not all organisms evolve at the same rate


Primate evolution example
  

Evolutionary relationships derived by comparing DNA sequences in a mitochondrial gene 3 branch points to examine (A,D, E) A- common ancestor diverges into siamangs and other species
 Gene

in siamangs more different than the gene in the other 7 species

Humans and siamangs have more differences than humans and chimpanzees because there has been more time for them to accumulate differences 2 chimp species diverged recently and have very similar gene sequences 34


Cladistic approach
Reconstructs phylogenetic tree by considering various possible pathways of evolution and then proposing plausible tree  Phylogenetic trees or cladograms  Compares traits shared or not shared

 Shared

trait – shared primitive character or symplesiomorphy  Not shared – shared derived character or synapomorphy

Branch point – 2 species differ in shared derived characters  Ingroup – monophyletic group we are interested in  Outgroup – species or group of species that is most closely related to an ingroup  All traits shared by the outgroup and the ingroup must have arisen in a common ancestor that predates the divergence of the 2 groups



 

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



Constructing a cladogram
1. 2. 3. 4.

Choose species Choose characters Determine order of character states

primitive or derived?

Group species (or higher taxa) based on shared derived characteristics



Build a cladogram based on
 

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

Strategies for a likely cladogram
 

Challenge in a cladistic approach is to determine the correct order of events May not always be obvious which traits are ancestral and came earlier, and which are derived and came later in evolution Different approaches can be used to deduce the correct order
  

Analyze fossils and determine the relative dates that certain traits arose Assume that the best hypothesis is the one that requires the fewest number of evolutionary changes (principle of parsimony) Maximum likelihood and Bayesian analysis for gene sequence data

4 taxa (A-D)  A is the outgroup

 Has

all the primitive states 3 requires fewest number of mutations so is the most parsimonous

3 potential trees
 Tree



Cooper and Colleagues Extracted DNA from Extinct Flightless Birds and Then Compared It with DNA from Modern Species to Reconstruct Their Phylogeny

Ancient DNA analysis or molecular paleontology  Under certain conditions DNA samples may be stable as long as 50,000 – 100,000 years  Discovery based sciences- gather data to propose a hypothesis  Sequences are very similar  New Zealand colonized twice by the ancestors of flightless birds

 First

by moa ancestor, then by kiwi ancestor

Ideal goal of taxonomy to place organisms in monophyletic groups


Many recent models propose several major groups, supergroups, as a way to organize eukaryotes into monophyletic groups Shows that protists played a key role in the evolution of diverse eukaryote species


Due to Horizontal Gene Transfer, the Tree of Life Is Really a “Web of Life”
    

Vertical evolution involves changes in species due to descent from a common ancestor Horizontal gene transfer is the transfer of genes between different species Significant role in phylogeny of all living species Still prevalent among prokaryotes but less common in eukaryotes Horizontal gene transfer may have been so prevalent that the universal ancestor may have been a community of cell lineages

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