CHAPTER 26 TAXONOMY AND SYSTEMATICS Brenda Leady, University of Toledo Prepared by Brenda Leady, University of Toledo Copyright (c) The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

Taxonomy and systematics Field of biology concerned with the theory, practice, and rules of 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

Taxonomy 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

Similarities 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

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 Domain Archaea 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

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

Systematics 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)

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

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

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 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

Example 4 taxa (A-D) A is the outgroup 3 potential trees Has all the primitive states 3 potential trees Tree 3 requires fewest number of mutations so is the most parsimonous

Ancient DNA analysis or molecular paleontology 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