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Course Weekly Lecture Plan

Week Topic
1 Weekly Course Chronology
1 -7th Feb History of Life on Earth
• Clock analogy for some key events in evolutionary history
• Introduction to prokaryotes
• Geologic time scale, important events in the history of life
• The origin of eukaryotes through serial endosymbiosis hypothesis
• The Cambrian explosion and “adaptive radiation”
• Fossil record – dating and “Living fossils”
• Prehistoric/historic extinctions and the diversity of life
• The rise and fall of dominant groups:
- Continental drift, mass extinctions, adaptive radiation
• Adaptive radiation of mammals

2 -14th Feb Evolution
• Evolutionary theory
• Darwinian evolution- descent with modification
• Natural selection
• The evidence for “descent with modification”
• Species - what are they? - One of the oldest problems in Biology
- Species Concepts - How do we define species?
- Biological Species Concept
- Morphospecies Concept
- Phylogenetic Species Concept
3 21st Feb Appreciation of diversity of life
• Levels of biological organization
• Biodiversity
- Definition and levels
- Values of biodiversity
- Estimating biodiversity
“How Many Species Are There on Earth and in the Ocean?”
- Biodiversity “hot spots”
- Threats, species extinctions and global biodiversity crisis
“Why Worry about How Many Species and Their Loss?” http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001130
• Conservation biology
4 -28th Feb Introduction to Phylogenetic Kingdoms
The Kingdom Monera - Eubacteria and Archaebacteria
The Kingdom Protista or Protoctista
5 -6th March MID-TERM I
The Kingdom Fungi
6 -13th Mar The Kingdom Plantae
• Major Groups of Plants:
- Bryophytes—nonvascular plants
- Pteridophytes — vascular, seedless plants
- Seed plants – Gymnosperms and Angiosperms
7 -20th Mar The Kingdom Animalia
• Invertebrates
• Sponges
• Cnidarians
• Worms
• Mollusks
• Arthropods
• Echinoderms
8 -27th Mar The Vertebrates
• Chordates
• Fish
- Agnatha (jawless fish/lamprey)
- Chondrichthyes (sharks, skates, rays)
- Osteichthyes (bass, tuna, salmon)
• Amphibians
• Reptiles
• Birds
• Mammals
* Phylogenetic Kingdoms Comparison Activity
9 -3rd Apr Introduction to Biological Systematics
How to organize the diversity of life? How to classify all this diversity?
• Biological systematics
• Its role and components
• Taxonomy
• Describing, Identification, Classification, Collections, Conservation
• To curate and manage depositories of Earth’s biodiversity
• “Mapping biodiversity” and finding “new” species, new traits
• Nomenclature
• Binomial nomenclature - Carolus Linnaeus
• International Code of Zoological & Botanical Nomenclature
• Dichotomous Keys Identify Organisms
• Classification
- Hierarchical Classification - 7 Taxonomic Categories
• Systematics
• Fossil records
• Comparative homologies
• Cladistics
• Comparative sequencing of DNA/RNA among organisms
• Molecular clocks
• Cladistics
- A clade and a cladogram
- Monophyletic, paraphyletic and polyphyletic grouping
- The outgroup comparison
• Phylogenetics
• Phylogenetic trees and timing
- Phylograms
- Ultrametric Trees
• Molecular Systematics
- Ribosomal RNA, chloroplast DNA, and mitochondrial DNA
- Maximum Parsimony and Maximum Likelihood
• The Universal Tree of Life
10 -10th April MID-TERM II
History of taxonomy
• Pre Lamarck, Pre Darwin - “Classification without phylogeny”
• Lamarck & Darwin to Hennig (et al.)
“Classification with phylogeny but without a reproducible method”
- Lack of a reproducible method resulted in explosion of
3 major approaches in1960s:
I. Phenetics
- Hennig (et al.) to today
- “Classification with phylogeny and a reproducible method”
II. Cladistics
III. Phylogenetics

11 -17th Apr Modern Taxonomy
• Tools - digital imaging, databases
• Dissemination – www
• Tools - Molecular data, species demarcation, phylogeography
“Taxonomy as an eScience” http://rsta.royalsocietypublishing.org/content/367/1890/953.full.pdf+html
• Phenotypic data management
• Molecular data
• Proteins, Chromosomes, DNA barcoding
“Towards writing the encyclopaedia of life: an introduction to DNA barcoding”http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1609222/pdf/rstb20051730.pdf
• DNA sequence data, PCR, Mitochondrial genome, rRNA genes, 22 tRNA genes
• Species demarcation using DNA
• Phylogeography
- MtDNA and Ecology
12 -24th Apr Biodiversity information/informatics
• Biodiversity information
“Towards a collaborative, global infrastructure for biodiversity assessment”
• key generations-DELTA
13 -1st May International and National perspective/efforts/DATABASES
• Biodiversity and Biological Collections Web Server
• Global Biodiversity Information Facility (GBIF)
• Biosis Taxonomy and Nomenclature
• Tree of Life
• TreeBase: A database of phylogenetic knowledge
• Barcode of Life
• TÜBİTAK-Türkiye Taksonomik Tür Veritabanı bioces.tubitak.gov.tr
• TÜBİTAK-Türkiye Bitkileri Veri Sistemi www.tubitak.gov.tr/tubives
• T.C Orman ve Su İşleri Bakanlığı- DKMP- BİB www.nuhungemisi.gov.tr
14 -8th May * Field Trip
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