Exam 1 - Notes

• Chapter 26
• Chapter 27-31
• Chapter 32 & 33
• Chapter 34

Chapter 26

Overview

• Taxonomy and Systematics
• Phylogenetic Trees
• Horizontal Gene Transfer

Taxonomy

The Science of describing, naming, and classifying living an extinct organisms and viruses.

Systematics

Study of biological diversity and the evolutionary  relationships among organisms, both extinct and modern.

• Taxonomic groups are based on hypothesis regarding evolutionary relationships from systematics 
• Hierarchical system involving successive levels
• Each group at any level is called a taxon
• Highest level is Domain
  • All life belongs to 3 domains
  • Bacteria, Archaea, and Eukarya
    • The Eukarya Domain is often divided into Kingdoms in the next level
      This is typically called the 4 Kingdom concept

Four Kingdoms

• Domains Bacteria and Archaea
  • Prokaryotic cells 
    • Lack nucleus
• Kingdom Protista, Fungi, Plantae, Animilia
  • Eukaryotic cells
    • True nucleus

Types of cells

Prokaryotic 

• Lack Nucleus
• Lacks membrane-bound organelles
• Typically singled celled

Eukaryotic 

• Well defined nucleus
• Membrane-bound organelles
• internal membrane system (compartments)

Binomial Nomenclature

• Genus name + Specific epithet
  • ex. Homo sapiens ('wise humans')
• Genus name is always capitalized
• Specific epithet is never capitalized
• Both names are either italicized or underlined 

Phylogenetic Trees

• Phylogeny
  • Evolutionary history of a species or group of species
• To propose a phylogeny,  biologist must use the tools of systematics
• Trees are usually based in morphological and genetic data
  • Subjective vs. Objective data
• Diagram that describes the phylogeny
• A hypothesis of evolutionary relationships among various species
• Based on available information

Monophyletic Group or Clade

• Group of species (taxon) consisting of the most recent ancestor and all of its descendants
• Smaller and more recent clades are nested within larger clades that have a common ancestor

Paraphyletic group

• Contains a common ancestor and some, but not all of its descendants

• Over time, taxonomic groups will be reorganized so that only monophyletic are recognized
• Reptiles were a paraphyletic group because birds were excluded
• In the class and lab, we are going to separate birds and reptiles

Systematics

Morphological Analysis

• First systematic studies focused on morphological features of extinct and modern species
• Most of early classifications were based upon morphological features

Molecular Analysis

• Analysis of genetic data (DNA, Amino Acids, rRNA) to identify and study genetic similarities and propose phylogentic trees
• DNA and Amino Acid sequences from closely related species are more similar to each other than sequences from more distantly related species

Horizontal Gene Transfer

• any process in which an organism incorporates genetic material from another organism without being the offspring of that organism (by means of asexual reproduction)

Vertical Evolution

• Changes in groups due to descent form a common ancestor (sexual reproduction)

 

Chapter 27-31

Prokaryotic Diversity

• Prokaryotes dated at 3.5 billion years old
• Modern Prokaryotes  are most abundant, lacking sexual reproduction

Domain Bacteria

• Proteobacteria
  • "true bacteria"
• Cyanobacteria
  • "Blue-Green bacteria"

Domain Archaea

• Have and "almost" nucleus
• specialized membranes
• surrounded by a cell wall
• old, can live in extreme conditions

Eukaryotic Diversity (Ch 28)

Kingdom Protista

• Earliest eukaryotes in fossil record
• most are microscopic and found in moist environments
• DNA many separate groups
• Most artificial category
  • "catch-all" category

Subgroups

Algae

• Plant-like organisms
• 10 groups
• autotrophic (self-feeding)
  • most are photosynthetic
  • few ingest food
• cell wall with

Protozoans

• Animal-like
• mostly netraothrophic (food-eating)

Slime Molds

• Fungal-like Protist
• Mostly saprothrophic (absorb-feeding)
• mostly multicellular

Kingdom Fungi (Ch 31)

• Conspicuous portion of the organism in the mushroom/yeast/mold/etc
• Saprothrophic (some are heterotrophic)
• Natures recyclers
• Composed of:
  • Mycelium
    • compacted mass of tubular filaments called hyphae
  • Fruiting body
    • site of spore production
  • Cell wall
    • composed of muramic acid/chitin

Kingdom Plantae (Ch 29 & 30)

• >330,000 species
• eukaryotic and multicellular
• autotrophic (mostly) self-feeding
  • capture sunlight to produce energy by photosynthesis
  • Food storage copound
    • starch
  • cell wall
    • cellulose
• Are referred to as "land plants"
• fossils dated to ~400mybp (million years before present)
• Ancestor stock
  • probably a group of algae (green)
• Life on land requires special innovation
  • Must be able to get water
    • ROOTS!

Phyla (divisions)

• 10 phyla 
• Typically combine these into 4 broad categories for convenience 

Bryophytes

• Phylum Hepatophyta
  • Liverworts
  • ~6500 species
• Phylum Anthocerophyta
  • Hornwarts
  • ~100 species
• Phylum Bryophyta
  • Mosses
  • ~12,000 species

Referred to as "mosses and their friends"

Characteristics

• Reproduce by spores (not seeds)
• non-vascular plants
  • lack conducting tissues 
    • xlem and phloem
• Small plants
• Require external H2O for reproduction

Pteridophytes

• Phylum Lycopodiophyta
  • lychophytes
  • 1000 species
• Phylum Pteridophyts
  • Ferns and allies
  • 12,000 species

Characteristics

• Sporangia
  • Where the spores are produce
• Reproduce by spores
  • no seeds
• vascular plants
  • xylem
    • water and minerals
  • phloem
    • food and solutes
• true roots, stem, and leaves
  • due to being vascular
• vascular allows for larger size
• Require external H2O for reproduction

Gymnosperms

• Phylum Cycadophyta
  • cycads
  • 300 species
• Phylum Ginkophyta 
  • Ginko
  • 1 species
• Phylum Gnetophyta
  • gnetophytes
  • 300 species
• Phylum Coniferophytes
  • conifers
  • 500 species

Means "Naked seeds"
Seeds are not enclosed

Biggest group are the conifers
(Cone bearing trees)

• Oldest
  • Bristle cone pine
    • Over 4600 years
• Biggest
  • Giant Sequoia
    • estimated 600 tons
• Tallest 
  • Coastal Redwood
  • 180 meters in height

Characteristics

• Vascular
  • more advanced that Pteridophytes
• Advance seed
  • It has more survival value
  • Contains:
    • Embryo
      • Offspring
    • Stored food
    • Integument
      • Seed coating
• Does not require external H2O for reproduction
  • Pollen tubes deliver sperm to egg location

Angiosperms

• Phylum Anthophyta
  • 300,000 species

Characteristics

• Enclosed seed
• produces flowers and fruits
• most advance vascular tissues
• Seeds advance
  • Enclosed in a vesses (fruit)
    • no survival value
  • Embryo
  • Stored food
  • 2 integuments
    • Seed coats
• Does not require external H2O for reproduction
• Flowers
  • Attract pollinators
• Fruit
  • Enclose and protect the seed
  • assist with seed dispersal

Chapter 32 & 33

Kingdom Animilia

• Over 1.5 million species
  • Estimated 73 million
• 35 Phylums
  • Over half are insects
• More similarities within animal genomes than other kingdoms

Characteristics 

• Multicellular
• Lack of cell wall
• Sexual reproduction
  • mobile sperm
  • larger non-motile egg
• Nervous Tissue
  • Complexity
  • Responsiveness
• Hox Genes
  • Special clusters of genes associated with the planning of the body

Metazoans

• All animals
• Multicellular animals
• Paratoans
  • Sponges
• Eumetazoans
  • "true" multicellular animals

Classification/Systematics

• Old
  • Morphology
  • Embryonic Development
• Recent
  • Molecular genetics

Body Plans

Morphological and Developmental Features

1. Body Symmetry
2. Number of tissue Layers
3. Patterns of Embryonic development 

Symmetry

• Eumetazoa
  • Divided by symmetry
• Radiata
  • Radial symmetry
  • Often Circular or tubular
• Bilateria
  • Bilateral symmetry
  • Dorsal
    • Back
  • Ventral
    • Front
  • Anterior
  • Posterior
  • cephalization
    • enlarged head

Tissues

• Metazoa
  • all animals
  • divided on weather or not they have specialized tissues
• Parazoa
  • Porfera
    • sponges
    • may have distinct cell types
• Enmetazoa
  • more than one type of tissue
  • organs
  • all other animals

Germ Layers

• Radial
  • 2 layers
  • Diploblastic
    • endoderm
    • ectoderm
• Bilateral
  • 3 layers
  • Triploblastic
    • endoderm
    • ectoderm
    • mesoderm

Embryonic Development

• Protostome
  • Blastopore becomes mouth
  • cleavage is determinate
    • fate of embryonic cells are determined early
• Deuterostome (second opening)
  • Blastopore becomes anus
  • cleavage is indeterminate
  • each cell produced by early cleavage can develop into a complete embryo 

Other Morphological Characteristics

Used in classification

• Presence or absence or coelom
• Body segmentation

Molecular data suggest these features are unreliable in terms of understanding evolutionary history

Body Cavity

Coelom

• • a fluid-filled body cavity
• Coelomate or eucolemate
  • true coelom
  • coelom completely lined with mesoderm
• Pseudocoelom
  • coelom only partially lined with mesoderm
  • rotifers and roundworms
• Acoelomate
  • lack of a body cavity and instead have mesenchyme
  • flatworms

Flatworm has no mesoderm

Functions of the Coelom

• Cushions internal organs
• Enables movements and growth of internal organs independent of the body wall
• Fluid acts as a simple circulatory system

Segmentation

• Body may be divided into regions called segments
• occurs in annelid worms, arthropods, and chordates
• allows specialization of body region

DO NOT worry about the number of species

Molecular views of Animal Diversity

• Scientist now use molecular techniques to classify animals
  • Compare similarities in DNA, rRNA, and Amino Acids
  • Closely related organisms have fewer differences than those more distantly related
• Advantages over morphological data in that genetic sequences are easier to quantify and compare
  • Example: A,T,G, and C in DNA

Genes used in Molecular Systematics

• Studies often focus on ribosomal RNA (rRNA)
  • Universal in all organisms
  • changes slowly over time
• Hox genes also studied often
  • Found in all animals
  • duplications in these genes may have led to evolution of body form
• Phylogenies constructed using rRNA and Hox genes are similar and often agree with those based on morphology

Invertebrates

• "without backbone"
• +95% of all species

Phylum Porifera

• Sponges
• lack tissues (organs)
• multicellular
• pores
  • filter H2O and food
• Invertebrates

Phylum Cnidaria

• Jelly fish, corals, anemones 
• Diploblastic development
  • Two tissue layers
• Mesoclea 
  • gelatinous covering
• Nerve net
  • interconnected nerve cells 
  • no brain
• One opening with gastrovascular cavity
• Protostomes
• Invertebrates
• Radial symmetry
• Salt and fresh water
• Stingers

Phylum Ctenophora

• Comb jellies
• Same characteristics as Cnidaria
• Strictly salt water
• No Stingers

Phylum Platyhelminthes

• Flatworms, tapeworms, flukes
• Triploblastic
• Organs and organ systems
• Enhanced nerve net
  • 2 cerebral ganglia
• One opening with gastrovascular cavity
• Protostomes
• invertebrates
• bilateral symmetry
• Acoelomate

Phylum Rotifera

• rotifers
• pseudocoelomate
• Triploblastic
• Two openings
  • complete gut tract
  • alimentary canal
• Protostomes 
• Corona
• simple brain
• invertebrates

Phylum Mollusea

• Snails, slugs, oysters, octopus, squid, clams, muscles
• Triploblastic
• Eucoelomate
• Complete gut tract
• Protostomes
• Invertebrates
• Three part Body
  • Foot
  • Visceral mass
  • Mantle
    • Many have outer shells

Phylum Annelida

• Segmented ring worms
• Triploblastic
• Eucoelomate
• Complete gut tract
• Protostomes
• Enhanced nervous system
• Invertebrates

Phylum Nematoda

• Roundworms
• Triploblastic
• Pseudocoelomate
• Complete gut tract
• Protostomes
• Invertebrates

Phylum Anthropoda

• Insects, crustaceans, spiders, ticks
• Highest diversity of animals
  • >1.5 million species
• Hardened Exoskeleton
• Protostomes
• Invertebrates
• Eucoelomate
• Triploblastic
• Complete gut tract
• Enhanced nervous system
  • Insects, in particular, have an enhanced brain
• segmented appendages

Phylum Echinodermata

• sea stars, urchins, sea cucumbers, sand dollars
• Triploblastic
• Eucoelomate
• Complete gut tract
• Deuterostomes
• Simple nervous system
• Endoskeleton
  • series of plates

Phylum Chordata

• Deuterstomes
• Complete gut tract
• Endoskeleton
• Few invertebrates
  • Mostly vertebrates
• Eucloemates
• Triploblastic

Four Critical Innovations of Chordate Body Design

1. Notochord
2. Dorsal, hollow nerve cord
3. Pharyngeal gill pouches
4. Post-anal tail

• These four features are exhibited at some point of life history/development
  • Only some Fishes exhibit all four

Notochord

• Cartilaginous supporting rod along the dorsal axis
• Replaced by jointed "backbone"
  • Vertebral column of hardened cartilage or bone

Dorsal, hollow nerve cord

• Expanded at the anterior end
  • Brian
• Enclosed/supported/protected by the Notochord

Pharyngeal gill pouches

• Gill slits
• pharynx
  • back of mouth cavity

Post-anal Tail

• Tail extends posterior of the anus

Humans

Notochord

• replaced by vertebrae
• only pieces left are the inter-vertebral discs between vertebrae 

Nerve cord

• Dorsal, hollow with largest brain capacity (compared to body size)

Pharyngeal Pouches

• Embryonic Development
• 1 pair retained as Eustachian tubes

Post-anal Tail

• One vertebra as a tail bone (coccyx)

Subphylum Urochordata

• tunicates
• invertebrates
• ~3000 species
• Marine
• Filter feeders

 

Subphylum Cephalochordata

• Lancelets
• Invertebrates
• 25 species
• marine
• Filter feeders

 

Chapter 34

Subphylum Vertebrata

• Vertebrates
• Chordates with a backbone

Chordate features as well as:

1. Vertebral column
   • Series of cartilaginous or bony elements
2. Cranium
3. Endoskeleton or cartilage or bone
4. Hox genes (lots of them)
5. Neural crest

Cyclostomes

• Jawless Fishes

Class Myxini

• Hagfishes
• lack jaws, eyes, fins vertebrae
• skeleton comprised of notochord and cartilaginous skull
• covered in slime

Class Cephalospidomorphi

• Lampreys
• Has notochord, and cartilaginous vertebral column
• lacks jaws and appendages (fins)
• Oldest fossil records 510 mybp

Class Chondrichthyes

• Cartilaginous fishes
• Sharks, skates, rays
• Cartilaginous skeleton and notochord as adults
• jawed fishes
• paired appendages (fins)
• < 900 species

Class Osteichthyes

• Bony fishes
• Most diverse vertebrate group with  < 26,000 species
• Bony skeleton (most do have this)
• Jawed
• paired appendages (fins)

Tertapod: Gnathastomes

• Four limbs with jawed mouth
• Transition to land involved adaptions for locomotion, reproduction, desiccation (drying out) prevention, and gas exchange
• Sturdy lobe-finned fishes became animals with four limbs
• Vertebral column strengthened, ship and shoulder bones braced against backbone
• relatively simple changes in gene expression, especially Hox genes

Class Amphibia

• >4000 species
• Amphibios
  • greek - "living double life"
  • split their life between aquatic and terrestrial stages
• Successfully invaded land but reproduce in water
• Lunges are and adaption to semi-terrestrial lifestyle
• Three chambered heart
  • Fishes only have a two chambered heart
• External Fertilization
• Larval stages are aquatic
  • Undergo metamorphosis
• Not completely separated from water

Order Anura

• Frogs and toads
• Nearly 90% of amphibians
• Carnivorous adults
  • Herbivorous tadpoles

Order Apoda

• Caecilians
• Nearly blind tropical burrowers
• Secondarily legless

Order Urodela

• Salamanders
• Often have colorful skin patterns
• Most have four limbs

Amniotes

• Tetrapods with a desiccation resistant egg
• Critical innovation
  • Development of a shelled egg
• Amniotic egg
  • Broke the tie to water
  • Three internal membranes
• Shell is permeable to Oxygen and CO2
  • Birds
    • Hard and Calcareous
  • Reptiles
    • Soft and Leathery
  • Most Mammals
    • Embryo embeds in uterine wall
    • Only three species lay eggs
      • These eggs are soft and leathery

Other Key Innovations of the Amniotes

• Desiccation resistant skin
  • contains keratin
• Thoracic breathing
  • Negative pressure sucks air in 
• Water conserving Kidneys
  • Concentrate waste prior to elimination
• Internal fertilization

Class Reptilia

• >8000 living species
• turtles, crocodilians, lizards, snakes
• Can live away from water
• thicker skin and scales
• larger brain
• larger limbs with muscles
• enhanced kidneys
• Amniotic egg
  • "indoor pond"

Vertebrate Reproductive Modes

1. Oviparous
   • Egg laying outside of the body
2. Ovoviviparous
   • live baring wuth retention of eggs
   • No maternal connection
3. Viviparous
   • live bearing with egg retained
   • Maternal connection

Class Aves

• Birds
• Evolved form small dinosaurs
• Fossils 150mybp
• Adaptions for flight
  • Feathers
  • Modified front limbs
  • Lightweight skeleton
  • Organ reduction
  • Lungs and air sacs
    • more gas exchange
• Oviparous
  • all leg layers
• Bill beak
  • Encloses mouth and nasal cavity
  • Adapted for environment

Endothermic

• "Internal temperature"
• Body temperature is primarily controlled by trapped metabolic heat.
• Birds and mammals

Ectothermic

• "External temperature"
• Body temperature is primarily related to external temperature
• Metabolic heat is generated but difficult to capture/maintain the heat
• Fishes, amphibious, reptiles

Class Mammalia

• Milk producing Amniotes
• Evolved from amniote ancestors (reptiles) earlier than birds
• >6000 species
• Appeared ~ 225mybp
  • Evolved from small mammal-like reptiles
• After dinosaur extinction, mammals flourished
• Range of sizes, body forms, and complexity unmatched

• Fish-like mammals
  • Marine mammals
• Bird-like mammals
  • Bats
• Reptile-like mammals
  • Three egg layers

Distinguishing Characteristics

• Mammary Glands
  • Secrete milk
• All have hair
  • In varying amounts
• Only vertebrate with multiple dentitions
  • Heterodont
    • Different types of teeth 
    • incisors, canines, molars, premolars
  • Thecodont
    • Teeth with long roots embedded in sockets of jawbone
  • Diphyodont
    • Milk teeth that are mostly replaced by "adult" teeth later in life
• Pinna
  • Flap of cartilage and lose connective tissue to channel and funnel sound
  • The "outer ear"
• Three middle ear ossicles (bones)
• Enlarged Skull
  • Brain enlarged in large skull
  • Larger Cerebrum
  • Single lower Jawbone (Dentary)
• Anucleate red blood cells

Order Primates

• Primarily tree dwelling species
• grasping hands with  opposable thumbs
• Large brain
• Some digits with flat nails
  • Not claws
• Binocular vision
• Complex social behavior and well-developed parental care 
• Enhanced sense of touch

Taxonomy of Humans

• Kingdom Animalia
  • Phylum Chordata
    • Subphylum Vertebrata
      • Class Mammalia
        • Order Primates
          • Suborder Anthropoidea
            • Superfamily Hominoidae
              • Family Hominidae
                • Subfamily Homininae
                  • Tribe Hominini
                    • Genus Homo
                      • Species Homo sapiens