Final Study Guide

Be able to apply macroevolutionary examples to discussion of speciation of chordates.

Macroevolution: broad patterns of evolutionary change above the species level, specifically the origin of new taxonomic groups.
- all chordates evolved from bilateria and deuterostomes
- deuterostomes include echinoderms, hemichordates, and chordates
  - hemichordates include marine worms
    - Often called "half-chordates"
    - they possess some chordate features but lack a true notochord
  - chordates include into urochorata, cephlachorata, vertebrates
    - Urochordates: Known as Tunicates.
      - invertebrates
    - Cephalochordates: Known as Lancelets.
      - invertebrates
    - Vertebrates: include lampreys (jawless fish)

Developmental Genetics and Animal Body Plans

HOX Gene Function (Animal Phyla):
- Hox Genes and Tagmatization:
  - Hox Genes: These genes specialize body regions, leading to the formation of tagmata (specialized body regions).
    - Hox genes are a group of related genes that specify the anterior-posterior axis and segment identity of metazoans during early embryonic development.
    - These genes act as "master switches," encoding transcription factors that control the expression of other genes responsible for building specific body structures.
    - The presence and order of Hox genes are highly conserved across animal phyla
    - Changes in the expression, number, and regulation of these genes (e.g., through gene duplication) are directly linked to the evolution of diverse body plans.
- Hox Gene Clusters:
  - Hox genes operate in clusters through a "combinatorial nature."
  - Complexity in higher animals (e.g., mammals vs. nematodes) is achieved through the duplication and refinement of these gene clusters.
  - Regulation: Specific genes regulate the "radius" or range of Hox gene expression. Changing these ranges determines the developmental fate of a segment (e.g., whether a segment becomes a leg, a swimmeret, or a mandible in a crustacean).

Animal Body Plan Determination:
- Metamerism: The condition of being constructed of linear series of repeat parts (segments) which are fundamentally similar in structure. Each segment is known as a metamere
  - Serial repetition of segments, seen in organisms like tapeworms or annelids.
- Tagmatization: The evolutionary process where adjacent metameres are fused or specialized into functional groups called tagmata (e.g., the head, thorax, and abdomen of an insect).
  - Facilitate increased locomotion, cephalization (concentration of sense organs in a head), and internal body structure specialization.
- Significance: These processes allow for increased complexity and specialization. Instead of every segment performing every function, specific tagmata can be dedicated to sensing, feeding, locomotion, or reproduction.
Diversification of Animal Phyla:
- HOX genes provide the genetic mechanism for diversification.
  - By shifting the boundaries of HOX gene expression, an organism can change the location or size of its body parts without needing entirely new genes.
- Body plan changes via HOX mutations allow for rapid evolutionary shifts, potentially explaining the "explosion" of diverse forms seen in the fossil record (e.g., the Cambrian Explosion).

Deuterostomia and the Phylum Chordata

Hemichordates vs. Chordates (Distinctions):

Hemichordata: Marine organisms that exhibit some, but not all, chordate characteristics. They possess pharyngeal slits and a dorsal (and sometimes ventral) nerve cord. However, they lack a true notochord
- instead, they have a stomochord, which is an anterior outpocketing of the gut.
- Characteristics of the phylum Hemichordata include the:
  - Marine, deuterostomate animals with a body divided into three regions:
    - proboscis
    - collar
    - trunk
  - coelom divided into three cavities (tripartite coelom)
  - Ciliated pharyngeal slits
  - Open circulatory system
  - Complete digestive tract
  - Dorsal, sometimes tubular, nerve cord
Chordata: Characterized by the presence of a true notochord and specific developmental hallmarks throughout their life cycle (or at least in the embryonic stage).
- bilaterally symmetrical deuerostomes
- have 5 unique characteristics:
  - Notochord: A flexible, rod-like structure providing skeletal support.
    - connective tissue sheath enclosing vacuolated cells
    - Becomes the intervertebral discs
  - Pharyngeal Slits/Pouch: Openings between the digestive tract and outside the body
    - may be in form of pouches
    - for filter feeding or used as gills for gas exchange
    - Develop into gill arches in fish for respiration; in land vertebrates (tetrapods), they form portions of the inner ear, tonsils, and thymus gland.
  - Dorsal Tubular Nerve Cord: Forms the central nervous system; located dorsal to the notochord.
    - expanded anteriorly into the brain
    - Develops into the central nervous system, which includes the brain and spinal cord.
  - Post-anal Tail: A muscular tail extending past the anus
    - Serves as a means of locomotion in aquatic animals or a tool for balance and signaling in many land animals. In humans and great apes, it is reduced to a vestigial tailbone (the coccyx).
  - Endostyle or Thyroid Gland: ventral aspect of the pharynx
    - secretes mucus used in filter needing
    - transformed into thyroid in adult lampreys or other chordates
  - Complete digestive tract
  - Ventral, contractile blood vessel (heart)
  - Muscles of the body well organized into paired blocks of
    muscles called myomeres.

Morphological Transformations:
- In many vertebrates, the notochord is largely replaced by the vertebral column (backbone).
- Pharyngeal slits in tetrapods become parts of the ears, tonsils, and thymus gland.
- The dorsal hollow nerve cord develops into the brain and spinal cord.

Hierarchy and Diversity of Chordate Classes

Superclasses and Subphyla:
- Invertebrate Chordates:
  - Cephalochordata (Lancelets): Small, blade-like organisms that retain all chordate hallmarks as adults. Use cilia for filter-feeding.
    - Maintain a notochord throughout their life, distinguishing them from urochordates
    - Aquatic filter feeders with a simple muscular structure and a defined nervous system layout
    - Key features of anatomy include:
      - Pharyngeal slits and gut structure for feeding and digestion
      - External fertilization, releasing gametes into the water.
  - Urochordata (Tunicates): Adults are often sessile filter-feeders; chordate hallmarks (like the notochord and tail) are most prominent in the motile larval stage.
    - Simplest chordates; they undergo metamorphosis from a swimming larva to a sessile adult.
    - Filter feeders characterized by their tunic, a protective outer layer that allows for water flow and food capture.
    - Unique structures:
      - Ciliary structures around the mouth for feeding
      - Use of pharyngeal slits for gas exchange and waste removal.
- Subphylum Craniata (Vertebrata): Chordates with a distinct skull (cranium) to protect the brain.
  - Skull surrounds the three-part brain, olfactory organs, eyes, and inner
    ear
  - Unique embryonic tissue
  - neural crest contributes to a variety of adult structures, including sensory nerve cells and some skeletal and other connective tissue structures.
  - have nodacord
  - hagfish and lampreys are the only vertebrates lacking a jaw
  - lack backbone but have a reduced vertebrae
    - Subphylum Craniata (Vertebrata) include:
      - Infraphylum Hyperotreti (Hagfishes):
        Fishlike, skull consisting of cartilaginous bars
        jawless
        no paired appendages
        mouth with four pairs of tentacles
        olfactory sacs open to mouth cavity
        5 to 15 pairs of pharyngeal slits
        ventrolateral slime glands.
      - Infraphylum Vertebrata: include lampreys (jawless fish)
        jawless vertebrates
        cartilaginous
        Vertebrae surround nerve cord and serve as primary axial support.
        2 sets of Hox genes (vs. tunicates that only have one)
        neural crest cells that give rise to various structures including the craniofacial cartilage

Major Vertebrate Groups:
- Superclass Gnathostomata: Hinged jaw structures
  - teeth used to grip and slice food
  - 4 sets of hox genes - skeleton from duplication of hox genes that are inverted
  - enlarged forebrain
  - enhanced senses of smell and vision
  - lateral line system, rows of organs sensitive to vibrations along body
  - paired appendages
  - vertebral column may have replaced notochord
  - three semicircular canals.
- Agnatha (Jawless Fish): (lampreys).
  - cartilaginous skeleton
  - lack jaw and paired fins.
  - Sucking mouth with teeth and rasping tongue
  - eel-shaped
  - prey on fish
  - have larval stages that are different from adults
  - seven pairs of pharyngeal slits
  - blind olfactory sac
  - The mouth of an adult is suckerlike and surrounded by lips that have sensory and attachment functions.
  - salivary glands with anticoagulant secretions
- Chondrichthyes (Cartilaginous Fish): Sharks, rays, saw fish and skates.
  - Possess jaws
  - cartilaginous skeleton, not bone
  - have paired fins
  - not buoyant, must swim or sink
    - require continuous swimming, keeps water flowing through gills
  - have a lateral line system which detects differences in water pressure (equivalent to our hearing)
  - traces of bone in scales
  - have pector and pelvic fins
- Osteichthyes: most familiar fish (perch, tuna, catfish)
  - most numerous out of al vertebrates
  - have jaws (osteo = bone)
  - bony skeletons
  - paired fins
  - in fish, O2 is exchanged through gills
    - gills are covered by operculum (body flap protecting gills of fish) which helps to draw water across/through gills
  - have swimmer bladder (an air sac used to control buoyancy)
    - can hold depth and not sink
- Tetrapods (Land Vertebrates):
  - four feet body plan - 4 limbs and feet with digits
  - neck independent from head
  - fusion of pelvic with backbone
  - include:
    - Amphibia: Frogs, salamanders, caecilians.
      - first land vertebrates
      - frogs go through metamorphosis
      - larvae are aquatic
      - eggs have no shell
        sperm can swim through water to the eggs and embryos develop in water
      - exothermic: maintain body temperature through external means such as water or sun
      - moist, glandular skin
      - large scales and claws
    - Reptilia: Includes lizards, turtles, snakes, and crocodilians.
      - dry, scaly skin
      - breathe by lungs
      - leathery shelled eggs
      - exothermic: maintain body temperature through external means such as sunning on rock or seeking. shade
      - need less food/energy to live
      - live longer than comparable sized mammals
      - debate weather dinosaurs were like modern day reptiles
      - Amniotic eggs allow for reproduction away from water.
    - Aves: Birds and subclass of reptiles
      - feathered
      - has wings
      - endothermic: control their body temperature from within
        warmblooded
        eggs and young birds are exothermic, must be brooded/incubated by parents
      - hard shelled eggs
        internal fertilization
      - scales on their feed
        thought that birds are descended from dinosaurs (because of scales on feet)
      - lightweight, have hollow bones
      - very good vision
      - mating is accompanied with elaborate courtship rituals
    - Mammalia: humans, rodents, whales, bats
      - hair on all parts of body
      - endothermic
        warmblooded
      - mammary glands that produce milk
        derived from modified sweat glands
      - have diaphragm to aid respiration
      - most bear live young and exhibit maternal care
fertilization:
- oviparous: eggs hatch outside
- ovoviviparous: hatch egg inside mother
- viviparous: no egg, born free