1. Lecture 10

2. Phylogenetic trees are hypotheses
- a phylogenetic tree is nothing more than an hypothesis.
- the tree may have very strong support, or it may have very little support.
- the former arises when there are a large number of characters supporting a specific topology.
- the latter arises when there are many possible trees that are difficult to exclude as possible alternatives.
- considerable caution must be exercised in the generation and testing of phylogenies, a point not appreciated by many researchers.

3. Gene trees are not the same as species trees
- species trees illustrate the evolutionary histories of a group of related species. - in other words, species trees record the details of speciation for the group. - gene trees show the evolutionary relationships among DNA sequences for a locus. - gene trees may not be the same as species trees for one main reason – the existence of ancestral polymorphism. - if this ancestral polymorphism is lost in some taxa but not in others, then one sequence isolated in species A may be more closely related to one in species B than to any other conspecific sequence. - the gene tree will thus be different from the true species tree. - the best way to guarantee that this will no occur is to use information provided by multiple independent loci!

4. Types of data
- any type of data can be used to reconstruct phylogenetic trees. - until recently, trees were constructed solely from morphological characters. - now, the vast majority of researchers use molecular data. - this molecular data can be in various forms: 1. Immunological distance. 2. DNA-DNA hybridization. 3. Allozyme data. 4. Restriction site data. 5. Amino acid sequences. 6. DNA sequences.

5. Skulls Skull is defining characteristic of "vertebrates"
modern term for phylum of animals to which humans belong is Craniates
Divisions of skull 1) functional
a) neurocranium - houses the brain
b) facial skeleton (viscerocranium) - surrounds oral and nasal cavities
2) developmental - skull divided into components by embryological / phylogenetic origin
a) chondrocranium - forms base of skull; as name suggests endochondral ossifications
b) splachnocranium - derived from pharyngeal arches; also endochondral ossifications
c) dermatocranium - remnant of ancestral exoskeleton; as name suggests dermal ossifications

6. Skull Anatomy Comprised of 22 separate bones divided into two groups:
Cranial bones – 8
Facial bones – 14
Cranial bones further subdivided into
Calvaria
Floor

7. Cranial Bones Calvaria Floor Frontal Occipital R. parietal L. parietal
Ethmoid
Sphenoid
R. temporal
L. temporal

8. Skull Anatomy
Sutures = fibrous joints that connect the bones of the skull
Coronal = between frontal and parietal bones
Sagittal = on top of head between two parietal bones
Squamosal = between temporal bone and the parietal bones
Lambdoidal = between occipital and the parietal bones

9. Sutures joint (G, arthroses) = articulation between two or more bones
joint classifications
1) relative mobility: syn-, amphi- and vs di-arthroses
2) structural:
a) fibrous (solid or non-cavitated joints) - collagenous fibers link articulating bones; sub-types distinguished by location and slight differences in histology
i) sutures - limited to skull
ii) syndesmoses (interosseous ligament) - post-cranial
iii) gomphoses (periodontal ligament) - bind teeth to alveolar bone
b) cartilaginous (solid or non-cavitated joints) - pad of cartilage interposed between bony elements
i) synchondroses (primary cartilaginous joint) - hyaline pad between
e.g., metaphyses, costal cartilage
ii) symphyses (secondary cartilaginous joint) - pad of fibrocartilage between hyaline covered bony elements
limited to median sagittal plane
c) synovial (cavitated joints)
actual gap (synovial cavity) between bony elements which are covered with thin layer of articular (hyaline cartilage)
encased within fibrous articular capsule line by synovial membrane

10. Splanchnocranium
Splanchnocranium phylogentically oldest part of skull, derived from pharyngeal arches
pharyngeal arches present in chordates (sister group of craniates (vertebrates))
pharynx ancestral respiratory and feeding organ
series of U-shaped bars separated by slits (incomplete in tetrapods), each bar containing a cartilaginous skeleton with associated muscles and nerves
these cartilaginous rods give rise to the bones and cartilages of the splanchnocranium
small but important part of cranial skeleton
derivatives of splanchnocranium
first or mandibular arch: cartilage splits into cranial (palatoquadrate) and caudal (mandibular) arches around which the dermal bones of the upper and lower form
palatoquadrate: incus (quadrate) and alisphenoid (greater wing of sphenoid)
mandibular cartilage: malleus (articular)
second or hyoid arch: stapes, styloid process, body and lesser horn of hyoid
third arch: greater horn of hyoid
fourth and fifth (sixth) arches: laryngeal cartilages

11. Chondrocranium
Chondrocranium phylogenetically second oldest part of skull
as name suggests, series of cartilages which form base of cranial cavity
derives from
1) series of paraxial mesodermal condensations (names not important), and
2) sensory capsules which form which form around the nasal, eyes and the inner ear organs
capsule and condensations turn to cartilage, expand and then ossify to form bones of the skull base
bones include: portions of occipital, temporal, and sphenoid and all of ethmoid and inferior nasal concha

12. during evolution (and development) note two trends:
Evolution of mammalian ear ossicles in earliest mammals (pelycosaurs), lower jaw reptilian like (see iguana)
1) lower jaw formed by multiple bones
tooth bearing dentary
multiple post-dentary bones
2) jaw joint (primary) formed by quadrate and articular
unique to mammals, however, is that tympanum carried not by quadrate (upper jaw) but by post-dentary angular bone
thus lower jaw functioned in both feeding and hearing
during evolution (and development) note two trends:
1) expansion of dentary
ultimately contacts squamosal and forms new (secondary) jaw joint (TMJ or sq/d)
2) reduction of post-dentary bones with eventual transferal from "jaw" to temporal bone
basically separates original dual functions of jaws (hearing and feeding) to increase acuity of hearing

13. Dermatocranium
Dermatocranium phylogenetically, remnant of ancestral exoskeleton
primitive condition for all vertebrates is to be encased in a bony exoskeleton of dermal origin
secondarily evolved exoskeletons common in many terrestrial vertebrates
as name suggests, dermatocranium represents intramembranous ossifications within the dermis of the skin
gives rise to the vast majority of bones covering the cranial cavity and face
dermal bones: frontal, parietal, zygomatic, nasal, vomer, lacrimal, palantine, maxilla, dentary (mandible) and portions of occipital, temporal and sphenoid

14. found in mammals and birds (endotherms)
Composite bones result from fusion between separate centres of ossification
found in mammals and birds (endotherms)
phenomenon accounts for apparent complex morphology of many cranial "bones"
temporal
fusion of elements from all three developmental components
dermatocranium > squamosal and tympanic annulus (angular)
chondrocranium > petrous (prootic and opisthotic) and mastoid
splanchnocranium > styloid process
sphenoid
also fusion of elements from all three developmental components
dermatocranium > pterygoid process (pterygoid, ectopterygoid and parasphenoid)
chondrocranium > oriboto-, pre- and basi-sphenoid
splanchnocranium > alisphenoid (greater wing)
occipital
fusion of chondocranial and dermatocranial elements
chondrocranium > basi-, paired exo-and supra-occiptal bones
dermatocranium > interparietal (post-parietal)

15. Why skulls?
two important assumptions about the characters used to build trees:
1. the characters are independent
2. the characters are homologous
- a homologous character is one shared by two species because it was inherited from a common ancestor.
- if a similar character or trait is possessed by two species but was not possessed by all the ancestors intervening between them, it is said to exhibit “homoplasy”.
- homoplasy can result from convergent or parallel evolution, or from evolutionary reversals.