Lecture 1:

Definition of paleobiology.
The study of the history and evolution of life, as revealed by the fossil record.
What kind of questions do paleontologists ask?
Those that Docu!ent historical patterns
"nvestigate the process of evolution
Devise the best !ethodology for acco!plishing both
What can fossils#fossil record teach us? $e.g. fossils provide direct record of life%
&ossils provide the only direct record of the history of life
Discovery of kinds of organis!s no longer living today
&ossils provide direct evidence of ancient environ!ents
&ossils provide critical evidence for ancient continental positions
&ossils provide the !eans of telling ti!e in geology
'ho( us that life today is a product of a long, co!ple)
&ossils are fascinating and beautiful*
+acroevolution: (e can e)a!ine patterns and hypothesi,e !echanis!s of evolutionary change over
long periods of ti!e
-no( longter! evolutionary patterns fro! the fossil record that are not predictable fro! living (orld.
'pecies longevity: 'pecies can e)ist for long and variable periods of ti!e
Ta)ono!ic turnover.igher ta)a $genera, fa!ilies, orders, etc.% turn over $change% at a high rate over
geological ti!e
/0)plosive1 diversification'udden appearance of !any higher ta)a.
+ass e)tinctions0pisodes of elevated rates of e)tinction have occurred, !ore than once.
Definition of a fossil
+inerali,ed re!ains of part or all of the body of an organis! preserved in any (ay
Types of fossil preservation
2er!inerali,ation filled pores3 petrified
4ecrystalli,ation: 5ltered change in !inerals: "nversion to less ordered state:
Loss of +g:
6hange in crystal si,e
Dissolution and replace!ent: 'keleton dissolves3 leaves a void that defines a !old, (hich can be cast
(ith !inerals.
6arboni,ation 7 4esidue of coallike carbon, fro! high organic content
8nderstand the biological characteristics that !ake an organis! !ore likely to be preserved. 9iological
characteristics (ere subdivided into anato!ical, ecological, and biogeographical categories.
5nato!ical : .ard $!inerali,ed%, thick, dense skeletons
'keletons of one part
+olted skeletons
Large body si,e
0cological: 5bundant individuals
'hallo( !arine habitat
9iogeographical :eographically (idespread
Why is it i!portant to understand biases of the fossil record?
"t is i!portant to be able to understand the nature of these biases,so (e don;t bother asking questions or
posing hypotheses that can;t be ans(ered or tested (ith evidence fro! the fossil record.
Lecture <:
&unctions of !inerali,ed skeletons
2rotection
+echanical
"on storage
"on purge
:ravity perception
-no( that skeletons have t(o pri!ary co!ponents $organic and inorganic%
=rganic: 2roteins: 6ollagen
'ilk
-eratin
2olysaccharides: 6ellulose
6hitin
"norganic: +ostly crystalline
&or!ed both intracellularly and e)tracellularly>
+ost enclose or are enclosed by an organic !atri)>
6o!posed of !a?or ele!ents, !inor ele!ents,trace ele!ents, and isotopes of ele!ents
"norganic co!ponent is either biologicallycontrolled or biologicallyinduced $understand the
differences bet(een the t(o types%
9iologicallycontrolled process: Te!plate of organic co!ponents is for!ed
"ons actively induced to site3 crystalli,e and gro(
+ineral type, structure, and orientation are genetically controlled
6o!!on in ani!als
9iologicallyinduced process: =rganis!s alter their che!ical !icroenviron!ent,thus inducing !inerals
to precipitate
@ot under strict genetic control
6o!!on in green algae
-no( the !ost co!!on !inerals are phosphates $apatite% and carbonates $calcite, high +g calcite, and
aragonite% $kno( an e)a!ple of each%.
phosphates $apatite%: dyna!ic bio!ineral in vertebrates3
re!odels continuously
e). Aertebrates, so!e brachiopods, conodonts
carbonates: calcite: e). &ora!inifera3 coccoliths3 so!e brachiopods3 parts of so!e !olluscs
high +g calcite: e). echinoder!s3 bryo,oans3 red coralline algae
aragonite: e). !olluscs3 corals3 green algae
-no(#understand the three rock types $and ho( they are for!ed% and the definition of rocks and
!inerals. 4ock cycle.
"gneous: 6ools and crystalli,es fro! hot liquid rock called !ag!a
+eta!orphic: /6hange for!1 "ncrease in T and 2 change characteristics of rock.
6an for! fro! any other rock type
'edi!entary: /settle out1 "nteraction of at!osphere and fluids on pree)isting rocks
&a!iliar rocks3 cover B#C of continental surfaces
cooling of !olten !ag!a DE igneous
increase T and 2 DE !eta!orphic
(eathering, transport, deposition DEsedi!entary

4ocks: +ade of minerals,(hich are natural inorganic solids $at surface T and 2%,that occur in a
crystalline $highly ordered% state, gro(,and have distinct physical properties resulting fro! their
internal structure and che!ical co!position
8nderstand the difference bet(een process and pattern and ho( they are related
Processes: Patterns:
> 0volution $over a long time% .istory of life
> 9iological and :eological record &ossil and rock
8nderstand the geological characteristics that !ake an organis! !ore likely to be preserved
$subdivided into depositional environ!ent, geological history, ti!e, discovery%.
Depositional environ!ent: Locations (ith active sedi!entation !ore likely to be preserved
:eological history: 9iases that increase the likelihood of preservation: Little che!ical dissolution of
skeletons
Little physical destruction or
disarticulation of skeletons
Ti!e: Longerlived species
:eologically younger species
+ore likely to be preserved and discovered in fossil record
Discovery: 0asy to recogni,e as a fossil organis!
"n a place (here other fossils have been found
We see (hat (e e)pect to see, so fa!iliar organis!s are !ore likely to be discovered and
collected
8nderstand stratigraphic, ecological, and biogeographical biases
'tratigraphic bias: erosion of already deposited rock creates gaps in recorded ti!e in rock#fossil record
0cological bias: (hen less than the co!plete ecological co!!unity is preserved
9iogeographical bias: (hen less than the full geographical range is preserved
8nderstand relative and absolute !ethods $including absolute dating !ethods%.
4elative co!paring t(o fossils# co!paring to so!ething (ith a kno(n age.
5bsolute 7 .alflife
:eologic ti!e scale:5ge of the 0arth FCGHH !illion years
0arliest fossils FBIHH !illion years
0arliest !ulticellular life FJHH !illion years
&irst abundant skeletoni,ed !ulticellular life FIIH !illion years
Lecture B K C:
8nderstand stable isotopes and ho( o)ygen isotopes allo(s us to dra( conclusions about past
enviorn!ents#te!peratures
'table isotopes of an ele!ent do not transfor! or decay.
=ccur naturally
=ne isotope is usually far !ore co!!on
@ot used to date rocks because they do not decay
.igher ratio of =)ygen1L isotope M 6ooler 6li!ate
Lo(er ratio of =)ygen1L isotope M War!er 6li!ate
-no( definition of taphono!y, biostratino!y, and diagenesis and (hat processes act during
taphono!y
taphono!y: The study of ho( the fossil record has co!e to be biased
Life D1DE Death D<DE 9urial DBDE Discovery
biostratino!y: decay, disarticulation, deposition
diagenesis: fossili,ation
Why should (e study taphono!y?
9etter understanding of these processes allo(s us to e)tract !ore useful infor!ation fro! the fossil
record in an intelligent and testable !anner.
-no( the LagerstNtten (e discussed and (hat they are kno(n for. -no( the geologic ti!e periods for
each. Oou do not need to re!e!ber the absolute dates.
o 9urgess 'hale M early, softbodied organis!s3 2ikaia Middle Cambrian
o +a,on 6reek M Tully !onster3 plants Carboniferous
o .ol,!aden M ichthysaurs Jurassic
o 'olnhofen M archeaoptery) Jurassic
o +essel M !any different land and air ani!als Eocene
PQRSTUVWVVSXYsites of exceptional preservation
.o( can (e describe a fossil#organis!?
[uantitative: +orphology
'cales of description
6he!ical co!position
9ehavior
2osition in space
2osition in ti!e
[ualitative: 2ictures
Words
8nderstand ontogeny and the different types of gro(th
=rigin and develop!ent of an organis!
-Accretion: addition of skeletal !aterial to e)isting structures
-Addition of new parts to old parts
+olting: 5llo(s rapid !orphological change to occur during gro(th
-Remodeling of bone: 6ontinual !inerali,ation K resorption.
5llo(s considerable change in shape
8nderstand the different types of variation and !orpho!etrics
'e)ual Di!orphis!: differences bet(een +#&
0cophenotypic variation: differences based on environ!ent
Taphono!ic Distortion: differences based on changes of the process of fossili,ation (hich ske(s the
organis!s
!orpho!etrics: [uantitative analysis of for!, a concept that enco!passes si,e and shape.
8nderstand allo!etry vs. iso!etry and ho( (e can recogni,e it. Why do !ost organis!s gro(
allo!etrically?
5llo!etry: 6hange in shape that acco!panies a change in si,e
Isometr M increase in si,e (ith no change in shape
Lecture I:
definition of populations and basics of population genetics
populations ::roups of conspecific organis!s that occupy a !ore or less (elldefined geograp!ic
region and e)hibit reproductive continuit fro! generation to generation
2opulation genetics: =rigin, !aintainance, evolutionary significance of genetic variation
.o( do proporations of genotypes change through ti!e? $e.g. natural selection%
@atural selection Aariation e)ists3 is heritable3 differential survival. Will increase those gene
frequencies that are !ore \fit\ in so!e environ!ents $!ore adaptive%.
'tabili,ing, directional, diversifying selection.+ost ubiquitous $influential% force in causing gene
frequencies to shift in large populations.
4ando! genetic drift chance fluctuation in gene frequency3 can have a greater effect than (as
thought previously, particularly in s!all populations
"nbreeding reduces genetic variability (ithin populations
+igration !i)ing together prevents genetic divergence
+utation occur spontaneously3 ulti!ate source of genetic variation 6an be beneficial, neutral, or
lethal, depending on environ!ent
Definition of species
"nteractions a!ong populations in space and ti!e
8nderstand the pros and cons of the 9iological species concept
4eproductive isolation is difficult to identify or verify
6an;t test reproductive isolation directly in the fossil record
9'6 doesn;t apply to ase)ual species
This !odel ignores evolution $change over ti!e% altogether
'peciation occurs over ti!e*
8nderstand isolating !echanis!s
8nderstand !odes of speciation
Allopatric speciation : :eographic isolation
Parapatric speciation : 2artial geographic isolation
"mpatric speciation : @o geographic isolation
8nderstand pros and cons of evolutionary species concept, !orphological species concept
evolutionary species concept : 5n evolutionary species is a lineage evolving separately fro! others,and
(ith its o(n unitary evolutionary role and tendencies
'ounds fine, but is A5:80: .o( do (e characteri,e and identify /evolutionary role1 ???
!orphological species concept
'pecies are defined on the basis of a particular distinguishing$diagnostic% set of features, often
qualitative
8nderstand anagensis vs cladogenesis
5nagenesis> gradual change in fossil populations over ti!e
6ladogenesis> splitting of lineages3 like allopatry in ti!e
Lecture G: 2hylogeny
definition of a clade, sister groups, paraphyletic group, polyphyletic group, evolutionary tree and basics
of phylogenetic syste!atics $basically all the ter!s (e (ent over%
6lades M groups that include all the descendants fro! a single co!!on ancestor are !onophyletic
group si!ply a relative pattern of ancestry $recent, distant%
'ister groups M t(o groups that share !ost recent co!!on ancestor
2araphyletic groups M include so!e, but not all descendants fro! a single !ore recent co!!on
ancestor
2olyphyletic groups M include so!e, but not all descendants fro! a single !ore distant co!!on
ancestor
0volutionary tree D hypotheses of ancestry. 0)plicit ti!e di!ension
8nderstand characters and character selection
6haracters: 2hylogenetic hypotheses $cladogra!s or evolutionary trees% are generated fro! characters
$features that are heritable%
.o!ology M features that share co!!on ancestry. 5re often, but not al(ays, si!ilar to one another.
5are infor!ative about evolutionary relationships
2olarity M direction of character transfor!ation in evolution
2ri!itive $plesio!orphic% M ancestral, !ore general
Derived $apo!orphic% M !ore specific
5nalogy $ho!oplasy% M features that are si!ilar, but @=T because of co!!on ancestry.
6onvergence3 parallelis!3 reversal
!ay be !isleading about evolutionary relationships
.o( are hypotheses of phylogenetic relationships constructed?
1.6hoose the groups of organisms (hose phylogeny you are interested in
<.'elect the c!aracters DE !omologues $not analogues%
B.'elect a point of reference DE polarit determination $pri!itive3 derived%
#utgroups $sister group%
'tratigraphy $lo(est%3 =ntogeny $youngest%
C.6riterion for evaluating alternatives DE parsimon$ maximum li%eli!ood
:iven the data in hand, the simplest e)planation to account for those
data is preferred over !ore co!ple) e)planations3
the statistically !ost likely e)planation is preferred.
I.2erfor! the p!logenetic analsis
2ros and cons of uses genetic data or !orphological data in phylogenetic reconstruction
!orphological data:
Advantages:
> is tangible
> relatively easy to observe
> !ore tests available for ho!ology hypotheses
> can use it to relate the organis! to the environ!ent
$functional !orphology, paleoecology, etc.%
&isadvantages:
> defining characters and character states is difficult
> relatively s!all nu!ber of characters can be specified
> (e don;t yet kno( !uch about rates of !orphological
evolution, and variation a!ong those rates
genetic data
Advantages of molecular se'uence data:
> 5bundant characters
> =nly four character states possible
> 4elatively easy to analy,e co!putationally $no(%
&isadvantages of molecular se'uence data:
> Difficult to relate to the environ!ent directly
> Difficult to assess ho!ology of nucleotide si!ilarity
> 5ssu!e clocklike rates of change D
@ot realistic in all cases
> 9ecause so fe( character states, ho!oplasy likely
9e able to read#interpret a phylogenetic hypothesis