Chordates Flashcards
Chordate zoology is what type of biology
whole-organism biology (not just cell, function, form,.. everything)
organismal biology
research at the level of the whole organism, integrated over structure, function, ecology, and evolution
organism structure
anatomy, morphology
organism function
physiology, behaviour
evolution
phylogeny
functional morphology
focuses on the link between form (morphology) and performance
ecological morphology
focuses on the link between performance and ecology (ecomorphs, ecomorphotypes)
ecomorph
species with the same structural habitat/niche, similar in morphology and behavior, but not necessarily close phyletically
ecomorphotype
Any morphological modification caused by, or related to, specific ecological conditions
integrative biology
near synonym for organismal biology; brings different aspects of organisms and their environment together
comparative biology
an area of research that attempts to explain biodiversity and its adaptive radiation in a phylogenetic (historical) framework (comparative method)
how phylogeny tests/explains hypotheses
natural history
scientific study of the organism in its natural surroundings
kinds of chordates
Tunicata
Cephalochordata
Vertebrata
Tunicata includes
tunicates and sea squirts
Tunicata was formerly called
Urochordata (also protochordates- not valid taxonomic name)
Cephalochordata includes
lancelets (amphioxus)
Numbers of chordate species
Tunicata - 2150
Cephalochorddata - 25
Vertebrata - 63 600
*numbers are always changing
tunicates
free-living larva, sessile adult
shared characteristics of chordates
notochord dorsal hollow nerve cord pharyngeal gill slits endostyle muscular postanal tail
notochord
incorporated in vertebral column in vertebrates
stiff, flexible rod, runs length of back, provides connections for body muscles, and support
dorsal hollow nerve cord
spinal cord with brain at anterior end in vertebrates
pharyngeal gill slits
slits in pharynx/throat region through which water passes and food particles are filtered out, involved in filter-feeding and gas exchange
retained in fish- gas exchange
tetrapods- gill slits disappear in adults
gill arches become jaws and other structures in vertebrates
endostyle
ciliated groove before larynx
secretes mucus to trap food
homologous with thyroid gland in vertebrates
muscular postanal tail
extension of the body that runs past the anal opening
only present in embryonic stage of humans
paedomorphosis
retaining juvenile characteristics into adult hood
sister group to vertebrates
urochordata (most current theory)
vertebrates and urochordates are sister group to cephalochordates
pattern vs. process
phylogeny vs. scenario
current phylogenetic theory (pattern), process (scenario) yet to be determined
myomeres
blocks of skeletal muscle tissue found commonly in chordates. commonly zig-zag, “W” or “V”-shaped muscle fibers
possible first chordate
Pikaia
aspects of morphology (anatomy)
comparative
functional
transitional
comparative morphology
similarities/differences between groups
ex. heart
functional morphology
how organisms are equipped to deal with different situations
transitional morphology
macroevolutionary change- how we go from one form to another
why study chordates
intrinsic interest vertebrates are us diversity evolutionary record model organisms
chordate diversity
masses range from 10^-4 - 10^5 kg! (larva to blue whale)
altitudes range 58km- deep ocean - over himalayans
why evolutionary record is important for studying chordates
they have the best preservation of all organisms
model organisms
amphibians- developmental biology
birds- population biology
vertebrates characteristics
internal skeleton vertebral column with cranium at anterior spinal nerve cord with brain at anterior neural crest HOX genes
vertebrate internal skeleton
bone and/or cartilage
vertebral column
individual vertebra, skull at end
rudimentary in lampreys
lacking in hagfish
full formed in gnathostomes
gnathostomes
jawed vertebrates
neural crest
cells/tissue- formed during embryonic development and migrate to head
HOX genes
do exist in inverts but more important in vertebrates
vertebrates have the most HOX genes
“grades” of vertebrates
“fishes”
Tetrapods
paraphyletic
composed of some but not all members descending from a common ancestor
fishes
paraphyletic- would be monophyletic if we include all groups that have come from fishes (including us)
31,000 species
mainly Osteichthyes
groups in fishes
Agnathans
Chondrichthyes
Osteichthyes
Agnathans
jawless vertebrates- hagfish and lampreys, Ostracoderms
Chondrichthyes
cartilaginous fish- sharks, rays, ratfish
Osteichthyes
bony fish
Crossopterygii, Actinopterygii
Cossopterygii
Actinistia + Dipnoi (lobe-finned fish- coelacanth + lungfish)
Actinopterygii
ray-finned fish (most fish)
Tetrapods
all the rest of the vertebrates
4 feet, lots of secondary loss examples
Tetrapod examples
Amphibia
Amniota
Aves
Mammalia
Amphibia
7000 species
lissamphibians- apodans salamanders, anurans
Amniota
amniotes– Reptilia
Reptilia
10,000 species- turtles, crocodiles, tuataras, lizards, snakes, amphisbaenians
Aves
10,000 species
directly derived from reptiles, make reptiles a non-taxonomic group
Mammalia
5500 species- mammals
mostly placentals, some monotremes and marsupials
Ectotherms
“fishes”
amphibians
“reptiles”
endotherms
generate own body heat metabolically
birds
mammals
Amniotes
“reptiles”
birds
mammals
(taxonomic group)
Anamniotes
“Fishes”
Amphibians
(not a taxonomic group)
Sauropsids
“reptiles”
birds
synapsids
mammals
lampreys
Agnathan- parasitize other fish
Fossil Agnathans
Ostracoderms- coats of bone armour, very different from living fish
Gnathostomata
defined by presence of jaws with teeth
usually have limbs
thought to be closest living relative of tetrapods
lungfish (3 species)
tetrapoda
limbs with digits for terrestrial locomotion
internal nostrils
tympanic membrane and stapes
strong skeleton
internal nostrils
breathing through nose
fish do not breath through nose (except lungfish)
tetrapod tympanic membrane and stapes
to detect airborne sounds- ear drum
in fish stapes supports skull, in tetrapod it is main bone by which sound is transported into inner ear
tetrapod strong skeleton
support against gravity (adaptation to terrestrial life)
Lissamphibia
3 major, distinct morphological groups
thin skin
complex life cycle
numerous departures from theme
Lissamphibia thin skin
highly permeable
respiratory gas exchange- skin covered in mucus to facilitate exchange
water exchange- drink by skin, lose water through skin– restricted to moist habitats
Lissamphibia complex life cycle
includes metamorphosis
aquatic egg– aquatic larva– aquatic/terrestrial juvenile and adult
Amphibian groups
salamanders
anurans
apodans
Salamanders
mostly north temperate zone mostly elongate body mostly limbed- some highly reduced some permanently aquatic retain larval form, some bipass larval form- direct development, lay eggs on ground, hatch into full formed adult some pedomorphosis, have gills
Anurans
hyper developed back legs
aquatic/terrestrial/arboreal (ex. tree frogs climb w/ suction cups)
no paedomorphic frogs
some cut out larval stage
larval/adult generally radically different
unique Anuran forms
one species- female swallows eggs and they develop in her stomach
Apodans
(Caecilians)
superficially resemble earthworms/snakes
mostly live hidden in the ground, least familiar order of amphibians, smallest group, carnivores, large mouth
aquatic/burrowing/nocturnal/terrestrial
some have complex lifestyle, some direct development
live bearing- no placenta, hyper developed gills, mostly viviporous
Amniota
amniotic egg- amniote surrounds embryo
exclusively internal fertilization
allantois
waste dump, highly vascularized (blood vessels)
develops to line membrane surrounding the egg- transport system for gas exchange
amniote shell
holds eggs together, has mating consequences- necessitates internal fertilization, must develop on land (oviparity)
oviparity
Oviparous animals are animals that lay eggs, with little or no other embryonic development within the mother
Reptilia
not a taxon group
thicker skin, covered with epidural scutes (keratin)
much more terrestrially adapted, lose water slower
scutes
scales
keratin provides mechanical protection, defense against water loss, protection of lipids
“reptile” groups
turtles tuataras lizards amphisbaenians snakes crocodilians
turtles
only vertebrate in which ribs are outside
lots of aquatic, some marine, some terrestrial
Tuataras
endemic to New Zealand, highly restricted, resemble most lizards, part of a distinct lineage
long, slow life style, last remaining species of diverse group
“lizards”
biggest group of “reptiles”
very diverse, worldwide, terrestrial, arboreal
lots of long slender bodies w/o limbs
Amphisbaenians
derived from lizards, sometimes called worm lizards
burrowing species, swim, mostly tropic, some subtropic, mostly lack limbs, different head shapes for specialization of burrowing
head types of Amphisbaenians
round head- soft sediment
wedge shaped head- hard substrate
snakes
mostly have no trace of limbs
many arboreal- long and slender to spread weight out over branches
rain snake
oval cross section
tail flattened to propel through water
Crocodilians
~22 species living forms all fairly similar body covered with osteoderms long, elongate skull extant are only aquatic tropical/subtropical
osteoderms
bony deposits forming scales, plates or other structures in the dermal layers of the skin
crocodile snout specialization
long, skinny snout- fish eating- quicker swiping through water
Aves
highly modified reptiles endothermic body covered with feathers (keratin) legs covered with epidermal scutes wings and other modifications for flight modified jaw with beak (keratin) and no teeth
bird feet/beak
tell a lot about overall life ecology
ex. flightless - marine
bird feathers
aid endothermy
major flight surface of wing
Mammalia
endothermic body covered with hair/fur (keratin, insolation) highly differentiated dentition numerous derived traits in skeleton pinna
derived traits in mammal skeleton
squamosal-dentary jaw joint
7 cervical vertebrae (neck vertebrae)- almost all mammals have 7
Pinna
the visible part of the ear that resides outside of the head
main groups of mammals
monotremes
marsupials
placentals
monotremes
lay eggs- platypus, echidna
only a few species
basically same as reptile eggs- hatch then female feeds milk via ducts (not nipples)
marsupials
wide diversity of form, mostly in Australia, bears, rodents, carnivores, koala, kangaroo, opossum, wombat
have placenta but not well developed
embryo develops in uterus for short period of time
born at early embryonic stage, crawls up to pouch and attaches until ready to be born
marsupial embryo pouch
marsupion
placentals
development until birth is in uterus
intimate connection between embryo and mother (nutrients, gas exchange)
important parts of evolution
genes, chromosomes, alleles, mutation (many neutral, some lethal), proteins (structural, hormones, enzymes), recombination, dominance, pleiotropy, polygenic traits, epistasis, regulatory genes
pleiotropy
single genes code for multiple parts of the body
epistasis
interactions between genes
effect of gene depends on presence/expression of other genes
regulatory genes
govern expression of genes
phenotype =
genotype * environment
phenotypic plasticity
ability of an organism to change its phenotype in response to changes in the environment
heritability
the proportion of observed variation in a particular trait (as height) that can be attributed to inherited genetic factors in contrast to environmental ones
reaction norms
expression of the phenotype of a particular genotype in different environments
no genotype environment interaction, reaction norm
phenotype vs. environment graph
variation is constant, parallel for 2 genotypes among different environments
genotype environment interaction, reaction norm
genotypes are not parallel or constant (lines may cross)
one genotype may produce multiple phenotypes
phenotypic flexibility
reversible changes within individuals
ex. plumage variation with season- changeable/reversible phenotype
types of selection
artificial selection (natural) selection adaptation directional selection balancing selection disruptive selection
natural selection
variation, heritability, differential survival/reproduction
variation has to be heritable for evolution to occur
adaptation
a trait that has arisen from natural selection
three modes of selection
stabilizing
directional
disruptive
stabilizing selection
balancing
extreme values are a disadvantage and are ‘pruned’
keep population at certain ‘optimum’
directional selection
one extreme is disadvantageous
leeds to a shift away from one extreme
disruptive selection
intermediates are disadvantageous
selection is for the extreme- split down the ‘middle’
example of directional selection
high proportion of unbounded snakes- selection against banding- population pushed primarily to unbounded
banded snakes remain in population due to migrations from mainland
balance between migration and selection
example of balancing selection
UK birth weights- low mortality in mid weight babies
small babies underdeveloped, large babies died during birth
selection for optimal birth size- med size babies were commonest, had best chance of survival, most likely to pass on their characteristics
selection isn’t the only factor that determines change
genetic drift
founder effect
genetic drift
genes that wouldn’t normally be passed on are passed due to small population- selection goes in different direction that it normally would
founder effect
small founding colony of individuals will have more limited make-up than the population they came from, depends on founding colony being small
species/speciation concepts
multiple species concepts discontinuities morphospecies biological species hybridization asexual reproduction
discontinuities
breaks between species (ex. morphology)
multiple species concepts
many definitions of species
the 2 we will focus on are biological species concept (BSC), morphological species concept
BSC
depends on sexual breeding, must be able to interbreed, hard to test, depends on species exhibiting sympatry
discontinuity- reproductive isolation
sympatry
species that occur in same geographic area
why species concept can be hard to test
if they don’t come together naturally there is no way of knowing if they naturally mate- bringing them together in the lab is artificial
morphospecies
different species should look different
domestic dogs- haven’t speciated
sibling species
different species that look identical
sibling species example
Hyla versicolor- tetraploid (gray tree frog)
Hyla chrysoscelis- diploid (Cope’s gray tree frog)
tetraploid
Triploid/tetraploid chromosomes are polyploidy
Polyploid organisms are those containing more than two paired (homologous) sets of chromosomes. Most species whose cells have nuclei (Eukaryotes) are diploid, one set inherited from each parent.
polyphyletic
does not include the common ancestor of all members of the taxon
paraphyletic
includes the most recent common ancestor, but not all of its descendents
species is used to
describe groups that we recognize
describe what the animals themselves recognize
stable hybrid zone
ranges of 2 species come together, where they meet there is a zone that consists of hybrids
hybrids usually not sterile but may be less fit
hybrid example
manitoba toads- meet in East manitoba, zone where there are hybrids (separate species)
yellow-rumped warbler (sub-species)
gray wolf/eastern wolf/coyote/red wolf/dogs
European water frogs
incipient speciation
evolutionary process in which new species form but are still capable of interbreeding; can be the first part of the larger process of speciation
yellow-dumped warbler hybrids
Audubon’s warbler / Myrtle warbler
100km hybrid zone
graphs show different traits within/outside of hybrid zone
introgression
(introgressive hybridization), movement of a gene (gene flow) from one species into the gene pool of another by repeated backcrossing of an interspecific hybrid with one of its parent species
3 known categories of asexual reproduction in vertebrates
recall that BSC requires sexual breeding
hybridogenesis
gynogenesis
parthogenesis
hemiclonal
half of females genome is passed on clonally
clonal
all of females genome is passed on clonally
hybridogenesis
male mates with female but males genetic contribution is discarded at mitosis
egg is fertilized but genetic info. not passed on in next generation
gynogenesis
mates with male but sperm are not used (salamanders, some fish)
diploid egg, sperm stimulates reproduction but doesn’t fertilize
female relies on sperm from heterospecific males to initiate embryogenesis
parthenogenesis
males not used at all, diploid, unfertilized egg (clonal)
most vertebrates are
bisexual- normal sexual reproduction
European water frogs hemiclonal hybridogenesis
Rana ridibunda x R. lessonae = R. esculenta
R. esculenta x R. lessonae = R. esculenta
R. esculenta x R. esculenta = R. ridibunda
R. esculenta x R. ridibunda = R. ridibunda
R. esculenta maintains itself by mating with parent species- at meiosis discards lessonae part of genome and reconstitutes itself
usually inviable offspring
R. esculenta x R. esculenta = R. ridibunda
origin of R. esculenta
R. ridibunda x R. lessonae = R.esculenta
why do males mate with female gynogens (gynogenesis)
selection should favor males that gynogenesis
sexual females increase their preference for males whom they observe consorting with female gynogens
elements of speciation
occur in variable orders/rates/ranges/time, process of species formation, multiplication of species, complex process that involves multiple phenomena
elements: reproductive isolation, genetic divergence, phenotypic divergence
Bulloch’s Oriole and Blatimore Oriole
two morphologically distinct species, but they are interfertile
two morphospecies, but one or two biological species?
interfertile
capable of interbreeding
cryptic species
morphologically similar, genetically distinct, incapable of interbreeding
cryptic species example
African Savanna Elephant, African Forest Elephant
speciation can occur
allopatrically, parapatrically/peripatrically, or sympatrically
allopatric speciation
geographically separate
parapatric speciation
geographically adjacent
sympatric speciation
geographically coincident (same area)
non-selective speciation
‘by accident’- random drift in small founding populations
natural selection speciation
mutation-order speciation
ecological speciation
ecological speciation
evolution of reproductive isolation between populations by divergent natural selection arising from differences between ecological environments
indirect or direct
indirect ecological speciation
by-product speciation
reproductive isolation occurs as an incidental by-product of adaptation to different environments
direct ecological speciation
selection directly favours reproductive isolation
ex. if hybrids are less viable
allopatric (geographic) speciation
vicariant event- splitting events/barriers cause species to adapt independently to conditions (ex. glaciation)
dispersal- disperse to new area (ex. island), may lead to founder effect (ex. galapagos finches)
Possible outcomes of secondary contact after long periods of separation
partial/complete reproductive isolation- basically separate species
hybrid zones
complete introgression- interbreed as if never separated
selection for reproductive isolation- behavioural differences
lentic
standing water
lotic
running water
ecological speciation changes in fishes
marine-freshwater physio-chemical transitions lotic-lentic transitions discrete river habitat water depth benthic-open water benthic substrate shifts piscivory durophagy intrinsic incompatibilities divergent sexual selection
piscivory
eating of fish
durophagy
eating behavior of animals that consume hard-shelled or exoskeleton bearing organisms, such as corals, shelled mollusks, or crabs
increasing potential for gene flow in absence of differentiation
decreasing spatial scale
allopatric– parapatric– sympatric
ecological speciation example
repeated parallel speciation in endependent populations of sticklebacks, regulation in gene due to reproductive isolation
deep water- prominent spine, predator protection
shallow water- absence of fin, harder for insect larvae to attach
Replicated (parallel) ecological speciation in lizards
habitat matching- different species show the same coloration changes to match light/dark soil habitats
punctuated equilibrium
little net evolutionary change for most of geological history, remaining in an extended state called stasis, disrupted by abrupt change
phyletic gradualism
speciation is slow, uniform and gradual
When evolution occurs it is usually by the steady transformation of a whole species into a new one
microevolution
microphylogeny, microecology
change over short time and small spatial scale
ex. population genetics, shifts in color patterns, polumorphisms
macroevolution
historical ecology, macroecology
change over long time scales and large spatial scales
taxonomic and transformational implications- major changes in body form
Historical Ecology
taxic– speciation, cospeciation
transformational- adaptation, coadaptation
macroevolutionary phenomena
origin of new structures discontinuities in 'adaptive space' rates of evolution causes and natures of radiations causes and natures of mass extinctions
fundamental to biology
phylogeny, taxonomy, systematics
why phylogeny/taxonomy/systematics are important in a world with decreasing biodiversity
different conservational issue depending on whether or not separate species
BC spotted frog
found to be 2 species; 1 restricted to coastal Oregon, BC; new species is very restricted and need immediate conservation help
Tuatara Sphenodon (lizard) endemic to NZ
one species found to be two, separate conservation plans had to be made
folk taxonomy
local and simple
classifying animals based on known plants, local
used in everyday language- ‘bugs’ ‘shrubs’
world exploration
disruption to local order
Linnaeus
1700s, Systema Naturae binominal system
subjective, based on intuition, experience, ‘umwelt’, mix of art and science
species names have 2 parts, first subjective system
evolutionary taxonomists
1800s, influenced by Darwin
classification should reflect evolutionary relationships
shift in point of view but not methods
a species is what a good taxonomist says it is
making taxonomy a science
1950s, injecting objectivity
numerical taxonomy
unweighted characters, quantitative
take as many characters as can, try to find similarities to make unbiased connections
molecular taxonomy
proteins, RNA, DNA, comparison of apples and oranges
differences between species in relation to proteins and DNA
first time characters could be compared in vastly different organisms
Cladistic taxonomy
phylogenetic taxonomy
shared evolutionary novelties
not all traits are useful, some are more important than others- shared derived traits
fungi are closely related
to animals (more than to plants)
classification
ordering of organisms into sets based on relationships
relationships defined in various ways- phylogeny, resemblance
identification
allocation of previously unidentified specimens to the correct sets, as in ‘keying’
taxonomy
the theoretical study of classification, including principles and procedures (rules)
taxon
general term for any taxonomic group of any rank
systematics
study of diversity and interrelationships of organisms, causes and origins of relationships including zoogeography
broader than taxonomy
nomenclature
very narrow term, having to do with actual naming
types of classification
cross-tabulation
linearly ordered list- alphabetical, numerical (not a good classification, just a list)
hierarchy- by some criterion of similarity
cross-tabulation
take 2 traits and compare them in 2x2 grid
ex. endothermy/ectothermy, eyes/no eyes
biological classifications
hierarchical - groups nested within groups
based on similarity- morphological, genetic
usually reflect evolutionary relationships
taxon ranks in Linnean classification system
Kingdom- Phylum- Subphylum- Class- Subclass- Order- Suborder- Family- Genus- Species (binomen)- Subspecies (trainmen)
plural of taxon
taxa
order names end in
a
Order Squamata - not the Squamata order
or we can talk about squamates, or squamate reptiles
family names end in
idea
Family Viparidae- not the Viperidae family
or “viperirds” or “viperid snakes”
subfamily names end in
inae
Subfamily Viperinae
or “viperines” or “viperine snakes”
nomenclature rules are found
in International Code of Zoological Nomenclature
kinds of similarity
similar origin (developmental or evolutionary) similar function similar structure
similarity in origin example
articulation of jaw in mammals- squamosal and dentary
in all tetrapods except mammals- articular and quadrate
articular and quadrate in mammals
middle ear- different fn and structure but similar origin
articular = malleus
quadrate = incus
middle ear ossicles
3 in mammals- incus, malleus, stapes
1 in other tetrapods- stapes (trace back to fish)
similarity in structure example
3 different kinds of wings- bird, pterosaur, bat
forelimbs of tetrapods- similar features; ulna, radius, humerus
parts shaped differently with same basic elements
similarity in function example
noise-making in snakes- rattling, tail-vibrating, hissing, stridulation, cloacal popping
rattling in snakes
Crotalus: series of interlocking segments make up rattle, special shaker muscle vibrates at rapid rate for long time,
add segments to rattle every time they shed their skin, babies only have one segment and can’t rattle
tail-vibrating and hissing in snakes
Pituophis: shake tail to make noise in dry leaves (confused with rattlers)
specialized keel increases loudness of hissing (~10 decibels higher with keel- decibels are log scale)
stridulation in snakes
Echis: (scale-rubbing) specialized scale on side of body, move body segments against each other to make noise
cloacal popping
Micruroides, Gyalopion: force air out of cloacal (opening for intestine, reproductive, urinary tract) and make a popping noise
kinds of similarity
homology
homoplasy
analogy
homoplasy
“false” evolutionary resemblance
parallelism, convergence, reversal, loss, mimicry
can confound construction of phylogenies
but can be used to make inferences about adaptation
“false” evolutionary resemblance
phenotypic similarities mislead us to relationship
reversal
loss of trait back to original state
confound construction of phylogenies
sorting out homoplasies from other similarities is key
Convergent evolution (this is the term we will use)
convergence- evolution of similar phenotypic features independently in different lineages, usually from different features and developmental pathways
Parallel evolution
parallelism- evolution of similar/identical features independently in related lineages, usually based on similar modification of the same developmental pathways
convergence in African Cichlids
fish in two different lakes look similar- mimic each other
fish in same lake look different but are more similar to each other than to fish in other lake
convergence in mammals
similar body forms through time many marsupials look similar to eutherians (placentals) mole-- marsupial mole flying squirrel-- sugar glider woodchuck-- wombat
convergence of echolocation
different kinds of echolocation arise independently multiple times (bats, dolphins)
homology
“true” evolutionary resemblance, a relative term
similarity of origin is important, to some extent
taxic or transformational
homology is determined from
comparative anatomy, fossil record, developmental biology, distribution of character states among taxa (using parsimony)
reptile to mammal transformation homology
jaw joint to middle ear ossicle
polarity of the trait = direction of change over time
taxic homology
shared evolutionary novelties that help define taxa
tetrapod wings
show how the level of analysis changes the definition, relative terms
homologous as tetrapod limbs
homoplasious as wings (bird, pterosaur, bat all independently derived wings)
cladistics
phylogenetic systematics
grouped based on 1+ shared unique characteristics from the group’s LCA
monophyletic group
ancestor plus all descendants
paraphyletic group
monophyletic group with some descendants missing
ex. “reptiles” birds missing, would be a correct taxonomic group if we included birds
polyphyletic group
group composed of members separated by two or more ancestors
usually constructed by homoplasies
homoplasy
character shared by a set of species but not present in their common ancestor
plesiomorphies
ancestral, ‘primitive’ traits
apomorphies
derived, ‘advanced’ traits
symplesiomorphy
shared ancestral trait
synapomorphy
shared derived trait
we want to construct phylogenies with only
synapomorphies (shared derived traits), only clades
ex. all vertebrates have hearts does not set them apart from other taxon
grade vs clade
grade- group of species united by morphological/ physiological traits, gives rise to another group differing from ancestral condition- not considered part of the ancestral group, same grade can be in different clades
ancestral group- not phylogenetically complete, doesn’t form a clade, represents a paraphyletic taxon
Linnaean classification of Vertebrates
Class Chondrichthyes- sharks, rays Class Osteichthyes*- bony fish Class Amphibia- lissamphibians Class Reptilia*- reptiles Class Aves- birds Class Mammalia- mammals * paraphyletic groups
anagenesis
change in form within a lineage
cladogenesis
splitting events
grades =
paraphyly, group which does not include all its descendents
“fish” and “birds” are paraphyletic
clades =
monophyly, taxon (group of organisms) which forms a clade, meaning that it consists of an ancestral species and all its descendants
grades can be attributable to
synapomorphy- monophyletic groups (grade = clade, mammals are a grade and a clade)
symplesiomorphy- paraphyletic groups (reptile, fish)
convergence- polyphyletic
symplesiomorphies
characters shared by everybody, everybody’s got these traits so they don’t help characterize one group
synapomorphies
unique traits that maybe can be used to categorize one group vs. another
autapomorphies
derived traits that are unique to a particular taxon
each person is, in certain respects like all other people, like some other people, and like no other person
all other people- symplesiomorphies
some other people- synapomorphies
no other people- autapomorphies
in phylogeny we are trying to recognize sister taxa
a synapomorphy is present only in 2 sister-taxa and is the inherited autapomorphky from their LCA. ID’ing a character as a synapomorphy is essential for recognizing sister taxa
phylogenetic systematics
taxa (clades) defined by shared derived traits only
evolutionary relationship (phylogeny) among taxa represented by a branching diagram (cladogram)
sister clades receive equal rank (no taxon labels)
all taxa are monophyletic
groups defined by shared ancestral traits have no taxonomic value (may be important in other ways)
dichotomous branching
each branch is a sister group
fully resolved phylogeny
each point has only two branches
>2 - polytomy
phylogenetically defined taxa are always
monophyletic
taxon = monophyletic group = lineage = clade
groups defined by shared ancestral traits have no taxonomic value (may be important in other ways)
ectotherms- not a natural grouping, has eco-physiological meaning
fossil problem
incomplete specimens incomplete record through time mostly hard parts, few soft tissues no molecular data maybe unique derived traits that we can not see
types of clades
node-based
stem-based
apomorphy-based
node-based
crown group
based on extant forms (more information)
just below node of sister group
stem-based
total group
consists of crown group + extinct forms (stem) that are part of the ancestral lineage of crown group
just above node below sister group
apomorphy based
based on first known appearance of a particular derived trait
ex. first appearance of limbs in fossil record
somewhere in between sister group node and node below
crown group defined
by extant groups but can contain extinct groups
why phylogeny is more useful than Linnean system
more complete and informative classification
phylogeny recoverable from taxonomy and vice versa
can use a list to create cladogram (isomorphic, equal rank get equal indentation)
phylogeny limitations
polarity and/or homology of many traits is not unambiguously established (whats the direction of change)
evidence is evidence not proof, many disagreements on ‘correct’ phylogeny (still much debate, where do turtles go)
molecules vs. morphology
everything is provisional
molecules vs. morphology
modern phylogenies usually derived from molecular data
we then can map other traits onto the phylogeny and interpret them (ex. convergences)
mostly, now, start with molecular phylogeny and then map morphological
ingroup
group of taxa whose relationships we want to resolve
outgroup
comparison taxon closely related to the taxa of interest
sometimes 2 or more outgroup taxa are used, one more closely related and one more distantly related
outgroups used to determine
how the cladogram should be rooted
ex. help determine polarity (direction) of changes in traits
calibrating phylogeny so branch lengths give estimate of time since separation
fossil record
base phylogeny on genes and calibrate via molecular clock
use ancient DNA
ghost lineage
incomplete history, missing fossil record implied by sister group
NGS
next-generation DNA sequencing (paleogenomics)
some contamination problems
can bring evidence on questions such as time since divergence
can sequence hundreds of thousands of years back
can give an idea of process rather than just pattern
Phylogeny
evolutionary chronicle branched chronological series of character state changes along lineages (what) clear methodology (cladistics)
Genealogy
historical narrative
casual statements, explanation, interpretations, evolutionary scenarios (how and why)
no clear methodology- gaps between taxa filled by fossils, extant taxa, imagination, intuition
the comparative method
using comparisons across species that have evolved independently
why should we care about systematics
systematics are fundamental to biology and can tell us alot
problems comparing characteristics
shared history- lineage specific effects (non independence)
phylogenetic effects/differences- history matters
independent comparison method for 2 characters in a single phylogeny
sister taxa are averaged to give node value
differences are taken between sister taxa for d1 and d2
differences are taken between nodes d3
differences compared for characters and then the 2 characters differences are plotted against each other
number of rooted, bifurcating, labeled trees for n species
(2n-3)! / (2^n-2)(n-2)!
problems constructing phylogenies
large number of possible tree topologies (15 trees for n=4)
different analytical methods give different answers
numerous different trees for same group
fossil forms incomplete
analytical methods of phylogeny
parsimony and variants compatibility (character "cliques") distance matrix methods likelihood methods others, all quantitative
consensus tree
constructed when we have 2 or more different trees for the same group
parsimony
Occam’s Razor
the simplest, most plausible hypothesis is the obvious place to start
if you hear hoofbeats, think horses not zebras
cladogram w/ fewest evolutionary steps is best starting hypothesis
inferring characters in poorly known taxa
modern analogues
extant phylogenetic bracket
extant phylogenetic bracket
if a character is exhibited by bracketing extant species, then most likely exhibited by internal branches (extinct species)
ex. parental care seen in crocodilians and birds, so probably in the dinosaurs ‘in between’
may have evolved independently but less parsimonious- more evolutionary steps
endothermy in dinosaurs?
crocodilians- 4 different dinosaurs- birds
we know that crocodilians are not endothermic, birds are
there are 5 equally parsimonious trees to explain the evolution of endothermy in to birds, so we can’t infer where it evolved
non-therian synapsids
all synapsids other than mammals
nocturnality in non-therian synapsids
study finds synapsids were nocturnal ancestrally
carnivores are predominantly nocturnal or cathemeral
cathemeral
irregularly active at any time of night or day, according to prevailing circumstances
myrmecophagy
feeding behavior defined by the consumption of termites or ants
convergence example
myrmecophagy in Dendrobatids (frogs)
echolocation in bats and dolphins
flightlessness in birds
endothermy in Scombroidean Fishes
species that overlap geographically are sister taxa
sympatric speciation
sister species do not overlap geographically
allopatric speciation
sister species do not overlap and the range of one is smaller than the range of the other
peripatric speciation
polymorphism
occurrence together in same habitat of 2 or more discontinuous forms, or “phases”, of a species in proportions that the rarest of them cannot be maintained merely by recurrent mutation (genetically determined variants)
polyphenism
phenomenon where two or more distinct phenotypes are produced by the same genotype
Multiple phenotypes in population (polymorphic), not based on genotype
phenotypic variation induced by an environmental cue
form of phenotypic plasticity
example of polyphenism
amphibian larvae – shifts in morphological phenotype
due to predators, competitors, and prey
cannibalism is induced when high density of conspecifics- leads to larger mouth and teeth
why nervous system is useful in phylogenetic research
lots of data to compare
lots of genetic markers
origin of chordates, old system and new system
old- vertebrates sister group to Amphioxus
new system- Vertebrates sister group to Tunicates
why were tunicates ‘moved’ in the phylogeny?
found to have a number of fast-evolving genes
very derived, even though they appear basal
no longer a kew organism in understanding
mosaic development
something happened early in tunicate development that allowed them to rapidly evolve in a different direction
serial mesoderm (segmented) evolution
‘hairy’ gene in Arthropods and Annelids
homolog of ‘hairy’ in chordates
~same gene, evolved once
chordate characters
pharyngeal gill slits dorsal nerve cord segmental muscles/mesoderm notochord postanal tail
pharyngeal gill slits
probably first to evolve, seen in hemichordates and maybe echinoderms
amphioxus doesn’t use as gills- filters food
large surface area for gas exchange
segmental muscles/mesoderm
serial myotoes/somites
other inverts. typically circular/longitudinal muscles
in vertebrates only around guts
postanal tail
anus not terminal, body extends over primary anus to form tail, new anus is formed (non-terminally)
dorsal nerve cord
ventral in proterostome
evolves separately in new place OR inversion, mouth migration (moves down in chordates)
mouth formation
delayed, area btw mouth and nerve cord expands
ventral mouth is a derived character– lead to face evolution
as mouth ‘moves’ pituatary ‘chases’ it- moves to oral cavity, then up to underside of nerve cord
model organisms for developmental biology of vertebrates
zebrafish, mouse, chick, frog
why frog?
easy to obtain large # of eggs, embryogenesis occurs outside body- eggs can be manipulated
frog cell cycle
rapid cell cycle- no G1, G2– increases # of cells in embryo (large cell #)
no zygotic transcription
blastula parts
animal pole (AP)- top, blastocoel, superficial cells Vegetal pole- cells more dense, comprise gut structures
gastrulation
series of coordinated cell rearrangements leading to germ layers
equatorial region forms dorsal blastopore lip- bottle cells ‘crawl’ and involute- displaces blastoceal
germ layers
ectoderm
mesoderm
endoderm
ectoderm
skin, nervous system
mesoderm
muscle, bone
endoderm
gut
results of gastrulation
endoderm cells were on outside before gastrulation
archenteron formed
AP moved equatorial
blastopore formed (future anus)
protostome gastrulation
starts at mouth
deuterostome gastrulation
starts at anus
upon completion of gastrulation
3 germ layers are evident and layered (endo, meso, ecto)
A-P and dorsal-ventral poles established
preliminary notochord present, terminating in dorsal blastopore lip
next stage after gastrulation
neurulation - dorsal ectoderm becomes CNS (central nervous system)
mammalian, chick embryo proper
flat sheet of cells, epiblast, prior to gastrulation
cells migrate through primitive groove to give rise to 3 germ layers
neural plate stage
neural tube formation
neuroectoderm– neural groove formation– neural fold– neural tube pinches off– neural crest cells disperse and notochord forms– epidermis on top
gives rise to brain and spinal cord
neural crest
one of defining features of vertebrates- novel
migrate to different regions- even non neural cells
neural crest derivatives
PNS- peripheral nervous system Endocrine and paraendocrine derivatives pigment cells facial cartilage and bone connective tissue
sometimes referred to as the 4th germ layer
neural crest
distinguishes vertebrates from other chordates
a9.49 cell
always gives rise to pigment- overexpression of ‘twist’ = loss of melanocyte– migration is similar to neural crest cell (may be a precursor)
closure of neural tube
—neurula stage- formation of somites, tailed, expansion of forebrain, gill area
failure of closure = spina bifida (.7/1000 births, folic acid deficiency)
notochord remnants
retained in lancelet, larval tunicate
supports vertebrae in mammals
notochord implicated in different cell type generation
signals ectoderm to form CNS
implicated in different cell type generation
move/remove notochord- induce cell diversity in dorsal part of neural tube, in a graded manner (1 22 1)
shh
sonic hedgehog secreting cells- gradient directs TF expression- 3TF = 5 domains
gradient of morphogen- cells respond to density = expression of different genes
one signalling factor gives rise to multiple factors
tadpole with yellow in head
remnants of yolk, starts feeding after thats gone
coqui
‘direct developers’
hatch as live frogs- no larval stage
much larger embryo and yolk, quicker maturation, nutritional endoderm, less reliant on water (eggs can be laid on land)
parallel evolution with amniotes
frog metamorphosis controlled by
thyroid hormone, T3 tri-iodothyrodine
nutritional endoderm
novel cell type, single cell containing yolk, doesn’t integrate into frog, connected for feeding, similar to amniote
allantois
stores waste
gas exchange
chorion
outer most membrane
gas exchange
mammals = placenta
polyembryony
more than one embryo from one egg
armadillos always give rise to 4 identical twins, all share same amnion and chorion (very rare in humans- 1% of human twins)
to make a phylogenetic tree start with
homologous DNA sequences that you have collected in the lab or downloaded from a database search
align sequences
BLAST
basic local alignment search tool - takes query, finds pairwise match, ‘hit’
Clustal W
gives multiple sequence alignments- doesn’t discriminate between non-homologous sequences- this is up to the biologist
correctly aligned, non-homologous
ACCTCATC
C____T
used to manipulate Clustal W results
BioEdit
distance matrix
how many differences between sequences
start with columns = sites, rows = sequences, count how many differences between sequences
make new grid, ex. sequences 234 vs. 123 with # differences
distance tree
tree branches add up to differences, sized based on differences
works best if you have same amount of data for each sequence- less similarities if comparing a short sequence- (not b/c the similarities don’t exist)
if you don’t have same amount of data for each sequence
use p-distances (proportions)
problems with number of differences/p-distances
unobserved mutations
A–G–T = 2 substitutions but only 1 is observed
A–G–A = 2 substitutions, none are observed
what we see is not always the whole story
attempt to correct for unobserved mutations
Jukes and Cantor formula
Jukes and Cantor
distantly related sequences likely to have experienced more substitutions than visible
mutations are more likely to occur at the same place given a large number of mutations
without Jukes and Cantor correction p-distance over time graph
asymptotes
Jukes and Cantor formula
gets rid of asymptote
distance = -(3/4)ln(1-(4/3)p)
p = proportion of changed sites, p-distance
if p= 0.18, JC distance =
0.206
influence of JC formula
distance btw similar sequences increases very little
distance btw distant sequences increases more
increases branch lengths in distant sequences
Actinopterygii
almost all fish
Sarcopterygii
lungfish, coelocanth
forgs, reptiles, mammals,..
relationship btw lungfish, lobe-fin, tetrapod, ray-fin
LF and Coelocanth (lobe fin) sister taxa
LF, C and T sister taxa
LF, C, T and RFF sister taxa
exons and introns
exons encode a.a.’s, introns dont
changes in interns less likely to have effect on proteins
we compare exons- more likely to be similar
exon vs. intron graph
more distance between families than within
more distance in introns (x-axis) then exons (y-axis)
red pandas
sister group of raccoons, badger, otter
more closely related to seals and sea lions than other bears
giants panda
at the base of the bear tree
other bears are more closely related to one another than to giant pandas
heyenas
are much more closely related to cats than to dogs
OLD convergence and parallelism
C- evolution of similar traits in unrelated taxa
P- evolution of similar traits in closely related taxa
NEW convergence and parallelism
C- evolution of similar traits in different lineages, involving different developmental pathways
P- evolution of similar traits in related lineages, involving same developmental pathways
new convergence and parallelism definitions based on
closeness of relatedness and molecular pathway
but don’t really need to say anything about relationship
C- results from different genetic mechanisms
toothlessness evolution
same genes are involved- parallelism
if we look at the relationships it would be convergence
evolution of body elongation
in sister taxa- same mechanism (increasing size of vertebrae) - parallelism
in more distantly related species- different mechanism (increasing # of vertebrae) - convergence
Pattern
the “what”?
ex. phylogeny
simple description of what we see
Process
the “how”?
genetic development/mechanism
process by which pattern arose
ex. giraffes have long necks b/c they expand size of vertebrae
and the “why”?
adaptive/selective scenario
assumed to be for feeding at higher levels
The integrated organism
diverse physiological processes all affect each other (ability, rate) one imposes trade-off on another
ex. water absorption through skin affects gas loss through skin, heat exchange, etc.
fluxes of mass
respiratory gases, organic and inorganic substances, water
fluxes of energy
heat, charge, potential energy
physiologic trade-off in Darwin’s finches
negative trade-off btw velocity and bite force- 2 separate muscles, can’t maximize both at the same time
endothermy trade-off
can live in cold parts of the world
must eat all the time to conserve thermoregulation processes
interacting organ systems of vertebrates
skin, skeleto-muscular, nervous, endocrine, respiratory, digestive, excretory, circulatory
all interacting
major transitions in evolutionary history of vertebrates
water to land (origin of tetrapods) land to water (origin of whales) origin of amniotes ectothermy-endothermy evolution of flight (origin of birds) origin of mammals origin of turtles origin of snakes all involve multiple systems at once
adaptations in the transition between land and water
density/viscosity changes - locomotion and support O2/CO2 content - gas exchange thermal capacity - thermoregulation refractive index - visual system velocity of sound - hearing apparatus'
evolution of endothermy
insulation - controlling heat loss/gain circulatory system respiratory system (endo. high O2 demand) metabolic rate musculoskeletal system
evolution of birds
endothermy flight wings pneumatic bones (air filled bones) feathers rhamphotheca (bill)
evolution of snakes
elongation of body reduction/loss of limbs repackaging of internal anatomy (long and skinny) modified locomotion modified feeding apparatus
correlated progression assumptions
incremental changes
natural selection
systems evolve in parallel
–traits can only change by one unit at a time, can be no more than one unit different than connecting traits, no obvious starting point
incremental changes in correlated progression
characters are highly integrated with each other, no one can evolve by more than a small amount at a time, without losing functional integration within organism as a whole
ex. can’t just grow a leg and become terrestrial
natural selection in correlated progression
natural selection tests the fitness of an organism as a whole, not any individual characteristics
ex. fitness of leg is not the issue, fitness of the organism is
systems evolve in parallel, correlated progression
all structures and functions evolve by respective sequences of small steps in loose correlation with each other to maintain continuous functional integration
your inner fish
all the parts mammals have are modified parts from fish ancestors
no parts are new parts, history matters
co-option
new use for old parts
gill arches
co-opted for other functions
arches 1-4 — jaws, ears, larynx, throat
bones, muscles, nerves, arteries develop inside these gill arches
every bone in our head can be traced to
plates, blocks, and rods (from fish)
plates- dermatocranium
blocks- chondrocranium
rods- splanchonocranium (jaws)
distinguishing feature of mammals (bone)
lower jaw only one bone- dentary
macroevolution
changes above or at a species level (speciation)
organisms are highly integrated
constrained by ancestral history- if we could build a new one it would be much different
linking micro and macroevolution
phenotypic plasticity- variation within individual species raw material for evolution of new species developmental biology (evo-devo)
graph of phenotypic plasticity in reaction norm
phenotype vs. environment is a linear graph where phenotype is able to vary with different environments
genetic assimilation
occupying on enviro.—unexpressed capacity for plasticity– enviro. changes– rxn norm allows population to persist– novel phenotype, no initial genetic change– phenotype becomes fixed– rxn norm loses plasticity
why reaction norm may lose plasticity
drift, cost associated w/ maintaining plasticity when it is not favoured by natural selection- old environment no longer favoured
macroevolutionary phenomena
origin of new structures discontinuities in "adaptive space" rates of evolution causes and natures of radiation causes and natures of mass extinctions
therapsids
mammal like reptiles
cause and nature of radiation example, therapsids
different lineages, showing increasingly mammalian characteristics, parallel changes in lineages
phylogenetic baggage
we are constrained by our evolution
exaptation
and the related term co-option describe a shift in function of a traits evolution
ex. trait can evolve because it served 1 function, but comes to serve another
preadaptation
large change in function is accomplished with little change in structure
mammals and vertebrae
7 cervical vertebrae almost always in mammals
exception- manatees have 6/7; sloths have recruited thoracic vertebrae to lengthen neck
why are mammals constricted to 7 cervical vertebrae?
morphological integration with other body parts, evo-devo- environmental biology evolved along with neck
each vertebra is restricted by a somite that produces myoblasts
C3-C5 migrated further back in body, responsible for formation of diaphragm
C6-C7 associated with muscles in shoulder area
largest known mammal necks
increase size of vertebrae not number (giraffe)
Annolis inovations
lizard- ‘pave the way’ for future evolutions
feet w/ hooks for climbing vertical surfaces- success of the species
key innovations can only really be determined to be key in hind sight
adaptation
feature that performs a specific function, arises as a result of selection
exaptation
one function taking over old function
new use will arise for a structure
in trade-offs be aware of
other variables that affect trade-offs
do simple correlation value and semipartial correlation values change
scaling relationships
how different characteristics are related to body size
allometry
statistical shape analysis in biology for differential growth rates of the parts of a living organism’s body
morphometrics, multivariate stats, homologous landmarks
morphometrics
quantitative study of shape, heavily statistical
landmarks
changes in position give change in shape
knowing distances between points to determine shape and convert it to data
example of landmarks as a beneficial study
determining landmarks in endangered species to determine sex (M/F) for rearing eggs
PCA
principle component analysis
using landmarks in salamanders
2 salamanders with overlapping ranges, occurring in allopatry and sympatry
IDing landmarks on heads to determine how they differ in allopatry and sympatry
isometric vs. allometric growth
Iso- no change in shape proportions of body parts- stay the same
Allo- body proportions change
ontogenetic change in shape
change in shape during growth, through life
cohort
born at the same time
longitudinal study
following a cohort, following a group through life
cross-sectional study
slice in time, harder to determine age
measuring and testing allometry, bivariate case H_o
H_o : isometry, b = 1
testing bivariate allometry, equation
Y = aX^b ln(Y) = ln(a) + b*ln(X)
testing for area
H_o: b = 2
testing for volume or mass
H_o: b = 3
results of Natrix natrix allometry regression
M have longer tails in absolute measurements, not in relative = isometry (M are smaller than F)
2 sexes are different but that is established right at birth, no change during life time- isometric
longer for copulation, reproductive organs
growth rate of head in humans
negatively allometric to body size in early life before head reaches full size
brain growth declines with age, relatively speaking
growth rate of heart in humans
about isometric to body size
proportionate difference in skull shapes of dogs and cats
dogs undergo greater shape changes than do cats
greater diversity of skull shapes in different breeds of dogs
dogs are tremendously allometric in skull growth
cats are close to isometric in skull growth
chameleon characteristics
highly derived- lots of apomorphves zygodactyly (2 fingers opposing other 2) highly projectile tongue independently moving eyes prehensile tail (to anchor)
slope of log(mass) vs. log(length)
mass = volumetric = 3 if isometric
< 3 is negatively allometric
>3 is positively allometric
allometric tail growth in chameleons
negatively allometric at posterior end, positively allometric at anterior end- prehensile tail- able to curl tightly at end because vertebrae are very small
adaptive significance of allometry in hatchling sea turtles
highly vulnerable to predation, swallowed whole by dolphinfish (mahimahi)- grow wider shell (positive allometry)
after week 5, probability of lethal encounter decreases quicker with wider shells
turtles- caretta caretta, chelonia mydas, lepidochelys kempii
intraspecific
same species
interspecific
different species
phylogenetic studies require
interspecific comparisons, representative measurements from different species
most important evolutionary force of overall color
camoflauge
patches of color
intraspecific signalling
types of concealment
crypsis, disruptive coloration/obliterative shading, irregular marks to break up bodies outline, lighter ventral surface
spotted species are generally found
arboreal (forests)
striped species are generally found
grasslands (blend in to blades of grass)
aposematism
prey advertise noxiousness/pugnacity
ex. skunk
discontinuous color variation
white or black
albinism- likely no adaptive significance, rare
melanism- common in tropical forests (black panther)
sexual dichromatism
rare in most mammals, common in primates
physiological coloration
reflet/absorb sunlight for thermoregulation, enhance/reduce evaporation, reduce glare (dark eyes)
thermoregulation coloration
pale species found in deserts- reflect sunlight
dark species found in tropics- enhance H2O evaporation, protect against UV
If plasticity was acting on lizard field experiment
would expect immediate difference in hindlimb length
not what was seen
problems inferring behaviour of extinct species
underlying assumption have to be made
have to rely on modern analogues when there may not be
behaviours exhibited were documented in crown groups, little know of stem taxa
wing skeleton and migration
migratory, semi-migratory taxa have proportionally longer wing skeleton than non migratory taxa
large crushing force with bill
exceeds force needed for herbivory– likely predation, scavenging
fossilized footprints
many found oriented in same direction along shoreline– moving in parallel, gregarious behaviour
modern avian behaviours exhibited by ancestor of crown birds
vegetative nests, extensive pre and post-hatching parental care, egg brooding
loss of hearing represents
regressive evolution
reduction of hair cell density indicates
involvement in high-freq hearing loss
fewer hair cells = fewer sites for signal transduction
how selection against production of unfit hybrids can lead to differentiation
ex. female choice selecting for a divergence in male secondary sexual traits that facilitates species recognition
reinforcement hypothesis
the ultimate explanation for a sympatric character divergence is that it reduces the probability of hybridization
selection against hybridization in sympatry
overrides sexual selection for elaborate traits
