FINAL TERM Flashcards
are different in
appearance and perform different
functions but are built on the same basic
pattern and have a common origin
(same source)
Homologous organs
the similarity in the basic structure of
organs of different animal groups based
on common ancestry or origin from
some common structural patterns
Homology
Similarity in the DNA sequences found in
different species
Existence of universal genetic code, the same 64 codons specify the same amino acids from
bacteria to man
Similarity in the structure of plasma membrane
Similarity in the mechanism of transcription and translation via same RNA polymerase
Use of ATP as energy currency
Similarity in the mechanism of DNA replication via DNA polymerase
Genetic homology
- is seen in the overall
process of development, form of the embryos of different groups and fate of particular embryonic tissues or organs.
Developmental homology
are similarities in adult
morphology in organisms of different groups and are the results of homologous genes .
Structural homology
Levels of homology in species
Genetic, developmental, and structural homology
Types of homology
Phylogenetic, Sexual, Serial, and Molecular homology
is similarity among animals or
among plants of different species. Ex: homology in the
hand of man and forelimbs of horse and bat)
Phylogenetic homology
is parallelism in the male and female
reproductive organs of the same species.
Sexual homology
has been observed among
invertebrates .
Serial homology
is similarity in the biomolecules,
such as DNA, the genetic material found from viruses to man.
Molecular homology
when the ancestral individuals of the same group migrate to different habitats, their organs undergo adaptive modifications in different environments and become different in form and/or function.
Divergent evolution
have almost similar appearance and perform the same function but they develop independently in totally different groups through parallel evolution and are not inherited from a common ancestor
Analogous or homoplasious organs
is the superficial similarity in appearance between organs of different animal groups because they carry out the same function.
Analogy
Organisms of the same or closely related groups when occupy different habitats, they assume different appearances and their homologous structures exhibit great divergence in the form and function.
Adaptive divergence
Organisms of distantly related or totally
unrelated groups are found to develop similar
adaptations, while living in the same or similar
habitat. Their analogous structures, though
apparently similar are constructed on different
basic plans
Adaptive convergence
Used the term “vestiges” and “Rudiments”
Jean Baptiste Lamarck
Used the term Rudimentary Organs
Charles Darwin
Popularized the term “Vestiges”
Robert Wiedersheim
Group 1 Presentation Title
Vestigial Structure in Postcranial Skeletons of Extant Mammals
Group 2 Presentation Title
Vestigial organs as opportunities for functional innovation the example of the penstemon staminode
structures that persist within a species but have lost their function
Vestigial structures
They are usually smaller than their homologues
in other species, and are sometimes described as
Atrophied
often modifies the androecium, resulting in either stamen loss or transformation of stamen
function from pollen production and
presentation to alternate functions
Floral evolution
stamens that have lost their primary
function of pollen production
“abortive stamen”
relatively uncommon, but widely
distributed taxonomically
32.5% of angiosperm families and 54.4%
of angiosperm genera.
Staminode
arise as intermediate structures during
reductive processes in the androecium.
decreases in stamen number typically
involve progressive suppression of
stamen development during
morphogenesis
Nonfunctional staminodes
commonly implicated staminode roles
include pollinator attraction through
visual conspicuousness and/or provision
of attractants and rewards, avoidance of
selfpollination, and facilitation of pollen
removal and receipt through various
trigger mechanisms
Functional staminodes
occurs when stamens initially serve
purposes in addition to pollen
production and presentation (e.g.,
pollinator attraction)
functional constraints should favor
‘‘division of labor’’
Direct evolution
the nonfunctional phase preceding
adoption of a new function allows
staminodes to assume novel functions
not expected of stamens
Indirect evolution
Beardtongue in English
the largest genus of flowering plants
endemic to North America (250 species;
Holmgren 1993)
Penstemon (Scrophularicaeae)
staminode hinders pollinator access to
nectar, increasing visit duration and
contact with sexual organs, thereby
increasing pollen receipt by stigmas and
controlling pollen removal from anthers.
the staminode acts as a lever that
enhances stigma contact with the
pollinator, so that staminode removal
reduced pollen receipt, but did not
affect pollinator attraction, visit
duration, or pollen removal.
Bee-pollinated
staminode removal from hummingbird pollinated species did not affect any measured aspect of pollination,
indicating that the staminode serves no
function in this derived pollination
system
Hummingbird- pollinate
Group 3 Presentation Title
VESTIGES OF THE NATURAL HISTORY OF
DEVELOPMENT - HISTORICAL HOLDOVERS REVEAL THE DYNAMIC INTERACTION BETWEEN ONTOGENY AND PHYLOGENY
evolution of biological
systems’ two main stages:
Evolutionary and Developmental change
Vestiges come from the Latin word “vestigium” which means
Footprint
what are the human vestiges
Vermiform appendix
tail bone (coccyx)
Wisdom tooth
He published “Vestiges of the Natural History of Creation”
Robert Chambers
is present in humans but in much-reduced form relative to other mammals. It is series of
physiological changes that take place in
the body in response to a mammal
holding its breath while submerged in
water
Mammalian dive
are a vestigial motor reflex pattern (of
glottal closure during inhalation, so that
the vocal folds slam shut) left over from
early tetrapod vertebrates, specifically
the tadpole larvae of amphibians
Hiccups
This bird is endemic to Fernandina and
Isabela Islands of the Galápagos
Archipelago, provides an excellent
example of vestigial attributes due ot its
noticeably stumpy, stubby wings that
are much too small to allow it to fly
flightless cormorant (Phalacrocorax harrisi)
reflex vestige of human babies
from ancestral primates, where offspring
needed a firm grasp of their mothers’ fur as they were carried
Palmar gasp
These are detours or shunts
(pulmonary to systemic, or ‘right to left’)
occurring in the shift from fetal to neonatal
mammalian circulation.
Remnants of the old circulation pattern and
blood supply network from the in utero phase
are left behind on the offspring after birth
Embryonic remnants of mammalian circulation
This bypass, essentially an oval-shaped hole in
the septum dividing the right and left atria,
normally closes when the pressure head in the
systemic (left) half of the mammalian circulation exceeds that of the pulmonary division, pressing a flap of tissue to close the hole. The tissues soon fuse and all that remains is an oval-shaped depression.
Foramen ovale → fossa ovalis
a bypass from the pulmonary trunk to the aorta, serves to shunt blood away from the lungs during fetal development. However after birth, it withers and closes to become a shriveled band of tissue
Ductus arteriosus → ligamentum arteriosum
is a vein present during fetal
development that carries oxygenated blood
from the placenta into the growing fetus. It is
open at birth but closes within a week. Just after closure, the umbilical vein is mostly removed except for a fibrous portion on the abdominal wall that remains as the
Umbilical vein → ligamentum teres hepatis
Aside from these circulatory artifacts, the best
examples of non-functional embryonic ‘vestiges’ come from the
Developing urogenital system
becomes the efferent or deferent duct that stores and transports sperm and seminal fluids. It is maintained by testosterone
Wolffian duct
The Wolffian duct develops in males into the vas deferens. In mammals testes normally descend permanently or temporarily into a scrotal sac for better spermatogenesis, In males, it transmits the spermatic cord, gonadal vessels, and lymphatics. In females, it transmits the round ligament of the uterus
Inguinal canal
In all mammals, nipples develop along the milk
line of the mammary ridge. But why should male mammals have nipples at all? Interestingly, Darwin (1871) perpetuated the myth that male nipples are true evolutionary vestiges that stem from lactation in male as well as female ancestral mammals.
Male nipples
Group 4 Presentation Title
The Evolution of Complex Organs
Special Issue: Persistent Unilateral Nictitating
Membrane in Eyes
Made up of a combination of different cells that works together to perform scientific functions. One of the example is the “eye”: 70 distinct types of cells work together to enable our visual perception.
Complex organs
how an organism develop their ability to
function successfully through time
Complexity
The notion of functional shifts is an old
one in evolutionary biology, having been
considered “an extremely important
means of transition” by Darwin.
A feature that arose for some reason
and subsequently acquired its current
function. (new role or function)
Exaptation
The duplication and individuation of
biological entities
Individuals with different form of the
feature will leave fewer offspring than
those with the original form, such that
there will not be changed in the
population from one generation to
another concerning this feature.
Duplication or Furcation
4 different outcomes in gene duplication event:
“pseudogene” “iso-functionalization” “subfunctionalization” and “neofunctionalization”
Complex Organs do not evolve from
scratch at each stage; instead, the
process builds upon and modifies what
is already present, whether through
direct adaptation or functional
adjustments
Bricolage (Tinkering) and Collage
A loss of a component that was formerly
required for the assembly of a complex
arrangement of parts. (the removal of
one or more compontents may render
the organ non-functtional)
Scaffolding
is a transparent and translucent third eyelid present in some animals that can be drawn across the eye for protection and moisten it while maintaining visibility
Nictitating membrane
Also known as semilunar fold
Plica semilunaris
encompasses the correct interpretation
and understanding of information about
evolutionary relationships.
Tree thinking
is observed in unused ones as
the mechanism of muscle atrophy is either ‘use
it or lose it’
Muscular decline
Group 5 Presentation Title
The plantaris and the question of vestigial muscles in man
Consists of the subsequent
muscles to be mentioned, the
gastrocnemius, soleus, and the
plantaris
Collectively, these muscles serve
to plantarflex the foot at the
ankle.
Triceps surae
most superficial among the trio
obvious as it bulges when we
raise ourselves up on our toes.
composed of multiple
multinucleated cells
producing maximum speed and
contraction during running and
jumping
Gastrocnemius
deepest muscle of the triceps surae,
is a large flat muscle so named
because of its resemblance to the flat
fish known as the sole.
muscle fibres in the bipennate
(feather-shaped) arrangement and
is referred to as the ‘antigravity
muscle’
Soleus
small muscle the runs along the
posterior region of the calf as also
described by Spina, (2007).
its functionality is still questioned as
to whether it is vestigial in nature or
still developing from being one
Plantaris
special sense of limb
position is called
Kinaesthesia
Archetypal examples of vestigial organs
wings in non flighted birds
eyes in blind species
vestigial limbs in snakes
providing an improved ability to hear potential predators and other hazards
Auricular (ear) musculature
proposed by Stephen Jay Gould and Elizabeth
Vrba in the 1980s as an alternative to
preadaptation
Exaptation
refer to traits or features that are the result of
evolutionary byproducts rather than adaptations that have evolved for a particular purpose
first used by evolutionary biologists Stephen Jay Gould and Richard Lewontin in 1979
Spandrels
is the change in biological populations’
heritable features over successive generations.
Every level of biological complexity benefits from the diversity provided by evolutionary processes
Evolution
begins when a characteristic is
declared nonfunctional or becomes a selected
liability outright as a result of environmental
alterations or bodily components that have
evolved out of function (Fong et al., 1995)
Vestigialization
Causes of Vestigialization
- Vestigial or missing structures may be a result of evolutionary trade-off
- Indirect Selection causes character loss
refers to the idea that the evolution of one trait
may come at the cost of another trait.
Evolutionary trade-offs
Occurs when a sensory system in an organism is reduced or lost, while another sensory system becomes more elaborated or enhanced to compensate for the lost sensory function
Compensatory sensory system trade-off
A particular trait or feature of an organism is no longer subject to the same level of selective pressure as it was in the past
Relaxation of natural selection
A process of natural selection
in which a trait is not directly favored or selected for, but instead, changes in the trait frequency occur as a result of selection acting on a correlated trait.
Indirect selection
A random process that can cause
changes in the frequency of alleles in a
population due to chance events, especially in
small populations.
Genetic drift
-is a change in the
DNA sequence that makes up a gene or a
chromosome.
-can result from errors
in DNA replication during cell division
Mutation
-adaptation for increased ballast, decreased risk of downstream drift, and increased reliance on cutaneous respiration in cool, swift, oxygen-rich upland Appalachian streams
-results from the selection for narrower heads or the evolution of terrestrial courtship and mating, increasing the reliance on cutaneous respiration.
Lungless plethodontids (salamander)
A laboratory strain of Drosophila mercatorum has been
used for an experiment called parthenogenesis. They
were isolated for 20 years without males. The laboratory
experiment resulted from female mating behavior as
nonfunctional trait.
Decay of Sexual Behavior
n behavior in the Village Weaver, Ploceus
cucullatus, a colonial nesting bird from Africa, had
probably evolved to counter brood parasitism by the
Didric Cuckoo, Chrysococcyx caprius. Hispaniola Village
Weavers are less discriminatory and reject a lower
percentage of foreign eggs than do their African
counterpart.
Decay of Egg-rejection behavior
Best website for Protein
PubMed/ NCBI
Applicable both to nucleic acid
sequences and protein sequences.
Sequence databases
- Very common applications in proteins.
- 2D and 3D
- Interaction with proteins.
- Nucleic acids
- Drugs
- Natural products (active
components)
Structure databases
– contains information of the
sequence or structure alone
* Data are derived experimentally.
* e.g. Swiss-Prot and PIR for
protein sequences, GenBank
and DDBJ for genome
sequences, and PDB for protein
structures
Primary database
contains derived
information from the primary database.
* Conserved sequence, signature
sequence, active site residues of protein
families, and conserved secondary
structure motifs
* e.g. Prosite, Pfam
Secondary database
amalgamates a variety of
different primary database sources.
* Removes the need to search multiple
resources
* e.g. NCBI and ExPASy
Composite database
Includes the following databases: UniProtKB, SwissProt,
STRING, SWISS-MODEL Repository, PROSITE, ViralZone,
and neXtProt
EsPASy
What is the tool used to compare the protein sequence of multiple species
ClustalO
is the name of a popular sequence alignment-and-database-scanning program
created by W.R. Pearson and D.J. Lipman in
1988.
FASTA
What is the difference between Protein sequence and DNA sequence?
Protein is composed of alphabet except BJOUXZ while DNA is composed of ATCG
that is generated by copying the DNA sequence
of a gene from beginning to end,
(including exons + introns).
Primary transcript
the mRNA, generated from the primary transcript by discarding the introns
Mature transcript
the open reading frame or ORF
Strict protein-coding region
an arbitrary identifier – is followed by a short definition line and a unique accession number
Locus name
- Lists article(s) relevant to the sequence
determination. - Can be quite long for large
sequences.
Reference section
- Lists the definitions and exact ranges of
multiple types of elements - Have been recognized in the
sequence
Features section
- Rounds out the GenBank entry,
- Nucleotides are listed between the
ORIGIN keyword and the final // that
signals the very end of the entry. - Numbering is provided to help relate the
location of the ORF to the actual
nucleotide sequence.
Sequence section
Used to compare protein to other protein sequences
BLAST (Basic Local Alignment Search Tool)
Is an assessment of the statistical
significance of the score.
E-value
- Involve lining up many similar proteins side by
side for the sake of comparison.
Multiple alignments
