Evidence for evolution

							          Evidence for evolution
 Inthe early 1800’s prevailing belief was
  that:
      organisms were specially created and
       unchanged since their creation
      Species created independently of each other
      Earth not old. Ussher’s estimate: for Earth’s
       creation 4004 BC
               Lamarck
 Fact of evolution proposed in late 1700’s
  early 1800’s.
 Jean Baptiste Lamarck 1809, 1815
  proposed that all species were derived by
  gradual evolution from other species.
 Lamarck’s idea was that evolution was
  driven by an innate tendency of organisms
  to become more complex over time.
        Inheritance of Acquired
            Characteristics
 Lamarck’s proposed mechanism of
 evolution was called the Inheritance of
 Acquired Characteristics (IAC)

 IAC suggested that modifications to
 organisms during their life could be
 passed on to their offspring (e.g., a giraffe
 stretching its neck during its life passes
 slightly longer neck to offspring).
          Inheritance of Acquired
              Characteristics
   Obviously, Lamarck’s ideas about the
    mechanism of evolution largely contradict
    current biological knowledge.

   The information required to build a body is
    stored in DNA and that information (influenced
    by the environment) determines the phenotype.
    Changes to the phenotype during life however
    do not affect the DNA sequence. Information
    flow is thus only in one direction from DNA 
    phenotype, not in the reverse direction.
             Epigenetics
 However,   recent research in the emerging
 field of epigenetics shows that Lamarckian
 effects may occur through changes in the
 control of gene expression caused by
 environmental effects e.g. food shortage
 during development.
                  Epigenetics
   Epigenetics is the study of heritable changes in
    gene expression caused by mechanisms other
    than changes in the DNA sequence.

   The DNA nucleotide sequence is not changed
    but whether and how much genes are
    expressed can be altered and some of these
    changes may be passed from one generation to
    another.
                 Epigenetics
   One way in which epigenetic effects have been
    shown to occur is through environmentally
    induced methylation in which a methyl group
    (CH3) is added to cytosine nucleotides
    converting them to 5-methyl-cytosine.

   More heavily methylated regions are translated
    and transcribed less frequently than non-
    methylated regions.
                    Epigenetics
   One well documented example of epigenetic effects
    resulted from the Dutch winter famine of 1944/45 at the
    end of WWII.

   The children of women pregnant during the famine were
    born smaller than normal (which was to be expected).

   However, the children of those children were also born
    smaller than average. This suggests the famine induced
    epigenetic changes in mothers pregnant during the
    famine that were passed to their offspring.
Charles Darwin
published
“On the origin
of species”
in 1859.
   Charles Darwin (1809-1882)
 Son  of a wealthy doctor.
 Dropped out of medical school.
 Studied theology, but was much more
  interested in natural history (e.g. he had a
  large insect collection).
 After college signed on as captain’s
  companion on The Beagle.
       Voyage of the Beagle
 Darwin companion for Captain Fitzroy on
Voyage of The Beagle (1831-1836).
 The Beagle’s mission was to map the
 coast of South America, but the ship
 traveled around the World.
 Sites visited included Galapagos Islands
 a group of volcanic islands (hence of
 recent origin) off the coast of Ecuador.
 Unique animals on Galapagos include
 giant tortoises, marine iguanas, and
 Darwin’s finches.




Galapagos Giant Tortoise
Sharp-
beaked
Ground
Finch
 Influence of geological thinking on
               Darwin
 By the time of “The Beagle” voyage the
  idea that Earth was young was being
  challenged.
 Opposition based on principle of
  Uniformitarianism.
 This is the idea that geological processes
  happening today are the same as have
  operated in the past.
 Influence of geological thinking on
               Darwin
 Uniformitarianism  contrasted with
 Catastrophism which proposed that
 current geological formations had resulted
 from catastrophic events (such as the
 biblical flood) which occurred on scale
 unknown today.

                 first proposed by James
 Uniformitarianism
 Hutton and championed by Charles Lyell.
 Influence of geological thinking on
               Darwin
 During   the voyage Darwin read Lyell’s new
  book “Principles of Geology.”
 Lyell emphasized two points:
 1. Gradualism: Geological features can
  be explained by the slow gradual action of
  processes we observe every day e.g.
  erosion by wind and water, deposition of
  sediments in rivers.
 2. The Earth is very old: there has been
  lots of time for change to occur.
 Influence of geological thinking on
               Darwin
 Huttonand Lyell inferred Earth must be
 very old based on measurements of rate
 of ongoing rock forming processes (e.g.
 deposition of mud and sand).

 Thesedevelopments in geology focused
 Darwin on the potential importance of
 gradual change in shaping structures.
       What Darwin observed
 On   the voyage Darwin noted many things
 that were puzzling from the point of view of
 a creationist explanation for the diversity of
 life.
         What Darwin observed
   1. South American fossils resembled living
    South American animals.
   2. Parts of the world with similar habitats and
    climates (e.g. Australia and South America) are
    populated by very different animals.
   3. Plants and animals on each continent are
    different from those on other continents.
   4. Many species on remote oceanic islands are
    found only there (endemic).
   5. Endemic species on islands closely resemble
    species found on adjacent mainland.
           What Darwin observed
   These observations taken together don’t make
    sense if organisms were specially created.
       Why should similar habitats in different parts of the
        world have different faunas?
       Why should remote islands have unique faunas that
        differ from but resemble those on adjacent land
        masses?
   Together these observations suggested to
    Darwin that species change over time i.e., that
    evolution occurs.
            Darwin and Wallace
   After returning from the voyage Darwin spent more than
    20 years developing his ideas and gathering the evidence
    to support them.

   In 1858 Charles Darwin and Alfred Russel Wallace jointly
    proposed natural selection as the primary mechanism by
    which evolution takes place.

   In 1859 Darwin published his book On the Origin of
    Species, which summarized his ideas about evolution and
    presented the evidence to support them.
      The “modern synthesis”
 Idea of evolution was accepted rapidly by
  scientists.
 Lack of understanding of heredity and
  population genetics, however, prevented natural
  selection being accepted as the principal
  mechanism of evolution until 1930’s.
 The “Modern Synthesis” in the 1930’s of
  combined the ideas of population genetics and
  natural selection to explain gradual evolution,
  speciation, and macroevolution.
         Evidence for Evolution
 Evidence    of change in organisms over
  time
 An example in a living species:
     evolution of beak length in soapberry bugs.
     Soapberry bugs use long beak to penetrate
      seeds in fruits and eat them.
     Native host plant is balloon vine which has
      thick fruits.
  Evolution of Soapberry Bugs
 In 1926 flat-podded Golden rain tree
  introduced to Florida. Has thin fruits.
 Today soapberry bugs feeding on Golden
  rain trees have much shorter beaks than
  those living on balloon vines.
Comparison of beak
lengths in areas
with and without
golden rain trees
Data from museum
specimens documents
change in beak length
over time.
Antibiotic resistance in bacteria
   In 1947 only four years after the mass
    production of penicillin began resistant strains of
    Staphylococcus aureus began to be reported.

   Antibiotic resistance is now widespread and in
    the US half of all S. aureus infections are
    resistant to multiple antibiotics including
    penicillin, tetracycline, erythromicin and
    methicillin.
        Antibiotic resistance
 Bacteria have evolved resistance quickly
 in part because of their rapid reproduction,
 but also because antibiotics were misused
 (e.g. by being overprescribed or
 prescribed for non-bacterial infections and
 by people not completing their course of
 antibiotics)
    The evidence for evolution
   Fossil evidence
   Vestigial structures
   Homologous structures
   Atavistic structures
   Other evidence
       Jerry-rigged structures
       Adaptive radiation
       Artificial selection
            Fossil evidence
 Fossilsare mineralized copies of the
  remains of organisms preserved in
  sedimentary rocks.

 In the process of fossilization a dead
  organism is covered by sediment and the
  organic matter is replaced by minerals
  leaving behind an impression of the
  organism.
   Fossil evidence of evolution
 Millions  of fossils have been collected and
  it is clear from fossil evidence that many
  species (in fact almost all that have ever
  existed) have become extinct.

 Equally clearly the faunas of different
  geological eras are very different and have
  changed over time.
   Fossil evidence of evolution
 Law   of Succession: Fossil and living
  organisms in same area are related to
  each other and differ from organisms in
  other areas.
 South America contains both fossil and
  living armadillos
Extinct glyptodont (2,000 kg) resembles the
modern-day South American armadillo (2 kg).
         Fossil evidence of evolution
    Similarly modern Australia is filled with
      marsupials and fossils in Australia are of
      similar marsupial forms.

    Extinct      short-faced kangaroo.




http://msnbcmedia2.msn.com/j/msnbc/Components/Photos/061226/061226_kangaroo_v
med_1p.widec.jpg
   Fossil evidence of evolution
 Transitional   forms
 If fossil organisms are ancestral to modern
  organisms then there should be
  transitional fossils that show
  characteristics intermediate between the
  older and more recent groups.
               Archaeopteryx
 Archaeopteryx   the oldest known fossil bird
  (name means “ancient wing) has mix of
  reptilian and avian features.

 Reptilian:   long tail, teeth, long clawed
  fingers

 Avian:feathers, ribs with uncinate
  processes, avian shoulder girdle.
Archaeopteryx
(oldest known
fossil bird)
Jurassic
150mya
         Evolution of mammals
   There are numerous excellent fossil series that
    document the transitions from ancestral species
    to later species.

   For example: the evolution of mammals from
    synapsid reptiles.

   An extensive series of fossils documents the
    changes in the synapsid lower jaw from a jaw
    made of multiple bones to the modern mammals
    single dentary and the incorporation of some
    synapsid jaw bones into the inner ear.
www.mun.ca/biology/scarr/142019_QA_to_DS_jaws.jpg
http://www.talkorigins.org/faqs/comdesc/images/jaws2.gif
             Tiktaalik roseae
 Another example is the evolution of the first
  amphibians from lobe finned fishes.
 The transitional fossil Tiktaalik roseae
  possesses an intermediate suites of characters.
 It has fish-like scales, palate and jaws, but an
  amphibian-like mobile neck and head, an ear
  that could hear in air, and the bones in its fins
  are intermediate between those of fish such as
  Eusthenopteron and Panderichthys and early
  amphibians such as Acanthostega.
Tiktaalik roseae 375 mya
Figure 25.01a
http://images.google.com/imgres?imgurl=http://www.bringyou.to/apologetics/SynapsidRe
ptileMammal.jpg&imgrefurl=http://www.bringyou.to/apologetics/p15.htm&usg=__xL62Y1i
gePmktGVlxKZ_0QKqfxo=&h=617&w=489&sz=118&hl=en&start=3&um=1&itbs=1&tbnid
=pvmoIlV49CGugM:&tbnh=136&tbnw=108&prev=/images%3Fq%3Dsynapsid%2Bto%2
Bmammals%2Bjaw%2Bevolution%26hl%3Den%26sa%3DG%26um%3D1
         Vestigial structures
 Many  organisms possess rudimentary or
 functionless versions of body parts that
 function in close relatives/ancestors.

 The fact that structures are rudimentary
 implies they had ancestors in which these
 structures were functional. This suggests
 an evolutionary history.
Examples of Vestigial structures
 Cave  populations of Mexican tetra fish
  have eye sockets, but no eyes.
 Kiwis have tiny, stubby wings
 Boas have tiny remnant hind limbs
http://news.nationalgeographic.com/news/2006/02/images/060217_kiwi.jpg
Mexican Tetra
    Human vestigial structures
 Coccyx:  vestigial tailbone at base of spine.
 Arrector pili muscle at base of hair follicles
  makes hair stand up.
 Appendix: reduced in size. Used in
  digestion of cellulose in herbivores e.g.
  rabbits.
  Vestigial developmental traits
 Adultchickens: three bones in forefoot
  (wing), four in hindfoot.
 However, digit 5 appears briefly during
  embryonic development before
  disappearing.
     Molecular vestigial traits
 Human  genome contains large numbers of
 pseudogenes that do not code for
 functional RNA or proteins. These are
 leftovers from evolutionary history once
 functional genes that have been turned off.

     there are several pseudogenes of
 E.g.
 hemoglobin. May be as many as 6,000
 pseudogenes in human genome.
        Homologous structures
   Homologous structures are those constructed
    from the same basic components which have
    been inherited from a common ancestor and
    then modified for different purposes.

   E.g. The forelimbs of a human, mole, horse,
    dolphin and bat are constructed from the same
    bones, but the bones differ in size and shape
    and the structures made from the bones are
    used in radically different ways.
     Homologous structures
 Homologous    structures make no sense if
 organisms were specially created, but they
 do if a set of organisms share a common
 ancestor and all inherited the same basic
 bone structure from that ancestor.

 Homologous  structures imply an
 evolutionary history and common
 ancestry.
Homologous structures (i.e. derived from a common ancestor). Even though the
forelimbs have evolved to carry out very different tasks they are all constructed
from the same bones.




                          FIG 2.11
             Homology vs. Convergent
                   Evolution
   Not all similarities between different species are due to
    homology.

   The streamlined shapes of sharks and whales are not a due to
    common ancestry but to convergent evolution.

   The same selection pressures to be able to swim efficiently in
    water have independently produced similarly shaped bodies
    instead of the traits being inherited from a recent common
    ancestor.
        Homology vs. Convergent
              Evolution
   Whales and dolphins evolved from terrestrial
    ancestors about 50 million years ago, whereas
    shark fossils as much as 350 million years old
    are known.

   The whales are most closely related to
    artiodactyls (hoofed mammals that include deer
    and hippos) and both whales and deer evolved
    from hoofed, carnivorous ancestors.
http://static.howstuffworks.com/gif/great-white-shark-1.jpg




www.seaworld.org/.../images/
killer-whale.jpg
     Homologous vs. Analagous
            structures
 Similarly, the wings of butterflies and birds
  are not homologous (because their
  structural components were not derived
  from a recent common ancestor) but
  perform the same function.

 Such  structures are analagous. They carry
  out the same function.
           Molecular Homology
   All organisms (with a few minor exceptions) use
    the same genetic code to specify which
    sequences of bases specify which amino acids
    when assembling proteins.

   The reason the code is essentially universal is
    that a mutation that altered the code would alter
    almost every protein produced and so would be
    lethal.
Figure 1.1.1. The standard genetic code and known variant nuclear codes.
(1) Candida, a unicellular yeast. (2) Micrococcus. (3) ciliated protozoans and green algae.
(4) Mycoplasma. (5) suppressor codon in bacteria. (6) Euplotes.
(7) the selenocysteine codon (8) Spiroplasma. (9) Micrococcus.
 (10) resume codon in ssrA RNA (Lehman 2001).

http://www.talkorigins.org/faqs/comdesc/section1.html
Molecular Homology: Genetic flaws
   shared by different species
 Chromosome     17 in humans PMP22 gene
  has duplicate sequence of DNA (CMT1A
  repeat) on either side of it.

 Itis the result of duplication and insertion
  of DNA and occasionally causes
  inaccurate crossing over during meiosis.
       Molecular Homology
 Humans   share CMT1A repeat with
 bonobos and chimpanzees, but not
 gorillas, orang-utans or other primates.

 Suggests CMT1A derived from common
 ancestor of bonobos, chimps and humans.
              Atavistic traits
 Atavistictraits are anatomical
  “throwbacks” that occasionally occur when
  a feature present in an ancestor reappears
  in a modern organism.

 For example, occasionally horses are born
  that have additional toes either side of
  their hoof. Similarly, sometimes people
  are born with a short tail.
http://atheistzoo.blogspot.com/2010/10/atavisms-blast-from-past.html
            Atavistic traits
 Suchoddities are due to errors in
 development that cause ancestral traits
 normally suppressed in the genome to be
 expressed.

 The presence of genes for such traits
 indicate an evolutionary history.
              Atavistic traits
 The  embryos of a diverse array of
  vertebrates are very similar in early
  development.

 Atavistic traits such as gill slits and a
  postanal tail, which are not present in the
  adult appear briefly before disappearing
  later in development.
Other evidence for evolution: jerry-
         rigged structures
 Jerry-rigged   structures e.g. the Panda’s
  thumb.

 In pandas, a wrist bone has been modified
  into a “thumb” that is used to grip bamboo
  stalks and assist in stripping leaves.

 The  “thumb” is not a very efficient solution
  to the problem of bamboo stripping.
http://www.athro.com/evo/pthumb.html
http://www.athro.com/evo/pthumb.html
              Panda’s Thumb

  Natural selection must work with the material
available to it. Process is more like someone
tinkering in their workshop and assembling an
object from spare parts than an engineer building a
structure from scratch.

   The jerry-rigged nature of the panda’s “thumb”
    implies pandas were not designed, but evolved.
    Other evidence for evolution:
         adaptive radiation
 Adaptive   radiation and clusters of species.

 Many remote islands are populated by
 morphologically diverse clusters of closely
 related species.

 Thispattern is difficult to explain without
 evolution.
  Process of adaptive radiation
 Ancestral   colonists arrive on island.

 Shortageof resident species means many
 niches are unfilled.

         colonizing species gives rise to
 Ancestral
 many species that occupy unfilled niches.
        Adaptive radiation
 Examples:Darwin’s finches on
 Galapagos Island, Drosophila on Hawaiian
 Islands.
          Darwin’s Finches
 On Galapagos Islands there are 13
 species of anatomically very different, but
 closely related species of finch.

 Theydiffer greatly in beak size and diet
 having evolved very different lifestyles.
          Hawaiian Drosophila
 More   than 25% of the world’s 1,250
    species of Drosophila fruit flies found on
    Hawaiian Islands.

   Few insect competitors so Drosophila
    have diversified to fill large number of
    niches.
 If faunas were created why are
there woodpecker finches, but no
 woodpeckers on the Galapagos
            Islands?
             Artificial Selection
   Artificial Selection. Humans as the agents of
    selection have selectively bred for desirable
    traits in domestic animals and plants for
    thousands of years.

   The tremendous diversity of body forms that
    have been produced in domestic dogs in very
    few generations show how quickly organisms
    can change in response to selection.
        Tameness in silver foxes
   One excellent example of artificial selection is
    Dimitri Belyaev’s work to breed tame Silver
    foxes.

   In each generation he bred only from the tamest
    individuals and in only six generations was able
    to produce foxes that were eager for human
    contact and behaved like domestic dogs rather
    than foxes.
        Tameness in silver foxes
   After about 30 generations 70-80% of the
    experimental population displayed extreme
    tameness.

   In addition many foxes lots their fox-like look,
    became piebald and resembled Welsh collies.
    These were side-effects of selection for
    tameness (an example of pleiotropy: genes
    having more than one effect).
  Silver fox after multiple generations of
  selection for tameness (upper left)




http://www.nature.com/scitable/nated/
content/42740/Belyaev_foxes_MED.jpg
        Creationism and “Intelligent
                  Design”
   The idea of evolution has been harshly criticized
    by religious fundamentalists since the
    publication of the Origin in 1859.

   This has been especially true in the U.S.

   Repeatedly, believers in the literal truth of the
    Bible have attempted to have alternatives to
    evolution (i.e., creationism) taught in the public
    schools and to have the teaching of evolution
    either banned or restricted.
     Creationism and “Intelligent
               Design”
 The U.S. Supreme Court has prohibited
 the teaching of creationism in public
 schools as a violation of the establishment
 of religion clause of the Constitution.

       attempt to insert creationism into
 Latest
 schools is the idea of “Intelligent Design.”
       Creationism and “Intelligent
                 Design”
   The concept of “intelligent design” is outlined
    most clearly in Michael Behe’s book “Darwin’s
    Black Box.”

   The central idea in “intelligent design” is that
    some structures in the body are so complex that
    they could not possibly have evolved by a
    gradual process of natural selection. These
    structures are said to “irreducibly complex.”
       Creationism and “Intelligent
                 Design”
 By “irreducibly complex” Behe means that
 a complex structure cannot be broken
 down into components that are
 themselves functional and that the
 structure must have come into existence in
 its complete form.
       Creationism and “Intelligent
                 Design”
 Ifstructures are “irreducibly complex”
  Behe claims that they cannot have
  evolved. Thus, their existence implies
  they must have been created by a
  designer (i.e. God, although the designer
  is not explicitly referred to as such).
    Creationism and “Intelligent
              Design”
 Behe’s main examples are various
 biochemical pathways in the body, the
 blood clotting system, and structures such
 as the bacterial flagellum.
     Creationism and “Intelligent
               Design”
 Sincethe publication of Behe’s book, it
 has been demonstrated repeatedly that
 things he has claimed to be irreducibly
 complex are not in fact so.

 E.g.the flagellum in eel sperm lacks
 several of the components found in other
 flagella, yet the flagellum functions well.
       Creationism and “Intelligent
                 Design”
 The  blood clotting system in dolphins lacks
  at least one component that the human
  system has, yet it too is functional.

 In addition, plausible gradual scenarios for
  the evolution of biochemical pathways
  including the Kreb’s cycle have been
  documented.
Evolution of complex structures
 The evolution of complex structures, such
 as the eye, appears difficult, but natural
 selection achieves this by the slow
 accumulation of minor improvements from
 one generation to the next.
Evolution of complex structures
   Each step on the evolutionary pathway from a
    simple light sensing cell to a complex eye
    capable of focusing and producing color vision,
    must be beneficial to the organism that possess
    it and a slight improvement on earlier versions.

   It is not necessary for a structure to be perfect or
    even very good, it just needs to be better than
    the alternatives to be favored by selection.
Variation in mollusc eyes from (a) pigment spot to (b) pigment cup to
(c) simple optic cup in abalone to (d) complex lensed eyes in a marine snail and
octopus.
Evolution of complex structures
 Computer simulations suggest that eyes
 can evolve easily and in nature eyes have
 evolved independently more than 40
 times.