The origin of species chapter 24'

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The origin of species chapter 24.

• Evolutionary theory must explain how new species
  originate.
• Two basic patterns in which evolution of one
  species into one or more other species occurs.

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The origin of species

• Anagenesis accumulation of changes over time
  gradually transforms a species into a different
  species.
• Cladogenesis Gene pool splits into two or more
  pools which each give rise to new species.

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The origin of species

• Biological Species Concept
• The species is a basic biological unit and humans
  seem to intuitively recognize species.

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• Why do species exist?
• Why dont we see a smooth continuous blending of
  one species into another?
• Because intermediate forms are selected against.

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• John Ray (1627-1705) gave first general
  definition of a species.
• A species consists of all individuals that can
  breed together and produce fertile offspring.

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A female donkey mated to a male horse produces
what?
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A mule (which is sterile) Hence, donkeys and
horses are separate species.
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Biological Species Concept

• Rays idea updated into the biological species
  concept.
• Species are groups of actually or potentially
  interbreeding natural populations, which are
  reproductively isolated from other such groups.
  Ernst Mayr.

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Reproductive Isolation

• There are a large number of potential barriers
  that prevent different species producing viable,
  healthy adults.
• These include both prezygotic and postzygotic
  isolating mechanisms (i.e., barriers that come
  respectively before and after mating).

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• But what about organisms that do not mate with
  another individual?
• E.g. single-celled animals, bacteria, fungi and
  many plants reproduce asexually.
• In practice, many organisms are assigned to
  species based on morphology or DNA.

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Speciation

• Two ways in which speciation can occur.
• Allopatric speciation occurs when a gene pool is
  divided into two
• Sympatric speciation occurs without geographic
  separation.

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Allopatric speciation

• Occurs when a population is divided by a barrier.
  
• Can occur because a barrier develops or because
  some members of population disperse to a new
  area.
• Once separated, the gene pools diverge as each
  population adapts to its local environment. Over
  time isolating mechanisms are likely to develop.

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Allopatric speciation

• If after many generations members of the
  allopatric populations are brought back together
  they may or may not be able to produce fertile
  offspring.
• Even if they can do so, those offspring may have
  intermediate characteristics which suit them to
  neither of the parental environments and thus
  they will be selected against.

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Allopatric speciation

• If intermediates are selected against, we would
  expect isolating mechanisms (barriers to
  reproduction) to be increasingly strongly favored
  by selection and ultimately that the two
  populations would become completely
  reproductively isolated and so new species.

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Allopatric speciation

• Examples.
• Two species of closely related antelope squirrels
  live on opposite sides of the Grand Canyon. The
  canyon is a barrier to their dispersal.
• In contrast, birds and other species that
  disperse well have not undergone speciation on
  opposite sides of the canyon

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Allopatric speciation

• Different Galapagos Islands contain different
  species of finches, which have evolved in the
  approximately 2 million years since the islands
  were first colonized from the South American
  mainland.

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Allopatric speciation

• Diane Dodd investigated development of
  reproductive barriers in fruit flies.
• Raised populations for several generations on
  either starch or maltose medium. Fly populations
  diverged each becoming better at digesting its
  food source.

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Allopatric speciation

• When flies from starch populations and from
  maltose populations brought together they were
  significantly more likely to mate with flies of
  their own population.
• Indicates that reproductive barriers between
  species can begin to form quickly.

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Sympatric Speciation

• In sympatric speciation, speciation takes place
  in geographically overlapping populations.
• Mechanisms of sympatric speciation include
  polyploidy and nonrandom mating that reduces gene
  flow.

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Sympatric Speciation

• Polyploidy is quite common in plants and many
  species have resulted from accidents in cell
  division that produce extra sets of chromosomes.
• For example a diploid plant (2n chromosomes) may
  become a tetraploid (4n). The tetraploid cannot
  produce fertile young with diploid plants because
  young will be triploid (3n chromosomes), but can
  self pollinate or mate with other tetraploids.

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Sympatric Speciation

• Polyploidy can thus result in speciation in just
  one generation.
• Polyploidy can also occur when two different
  species produce a hybrid. The offspring are
  often sterile because chromosomes cannot pair up
  during meiosis. However, the plant can often
  reproduce asexually.

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Sympatric Speciation

• Subsequently, various mechanisms can convert
  sterile hybrid into fertile polyploid called an
  allopolyploid.
• The allopolyploids are fertile with each other,
  but not other species and so are a new species.

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Sympatric Speciation

• Many important crops are polyploids. For
  example, the wheat used for bread is an
  allohexaploid (six sets of chromosomes, with two
  sets from each of three different species).

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Sympatric Speciation

• Non-random mating. Reproductive isolation can
  occur when genetic factors enable a subpopulation
  to exploit a resource not used by the parental
  population.

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Sympatric Speciation

• Example North American Apple maggot fly.
  Original habitat was hawthorn trees, but about
  200 years ago some populations colonized apple
  trees.
• Apples mature faster than haws (hawthorn fruit)
  so apple-feeding flies have been selected for
  rapid development.

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Sympatric Speciation

• Apple-feeding flies now temporally isolated
  (isolated in time) from hawthorn-feeding flies.
  Speciation appears well underway.

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Sympatric Speciation

• Lake Victoria cichlids. Lake Victoria about
  12,000 years old but home to more than 500
  species of cichlids (fish).
• There has been rapid speciation and some of it
  appears to have been caused by non-random mating
  in which females choose males based on their
  appearance.

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Sympatric Speciation

• Researchers studied two closely related species
  one which has a blue-tinged back and the other a
  red-tinged back.
• In an aquarium with natural light females mated
  with males of their own species exclusively.
  However, in an aquarium under monochromatic
  orange light (where blue and red could not be
  distinguished), females mated indiscriminately
  and offspring were fertile.

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Sympatric Speciation

• Researchers concluded mate choice by females
  based on coloration is main barrier keeping gene
  pools separated.
• Because fertile young are produced in
  interspecific crosses the speciation probably
  occurred recently.

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Phylogeny and Systematics

• Phylogeny is the evolutionary history of a
  species or group of species.
• Systematics is science of understanding the
  diversity and relatedness of organisms.

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Phylogeny and Systematics

• Traditionally morphological similarities used to
  infer evolutionary relationships.
• More recently, comparisons of DNA, RNA and other
  molecules used to infer relationships molecular
  systematics.

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Phylogeny and Systematics

• Phylogenetic trees are based on common ancestry
  and data from various sources used to construct
  them
• Fossil evidence
• Molecular evidence
• Morphological evidence

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Phylogeny and Systematics

• In constructing phylogenies important to
  distinguish between homologous structures
  (similar due to common descent) and analagous
  structures (similar because of convergent
  evolution).
• Australian sugar glider a marsupial and North
  American flying squirrel a eutherian mammal are
  examples of convergent evolution. Both possess
  gliding membrane, but otherwise only distantly
  related.

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Phylogeny and Systematics

• Analagous structures that have evolved
  independently are called homoplasies.
• Deciding whether structures are homologous or
  analagous requires various types of evidence to
  be assessed.

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Phylogeny and Systematics

• Corroborating similarities in other structures
• Fossil evidence
• Complexity of characters being compared. The
  more points of resemblance there are between two
  structures the less likely it is they evolved
  independently.

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Phylogeny and Systematics

• Evaluating molecular homologies. Comparison of
  DNA sequences usually done using computer
  programs that match up sequences taking into
  account effects of insertions and deletions.

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Phylogeny and Systematics

• Science of systematics dates to Linnaeus in the
  18th century who devised basic systems of
  binomial nomenclature and hierarchical
  classification in use today.
• All organisms have a unique binomial name
• E.g. Humans are Homo sapiens

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Phylogeny and Systematics

• Organisms are classified into hierarchical
  classifications that group closely related
  organisms and progressively include more and more
  organisms.

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Phylogenetic trees

• Branching diagrams called phylogenetic trees
  summarize evolutionary relationships and
  hierarchical classification is represented in
  finer branching of phylogenetic trees.

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Phylogenetic trees

• In a phylogenetic tree the tips of the branches
  specify particular species and the branch points
  represent common ancestors.

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Cladistics and construction of phylogenetic trees

• Cladograms are diagrams that display patterns of
  shared characteristics.
• If shared characteristics are due to common
  ancestry the cladogram forms basis of a
  phylogenetic tree.

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Cladograms

• Within a tree a clade is defined as a group that
  includes an ancestral species and all of its
  descendants.
• Cladistics is analysis of how species may be
  grouped into clades.

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Shared derived characters

• Cladograms are largely constructed using shared
  derived characters.
• These are characteristics that are evolutionary
  novelties, new developments that are unique to a
  particular clade.

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Shared derived characters

• Shared derived characters are unique to the
  clade. For example, for mammals hair is a shared
  derived character

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Shared primitive characters

• Shared primitive characters are characters that
  are shared beyond the taxon we are interested in.
  Among vertebrates the backbone is an example
  because it evolved in ancestor of all
  vertebrates.
• If you go back far enough in time shared
  primitive characters will be shared derived
  characters. Thus, the backbone is a shared
  derived character that distinguishes vertebrates
  from all other animals.

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Constructing a cladogram

• Outgroup comparison is used to begin building a
  cladogram.
• An outgroup is a close relative of the members of
  the ingroup (the various species being studied)
  that provides a basis for comparison with the
  others.

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Constructing a cladogram

• The outgroup in a cladogram is determined using
  data different from that being used to construct
  the cladistic tree.
• The outgroup roots the tree. The outgroup is
  based on the assumption that homologies in the
  outgroup and ingroup are primitive characters.

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Constructing a cladogram

• Having the outgroup for comparison enables
  researchers to focus on those characters derived
  after the separation from the outgroup to figure
  out relationships among species in the ingroup.

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Constructing a cladogram

• Cladogram of various vertebrates leopard, tuna,
  salamander, turtle and lamprey.
• Use lancelet as outgroup (is a chordate, but has
  no backbone).
• Table summarizes data about character traits and
  which organisms possess them.

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Constructing a cladogram

• In the cladogram new characters are marked on the
  tree where they originate and these characters
  are possessed by all subsequent groups.
• The cladogram of vertebrates is a step towards
  constructing a phylogenetic tree, but such a tree
  would need to be based on much more data.
  Unfortunately, additional data and additional
  species make it hard to decide on a best tree.

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Identifying the best trees

• When constructing a phylogenetic tree that
  involves many species there are billions of
  possible ways to arrange a tree.
• We try to build tress that are the most likely.
  Generally these are trees that are the most
  parsimonious (require the fewest evolutionary
  changes) to construct.

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Homology and analogy

• The most parsimonious tree may not always
  correct.
• If analogy versus homology mistakes are made the
  tree will be incorrect.
• Which of the next two trees is the best tree?

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Homology and analogy

• If mammal and bird four-chambered hearts are
  homologous, then tree A is most parsimonious.
• However, lots of data suggest birds and reptiles
  more closely related, so tree B is better tree.
  Four-chambered heart evolved more than once.

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Phylogenetic trees are hypotheses

• Important to remember that phylogenetic trees are
  hypotheses for the evolutionary pathways.
• Trees that we will have most confidence in will
  be supported by multiple lines of evidence (e.g.
  molecular, morphological and fossil evidence).

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Molecular clocks

• Trees of relatedness can be dated by using fossil
  evidence, but also by using molecular clocks.
• Based on observation that some genes appear to
  evolve at fairly constant rates.

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Molecular clocks

• Assumption is that the number of changes in genes
  is proportional to the amount of time since two
  species branched from their common ancestor.
• Molecular clocks are calibrated against the
  fossil record.

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Molecular clocks

• Molecular clocks are not perfect as genes may
  evolve in fits and starts (because of effects of
  selection) and not be very clocklike.

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Molecular clocks

• Some good markers to use for molecular clocks are
  silent mutations (changes in genes that do not
  change the amino acid coded for) because these
  will have no effect on selection. However, these
  are most useful over only relatively short time
  periods.

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Applying a molecular clock HIV

• HIV is descended from viruses found in chimps and
  monkeys (SIV simian immunodeficiency virus).
• To date the time the virus jumped to humans
  scientists have compared current HIV-1 M samples
  to some from tissue samples preserved in 1959.

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Applying a molecular clock HIV

• Samples showed virus has evolved at steady rate
  and by extrapolating back using the molecular
  clock have estimated that HIV-1 M first infected
  humans in the 1930s.