Lecture 8/9 Evolution of Species, genes, and genomes Natural Selection Flashcards
Comparing sequences and genomes
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A - Evolution of Genes: Key Concepts
➢ Human Genome Project and DNA sequencing technology.
➢ Analysis of genomes using Bioinformatics
➢ Comparing the composition of the genomes
➢ Comparing genome sequences
Definitions
Genomics - study a whole set of genes and their interactions
Bioinformatics - application of computational methods to store an analyze biological data
Reference genome - full sequence that best represents the genome of the species
The Human Genome Project - mapping human genome
● Start 1990 the sequencing of the human genome
● Published in 2006
● Sequenced DNA was pooled from a few individuals
● Scientists reviewed the results and agreed on a
reference genome, a full sequence that best
represents the genome of a species
● Goal - determine the complete nucleotide sequence
of each chromosome
● Techniques:
○ Dideoxy chain termination method
○ Whole-genome shotgun approach
Sequencing using a whole Genome shotgun approach
Cloning and sequencing of fragments of
randomly cut DNA followed by assembly into a
single continuous sequence
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Consequences:
● Centralized Resources to analyze genome Sequences
● The National Library of Medicine (NLM) and
● National Institutes of Health (NIH)
○ National Center for Biotechnology Information (NCBI)
○ Database of sequences is called GenBank
○ BLAST (Basic Local Alignment Search Tool)
● European Molecular Biology Laboratory
● DNA Data Bank of Japan
● BGI in Shenzhen, China
NCBI website
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GenBank: NCBI database of sequences
● 214 million fragments of genomic DNA (366 billion
base pairs) Data from 2019
● Software programs
○ BLAST (Basic Local Alignment Search Tool)
○ compare a DNA sequence with every
sequence in GenBank
○ comparison of protein sequences
○ Protein Data Bank - search any protein
sequence for conserved (commo) stretches of
amino acids (domains) for which a function is
known or suspected
Comparing Genome sizes
● Eukaryotic genomes tend to be larger
● Number of genes is not correlated to genome size
● Vertebrate genomes can produce more than one
polypeptide per gene because of alternative splicing of RNA transcripts
● Humans and other mammals have the lowest gene density
● Multicellular eukaryotes have many introns within
genes and a large amount of noncoding DNA
between genes
Comparing Genome sizes
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Comparing Genome sizes
● Human genome - 98.5% does
not code for proteins, rRNAs, or
tRNAs
● Gene regulatory sequences and
introns account for 5% and 20%,
respectively,
● Noncoding DNA, found between
genes, includes:
○ Pseudogenes, former genes
that have accumulated
mutations and are
nonfunctional
○ Repetitive DNA, present in
multiple copies in the
genome (short tandem
repeat (STR)
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Compare the chromosomal organizations of different species
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Compare the chromosomal organizations of different species
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Comparing Genome sequences: clues to evolution
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B - Evolution and Natural Selection: Key concepts
● Compare Darwin’s concept of descent with
modification to the prevailing ideas of his time.
● Explain how, over time, natural selection results in
organisms’ adaptation to their environment.
● Use examples to show how evolution is supported by scientific evidence
- Origin of Species
Charles Darwin published on the Origin of
Species by Means of Natural Selection in 1859
Darwinism
Two main points:
1. Species showed evidence of “descent with
modification” from common ancestors
2. Natural selection is the mechanism behind
“descent with modification”
Darwin’s theory explained the duality of
unity and diversity
Descent with Modification by Natural Selection
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The intellectual context of Darwin’s ideas
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Darwin’s Focus on Adaptation: Voyage of Beagle
● Darwin observed many examples of adaptations : inherited characteristics of
organisms that enhance their survival and reproduction in specific
environments
● How do adaptations arise?Natural selection, a process in which individuals
that have certain inherited traits tend to survive and reproduce at higher rates
than do other individuals because of those traits.
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Examples of beak variation in Galápagos finches
The Galápagos Islands are home to more than a dozen species of closely related
finches, some found only on a single island. A striking difference among them is
their beaks, which are adapted for specific diets.
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- Descent with Modification
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Artificial Selection, Natural Selection, and Adaptation
Darwin proposed the mechanism of natural selection to explain the observable patterns of evolution: process in which individuals with certain inherited traits tend to survive and
reproduce at higher rates because of those traits
● Artificial selection - selective breeding of domesticated plants and animals
● Natural selection - similar process occurs in nature
○ Variation in a population - Members of a population often vary in their inherited traits
○ Overproduction of offspring - All species can produce more offspring than their environment can
support (Figure 22.11), and many of these offspring fail to survive and reproduce.
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Mutation: source of biodiversity
● A change in the environment favors a mutation that had previously been
neutral or even somewhat harmful
● Through natural selection, a beneficial mutation tends to increase in
frequency in a population over generations
● Mutations are the source of Earth’s staggering biodiversity
● How much do genes and other DNA sequences vary from one individual
to another?
● Genetic variation at the whole-gene level (gene variability) can be
quantified as the average percentage of loci that are heterozygous
Effect of environment: Non Heritable variation
● Some phenotypic variation does not result from genetic differences
among individuals
● These caterpillars of the moth Nemoria arizonaria owe their different
appearances to chemicals in their diets, not to differences in their
genotypes.
a. Caterpillars raised on a diet of oak flowers resemble the flowers,
b. their siblings raised on oak leaves resemble oak twigs.
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Source of Genetic Variation
● Morphological, physiological, and behavioral traits with a heritable basis
● Variations within a population arise from different alleles of shared
genes
○ Dimorphic: a trait with only two forms
○ Polymorphic: traits with more than two distinct forms
Role of Mutations in evolution
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Features of Natural Selection
● Natural selection is a process in which individuals that have certain
heritable traits survive and reproduce at a higher rate than do other
individuals because of those traits.
● Natural selection can increase the frequency of adaptations that are
favorable in a given environment
● If an environment changes, or if individuals move to a new environment,
natural selection may result in adaptation to these new conditions,
sometimes giving rise to new species
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Conclusions
● Individuals do not evolve;
● Populations evolves over time
● Natural selection can only increase or
decrease heritable traits that are variable in
a population
● The environment varies from place to place
and over time;
● Favorable traits vary with the environment
- Scientific evidence
a. Direct observations
b. Homology
c. Fossil record
d. Biogeography
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a. Direct observations
● Response to Introduced Species
● What happens when herbivores switch to a new food source with
different characteristics?
● Study of soapberry bugs: use their “beak”—a hollow, needlelike
mouthpart—to feed on seeds located within the fruits of various
plants
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Direct observations
Evolution of Drug-Resistant Bacteria
● ongoing natural selection
● bacteria and viruses because they can produce new generations
in a short period of time
● resistant strains of these pathogens can proliferate very quickly.
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b. Homology
Analyzing similarities among different organisms
● evolution is a process of descent with modification
● Characteristics present in an ancestral organism are altered over
time
● Result: related species can have characteristics that have an
underlying similarity yet function differently
● Homology = Similarity resulting from common ancestry
● homologous features share common ancestry, but not
necessarily similar function.
Mammalian forelimbs: homologous structures.
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Anatomical similarities in vertebrate embryos
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Tree thinking: reflect hypotheses about the relationships
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Convergent Evolution
● Distantly related organisms can resemble one another
● Independent evolution of similar features in different lineages
● Analagous structures - share similar function, but not common ancestry
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c. The Fossil Record
● Documents the pattern of evolution,
● Shows that past organisms differed from present-day organisms
● Shows that many species have become extinct
● Shed light on the origins of new groups of organisms
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The transition to life in the sea
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d. Biogeography
● Scientific study of the geographic distributions of species
● Influenced by many factors, including continental drift, the slow movement of Earth’s continents over time.
Evolution also explains biogeographic data.
For example, a group of three species of
freshwater fish in the family Galaxiidae are
found in regions separated by wide
stretches of open ocean
