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POB 2 > Lecture 8/9 Evolution of Species, genes, and genomes Natural Selection > Flashcards

Lecture 8/9 Evolution of Species, genes, and genomes Natural Selection Flashcards

1
Q

Comparing sequences and genomes

A

slide 2

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2
Q

A - Evolution of Genes: Key Concepts

A

➢ Human Genome Project and DNA sequencing technology.
➢ Analysis of genomes using Bioinformatics
➢ Comparing the composition of the genomes
➢ Comparing genome sequences

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3
Q

Definitions

A

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

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4
Q

The Human Genome Project - mapping human genome

A

● 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

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5
Q

Sequencing using a whole Genome shotgun approach

A

Cloning and sequencing of fragments of
randomly cut DNA followed by assembly into a
single continuous sequence

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6
Q

Consequences:

A

● 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

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7
Q

NCBI website

A

slide 8

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8
Q

GenBank: NCBI database of sequences

A

● 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

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9
Q

Comparing Genome sizes

A

● 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

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10
Q

Comparing Genome sizes

A

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11
Q

Comparing Genome sizes

A

● 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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12
Q

Compare the chromosomal organizations of different species

A

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13
Q

Compare the chromosomal organizations of different species

A

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14
Q

Comparing Genome sequences: clues to evolution

A

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15
Q

B - Evolution and Natural Selection: Key concepts

A

● 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

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16
Q
  1. Origin of Species
A

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

17
Q

Descent with Modification by Natural Selection

A

slide 18

18
Q

The intellectual context of Darwin’s ideas

A

slide 19

19
Q

Darwin’s Focus on Adaptation: Voyage of Beagle

A

● 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.

slide 20

20
Q

Examples of beak variation in Galápagos finches

A

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.

slide 21

21
Q
  1. Descent with Modification
A

slide 22

22
Q

Artificial Selection, Natural Selection, and Adaptation

A

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.

slide 23

23
Q

Mutation: source of biodiversity

A

● 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

24
Q

Effect of environment: Non Heritable variation

A

● 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.

slide 25

25
Q

Source of Genetic Variation

A

● 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

26
Q

Role of Mutations in evolution

A

slide 27

27
Q

Features of Natural Selection

A

● 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

slide 28

28
Q

Conclusions

A

● 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

29
Q
  1. Scientific evidence
A

a. Direct observations
b. Homology
c. Fossil record
d. Biogeography

slide 30

30
Q

a. Direct observations

A

● 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

slide 31

31
Q

Direct observations

A

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.

slide 32-33

32
Q

b. Homology

A

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.

33
Q

Mammalian forelimbs: homologous structures.

A

slide 35

34
Q

Anatomical similarities in vertebrate embryos

A

slide 36

35
Q

Tree thinking: reflect hypotheses about the relationships

A

slide 37

36
Q

Convergent Evolution

A

● Distantly related organisms can resemble one another
● Independent evolution of similar features in different lineages
● Analagous structures - share similar function, but not common ancestry

slide 38

37
Q

c. The Fossil Record

A

● 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

slide 39

38
Q

The transition to life in the sea

A

slide 40

39
Q

d. Biogeography

A

● 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

POB 2 (25 decks)

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