Starting Day 1 of Scott... Flashcards

Question 1

Q

Science Caveats

Answer

A

Most of what you learn in every class are abstractions

Abstraction:
1. Something that only exists as an idea
2. A simplified, generalized depiction
To Abstract:
To reduce the information content by omitting irrelevant info
EX: Map of Europe, chemical bonds

Species are Abstractions

It’s a map of biological organisms

Species is a unit of classification

Species is a taxonomic construct

Question 2

Q

Before Darwin

Answer

A

Mythology – Adonai/Allah/Ahura Mazda/Jehovah/Marduk/Yahweh etc. made all the organisms in the world perfect and as they are today

Aristotle – Scala Naturae (Scale of Nature)

Carl Linnaeus – “God created, Linnaeus organized.”

Linnean Organization

Question 3

Q

Traditional Darwin Story

Answer

A

Darwin boards the HMS Beagle in 1832 for a five year trip around the world, collecting, and observing
He was greatly impressed by the constantly changing variety of organisms
???
“Evolution!”

Question 4

Q

Darwin’s Finches

Question 5

Q

Darwin’s Influences - Stratigraphy

Sedimentary Rock

Stratum

Answer

A

Stratigraphy: Study of rock layers

Sedimentary and volcanic rock is deposited in layers

These layers can be counted and compared

Sedimentary rock –formed from the deposition of material

Stratum – a layer of sedimentary rock that is internally consistent and distinguishable form other layers

Question 6

Q

Strata

Answer

A

Stratum – a layer of sedimentary rock that is internally consistent and distinguishable form other layers

Question 7

Q

Stratigraphy

Answer

A

Stratigraphy: Study of rock layers

Sedimentary and volcanic rock is deposited in layers

These layers can be counted and compared

Question 8

Q

Darwin’s Influences – Charles Lyell

Answer

A

Leading Geologist of the time and close friend of Darwin

He stated that the mechanisms of change are constant over time

He stated that the earth is very old

Question 9

Q

Darwin’s Influences - Paleontology

Answer

A

Paleontology - the study of fossils

Developed by Charles Cuvier

Cuvier noted that:
Different strata had different fossils
Species appear and disappear
The older the strata the more dissimilar the organisms are to organisms today

Question 10

Q

Darwin’s Influences – Thomas Malthus

Answer

A

An Essay on the Principle of Population (1798)

Populations are kept in check by their food supply

When the food supply is exhausted there is a competition for scarce resources

“In October 1838, that is, fifteen months after I had begun my systematic inquiry, I happened to read for amusement Malthus on Population, and being well prepared to appreciate the struggle for existence which everywhere goes on from long- continued observation of the habits of animals and plants, it at once struck me that under these circumstances favourable variations would tend to be preserved, and unfavourable ones to be destroyed. The results of this would be the formation of a new species. Here, then I had at last got a theory by which to work”.

Charles Darwin, from his autobiography. (1876)

Question 11

Q

Darwin’s Influences - Lamarck

Answer

A

Jean-Baptiste Pierre Antoine de Monet, Chevalier de Lamarck proposed that new species come from old species

He proposed a mechanism involving:

1) use and disuse
2) the inheritance of acquired characteristics

He also coined the word “biology”

Lamarkism: Parts of the body that are used become more developed and parts that aren’t deteriorate

These acquired characteristics are passed on to offspring

Question 12

Q

Lamarckism Today

Answer

A

Epigenetics - the study of changes in gene expression caused by mechanisms other than changes in the DNA sequence

Some epigenetic changes are heritable

Mechanisms for these changes include the methylation of DNA and vertical transmission of small RNAs

Question 13

Q

Darwin’s Influences – Alfred Russel Wallace

Answer

A

Came up with Natural Selection independently

Wrote Darwin about it

Had his work published w/some of Darwin’s work added

Made Darwin hurry up and publish Origin of Species before he was completely scooped

Question 14

Q

Origin of Species by Means of Natural Selection (1859)

Answer

A

Darwin never used the word evolution, instead he used “descent with modification”

Natural Selection is the mechanism that explains evolution

Question 15

Q

Natural Selection

Answer

A

One of the key mechanisms of evolution

The gradual process by which biological traits become either more or less common in a population. This is due to the differential reproduction of the organisms bearing these traits.

Different individuals in a population of organisms have slightly different traits.

These traits affect the fitness of an organism to make copies of itself.

These traits are inherited by subsequent generations of organisms.

Nature selects against organisms that are not fit, and selects for ones that are.

Nature changes over time so traits change over time.

Really long time spans result in the diversity we see today

Question 16

Q

Artificial vs. Natural Selection

Answer

A

Artificial – Man deliberately decides who gets to reproduce through breeding

Natural – Indifferent Nature decides who gets to reproduce and therefore what traits are maintained. A lot of luck is involved.

Question 17

Q

Artificial Selection

Answer

A

Wild mustard/cabbage became; broccoli, brussels sprouts, cabbage, savoy, cauliflower, kale, kohlrabi, and collard

Dog breeding

Question 18

Q

Natural Selection

Answer

A

It’s not about the individual

It’s not about the species or where it’s going in time

It’s mostly about which information encodes for proteins that are useful right now

Survival of the Fittest

Reproduction of the information best at reproducing right now

It’s not about the individual.

It’s not about the species.

Question 19

Q

Theory of Natural Selection

And Evidence for Evolution

Answer

A

Evolution is a fact

Natural selection is the theory that explains evolution

Evidence For Evolution

Direct Observations

Homologies

The Fossil Record

Biogeography

Question 20

Q

Evidence For Evolution : Direct Observations

Answer

A

It has been carefully observed and measured by Scientists.

We can make it happen in a controlled laboratory setting

Evolution under controlled conditions

Evolution is scale invariant – it affects molecules, organisms, ecosystems, etc.

Since bacteria can reproduce quickly, their evolution is easier to observe and measure

Techniques have been developed to evolve organisms and even molecules for desired functions

Question 21

Q

E. coli long term evolution experiment

Answer

A

E. coli long term evolution experiment

Started in 1988 with 12 identical populations of E. Coli

Grow E. Coli in liquid in flasks

Take a little out every day and put into fresh growth media

Take a little out every 75 days and freeze for a frozen fossil record

So far, their cultures have gone through over 56,000 generations

Some adaptations happened in all 12 cultures, some only to some of the cultures

All cultures now grow faster than the initial culture

One culture evolved the ability to consume citrate in the growth media

Question 22

Q

Sexual PCR

Answer

A

The polymerase chain reaction (PCR) is a biochemical technology in molecular biology to amplify a single or a few copies of a piece of DNA across several orders of magnitude, generating thousands to millions of copies of a particular DNA sequence.

A technique used to evolve molecules for specific functions

The DNA that encodes for the molecule is shuffled via PCR

The resulting gene products are screened for the desired function and the winners isolated

Subsequent rounds of shuffling are performed on the winners

Repeat

Question 23

Q

Evidence For Evolution : Fossils

Answer

A

Evidence For Evolution : Fossils

It is extremely rare for an organism to become a fossil

They have to die in just the right conditions to become fossilized

And yet there are so many fossils

This is due to the extreme age of the earth

Question 24

Q

Problems with the Fossil Record

Answer

A

Problems with the Fossil Record

The fossil record is patchy

This makes sweeping generalizations difficult

For example, “What killed the dinosaurs?”

Question 25

Q

Problems with the Fossil Record – Dinosaur Extinction

Answer

A

Problems with the Fossil Record – Dinosaur Extinction

Birds are dinosaurs

There is only one area of the world that has good strata through the proposed extinction event

There are only 2 non-avian dinosaurs in this strata

Nothing killed the dinosaurs, they died out

Question 26

Q

Evidence For Evolution : Homology

Answer

A

Evidence For Evolution : Homology

Related species can have features that are similar but function differently

Homology – similarity resulting from common ancestry

Homologous

“The same organ in different animals under every variety of form and function” – Owen 1834

Traits of organisms that are evolutionarily related

Either it’s homologous or it isn’t. There is not such thing as “highly homologous” or “% homology”

Question 27

Q

Homologous Structures

Question 28

Q

Homology

Question 29

Q

Divergent Evolution

Answer

A

Divergent Evolution

If enough differences accumulate between groups within a population, 2 new distinct populations may form

When 2 groups of organisms are isolated reproductively or subjected to different selection pressures their traits diverge

Gives rise to homologous features

Question 30

Q

Convergent Evolution

Answer

A

Convergent Evolution

The appearance of a similar trait or traits in unrelated organisms

When groups organisms are subjected to the same selection pressure they tend to evolve similar designs

Often gives rise to analogous features

Question 31

Q

Analogous Features

Answer

A

Analagous Features

A trait that appears similar in two unrelated organisms

Not evolutionarily related

Question 32

Q

Evidence For Evolution : Homology

Answer

A

Evidence For Evolution : Homology

Evolution can be viewed as a nested pattern of homologous characteristics

Each group shares the deepest layer but adds it’s homologous features to form it’s own group

This method lends itself to the creation of phylogenetic trees

Question 33

Q

Phylogenetic Trees

Answer

A

Phylogenetic Trees

AKA Evolutionary Trees

Branching diagram depicting the evolutionary relationships among organisms based on their genetic and/or physical characteristics

The organisms inhabiting the tree are implied to have descended from a common ancestor

Question 34

Q

The Tree of Life

Question 35

Q

Evidence For Evolution : Biogeography

Plate Tectonics

Answer

A

Evidence For Evolution : Biogeography

Biogeography – the geographic distribution of species

This distribution is influenced by the movement of land masses

Large areas of the surface of the Earth move slowly

This has been going on for a long time

Question 36

Q

Several Conditions Necessary for Natural Selection to Occur

Answer

A

Variability: Individuals within a population must be different from each other. These differences may involve characteristics such as resistance to cold, susceptibility to disease, photosynthetic efficiency or the ability to attract a mate, to name just a few.
Heritability: Some of the variability between individuals must have a genetic basis. Thus offspring will tend to resemble their parents and have the same traits.
Differential Reproduction. Invidivuals with some traits will leave more descendants than others. This could be either because they survive longer (e.g. faster animals are better at escaping from predators) or because they have a higher reproductive rate (e.g. a bird with more colorful plumage may attract more mates.)

Question 37

Q

Population

Answer

A

Population

A population is a localized group of individuals capable of interbreeding and producing fertile offspring

Question 38

Q

Microevolution & 3 mechanisms that cause it

Answer

A

Microevolution

It is common to make the distinction between micro and macroevolution

This is the same distinction between micro and macroscopic

Microevolution

A change in allele frequencies in a population over generations

“Evolution on it’s smallest scale” according to your textbook

Microevolution

A change is DNA sequences in a population over time

3 mechanisms cause microevolution:
Natural Selection
Genetic Drift
Gene Flow

Question 39

Q

Alleles

Answer

A

Alleles

Alleles are alternative forms of the same gene or same genetic locus

They can be thought of as flavors in abstract ways such as Genetics

In reality, alleles arise from differences in DNA sequence

These differences in DNA sequence are not just single base pair changes, they can result from insertions, deletions, duplications, re-arrangements etc.

Question 40

Q

Genetic Loci

Answer

A

Genetic Loci

The specific location of a gene or DNA sequence or position on a chromosome

Question 41

Q

Genetic Variation

Answer

A

Genetic Variation

Within a population the individual organisms have various differences

These differences are a result of different DNA sequences

The genetic variation among individuals of a population is a result of the difference in nucleotide sequence

Question 42

Q

Gene Pool

Answer

A

Gene Pool

The set of all genes in any population, usually of a particular species

Question 43

Q

Natural Selection and Variation

Answer

A

Natural Selection and Variation

If variation exists within a population, then evolution does not act equally on all the members of that population

Question 44

Q

Discrete Characters

Answer

A

It’s one character or the other with no in between

Like flavors, or handedness and not continuous like height and weight

Trait can be the result of a single gene or genetic locus

Rare

Lead to abstract mathematical modeling

What Mendel focused on to prove his model

Question 45

Q

Variation

Answer

A

Variation

Variation can be discrete or quantitative (continuous)

Question 46

Q

Discrete Variation - Polymorphisms

Answer

A

the occurrence of different forms among the members of a population
two or more clearly different phenotypes exist in the same population

This term is used differently for different types of biology

EX: 1 Hawk - 2 Morphs

Question 47

Q

Quantitative Characters

Answer

A

Quantitative Characters

AKA continuous variation

Like weight and height

Trait can be the result of a multiple genes or genetic loci

Common

Lead to histograms and statistics

Continuous Variation Can Appear Discrete

Question 48

Q

Measuring Genetic Variation

Answer

A

Measuring Genetic Variation

Can measure the variation in genes – average heterozygosity

Can measure the variation in nucleotide sequence – nucleotide variability AKA sequence identity

Question 49

Q

Average Heterozygosity

Answer

A

Average Heterozygosity

The average percentage of loci that are heterozygous

Compare all the loci on one chromosome vs. another

Only works for diploids

Nobody does this anymore

Question 50

Q

Nucleotide Variability

Answer

A

Nucleotide Variability

Compare the DNA sequence between individuals in a population

~1% of the nucleotides are different between 2 fruit flies

~0.1% of the nucleotides are different between 2 humans

Question 51

Q

Geographic Variation

Answer

A

Geographic Variation

Genetic Variation exists not just through time, but space as well

Variations in population exist along spatial axes

Geographic Variation Example

Mice introduced to island in 1400s

Mice populations isolated by mountains

2 different populations today

Different populations have different numbers of chromosomes

This is probably a result of genetic drift

Question 52

Q

Geographic Variation - Clines

Answer

A

Geographic Variation - Clines

Geographic variation can occur as a cline

A cline is a slope or a gradual and continuous change

In biology, a cline is a graded gradient in a trait along a geographic axis

Question 53

Q

Sources of Genetic Variation

Answer

A

Sources of Genetic Variation

Genetic Variation has to happen in the germ line cells of multicellular organisms for it to be passed on

Question 54

Q

Random Sources of Genetic Variation

Answer

A

Random Sources of Genetic Variation

Genetic variation comes from random changes to the DNA sequence from base pair changes, insertions, deletions, duplications, re-arrangements, horizontal gene transfer etc.

Question 55

Q

Directed Sources of Genetic Variation

Answer

A

Directed Sources of Genetic Variation

Organisms have evolved to generate genetic variation through independent assortment, crossing over, random fertilization, etc.

Organisms have evolved to generate genetic variation through base pair changes, insertions, deletions, duplications, re-arrangements, horizontal gene transfer etc.

Question 56

Q

Sources of Genetic Variation – Point Mutations

Answer

A

Sources of Genetic Variation - Point Mutations

A point mutation is the change in one base of a gene

Often harmless due to the prevalence of non-coding regions and the redundancy of the genetic code

Can be harmful as in sickle cell anemia

Question 57

Q

Sources of Genetic Variation – Changing Gene Number or Position

Answer

A

Sources of Genetic Variation - Changing Gene Number or Position

Pieces of DNA in a chromosome can be duplicated, deleted, re-arranged, inverted, or moved to another location.

Chromosomes can be fused or split

Duplicated genes can evolve new functions by further mutation

This is what Eukaryotes do

Question 58

Q

Genetic Variation Sources – Gene Duplication

Answer

A

Genetic Variation Sources – Gene Duplication

Duplicated genes can evolve new functions by further mutation

Duplicated regions can increase genome size, increasing the material for evolution

1 ancestral odor-detecting gene has duplicated into over 1000 in humans

Question 59

Q

Genetic Variation Sources – Rapid Reproduction

Answer

A

Genetic Variation Sources – Rapid Reproduction

Some Prokaryotes can reproduce every 20 minutes

Prokaryotes can also exist at high population densities

This leads to high genetic variation

Question 60

Q

Genetic Variation Sources – Sexual Reproduction

Answer

A

Genetic Variation Sources - Sexual Reproduction

In prokaryotes, new DNA sequences are just one plasma membrane away, but multi-cellular eukaryotes have to incorporate changes into the germ line cells

The random mutation rate is too slow for multi-cellular organisms who reproduce slowly and do not exist at high population densities

Sexual reproduction evolved to overcome these problems

Sexual reproduction re-arranges alleles into new combinations

Sexual organisms rely on recombination of alleles more than mutation to produce genetic variation

Question 61

Q

Genetic Variation Sources – Horizontal Gene Transfer

Answer

A

Genetic Variation Sources – Horizontal Gene Transfer

AKA lateral gene transfer

Horizontal gene transfer (HGT) is the transfer of genes from one organism to another in a manner other than reproduction

There are many mechanisms to do this, and some organisms do it on their own

Horizontal gene transfer drives the microbial world

Question 62

Q

The Gene Pool is Leaky

Answer

A

The Gene Pool is Leaky

Genes from one organism can become part of genome of another organism

Nature has been making recombinant DNA too, a lot, and for a very, very long time

Genetic material can be transmitted vertically and horizontally

Question 63

Q

Genetic Transmission

Answer

A

Genetic Transmission

The transfer of genetic material from parent to offspring during reproduction is called vertical

The transfer of genetic material from one organism to another is called horizontal

Question 64

Q

Evidence for HGT

HGT and The Tree of Life

Answer

A

Evidence for HGT

181 prokaryotic genomes were examined

By their criteria, 80% of the genes had been horizontally transferred

HGT and The Tree of Life

HGT complicates phylogenetic trees, especially the tree of life

Answer 61

A

The Ring of Life

If the early Earth harbored a pool of genes, perhaps this shared pool gave rise to the 3 distinct lineages we observe today

Answer 62

A

Revised “Tree” of Life

Answer 63

A

Hardy Weinberg Equation

Can be used to test whether a population is evolving

Early attempt develop mathematical methods to describe biology

When aren’t populations evolving?

Over short time scales or when looking at single nucleotides

Hardy Weinberg Principle: A population that is not evolving can be described by the HW principle

A population is evolving if it does not meet the criteria of the HW principle

The frequencies of alleles and genotypes in a population remain constant from generation to generation

When gametes contribute to the next generation randomly, allele frequencies will not change in a given population

This population is at Hardy – Weinberg Equilibrium

Answer 64

A

Harvey Weinberg Caveats

The population at HW equilibrium must fulfill these 5 criteria:

No mutations

Random mating

No natural selection

Extremely large population size

No gene flow

Answer 65

A

HW Equillibrium

Populations can be evolving at some loci, while being in Hardy-Weinberg equilibrium at other loci

Answer 66

A

Changing Allele Frequencies

Three major factors alter allele frequencies

1) Natural selection
2) Genetic drift
3) Gene flow

Answer 67

A

Natural Selection and Variation

If variation exists within a population, then evolution does not act equally on all the members of that population

Certain alleles are passed to the next generation in greater proportions due to differential success in reproduction

Answer 68

A

Changing Allele Frequencies - Genetic Drift

Genetic drift is the change in the frequency of an allele in a population due to randomness

The alleles in an offspring are a sample of those from their parents

Whether a given individual survives and reproduces is random

Genetic drift can cause alleles to disappear completely and reduce genetic variation

Answer 69

A

Effects of Genetic Drift

Founder Effect: Occurs when a few individuals become isolated from a larger population

Allele frequencies in the founder population can be different from those in the parent population

Happens to island organisms or cults

Bottleneck Effect: A large reduction in the size of a population due to random events

Certain alleles can be over-represented in the survivors, while others can be absent

Answer 70

A

Genetic Drift in Action

Humans kill almost all of a particular species

Survivors suffer low genetic variability and are less fit

This has happened many times

Answer 71

A

Genetic Drift Summary

Genetic drift is significant in small populations

Genetic drift causes allele frequencies to change at random

Genetic drift can lead to a loss of genetic variation within populations

Genetic drift can cause harmful alleles to become fixed

Answer 72

A

Changing Allele Frequencies - Gene Flow

Gene Flow is the transfer of alleles from one population to another

Alleles can be transferred by reproduction between members of the 2 populations

Alleles can be transferred by the movement of gametes (pollen)

Alleles can be transferred horizontally

Gene flow can reduce (homogenize) genetic variation

Answer 73

A

Genetic Drift and Natural Selection

Genetic drift may be random, but the outcome of natural selection consistently increases the frequencies of alleles that confer a fitness benefit

Natural selection accomplishes this through ecological selection

Answer 74

A

Gene flow can increase fitness

Antibiotic resistance genes can be transferred horizontally between microorganisms of different species

Gene flow can decrease fitness

Island birds can breed with mainland birds

Gene flow decreases the genetic diversity in the island birds

Mainland birds are less adapted to island and are less fit

Gene flow from mainland to island makes island birds less fit

Answer 75

A

Types of Natural Selection

Ecological – natural selection minus sexual selection

Sexual – maximize reproduction through sexual behavior

Answer 76

A

Types of Ecological Selection

Directional – One phenotype is favored causing the population to shift towards that phenotype

Disruptive – extreme phenotypes of a trait are favored, dividing the population into 2 different groups

Stabilizing - genetic diversity of a trait decreases as population stabilizes around one phenotype

Answer 77

A

Types of Ecological Selection

Answer 78

A

Sexual Selection

Organism attracts mates

Organism defeats rivals

Done only by sexual creatures

Used to explain any feature on an organism in the fossil record that doesn’t make ecological sense

Sexual Selection

Can result in, marked differences between the sexes called sexual dimorphism

Answer 79

A

Sexual Selection

Intrasexual - selection within the same sex among individuals for mates of the opposite sex

Intersexual - AKA mate choice, selection of sex partners

Male showiness can increase a male’s chances of attracting a female and decrease his chances of survival

Answer 80

A

The Tree of Life I keep showing is based on nucleic acid sequences

The tree is built by comparing the nucleic acid sequences for all the organisms depicted

Which sequence(s)?

Answer 81

A

Preservation of Genetic Variation

If natural selection is directional and stabilizing, why isn’t genetic variation wiped out?

Neutral variation is variation that doesn’t confer advantages or disadvantages

Other mechanisms exist

Preservation of Genetic Variation - Ploidy

Additional copies of the genome can have less favored alleles that can be hidden from selection

When conditions change, these alleles could be useful

Answer 82

A

Preservation of Genetic Variation – Balancing Selection

Balancing selection occurs when natural selection maintains stable frequencies of two or more forms in a population

Balancing selection includes:
Heterozygote advantage
Frequency-dependent selection

Answer 83

A

Phylogenetics is the study of evolutionary relationships

Phylogeny is the evolutionary history of an organism, organ, people, etc.

Answer 84

A

ALL organisms have ribosomes

There are no other molecules that can substitute for rRNA so they are essential

The rRNA sequences are usually the same within an organism

Answer 85

A

16S/18S rRNA Tree

16S/18S rRNA has a structural role in the ribosome
16S rRNA is part of the prokaryotic ribosome

18S rRNA is part of the eukaryotic ribosome

16S is used to build the prokaryotic part of the tree and 18S is used to build the eukaryotic part

Answer 86

A

16S/18S rRNA

rRNA often has highly conserved sequences that flank its sequence or are within its sequence

Conserved sequences are DNA, RNA, or protein sequences that are similar or identical between organisms

These conserved sequences make it easy to use PCR to amplify rRNA genes from a variety of organisms

In biology, conserved sequences are similar or identical sequences that occur within nucleic acid sequences (such as RNA and DNA sequences), protein sequences, protein structures or polymeric carbohydrates across species (orthologous sequences) or within different molecules produced by the same organism (paralogous sequences). In the case of cross species conservation, this indicates that a particular sequence may have been maintained by evolution despite speciation. The further back up the phylogenetic tree a particular conserved sequence may occur the more highly conserved it is said to be. Since sequence information is normally transmitted from parents to progeny by genes, a conserved sequence implies that there is a conserved gene.

Answer 87

A

Using rRNA Sequences

Get organism or part of organism

Extract DNA

Use PCR to amplify 16S/18S

Use algorithm(s) to build the tree

Answer 88

A

Using Algorithms

Algorithm - A process or set of rules to be followed in calculations or other problem-solving operations, especially by a computer

Different algorithms can be used in phylogenetic analyses, often resulting in different phylogenetic trees

Answer 89

A

Problems with using rRNA in tree building

Only works for extant organisms

Eukaryotic trunk is really long and the deeply branching protist limbs are really long too

Prokaryotes often have many copies of rRNA in their genomes and sometimes they are different

Answer 90

A

Balancing Selection - Heterozygote Advantage

Heterozygote advantage occurs when heterozygotes have a higher fitness than homozygotes

Two or more alleles will be maintained at that locus

The sickle-cell allele causes mutations in hemoglobin but also confers malaria resistance

Answer 91

A

Balancing Selection – Frequency Dependent Selection

In frequency-dependent selection, the fitness of a phenotype decreases if it becomes too common in the population

Selection can favor whichever phenotype is less common in a population

Answer 92

A

Balancing Selection – Frequency Dependent Selection

The surprise left hook may influence the prevalence of left- handed humans

Answer 93

A

Why Natural Selection Cannot Fashion Perfect Organisms

Selection can act only on existing variations

Evolution is limited by historical constraints

Adaptations are often compromises

Chance, natural selection, and the environment interact

Answer 94

A

Selection can only edit existing variations

Natural selection favors the fittest, which may not be the ideal for long term

New alleles do not arise on demand

Answer 95

A

Evolution is Limited by Historical Constraints

Evolution can’t scrap everything and start over from the ground up

Evolution co-opts existing structures and adapts them to new situations

Answer 96

A

Exaptation

An exaptation is when a trait that evolved for one function becomes useful for another

Feathers evolved for heat regulation later became useful for sexual displays and still later became useful for flight

Deinococcus radiodurans evolved DNA repair for desiccation stress but it’s also useful for radiation stress

Answer 97

A

Adaptations are Often Compromises

The flippers of a seal must allow it to walk on land AND swim efficiently

The design of seal flippers is a compromise between these functions

Answer 98

A

Chance, natural selection, and the environment interact

Studying biology is a lot like studying history because both are the result of so many random events

Answer 99

A

Chromosomal crossover (or crossing over) is the exchange of genetic material between homologous chromosomes that results in recombinant chromosomes. It is one of the final phases of genetic recombination, which occurs during prophase I of meiosis (pachytene) in a process called synapsis. Synapsis begins before the synaptonemal complex develops, and is not completed until near the end of prophase I. Crossover usually occurs when matching regions on matching chromosomes break and then reconnect to the other chromosome.

Answer 100

A

Mendel’s Law of Independent Assortment

This law states that allele pairs separate independently during the formation of gametes. Therefore, traits are transmitted to offspring independently of one another.

Independent assortment
Independent assortment of chromosomes generates haploid daughter cells with a combination of maternal and paternal chromosomes. In this example, the offspring can have any of four combinations: ry, RY, rY, or Ry, each leading to a specific phenotype.

Independent assortment describes the combination of maternal and paternal chromosomes that make up the chromosome set in the haploid gamete.

Answer 101

A

Random fertilization

According to random fertilization, any male gamete can combine with any female gamete. Given that there are 2^n different combinations of chromosomes for each gamete, each zygote can have (2^n) x (2^n) or 2^2n combinations of chromosomes.

By affecting the combinations of alleles at different loci in a gamete, chromosomal behavior during meiosis contributes to genetic variation in three ways: an independent assortment of chromosomes, crossing over, and random fertilization of egg and sperm.

Answer 102

A

Genes

Definition: Genes are segments of DNA located on chromosomes. Genes exist in alternative forms called alleles. Alleles determine distinct traits that can be passed on from parents to offspring. The process by which genes are transmitted was discovered by Gregor Mendel and formulated in what is known as Mendel’s law of segregation.

Genes contain the codes for the production of specific proteins. The information contained within DNA is not directly converted to proteins, but must first be transcribed in a process called DNA transcription. This process takes place within the nucleus of our cells. Actual protein production takes place in the cytoplasm of our cells through a process called translation.

Answer 103

A

Conserved Sequence

In biology, conserved sequences are similar or identical sequences that occur within nucleic acid sequences (such as RNA and DNA sequences), protein sequences, protein structures or polymeric carbohydrates across species (orthologous sequences) or within different molecules produced by the same organism (paralogous sequences). In the case of cross species conservation, this indicates that a particular sequence may have been maintained by evolution despite speciation. The further back up the phylogenetic tree a particular conserved sequence may occur the more highly conserved it is said to be. Since sequence information is normally transmitted from parents to progeny by genes, a conserved sequence implies that there is a conserved gene.

Answer 104

A

Anagenesis – the evolution of an entire population that transforms into a new species (gradual evolution)

Cladogenesis – the splitting of a gene pool into 2 or more groups or clades giving rise to at least one new species

Your book doesn’t talk about either one

Your book assumes Cladogenesis

Answer 105

A

Speciation

Speciation is the process by which one species splits into two or more species

It explains the differences and similarities between species

Forms a conceptual bridge between macroevolution and microevolution

Answer 106

A

Micro vs Macroevolution

Microevolution consists of changes in allele frequencies within a population

Macroevolution refers to evolutionary change at or above the species level

Answer 107

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What makes a group a species?

Traditionally, morphology was used to describe species

More recently, biochemistry and physiology were used

Now, nucleotide sequences are the norm in extant organisms

Answer 108

A

The Species Concept

“But Scott, I thought you said species were and abstractions and not really real.”

It depends on which organisms you are looking at and how you define “species”

So yes, they aren’t real, but neither are chemical bonds as we understand them

The Species Concept

It has utility

It allows us to describe some things accurately

Like Newtonian Physics, it works fine for large, slow moving things

Answer 109

A

Approaches to the Species Concept

Biological – reproductive isolation

Morphological – anatomical differences

Ecological – roles in the environment

Phylogenetic – smallest group on organisms sharing a common ancestor as determined by morphology or molecular sequences

Answer 110

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The Biological Species Concept

A species is a group of populations whose members have the potential to interbreed and produce viable, fertile, offspring

A species cannot reproduce with members of other species, which is known as reproductive isolation

Answer 111

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Two “Different” Species

Eastern vs. Western Meadowlarks

One lives in the East US and the other the West

Your book says their songs and other behaviors are different enough to prevent interbreeding in the wild

Ornithologists say their territories overlap in the central US and they hybridize

Answer 112

A

Reproductive Isolation

Gene flow occurs between populations of a species and this keeps the species together

Reproductive isolation stops this gene flow and causes speciation

Reproductive isolation prevents the creation of hybrids that result from mating between species

Answer 113

A

Barriers to Reproduction

Prezygotic barriers prevent mating or fertilization

Postzygotic barriers prevent the zygote from developing into a viable and fertile adult

Answer 114

A

Prezygotic Barriers

Habitat Isolation
Temporal Isolation
Behavioral Isolation
Mechanical Isolation
Gametic Isolation

Answer 115

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Prezygotic Barriers - Habitat Isolation

2 species can share the same geographic location but live in different habitats and thus never meet to mate

Answer 116

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Prezygotic Barriers - Temporal Isolation

Species that are active at certain times of day can’t mate with members of species active at other times of the day

Species that breed at a specific time of day, season, or year cannot mix

Answer 117

A

Prezygotic Barriers - Behavioral Isolation

Behaviors such as courtship rituals that are unique to a species prevent interspecies mating (and intraspecies mating too)

Answer 118

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Prezygotic Barriers - Mechanical Isolation

“Mating is attempted but morphological differences prevent it’s successful completion.”

Answer 119

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Prezygotic Barriers – Gametic Isolation

The sperm and eggs can mix but the sperm can’t fertilize the egg

Answer 120

A

Postzygotic Reproductive Barriers

Reduced Hybrid Viability

Reduced Hybrid Fertility

Hybrid Breakdown

Answer 121

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Postzygotic Barriers - Reduced Hybrid Viability

Genetic incompatibility can abort development of the hybrid or produce a hybrid that is frail

Answer 122

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Postzygotic Barriers - Reduced Hybrid Fertility

Even if the hybrid matures normally, chromosomal differences between the parents can impair meiosis in the hybrid resulting in the hybrid producing abnormal gametes

Answer 123

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Postzygotic Barriers - Hybrid Breakdown

Even if the hybrid matures normally and is fertile, if it breeds with either parent species, or with each other, the resultant offspring are feeble and/or sterile

Answer 124

A

What are these domains?

The rRNA tree is broken into 3 domains:
Archaea, Bacteria, and Eukarya

These domains supersede Kingdom level designations

They supersede Linnaean taxonomy

Answer 125

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Traditional Taxonomic Organization

Before molecular methods, the old Linnaean taxonomic ranking did not include domains

The traditional hierarchy goes: Kingdom, Phyla, Class, Order, Family, Genus, Species

Mnemonic: King Phillip Came Over For Good Sex

Answer 126

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The 3 Domain System

Carl Woese

ALL life on Earth is divided into 3 domains

Introduced by Carl Woese in 1977

Arguably the most important evolutionary scientist since Darwin

Established molecular methods for determining phylogenetic relationsips

Proposed horizontal gene transfer

Proposed the RNA World hypothesis

Did not get a Nobel Prize

Answer 127

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Prokaryotes vs. Eukaryotes

Answer 128

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Prokaryotes:

By definition, prokaryotes do not have membrane bound nuclei

Archaea and Bacteria are prokaryotes

Maybe the first living cells. Maybe

Unicellular and multicellular
Reproduce by binary fission

Transfer DNA between cells

Answer 129

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Eukarya

By definition they have nuclei, but also contain other internal membranes/organelles

Have mitochondria, or had at some point

Have a lack of diversity in cellular metabolism

Unicellular and multicellular
Don’t often transfer DNA between cells

Reproduce cells through mitosis

Have specialized cellular reproduction called meiosis

Answer 130

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Differences in Gene Expression

Prokaryotes have many, many genes organized into operons while this is not as common in Eukaryotes

Eukaryotes genes have many introns while prokaryotes have a few

Answer 131

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Operon

Its a cluster of adjacent genes

They are co-regulated and transcribed together

The genes often perform related functions

The resulting mRNA is referred to as polycistronic (vs. monocistronic)

Answer 132

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Intron

It is sequence within a gene that is removed before translation

Introns are more common in eukaryotes

Answer 133

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In molecular biology and genetics, translation is the process in which cellular ribosomes create proteins. It is part of the process of gene expression. In translation, messenger RNA (mRNA) produced by transcription is decoded by a ribosome complex to produce a specific amino acid chain, or polypeptide, that will later fold into an active protein. In bacteria, translation occurs in the cell’s cytoplasm, where the large and small subunits of the ribosome are located, and bind to the mRNA. In eukaryotes, translation occurs across the membrane of the endoplasmic reticulum in a process called vectorial synthesis. The ribosome facilitates decoding by inducing the binding of tRNAs with complementary anticodon sequences to that of the mRNA. The tRNAs carry specific amino acids that are chained together into a polypeptide as the mRNA passes through and is “read” by the ribosome in a fashion reminiscent to that of a stock ticker and ticker tape.

Answer 134

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DNA Transcription

DNA transcription is a process that involves transcribing genetic information from DNA to RNA. The transcribed DNA message, or RNA transcript, is used to produce proteins. DNA is housed within the nucleus of our cells. It controls cellular activity by coding for the production of proteins. The information in DNA is not directly converted into proteins, but must first be copied into RNA. This ensures that the information contained within the DNA does not become tainted.

Answer 135

A

Prokaryotic and Eukaryotic Gene Organization

Answer 136

A

Bacteria

Live in every environment on Earth

The dominant life form on Earth, in terms of mass and total numbers

Have diverse metabolisms

Drive every nutrient cycle

Prokaryotic pathogens are bacteria

Answer 137

A

Archaea

Originally isolated from extreme environments but found everywhere on Earth

Despite the fact that archeans can live in the human body, no known pathogens exist, yet

Answer 138

A

Extreme Environments

Some environments are physically or geochemically detrimental to most life

Extremes can be temperature, pH, pressure, or salinity

Organisms that thrive in these environments are called extremeophiles

Answer 139

A

Archaea

More closely related to Eukarya than Bacteria

Share a gene pool with Bacteria

Have features in common with both domains, and features unique to themselves

Answer 140

A

They both change frequencies of alleles within a population

Gene Flow is the transfer of alleles from one population to another

It’s the movement of alleles into and out of a gene pool

Gene Flow vs. Speciation

In speciation, one population becomes reproductively isolated and alleles no longer flow between them and another population

In gene flow, the opposite happens and alleles flow between 2 different populations

Answer 141

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Genetic Drift

Genetic drift is the change in the frequency of an allele in a population due to randomness

Genetic drift can cause alleles to disappear completely and reduce genetic variation

Examples: The founder and bottleneck effects

Drifting is a stunt in motor sports

It’s a controlled skid around sharp turns

It still subject to randomness when they crash

The genetic diversity can crash due to genetic drift

Answer 142

A

The allelic frequency of allele A in a population is the fraction of all the alleles in the population’s gene pool that are A. For example, if all the organisms in the population have the genotype Aa, then the frequency of allele A is 0.5 (because half the alleles are A). Note that the allelic frequency is not the fraction of the organisms that have an A allele, or the fraction that have a particular genotype or phenotype.

Answer 143

A

Frequency of A = 1X.1 + .5X.6 + 0X.3 = .4

Frequence of a = 1-.4=.6

Answer 144

A

Genotypic frequency is the fraction of the population that is a particular genotype. For example, if a population is 20 percent AA, 20 percent Aa, and 60 percent aa, the gentypic frequencies are .2AA, .2Aa, and .6aa.

If we cannot assume HW equilibrium, there is no necessary relationship between allelic frequencies.

Answer 145

A

An allele frequency is the fraction of all alleles in the population’s gene pool that are of that allele. For example, if all the organisms in the population have the genotype Aa, then the frequency of allele A is .5.

Answer 146

A

If you have a complete list of genotypic frequencies for apopulation, you can calculate allelic frequencies if the populations are in Hardy-Weinberg equilibrium. However, if those populations are not at HW equilibrium, it is not possible to determine allelic frequencies.

Answer 147

A

A simple Mendelian trait has two alleles, D and d.

If a population is in HW equilibrium and is 49 percent homozygous dominant, what percentage is heterozygous? What are the allelic frequencies in the population?

DD = 49%

49% = dd

Dd = 2%

Allelic frequency of D is .5

Allelic frequency of d is .5

Answer 148

A

If you know allelic frequencies, you can calculate gentypic frequencies if the population is at HW equilibrium, where the frequency of A = p, and the frequencey of a = q, we will always see the following genotypic frequencies:

AA = p^2

Aa = 2pq

aa = q^2

If we cannot assume HW equilibrium, there is no necessary relationship between allelic frequency and gentypic frequencies, and so we cannot determine genotypic frequencies.

Answer 149

A

The field devoted to the classification of organisms

Answer 150

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What ecological conditions might result in the rapid diversification of some lineages?

Rapid diversification occurs oftentimes after an extinction event, and the survivors have access to additional resourcees. Diversification can also occur when a species occupies a new niche, and adapts to the new environment in this niche.

Answer 151

A

In the real world, what factors might increase or decrease the probability of a species going extinct?

A species is more likely to go extinct if it is small and specialized. Generalized species tend to avoid extinction more easily. Also, extinction may be more likely during habitat destruction due to catastrophic weather events. Elevated predation can increase extinction rates as well. For example, predation of the elephants by humans for their ivory nearly drove them to extinction.

Answer 152

A

vestigial structures have lost most if not all of their originial function through evolution. EX: The appendix in humans previously had digestive functions. Also, the ear muscles in humans are vestigial structures that are remnants of the muslces that human’s ancestors utilized to better hear potential predators.

Answer 153

A

cladistics

An approach to systematics in which common ancestry is the primary criterion used to classify organisms

Answer 154

A

parsimony

The most parsimonious tree (which is the most likely) requires the least evolutionary events (molecular changes) to have occurred

Answer 155

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synapomorphy

a synapomorphy is a trait that is shared by two or more taxa and inferred to have been present in their most recent common ancestor, whose own ancestor is inferred to not possess the trait

Answer 156

A

apomorphy

any character that the outgroup lacks. An apomorphy is a “derived,” specialized,” or “advanced” character.

The cladist assumes that the common ancestor of the ingroup and outgroup possessed only ancestral characters, and that they still are prevalent in the outgroup. Thus, any character that the outgroup displays must be a plesiomorphy, and any character that the outgroup lacks must be an apomorphy

Answer 157

A

ingroup

In cladistics, the monophyletic group that includes all taxa of interest to the current study

Answer 158

A

outgroup

a species or group of species from an evolutionary lineage that is known to have diverged before the lineage that includes the species we are studying (the ingroup)

Answer 159

A

systematics

a discipline focused on classifying organisms and determining their evolutionary relationships. Systematists use data from fossils to molecules and genes to infer evolutionary relationships.

Answer 160

A

character state

Characters (heritable traits) are usually described in terms of their states, for example: “hair present” vs. “hair absent,” where “hair” is the character, and “present” and “absent” are its states.

Answer 161

A

plesiomorphy

A plesiomorphy is an ancestral, less specialized, or primitive character. Any character that the outgroup displays must be a plesiomorphy, and any character that the outgroup lacks must be an apomorphy.

Answer 162

A

monophyletic group

A monophyletic group (clade) is one ancestor and all of its descendants. It is defined by at least one Synapomorphy (all gropu members have the synapomorphy or synapomorphies).

Answer 163

A

A paraphyletic group consists of an ancestor and some of its descendants. A paraphyletic group is an incomplete clade, or a grade. It is defined by the absence of at least one character (all group members lack some particular character(s).

Answer 164

A

A polyphyletic group includes two or more taxa (populations of organisms), but not the common ancestor of those taxa. A polyphyletic group is defined by at least one similar character that evolved independently (by convergent or parallel evolution) in each group member. Taxa are placed in a polyphyletic group because they share some superficial similarity, not because they are closely related to one another.

Answer 165

A

Everything alive today has evolved a lot

All living organisms have spent the same time under the hammer of natural selection

They just have evolved to do different things than you

Answer 166

A

Taxonomy

Taxonomy = Naming Things

One of the oldest human endeavors

Being able to agree on a word for something is essential to communication

It is part of the “triumph of man.”

Taxonomy as the basis of language

Animals consume a huge variety of plants

Stone age people used a even larger variety of plants

People needed to be able to remember and talk about the plants and animals they were using

There are a lot of plants!

Answer 167

A

Taxonomy Needs to be Anal

Common names are too varied and things need to be exact!

Specific names are needed for specific things.

Everyone who cares agrees on these names.

Every field does this.

Argot = the special vocabulary and idiom of a particular profession or social group

Answer 168

A

History of Biological Taxonomy

1500 BC Medicinal plants in ancient Egyptian paintings

350BC Aristotle divides invertebrate animals from vertebrate animals

“Insects, jelly fish, and crabs are different from fish, frogs, and humans.”

This system says things are different because of their features or morphology

Answer 169

A

Morphology

Study of the form and structure of organisms and their structural features

Anatomy is the study of the form and structure of the internal features of an organism

Nobody studies the form and structure of just the external features of an organism anymore

Answer 170

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History of Biological Taxonomy

Started by the Greeks and continued by the Romans

Later done by educated rich men in different places

Latin was still their common language

Therefore we use Latin names today
—

15th century long Latin names

Tomato: Solanum caule inermi herbaceo, foliis pinnatis incisis

Or, “solanum with the smooth stem which is herbaceous and has incised pinnate leaves.”

Answer 171

A

Father of Biological Taxonomy

Carl von Linne
(AKA Carolus Linnæus)

1735 Systema Naturæ

“No man has ever transformed
science in the way that I have.”

“Jehovah created,
Linnæus organized.”

Answer 172

A

Systema Naturæ

All matter is in one of 3 kingdoms: animal, vegetable, or mineral

Linnaean Taxonomy:

Binomial Nomenclature

Classification System

Answer 173

A

Binomial Nomenclature

A system of naming organisms by giving them a name composed of two parts, both in Latin

“Latin Name”

The first name is the genus and the second name is the species

Answer 174

A

Classification System

Categorize organisms into groups called taxa

There is a hierarchy to these groups

5 Initial levels: Kingdom Class, Order, Genus, Species

7-8 Level Classification System

Phylum and Family added

Minerals kicked out

Domain slapped on top

Answer 175

A

5 Kingdom System

Answer 176

A

Problems with Linnaean Taxonomy

It’s based on opinion

“This is a taxonomic group because I say so”

Even when rationalized by morphological analyses, it’s still essentially qualitative.

“It lives in the water so it’s a fish.”

It has nothing to do with evolution.

Answer 177

A

Modern Taxonomy

1960: Cladistics

AKA: Phylogenetic Systematics

Cladistics

Categorize organisms into groups called clades

A clade is an ancestor organism and all their descendents

Still based on morphology but now it’s systemized

Grouping organisms is no longer a matter of opinion, there are rules

Now taxonomy includes evolution

Answer 178

A

Cladogram

Answer 179

A

Cladogram

Answer 180

A

Cladogram

A cladogram is a phylogenetic tree formed by using cladistics

Answer 181

A

Rotating Branches

Answer 182

A

Reading a Cladogram

Answer 183

A

Synapomorphy

A derived character (or trait) shared by 2 or more taxa that was present in their most common recent ancestor

Plesiomorphy

A primitive character (or trait) shared by 2 or more taxa

Answer 184

A

Reading a Cladogram

Answer 185

A

Monophyletic Group

An ancestor organism and all its descendants

It is defined by at least one synapomorphy

Polyphyletic Group

Two or more taxa, but not the common ancestor

Can be the result of convergent evolution

Paraphyletic Group

An ancestor organism and some of its descendants

Reptiles is a paraphyletic group if it does not include birds

Mono vs. Poly vs. Paraphyly

Answer 186

A

Molecular Phylogenetics

Instead of looking at the features or morphology look at the DNA sequence

Conceived in the 1960s

Begun in earnest in the 1970s

–

Get the DNA sequence and compare between organisms

This is how it’s done now.

As long as you can get DNA…

Get DNA sequence

Compare the sequence of gene(s)

Make tree based not on physical characteristics, but nucleotide sequence

–

Molecular Phylogenetic tree

Answer 187

A

Phylogenetic Tree vs. Cladogram

The terms phylogeny, evolutionary tree, phylogenetic tree, and cladogram are often used interchangeably

Technically this is incorrect

–

A phylogenetic tree can contain information about evolutionary distance. This information is included in the length of the branches

In a cladogram the branch lengths are arbitrary and have no meaning

Answer 188

A

Phylogenetic Tree Branch Length

The length of a branch in a phylogenetic tree can indicate evolutionary distance

This can be described by time or number of changes

Number of changes can be described by morphological changes or changes in nucleotide sequence

Answer 189

A

Multifurcation vs. Bifurcation

Bifurcation - the division of something into two branches or parts

Multifurcation – the division of something into more than two branches or parts

Cladistics uses bifurcation only

Molecular methods include multifurcation

–

Multifurcation is Acceptable

Answer 190

A

Rooted vs. Unrooted Trees

Phylogenetic Trees can be either rooted or unrooted

A rooted tree assumes a common ancestor

An unrooted tree does not

Answer 191

A

Rooting Trees

Answer 192

A

Rooted Tree

One unique node on the tree is the common ancestor of everything else on the tree

Often trees are rooted by choosing an outgroup

Answer 193

A

Unrooted Tree

Unrooted trees depict the relationships between the members on the tree without assuming a common ancestor

Computational methods often generate unrooted trees, and people pick outgroups to root them

Answer 194

A

How many trees are possible?

If I have 4 groups, 3 unrooted trees are possible

5 species, 15 possible trees

6 species, 105 possible trees

…60 species, 10^70 trees possible!

Answer 195

A

You had 105 trees to chose from in lab

Answer 196

A

How many trees are possible?

Researchers routinely make trees with many groups

They can’t possibly screen all the possible trees for the best tree

They use tricks to reduce the number of possible trees

For example, the most likely tree has the fewest evolutionary events (i.e. parsimony)

Answer 197

A

Parsimony

Parsimony is the adoption of the simplest assumption in the in the interpretation of data

Occham’s razor – principle stating that the hypothesis that has the fewest assumptions is the best

Answer 198

A

Computational Phylogenetics

Traditional phylogenetics uses morphological features to make trees

Molecular phylogenetics uses nucleotide sequence to make trees

Computational phylogenetics uses algorithms to make trees

Answer 199

A

An algorithm is a process or set of rules to be followed in calculations or other problem-solving operations, especially by a computer

Answer 200

A

Computational Phylogenetics

You can use computational phylogentics on morphological and molecular data

When using morphological data, you have to pick and define characters to use to make the tree

When using molecular data, the characters are already defined

Answer 201

A

Using Computational Phylogenetics

There are many different techniques

They can generate many, many different trees
—

What features should be used to construct a tree?

Morphological features are used when molecular data is unavailable

Use features the are homolgous

Answer 202

A

Homologous

Features of organisms that are evolutionarily related

These features can be organs or nucleotide sequences

Either it’s homologous or it isn’t. There is not such thing as “highly homologous” or “% homology”

Homologous Organs

Answer 203

A

Homologous Genes

Two or more genes that are derived from the same ancestral gene

PAX6 is a gene in humans that regulates eye development

Similar genes exist in many, many animals that encode for proteins that also regulate eye development

The most parsimonious explanation is that these genes are homologous

Answer 204

A

Multiple Sequence Alignment

These are proteins that are made up of amino acids!

DNA = Brain or “blue print”

RNA = thoughts

proteins = doing

Answer 205

A

Multiple Sequence Alignment 2

3 or more DNA, RNA, or protein sequences that are aligned usually to indicate evolutionary relationships

It’s a character matrix of sequences

You did character matrices in the cladistics labs

Answer 206

A

Data Matrix in Lab

Answer 207

A

Molecular Data Matrices

Answer 208

A

One Letter Code for Amino Acids

Answer 209

A

Using Computational Phylogenetics

Use homolgous genes and align them

Use alignment to build tree

There are many methods to do this

A popular method is maximum parsimony

Answer 210

A

Building a tree with Maximum Parsimony

Create all possible trees

Choose the tree that has the minimum number changes

Answer 211

A

Feeding

All living things do it

Called –trophy

Both energy and reduced carbon are needed

Answer 212

A

Energy vs. Reduced Carbon

Energy is used to do work

Reduced carbon is used in the synthesis of biological molecules

One food source can be both energy and reduced carbon

Answer 213

A

Naming Organisms Based on Lifestyle

ALL organisms can be grouped by the methods they use to solve their feeding needs

Some organisms can switch methods

–

Needs

All living things need:

Energy - needed for work
Electrons – needed for redox reactions
Reduced Carbon- needed for biosynthesis

The source of electrons is often omitted when naming groups

Answer 214

A

Named by Nutritional Needs Example

Chemoorganoheterotroph

Answer 215

A

Energy Needs

Energy is needed for movement, growth, development, and for chemical reactions

The energy is stored as potential energy in the chemical bonds in nucleotides, carbohydrates, proteins and fats (sort of)

Answer 216

A

Energy source + -troph

Phototrophs get their energy from sunlight

Chemotrophs get their energy from the oxidation of electron donors

Answer 217

A

Reduced Carbon Needs

Reduced carbon is used in the synthesis of biological molecules

Reduced carbon is needed to make all 4 classes of biological molecules

Answer 218

A

Carbon source + -troph

Autotrophs get their energy from CO2

Heterotrophs get their carbon from organic compounds

Answer 219

A

Combining Names

Answer 220

A

Reduced Carbon

CO2 + 4e- + 4H+ → CH2O + H2O

The carbon in CO2 is not biologically available

By reducing it, it becomes available for biosynthetic reactions

Answer 221

A

Fixing Carbon

Organisms take CO2 from the environment and make it into reduced carbon

This process is called fixing carbon

This takes energy

The reduced carbon is used to make biological molecules

Answer 222

A

Redox Reactions

Redox stands for reduction - oxidation

Redox reactions involve the transfer of electrons between atoms

Reduction is the gain of electrons

Oxidation is the loss of electrons

OIL RIG or LEO says GER

Answer 223

A

Electron Needs

Electrons are needed in redox reactions that involve the transfer of energy

The electrons can come from organic or inorganic sources

This distinction is only common amongst the Chemotrophs

Answer 224

A

Electron source + -troph

Organotrophs get their electrons from organic compounds

Lithotrophs get their electrons from inorganic compounds

Answer 225

A

Heterotroph Examples

Chemoorganoheterotrophs – use organic reduced carbon sources for energy, electrons, and biosynthesis

Chemolithoheterotrophs – use reduced inorganic substrate for energy and electrons and eat molecules for biosynthesis

Photoheterotrophs- use light for energy but consume reduced carbon from the environment

Answer 226

A

Chemoorganoheterotrophs

Decomposers

You

Answer 227

A

Chemolithotrophs

They can oxidize minerals such as Sulfur, Iron, Uranium, or even Hydrogen

Answer 228

A

Photoheterotrophs

They use light for energy

They eat fatty acids, sugars, and alcohols

Aphids may have symbiotic photoheterotrophs

Answer 229

A

Autotrophy

“Self feeding”

Primary producers – base of the food web

Harness light or chemical energy in the environment to make cellular energy and make complex organic compounds

Answer 230

A

Types of Autotrophs

Chemoautotrophs – get energy from oxidation of electron donors in their environments

Lithoautotrophs - get energy from reduced compounds of mineral origin

Photoautotrophs – get energy from light

Answer 231

A

Photoautotrophy = Photosynthesis

Use sunlight to get energy

Use CO2 to fix carbon

Answer 232

A

Homologous Genes

The claim than genes are homologous is not verifiable without a time machine

However, the higher the similarity in two sequences the lower the probability that the two sequences originated independently due to chance

This probability can be calculated

Homologous Genes Example

Compare a:
100 nucleotide sequence from organism A
and a
100 nucleotide sequence from organism B

If the sequences are 80% the same the probability that they evolved independently in the last 4 billion years is very, very low

Answer 233

A

Nutritional Modes (Wikipedia)

Answer 234

A

Carbon source + -troph

Autotrophs get their carbon from CO2

Heterotrophs get their carbon from organic compounds

Answer 235

A

2 Names Are Not Enough For Chemotrophs

Chemoheterotrophs and Chemoautotrophs can be further subdivided into 2 more groups depending upon where they get their electrons for electron transport

Answer 236

A

Lithotrophy

Lithos means rock

So they are rock eaters

Rock eaters!

Why are chemolithoautotrophs important?

They don’t rely on sunlight for energy or need to eat photoautotrophs or heterotrophs

They make life on other planets much more likely

Answer 237

A

Chemolithoautotrophs II

Most are bacteria

Most, but not all are extremophiles

Participate in biogeochemical cycling

Found 2 miles below the surface of the earth

Help make soil from rock

Answer 238

A

“Kingdom” Protista

Protists, Protozoans and Protista

The traditional view:

Protists are single celled eukaryotes including protozoans and algae

Protista is a kingdom level taxanomic unit that is composed of protists

Protozoans are unicellular eukaryotic heterotrophs, usually motile

Wastebasket Taxa

Wastebasket taxa are used to classify organisms that do not belong anywhere else

Many eukaryotes are not plants, animals, or fungi, so they were all lumped together in one taxon, protista

Invertebrates is another wastebasket taxon

Answer 239

A

Protists are a paraphyletic group!

Answer 240

A

So what do we call them?

This is still a hotly debated issue

Molecular phylogenetics destroyed many earlier assumptions

Wait a few years for a better view of the organization of this group

Protist/Protozoan is still commonly used

Single celled eukaryotes is also common but technically incorrect as there are many colonial organisms in this group

Eukaryotic microbes or Eukaryotic microorganisms is also used, but incorrect due to microscopic eukaryotic animals

Eukaryotes that aren’t plants, animals, or, fungi is too long

Tissueless Eukaryotes is probably the best term, but not popular because I just made it up

My made up term also depends on the definition of tissues

Answer 241

A

Tissue

A tissue is a group of specialized cells from the same origin performing the same function

Answer 242

A

Tissue in the Multicellular Hierarchy

Tissues are made up of cells
Organs are made up of tissues
Biological systems are made up of organs
An organism is made up of biological systems

Answer 243

A

Tissue in the Multicellular Hierarchy II

Answer 244

A

Protists Don’t Have Tissues

While this group contains colonial organisms, their cells are not differentiated into tissues

Or are they?

Chlamydomonas

Unicellular flagellated “algae”

Swims

Has a chloroplast

Has an eyespot

Answer 245

A

Volvox

Volvox is basically a bunch of Chlamydomonas stuck together

It’s a colonial “alga” with up to 50,000 cells

Their flagella beat together to propel the colony like a tissue

They have specialized reproductive cells

Answer 246

A

Volvox is basically a bunch of Chlamydomonas stuck together

It’s a colonial “alga” with up to 50,000 cells

Their flagella beat together to propel the colony like a tissue

They have specialized reproductive cells

Can reproduce by making daughter colonies or sexually

Has specialized reproductive cells that make sperm and eggs

Some species are diecious

Monoecious (Greek for one household) species are hermaphroditic and contain all sexes

Dioecious species are divided into genders

Even though Di means two, there are many species that have more than one gender

Answer 247

A

Protist Examples - Amoeba

Genus level taxon

No definite shape – moves by pseudopods

10X the genome of humans

Originally thought to be asexual but this view is changing

Answer 248

A

Protist Examples - Euglena

Genus level taxon

Unicellular and flagellated

Can do chemoorganoheterotrophy or photoatutotrophy

Originally thought to be asexual but this view is changing

Answer 249

A

Protist Examples - Paramecia

Genus level taxon

Unicellular and cilliated

Have multiple nuclei

Have sex

Answer 250

A

Deinococcus radiodurans

Most radiation resistant organism known

500-1000 rads will kill a person

Deinococcus can survive 1,500,000 rads

Can survive toxic environments

Can survive desiccation

Doesn’t make spores

Instead of hiding in a spore it can repair its DNA from fragments

Has multiple copies of its genome to serve as templates

DNA repair helps it survive desiccation

Answer 251

A

exaptation

An exaptation is when a trait that evolved for one function becomes useful for another

Feathers evolved for heat regulation later became useful for sexual displays and still later became useful for flight

Deinococcus evolved its DNA repair for desiccation stress but it’s also useful for radiation stress

This means Deinococcus didn’t evolve for space travel, but perhaps could survive it now

Answer 252

A

spores

Made by bacteria, fungi, plants, algae, and protozoans for dispersal

Like a seed but smaller and tougher

Can remain dormant for millions of years

Resistant to radiation

Answer 253

A

bacterial endospores

DNA and protein surrounded by a protein coat

Not a true spore as it’s not produced by reproduction

It’s a place for the bacteria to hide when times are tough

When times are good the spore germinates

Don’t need food

Can survive high temperatures, extreme freezing, ultraviolet radiation, desiccation, and chemical disinfectants

Contains internal proteins that protect DNA from UV damage

Have been isolated from inside rock

Have been germinated after 25-40 million years

Answer 254

A

Endospore Formation

Answer 255

A

Interplanetary Panspermia is Happening Now

The methods exist

The organisms exist

Very hardy forms of life are leaving the Earth and traveling into space

If Panspermia can be interstellar, then life is more prevalent in the Universe

It makes evolution on many worlds easier

However life still had to evolve at least once somewhere

Answer 256

A

Abiogenesis

The study of how life could evolve from inorganic matter

Describes how life could have arose on Earth

Answer 257

A

Elements in Biology

Sulfur
Phosphorus
Oxygen
Nitrogen
Carbon
Hydrogen

SPONCH

The key elements that compose living things.

Answer 258

A

Early Earth

Atmosphere was probably different

There was little oxygen, so the atmosphere was not oxidizing

The early atmosphere was reducing and contained sulfur, oxygen, nitrogen, carbon, and hydrogen

All we need is phosphorus and the atmosphere is SPONCH

Answer 259

A

Urey-Miller Experiment

Recreate the hypothetical early Earth atmosphere

Subject it to artificial lightning

Make amino acids, nucleotide bases, and energy rich hydrocarbons

Make molecules similar to the ones found on Titan

It’s very easy to make adenine

Answer 260

A

ATP: Adenine to Adenosine

Answer 261

A

ATP: Adenosine Triphosphate

Answer 262

A

Adenosine vs. Deoxyadenosine

Answer 263

A

NAD+

Nicotinamide adenine dinucleotide

Found in all living cells

Involved in electron transfer

Used to shuttle electrons from Glycolysis and the citric acid cycle to the electron transport chain

Answer 264

A

Redox and NAD(P)H

Answer 265

A

FAD+

Nicotinamide adenine dinucleotide

Found in all living cells

Involved in electron transfer

Used to shuttle electrons from the citric acid cycle to the electron transport chain

Answer 266

A

Acetyl-CoA

Answer 267

A

Kreb’s Cycle, etc.

Answer 268

A

T/F: Plant cells contain mitochondria

True!

Answer 269

A

T/F: Polymorphisms are a result of discrete variations of traits within a population

True!

Answer 270

A

Photosynthetic organisms are photoautotrophs T/F?

True!

Answer 271

A

Metabolically, eukaryotes are not a very diverse group of organisms: T/F

True!

Answer 272

A

Urey Miller Experiment (Picture)

Recreate the hypothetical early Earth atmosphere

Subject it to artificial lightning

Make amino acids, nucleotide bases, and energy rich hydrocarbons

Make molecules similar to the ones found on Titan

It’s very easy to make adenine

Answer 273

A

RNA World Hypothesis

RNA can store information and catalyze reactions

What if the reaction you are catalyzing makes more of you?

RNA can regulate transcription

RNA can bind substrate and direct transcription

Answer 274

A

Organic Soup Model

The early earth’s reducing atmosphere was exposed to energy through sunlight and lightning

This produced simple organic compounds or monomers

These compounds accumulated and concentrated at various locations and localized sources of energy

By further transformation, more complex organic polymers developed

Answer 275

A

From Molecules to Cells

Phospholipids

Can form structures called coacervates in water, abiotically

Make up the cell membrane

Coacervates

A microscopic sphere of lipid molecules held together by hydrophobic forces from a surrounding liquid

Can form spontaneously

Are selectively permeable

Plasma membrane

Surrounds the cell

Made of a phospholipid bilayer

Selectively permeable

Coacervates (picture)

Answer 276

A

First life on Earth

Only known from fossilized stromatolites 3.5 billion years old

Life probably began earlier

Stromatolites

Microorganism collects sediment and deposits it around itself

After a long time this sediment builds up and forms rock

Can also be produced abiotically

Answer 277

A

Ecological Questions

Who is where?
Study the distribution of organisms or biodiversity
What are they doing?
Study nutrient and energy cycling

Ecology

Ecology is the study of the interaction between organisms and their environment

It’s also study of relationships between organisms

The fact that humans are organisms causes some confusion

Ecology includes abiotic factors like weather, climate, seasonality, and geography

Its complexity lends itself to statistics heavy analyses

Ecological studies often favor holistic approaches rather than traditional reductionism

Answer 278

A

Reductionism is the idea that a complex system is the sum of its parts

Naive reductionism is the belief that reductionism leads to a complete understanding of a phenomenon

Answer 279

A

Holism

Holism is the idea that a complex system should be seen as a whole and not a sum of its parts

Naive holism is the belief that a qualitative and subjective assessment leads to a complete understanding of a phenomenon

Holism is popular now

Holism Example and Reductionist Rebuttal

The Yankee$ have the best players, but don’t always have the best team

A baseball team is more than the sum of it’s players

Reductionists would say you didn’t study enough parts and try to measure things like morale and esprit décor

Answer 280

A

Systems Theory

Systems theory is the interdisciplinary study of systems in general with a focus on the interrelatedness of all phenomena

The goal of systems theory is to elucidate principles that can be applied to all types of systems at all nesting levels in all fields of research

Something that can not be reduced to it’s component parts is called a system

Answer 281

A

Systems Biology

Systems Biology is the study of interactions within biological systems using a more holistic approach

Systems Ecology is interdisciplinary ecology with a holistic approach

Hasn’t ecology always been that way?

Answer 282

A

It must be a real field because it has a journal

Answer 283

A

Nested Levels

From smallest to largest:
atoms, molecules, macromolecules, cells, tissues, organs, organ systems, organisms, populations, communities, ecosystems, biomes, biosphere

Answer 284

A

Nested LEvels 2

From smallest to largest:
atoms, molecules, macromolecules, cells, tissues, organs, organ systems, organisms, populations, communities, ecosystems, biomes, biosphere

Answer 285

A

Nested Levels 3

From smallest to largest:
atoms, molecules, macromolecules, cells, tissues, organs, organ systems, organisms, populations, communities, ecosystems, biomes, biosphere

Answer 286

A

Population

A population is a localized group of individuals capable of interbreeding and producing fertile offspring

Community

A community is all of the organisms that inhabit a particular area

It’s an assemblage of populations of different species that can interact

Answer 287

A

Biome

A biome is one of the worlds major ecosystem types

Terrestrial biomes are classified by predominant vegetation and weather

Aquatic biomes are classified by physical environment

Answer 288

A

Biosphere

The biosphere is the entire portion of earth that is inhabited by life

It is the sum of all biomes

–

How big is the biosphere?

Microbes have been isolated at an elevation of 41 km (25 mi)

Microbes have been isolated from 11km (6.8 mi) deep in the ocean and 5km (3 miles) deep on land

Answer 289

A

Population Ecology

It’s the study of populations in relation to their environment

It’s concerned with the density, distribution, size, and age structure of a population

Answer 290

A

Population Density

It’s the number of individuals per unit of area or volume

Dispersion is the pattern of spacing among individuals within the boundaries of the population

Answer 291

A

Population Dynamics

Population dynamics studies changes in the size and age composition of populations, and the biotic and abiotic processes influencing those changes

It deals with birth and death rates, immigration and emigration, and studies topics such as aging populations or population decline

Answer 292

A

Emigration is leaving a population

Immigration is entering a population

Answer 293

A

Metapopulation

A metapopulation is a number of linked local populations

It’s of a group of spatially separated populations of the same species which interact at some level

It’s a population of populations

Answer 294

A

Population Dynamics

Answer 295

A

Population Ecology Methods

Counting organisms

Estimating the amount of organisms by counting evidence of organisms

Estimate life expectancy of individuals

Estimate reproductive rates

Study demographics of a population

Answer 296

A

Demographics

Demographics are the quantifiable statistics of a population

Demography is the study of the statistics of a population and how they change over time

What statistics are studied depends on who is doing the studying

Demographics are used extensively by marketers, advertisers, politicians, and other parasites

Answer 297

A

community ecology

It’s the study of the interactions between species in communities.

It includes the study of the distribution, structure, abundance, demography, and interactions between coexisting populations

What constitutes a community and the size of it’s territory is open to debate

Answer 298

A

Interactions Between Species

Different species within a community can interact with each other

These interactions are classified by ecologists into competition, predation, symbioses, and facilitation

Interactions Between Species

Competition
Predation
Symbioses
>Parasitism
>Mutualism
>Commensalism
Facilitation

Answer 299

A

Competition

Interspecific competition is when different species compete with each other over finite resources

The species can compete for food, habitat, sunlight, etc.

If 2 species occupy the same niche, one of them is going to die

Answer 300

A

Ecological Niche

An ecological niche is the sum of a species’ use of the biotic and abiotic factors in its environment

It’s a species way of life

It’s analogous to a species’ job

Can be pronounced neesh, nitch or nish

Answer 301

A

Organisms Occupying the Same Niche Can Evolve the Same Traits

Convergent Evolution

Answer 302

A

Ecological Niche Modeling

Its hard to determine where a species is and where it likes to live

Instead, combine the observations of a species with abiotic data (temperature, altitude, rainfall, etc.)

Use an algorithm to build a model of the tolerances of the species and find it’s niche

Answer 303

A

Ecological Niche Modeling II

Answer 304

A

Predation

Predation is when one species eats another species

The predator doesn’t always kill the prey nor always consume the entire living organsim

This includes herbivory, the eating of plants and algae

Predation overlaps with parasitism in the case of parasitoids

Predation and predator defense drive evolution in many organisms

Answer 305

A

Predator Adaptations

Teeth, claws, speed, patience, venom, smell, vision, echolocation, camouflage, social behavior, etc.

Anti-predation Adaptations

Mimicry, camouflage, poison, detachable tails, speed, smell, vision, social behavior, thorns etc.

Answer 306

A

Evolutionary Arms Races

An evolutionary arms race is a fight between competing sets of co-evolving organisms or genes that develop adaptations and counter-adaptations against each other

The war can be fought between predator and prey or parasite and host

Answer 307

A

Co-evolution

Co-evolution is the joint evolution of two interacting species, each in response to selection imposed by the other

It can occur at the species level or the molecular level

It can occur in predator/prey, host/parasite, and mutualistic relationships

Darwin wrote about it

Answer 308

A

Warning Coloration

Anti-predator adaptation

Advertising that the potential prey tastes bad or is poisonous

The coloration can be mimicked by other organisms

Answer 309

A

Mimicry

Mimicry - The similarity of one species to another conferring an evolutionary advantage to one or both species

Camouflage – When a species resembles its surroundings

Can be visual, aural, or olfactory

EX Below (and butterflies!)

Answer 310

A

Interactions Between Species

Competition
Predation
Symbioses
>Parasitism
>Mutualism
>Commensalism
Facilitation

Symbiosis

A symbiosis is an ecological relationship between two different species that live together in direct contact

Symbioses can be bad for one of the species

Types of symbioses are parasitism, mutualism, and commensalism

Answer 311

A

Parasitism

Parasitism is a symbiotic relationship where one organism benefits at the expense of the other

The parasite lives either on (ectoparasite) or inside (endoparasite) of the host and feeds on cell components, tissues, or body fluids

Parasites don’t usually kill the host as this would deprive them of a host

EX: Worms infect 3.8 billion people in the world

Answer 312

A

Parasitoids

A parasitoid lives attached to or within a single host organism in a parasitic relationship, but eventually sterilizes or kills, and sometimes consumes the host

Insects are most famously parasitoids, but other arthropods, prokaryotes, vertebrates, and even plants can be parasitoids

Answer 313

A

Parasitoid Wasp

Answer 314

A

Plants Use Parasitoids for Defense

Answer 315

A

Mutualism is a symbiotic relationship where both organisms benefit

EX Below, and Nemo & Sea anenome

Answer 316

A

A mycorrhiza is a mutualistic association between a fungus and the roots of a vascular plant

95% of plants have mycorriza

Sometimes these associations are pathogenic

Answer 317

A

Commensalism

Commensalism is a symbiotic relationship where one organism benefits and the other is neither harmed nor helped

Some relationships appear commensal but are not when viewed more carefully or are not commensal for all members of the population

Commensalism?

Remora fish hitchhike on larger organisms

Sometimes the remoras clean the larger organism’s teeth (mutualism) sometimes the remoras eat their poop

Sharks have been observed eating remoras attempting to attach onto them

Answer 318

A

Demodex

Demodex is a mite that lives in human hair follicles

Not everybody has them, but most do

They eat your skin cells and oil

They mate, lay eggs, defecate, and die in hair follicles

They crawl out at night

Considered to be a commensal skin organism

Can cause skin problems in some people

May cause acne in some people

Answer 319

A

Lichens

Lichens are a symbiosis between fungi and algae or bacteria

Their associations can be mutualistic, commensal, or parasitic depending on species

Answer 320

A

Endosymbiotic Theory

Endo = within, sym = together, biosis = living

Several eukaryotic organelles were originally free living microorganisms

They now live with Eukaryotes in a symbiotic relationship

Secondary endosymbioses have occurred

Answer 321

A

Facilitation

Facilitation is an interaction where one species has a positive effect on the survival of another species without the intimate association of a symbiosis

Some plants may make it easier for other plants to grow in the area

Answer 322

A

Ecosystem

All of the organisms in a given area and the abiotic factors they interact with

One or more communities and physical environment around them

The biotic and abiotic factors of an ecosystem interact through nutrient cycles and energy flows

Answer 323

A

Ecosystem Ecology

Ecosystem Ecology is the study of energy flow and the cycling of chemicals among the various biotic and abiotic components in an ecosystem

The cycling of nutrients and energy are regulated by physical laws

Answer 324

A

Energy

Energy is the ability to do work

Energy is defined by the laws of thermodynamics

Answer 325

A

First Law of Thermodynamics

Energy can be changed from one form to another, but cannot be created or destroyed. The total energy of a system remains constant.

You can’t win

You can’t get something for nothing

Example: The energy in sunlight is stored in chemical bonds by plants and then released again when we eat them

Answer 326

A

First Law of Thermodynamics in Biology

Answer 327

A

Second Law of Thermodynamics

In all energy conversions, the potential energy of the final state will always be less than the potential energy of the initial state

You can’t break even

There is always an increase in entropy (disorder) when energy is transferred

Example: When a cow eats a plant, only 10% of the energy stored in the plant gets used by the cow

When a human eats a steak, only 10% of the energy stored in the steak gets used by the human

Every time you go up a trophic level, most of the energy is lost as heat

Answer 328

A

Trophic Structure

The trophic structure is the different feeding relationships within an ecosystem which determine the route of energy flow and the pattern of chemical cycling

A trophic level of an organism is it’s position in a food web

Answer 329

A

How Organisms Get Food

Producers – reduce carbon. They are autotrophs

Consumers – eat reduced carbon in the form of living organisms. They are heterotrophs

Decomposers – eat reduced carbon in the form of dead organisms. They are heterotrophs

Answer 330

A

Food Web

A food web demonstrates feeding relationships in an ecosystem

It includes a feeding hierarchy with trophic levels

Energy is lost each time you go up a level due to the 2nd law of thermodynamics

Primary producers consist of 1000 kg of plant material. This is 2-3 bales of hay

Herbivores consist of 100 kg of biomass, about the size of a large male deer

Predators consist of 10 kg of biomass

What a 10kg predator looks like → (puppy!)

Answer 331

A

Food Web II

Answer 332

A

Food Web III

Answer 333

A

Biomagnification

In the food web, predators consume many prey animals

Predators of predators consume many predators

Top predators then represent an accumulation of material from many lower animals

If there are molecules in the environment that are not readily broken down or metabolized, they can reach high concentrations in top predators through biomagnification

Answer 334

A

Rainforest Layers

Answer 335

A

Biomagnification in Your Meal

Also, “Eat this, not this (for SF Bay)

Answer 336

A

Nutrient Cycles

AKA Biogeochemical cycles

Pathway by which an element moves through biology and the environment

Answer 337

A

Water Cycle

Answer 338

A

Carbon Cycle

Answer 339

A

Nitrogen Cycle

Answer 340

A

Sulfur Cycle

Answer 341

A

Lumpers vs. Splitters

Any field that has defined categories can have lumping and splitting tendencies

Lumpers have a holistic view and define groups broadly

Splitters are precise and create new categories to further subdivide groups

–

Lumpers use fewer groups than splitters

The more you care about a field, the more likely you are to be a splitter within that field

Answer 342

A

Terrestrial Biomes (List)

Deserts and xeric shrublands
Tropical and subtropical moist broadleaf forests
Tropical and subtropical dry broadleaf forests
Tropical and subtropical coniferous forests
Temperate broadleaf and mixed forests
Temperate coniferous forests
Boreal forests/taiga
Tropical and subtropical grasslands, savannas, and shrublands
Temperate grasslands, savannas, and shrublands
Flooded grasslands and savannas
Montane grasslands and shrublands
Tundra
Mediterranean forests, woodlands, and scrub or sclerophyll forests
Mangroves

Answer 343

A

Deserts and Xeric Shrublands

Xeric means of, characterized by, or adapted to an extremely dry habitat

This group varies by amount of rainfall but dry conditions and evaporation rule

This group varies by temperature

–

Located around the world

Created by man in some regions through the process of desertification

Have uniquely adapted flora and diverse reptile fauna

Answer 344

A

Tropical and subtropical moist broadleaf forests

This group includes:
Tropical rainforests
Moist deciduous forests
Montane rain forests
Flooded forests

This group is characterized by low temperature variability and high rainfall

–

Dominated by semi-evergreen and evergreen deciduous tree species

High species diversity – half the world’s terrestrial species live here

An estimated 17,000 species disappear from this biome annually due to deforestation

Answer 345

A

Tropical and subtropical dry broadleaf forests

Characterized by moderate temperatures but long dry seasons

Dominated by deciduous trees, many that lose their leaves during the dry season

Loss of leaves in the canopy allows the under canopy and shrub layers to receive more light

Have less diversity than rainforests

Have higher mammalian biomass than rainforests

Answer 346

A

Tropical and subtropical coniferous forests

Characterized by low rainfall and moderate variability in temperature

Populated by diverse groups of conifers whose needles are adapted to low rainfall and variable temperatures

Thick canopy often leaves only ferns and fungi capable of living on the ground

Answer 347

A

Temperate broadleaf and mixed forests

Characterized by variable temperatures and variable rainfall

Includes conifers in the canopy layer

Answer 348

A

Temperate Coniferous Forest

Characterized by warm summers and cool winters and enough rainfall to sustain a forest

Dominated by evergreen conifers

Have the highest levels of biomass of any terrestrial biome

Include temperate rainforests

Answer 349

A

Boreal forests / Taiga

Characterized by low rainfall and cold temperatures

Located in Northern latitudes

Dominated by conifers

World’s largest land biome (29% of the world’s forest cover)

Still has relatively undisturbed large animal migrations

Under threat due to climate change

Answer 350

A

Tropical and subtropical grasslands, savannas and shrublands

Characterized by low rainfall (not enough to sustain a forest) and moderate to warm temperatures

Dominated by grasses with some trees

Home to large mammals

Soon to only exist in natural parks

-

Characterized by low rainfall (not enough to sustain a forest) and moderate temperatures

Dominated by grasses with few trees

Home to large mammals

AKA prairie, which doesn’t exist anymore in the US

Answer 351

A

Flooded grasslands and savannas

AKA swamps

Located tropically or sub-tropically and flooded seasonally or year round

High avian diversity with both resident and migratory birds

Answer 352

A

Montane grasslands and shrublands

Located at high altitude (alpine or subalpine) and above or below the treeline

Plants adapted to cool temperatures and high light

Answer 353

A

Tundra

Treeless cold climate

This group includes:
Artic – polar desert
Antarctic – polar desert
Alpine – above the treeline

Dwarf vegetation and lichens

Answer 354

A

Mediterranean forests, woodlands, and scrub

AKA Chaparral, maquis etc.

Characterized by dry summers and rainy winters

Most plants are fire adapted

Highly distinctive fauna with many endemic plants

Only 5 places in the world are a part of this biome

10% of all plant species in the world are here

40% of the plant speices in US and Canada are here, in an area the size of Maine

Answer 355

A

Mangroves

Waterlogged salty coastal soils in the tropics and subtropics are home to a forest of various mangrove trees

Plants uniquely adapted to temporally flooded, brackish, low oxygen conditions

Protect against storms and tsunamis

50% of this biome is gone compared to 100 years ago

Answer 356

A

Aquatic Biomes

Lakes
Wetlands
Streams and Rivers
Littoral Zone
Pelagic Zone
Coral Reef
Benthic Zone

Answer 357

A

Lakes

Standing body of water that can be large or small

Surrounded by land and localized in a basin

Weak tidal forces

More temporary than an ocean in geologic time scales

The Caspian Sea is a lake

Sensitive to pollution

Answer 358

A

Wetlands

AKA marshes, swamps, bogs, and fens

A wetland is a habitat that is inundated with water at least some of the time and that supports plants adapted to water-saturated soil

Includes mangroves and flooded grasslands and savannas

By 1993, half the worlds wetlands were drained

Answer 359

A

Streams and Rivers

Characterized by flowing water

Upland headwaters tend to be faster, cooler, clearer, and more turbulent while lowland downstream water tend to be slower, warmer, turbid, and less turbulent

Answer 360

A

Littoral Zones

Contains both the intertidal zone and estuary zones

Answer 361

A

Intertidal Zone

Flooded with water twice a day

Has sub-zones depending on amount of flooding. These sub-zones are compressed into narrow bands

Biologically productive despite harsh conditions

Answer 362

A

Estuaries

An estuary is where a freshwater stream or river merges with the ocean

It’s a transition zone with temporal variation in salinity and temperature

Very productive, but very impacted

60% of the world’s population lives here

Answer 363

A

Coral Reef

A coral reef is a warm water tropical ecosystem dominated by the hard skeletal structure secreted by corals. Some also exist in cold and/or deep waters

Disappearing faster than rainforests and could be gone in 100 years

Answer 364

A

Pelagic Zone

AKA The water column

The pelagic zone is the open water component of aquatic biomes

It’s not near the shore or the bottom

Primary producers are phytoplankton

Answer 365

A

Benthic Zone

The benthic zone is the bottom surface of any aquatic environment

Begins at the shoreline and extends down the continental shelf

The deeper regions are dark and nutrients come from detritus raining down from above or thermal vents from below

Answer 366

A

The 6th Great Extinction

There have been great extinctions many times in the history of the world

There is a man made one occurring right now

It’s your fault

Stop it

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