

Bio Midterm #1


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Example of phenotypes??
If you were to grow two plants that had an identical genotype in two different environments, you would get two very different phenotypes. For example, if one had insufficient water, it would be much shorter than the one with sufficient water. In this example, all the differences would have been due to the environment. Organisms such as plants are especially phenotypically plastic. They cannot move to a new environment like a mobile animal could, so to acclimate to environmental differences, they adjust their phenotypes instead
occurs when an allele affects more than one trait
refers to characters, such as leg length, that are controlled by many genes
Post zygotic
after mating, refers to reproductive isolation. Examples include, abortion of embryos, reduced fitness of hybrids, hybrid sterility
before mating, in reference to reproductive isolation. Examples include seasonal and habitat isolation, behavioral isolation, mechanical isolation
Zygotes are diploid cells formed when two gametes (haploid sex cells) fuse. Zygotes are thus diploid and have all the genetic information needed to form a whole organism.
Species are not easy to define simply, as you will learn later in the course. For now, I will give a definition that will seem "fuzzy" to you, but you will understand it better later
Mitosis refers to the process by which chromosomes in a nucleus are replicated before cells divide to make new cells. During replication, the chromosomes must also replicate. The process of mitosis produces daughter cells that are also diploid like the parental cells.
include phenomena such as inversions, duplications and chromosome gains and losses. Inversions and duplications can lead to the formation of new genes.
Monophyletic groups
are those species or groups of species (or populations, depending on the analysis) that have descended from a single common ancestor. On a phylogenetic tree, this is easy to see. All the branches would come from a single common ancestor
Mutations are changes in the genetic material. There are two large classes of mutations: micro mutations which lead to new allele s and macro mutations that lead to new genes or to large changes in chromosomes
Runaway selection
Runaway sexual selection can occur when a female is intrinsically attracted to a trait. If a mutant male arises with this trait, the females will prefer it. The offspring of this mating will inherit both their father's trait and their moth's preference for it. In each generation, the trait becomes more and more exaggerated until natural selection limits it. Example: red preference in Zebra finches
The state of bearing only a single set of chromosomes in the cell (in higher organisms, the haploid state only occurs in the gametes
the physical and biochemical characteristics of an organism. These characteristics have an underlying genetic basis (the genotype), but they can also be modified by the organism's response to the environment that it lives in. Thus the phenotype is usually a combination of "nature" (genes) and nurture (the environment of growth)
Crossing over is also sometimes called??
--First fossil evidence of life, cyanobacteria
from about 3.46 b.y
occur during DNA replication. Point mutations are when a single base is incorrectly substituted into the new DNA chain. Point mutations lead to the formation of new alleles. Frameshift mutations occur when a new base is inserted or deleted. Frame shift mutations can cause many changes and are usually extremely deleterious.
are groups of populations that are infrequently connected by gene flow, or that have been geographically separated and look different, but can still hybridize. It was the existence of many "semispecies" when the strict biological species concept was applied that made many biologists question the validity of the biological species concept and choose a more evolutionary species concept instead. Some examples of "semispecies" are ring species, such as arctic gulls.
see sexual dimorphism
refers to an evolutionary (heritable) change in the rate of developmental timing. For example, differences in dog, wolf, and coyote heads result from when and how fast they grow and when they stop growing.
the condition in which there is allelic variation at a locus. One variant is inherited from the mother, the other from the father. For example, the AB blood type is an example of a heterozygous condition
the condition at a locus where both alleles are the same kind. For example, AA
Operational Sex Ratio (OSR
ratio of sexually active males to sexually active females in a population. When the OSR is male biased, males tend to do little care and are polygamous (as in the example of Elk). When the OSR is about equal, both sexes raise the young and the mating system tends towards monogamy (as in many birds). When the OSR is female biased, the male does most of the young raising and the female is polygamous (as in the Jacana birds).
is the retention of juvenile traits by adults. For example, dog's skulls are broad for their length, they whine, bark and are submissive. Wolves outgrow these traits.
Aspects of an organism's biology that are seasonal and are correlated with climate. For example, bird migration, end of hibernation, start of flowering
is a plant or animal's ability to respond to photoperiods
The evolutionary history of a group is called a phylogeny
phylogenetic tree
is a graphical summary of a phylogenetic history. The tree describes the pattern of relationships among species or populations, and sometimes (depending on the kind of tree) can also show the timing of speciation events. The technique of phylogenetic analysis can be used for classification, but more importantly, it allows us to trace evolutionary history.
Point mutation
The simplest kind of mutation when a single base in a chain of DNA changes. Even a simple base change can have profound physiological consequences. Here, a C substituted for an A and the shape of blood cells changed drastically. The cells on the left are normal and the cells with the mutation are sickled. Sickled cells do not carry oxygen as well as normal cells do and people with the mutation are either chronically anemic (if they inherited only one allele from one parent) or they are likely to die (if they inherited sickling from both parents). However, when malaria is present, people with one sickling allele (the heterozygotes) are not as susceptible to it because the causal agent of malaria, Plasmodium, cannot ride on the deformed cells. Thus this mutation is beneficial when malaria is present, but not when it is absent.
is a common kind of mutation in which chromosomes are present in more copies than the usual two. Polyploidy is important because it can lead to speciation or to the evolution of new functions in the duplicated genes.
Symbiotic origin of mitochondria and chloroplasts from bacteria
at least 1.4 b.y.a
Give an example of polyploidy in how we use it in class
In this class, polyploidy comes up in the discussion of the evolution of domesticated plants. For example, the wheat we eat today is polyploid and was derived from diploid ancestors. Polyploid plants are usually larger than their diploid relatives. One of the consistent things we prefer in our crops is larger and larger size of the edible part. This means that when polyploidy has arisen in our domesticated plants, we have selected these individuals because they are larger and have continued to propagate them
refers to the condition of mating among genetic relatives. It is any circumstance in which the father (sire) and mother (dam) have common ancestors. Inbreeding reduces genetic variation and increases homozygosity, which can lead to the expression of deleterious alleles (i.e. genetic defects). Inbreeding may occur during selective breeding, when we choose to mate relatives, during marriage among relatives, and from self-fertilization. Self fertilization is common in many plants and in a few animals such as snails
Inbreeding Depression
is a decrease in fitness as a result of inbreeding. In inbreeding, genetic diversity and heterozygosity go down because the same allele is passed from one relative to the next. This means that the number of recessives that occur together goes up, and deleterious alleles are exposed to selection. Inbred individuals thus have lower fitness, which is what the term "depression" is referring to: the lower fitness exhibited by inbred individuals. Why are homozygotes at a disadvantage? Many mutations cause a loss of function. If this occurs in a recessive allele, the organism is still okay as in the heterozygous condition, enough protein can still be made. Thus, many deleterious mutations litter the genome of most individuals-they are simply not expressed as the heterozygous condition still functions properly. However, when inbreeding occurs, the alleles present at the same locus are more likely to be identical, and thus these recessive alleles are ere expressed, and selection acts upon them. An example of inbreeding depression is the increased death rate of children born to first cousins
Founder Effect
occurs when one or a few individuals for a new population. When this happens, only a subset of the possible genetic material present in the larger population can possibly be present in the new, small one. The founder effect is a type of genetic drift because gene frequencies changed by chance alone, and not for an adaptive reason.
Haploid (one set of chromosomes present) reproductive cells (such as sperm or eggs) that can fuse with another haploid reproductive cell to form a new diploid cell called a zygote (zygotes thus have all the genetic information required to develop into a whole organism). That is, our sperm and eggs are gametes until they fuse, once they have fused the new diploid cell is a zygote.
The genotype of an organism is the genetic makeup it has inherited. The phenotype or appearance of an organism is controlled partially by its genotype and partially by it's interactions with the environment.
Epigenesis, Epigenetic
these terms refer to developmental processes above the level of individual gene action. All cells have the same genetic information, but cells differentiate because different cells are turned on or off. This leads to new types of cells and to tissue differentiation. I was talking about epigeneisis in terms of why complexity tends to increase over the fossil record. Without epigenetic, developmental differences, all organisms would have just a single cell type. With differences in development we have more variation and more complexity
Hybridization means the sexual crossing of individuals from dissimilar populations. There are different levels of dissimilar when discussing hybrids. The least dissimilar would be varieties of a single species that either through artificial or natural selection have somewhat different gene pools. In these cases, there is usually no barrier to forming a hybrid. For example, if you have a variety of corn that has been selected to have red kernels and you cross it with a variety that has yellow kernels. Note that when you form a hybrid, such as the one I just described, it will have a mixture of the characteristics of both parents (i.e., genes for both red and yellow corn). Thus if you save the seeds from hybrids and plant them, in the next, or F1 generation, some of the progeny will have yellow corn and some will have red corn and some will be mixed. Thus hybrids do not "breed true".
Linkage is the tendency for alleles of different genes to assort together at meiosis. Genes on the same chromosome, for example, are more likely to be inherited together. An example of linkage is that in Dalmatians, a gene that causes a defect in uric acid metabolism, which leads to crystals in the urine and blockage, is linked with the gene that causes the characteristic spots on Dalmatians. Thus, you cannot get Dalmatian coloring without this defect.
a locus is the place on a chromosome where a particular gene resides
This is the reduction cell division that produces haploid gametes (e.g., sperm and eggs) from diploid cells. Meiosis leads to a halving of chromosome numbers. During meiosis genetic recombination also occurs because like chromosomes (one from each parent) exchange parts during a process called crossing over.
crossing over
For example, chromosome one from the mother and chromosome one from the father (and all the other chromosomes) line up with the other part of the pair and exchange parts during crossing over.
Evolutionary Species concept
a species is a group of populations under the same selection pressures. Species form a boundary for the spread of alleles (i.e., there is no or reduced gene flow between species). This means that mutation, selection, and drift operate on each species separately, consequently, different species follow different evolutionary trajectories.
the death of a species (or another taxonomic group, such as an order or family).
Mass extinctions
in which large numbers of species go extinct in a short period of time
Background extinctions
which are slower and more constant. Background extinctions result from natural selection, whereas mass extinctions result from unique, chance events. Background extinctions are based on changes in the fitness of individuals within populations, mass extinctions eliminate individuals regardless of their fitness.
Female choice
one of the mechanisms by which sexual selection operates. The female chooses to mate or not based on some characteristic of the male
The simplest definition of a gene is a segment of DNA that codes for a specific product such as a protein or RNA
Genetic Code:
DNA sequences are a kind of instruction book Each sequence is "read" in sets of triplet bases or codons that are translated through mRNA into an amino acid. Amino acids are linked together form proteins. You can think of the individual bases as the alphabet, the amino acids as the words, and the protein as the sentence in a book of instructions. (You do not need to know all the complicated biochemical details of how DNA is translated into proteins. You just need to understand what I say above).
Diversification of animal phyla near beginning of Cambrian
about 543 m.y.a
Invasion of land by plants in Silurian and lower Devonian
about 400 m.y.a.
Genetic drift
refers to changes in the frequencies of alleles in a population that happen by chance alone (i.e., are not adaptive). There are several ways this can happen (1) When small numbers of individuals form a new population, they carry only a subset of the alleles present in the source population (=founder effect). (2) When a population faces a catastrophic loss of individuals, but those that survived did so by "luck" lone, not for adaptive reasons (this is the so called, bottleneck effect"). (3) when gametes are drawn from the gene pool to make zygotes, it is possible for the allele frequencies to not be exactly as they are in the population at large. Genetic drift results in non-adaptive evolution.
Gene duplication
gene duplication occurs when there is unequal crossing over during meiosis
Gene Pool
The set of all alleles in a population that could be contributed to the next generation.
Geological Timescale:
The geologic timescale is a graphic tool for visualizing and organizing deep time. The time scale is divided into periods that reflect major events. Most of the divisions between them, for example are there because most of the previously found fossils disappeared as a result of mass extinctions. The dates in the timescale have been established through the use of radioactive isotopes of various minerals that decay (undergo spontaneous change) at known rates. Isotope measurements work because once a mineral crystallizes that it forms a closed chemical system and any decay products are produced at a constant rate. Some memorable dates:
Origin of earth between
4.5 and 4.6 b.y.a.
Solid crust
by about 4 b.y.a
Largest mass extinction event (95%) at the end of the Permian
about 251 m.y.a.
The earliest fossil hominids (proto-humans) date from the early Pliocene
about 4.4 m.y.a
Bottleneck effect
this is when the original source population undergoes a tremendous mortality event that a few accidentally (i.e., not by means of any special adaptation) survive. Bottlenecks are a kind of genetic drift-chance changes in gene frequencies.
DNA sequences are a kind of instruction book. Each sequence is "read" in sets of triplet bases or codons. Each codon encodes an amino acid.
Habitat Fragmentation
A habitat has been fragmented when it is subdivided into smaller units that are spatially segregated. Habitats become fragmented through natural causes such as fire, wind (e.g., Hurricane Andrew), volcanoes, and floods. However, most habitat fragmentation that is occurring now is human-caused. Human caused fragmentation occurs from clearings, development, highways and logging. Habitat fragmentation and degradation can lead to changes in population structure and the environment. Small populations are vulnerable to increased inbreeding, demographic problems (such as too few males) and genetic drift, all of which can lead to further declines in population size. As populations get smaller they may also be subject to allele effects, processes that cause the rate of decline to accelerate, leading to a higher probability of population extinction
Antigenic drift
The flu virus evolves in two different ways. Antigenic drift is the normal modification of the flu virus through natural selection (our immune systems do the selecting). The antigenic sites are the most selected. Thus, the flu virus changes all the time and in the process, evades our immune system. The reason it is called antigenic drift is that a phylogeny of flu strains shows a pattern of change in which most strains die out and only one strain, the one newest and most different than those that came before (and thus the hardest for our immune system to evade) starts the next generation. The pattern of change looks like it is "drifting" even though in actuality, the favored strain is the most fit. Antigenic drift creates new flu strains that are not very much different from the one before. They are all clearly related.
Antigenic sites
are the parts of the flu virus that the immune system encounters, recognizes and remembers. Two proteins, hemaglutinin (HA) and neuraminidase (NA) form key antigenic sites on the surface of the virus. They control the influenza virus's ability to attach to a cell.
Antigenic shift:
Antigenic shifts represent more drastic changes of the influenza virus genome. They are probably caused by reassortment (recombination) of different strains of flu within a single host. One of the strains involved in recombination is likely to have originated in a different host species than us (i.e., it "shifted" over from another species). Swine and farmyard birds such as ducks and chickens are likely sources of new antigenic variants. Antigenic shifts create very new strains of the flu that are very different than what came before. Influenzas that originate as a result of antigenic shift are so different that there is virtually no resistance to them, these are thus more virulent strains.. It is thought that antigenic shifts are what created the three major flu pandemic s in the last century in which hundreds of thousands or millions of people died.
refers to the building blocks of DNA and RNA. The bases are: A=adenine, T=thymine, C=cytosine, G=guanine plus U=uracil, which replaces T in RNA
Base pairs:
DNA is usually double-stranded and helical in form (like a twisted ladder) because each base is attached to its complement. A pairs with T, G pairs with C in DNA and U with A and G with C in RNA.
Biological Species Concept
groups of actually or potentially interbreeding natural populations, which are reproductively isolated from other such groups" (Mayr 1963)
candelabra models
of human evolution assume that genetic distances reflect time of divergence from a common ancestor
is the most recent common ancestor of all extant organisms
mutualism) is the term for actions that result in fitness gains for both individuals
Chromosomes contain genes. They are long sequences of double-stranded DNA containing millions of bases. In many organisms, including us, the DNA in chromosomes combines with some proteins to form the rod-like shape you might be familiar with.
Chromosome inversions
chromosome inversions result when during replication a chromosome breaks in two or more places and one or more segments is flipped (inverted) during repair. Genes on inverted chromosomes are more likely to be linked (to be inherited together
Demographic risks
also called demographic stochasticity): small population sizes can lead to demographic problems, such as too few males or females for reproduction.
Deoxyribonucleic acid. The molecule that carries genetic information in its sequence of bases (A=adenine, T=thymine, C=cytosine, G=guanine).
The state in which cells have two sets of chromosomes in the nucleus. Human cells are mostly diploid, the exception being the gametes (sperm and eggs), which are haploid. At fertilization, a haploid sperm fuses with a haploid egg to form the diploid embryo
What does sexual reproduction ensures?
that we each receive a set of chromosomes from each parent. This means that for each gene, we each receive one copy from one parent and one from the other.
refers to the ability of organisms to ecologically and physically adjust to their environment. Some examples for animals include winter fat, hibernation, choosing cooler (or warmer) places to rest, and migration to better places. Plants can produce new leaves in response to environmental factors and can also loose their leaves.
refers to an evolutionary response to an environment that allows better performance in that environment. Natural selection favors those traits that enable an organism to be better suited to the current environment
Allee Effect
Is a decrease in the population rate of increase that occurs when populations are small. It has many causes, for example small plant populations may not be attractive to pollinators and thus may not get pollinated and thus the population will shrink even further. For another example, wild dogs require a certain size pack to bring down prey. If the population is too small, they will go hungry, and the population will continue to decrease in size.
Alternative DNA sequences of the same gene. Each allele is slightly different in its DNA sequence, which means that each allele codes for a slightly different protein structure. However, since the function of the protein remains the same, we consider these different forms to be alternative expressions (alleles) of the same gene.
What is an example of alleles that was used in class?
An example of alleles that was used in class was for the ABO antigens, which are recognized by antibodies and are important in matching blood types for transfusions. There are three alleles: A, B, and O.
Allopatric speciation, sometimes called geographic speciation
has three important elements: physical separation between populations, divergence in mating tactics or habitat use and reproductive isolation. There are two kinds of Allopatric speciation: those initiated by a dispersal event and those called Vicariance, where a physical barrier divides a species range (as in glaciers or new mountains or the ocean widening between once connected continents). An example of speciation via dispersal was the initial colonization and adaptive radiation of fruit flies (Drosophila) in Hawaii. An example of a vicariance speciation event concerned Warblers in North America. The barriers were repeated ice ages.
represents cases in which the individual instigating the action pays a fitness cost and the individual on the receiving end benefits
Amino acids
Amino acids are the building blocks of proteins. The four base "letters" in a DNA sequence are read as a series of triplet codons to form an amino acid. There are 20 basic amino acids that make up the proteins in all living organisms. These are: Ala (alanine), Arg (arginine), Asn (asparagine), Asp (aspartate), Cys (cysteine), Gln (glutamine), Glu (glutamate), Gly (glycine), His (histidine), Ile (isoleucine), Leu (leucine), Lys (lysine), Met (methionine), Phe (phenylalaine), Pro (proline), Ser (serine), Thr (throenine),Trp (tryptophan), Tyr (tyrosine), Val (valine).
Antibodies are proteins produced by white blood cells in response to foreign antigens.
Antigens are proteins or carbohydrates from foreign sources (e.g., someone else's blood type, bacteria, viruses) that are not part of the "self" and that thus stimulate the production of antibodies

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