Evolution - AP biology

Number of Genes

-Free-living bacteria and archaea have 1,500 to 7,500 genes -Unicellular fungi have about 5,000 genes and multicellular eukaryotes up to at least 40,000 genes

Multicellular eukaryotes have a lot of noncoding DNA and many multigene families

-Sequencing of the human genome revealed that 98.5% does not code for proteins, rRNAs, or tRNAs -Gene regulatory sequences and introns account for 5% and 20%, respectively, of the human genome

Eukaryotic transposable elements are of two types:

-Transposons move by means of a DNA intermediate and require a transposase enzyme --Transposon is copied from DNA of genome into a mobile copy of transposon and inserted into the DNA of genome as a new copy of transposon -Retrotransposons move by means of an RNA intermediate using a reverse transcriptase --Movement begins with the synthesis of a single stranded RNA intermediate. Reverse transcriptase synthesizes the first DNA strand and then the second strand is synthesized, creating a mobile copy of retrotransposon. It is inserted into the DNA As a new copy of retrotransposon

whole-genome shotgun approach

1. Cut the DNA from many copies of an entire chromosome into overlapping fragments short enough for sequencing 2. Clone the fragments in plasmids or other vectors 3. Sequence each fragment 4. Order the sequences into one overall sequence with computer software

Effects of Genetic Drift

1. Genetic drift (GD) is significant in small populations 2. GD can cause allele frequencies to change at random 3. GD can lead to a loss of genetic variation within populations 4. GD can cause harmful alleles to become fixed Each of the effects above are more likely when the population size is small.

What are three key features of natural selection?

1. Natural selection is a process in which individuals that have certain heritable traits survive and reproduce at a higher rate than do other individuals because of those traits 2. Over time natural selection can increase the frequency of adaptations that are favorable in a given environment 3. If an environment changes, or if individuals move to a new environment, natural selection may result in adaptation to these new conditions, sometimes giving rise to new species -Individuals do not evolve; it is the population that evolves over time -Natural selection can only increase or decrease heritable traits that are variable in a population

Darwin's observations that drive changes in species over time

1. Variations in traits exist. 2. These variations (traits) are heritable. 3. Species overproduce. 4. There is competition for resources; not all offspring survive. Observation #1: Members of a population often vary in their inherited traits Observation #2: All species can produce more offspring than the environment can support, and many of these offspring fail to survive and reproduce

Do antibiotics cause bacteria to become resistant? Explain your response.

A drug does not create resistant pathogens; it selects for resistant individuals that are already present in the population.

homeobox

A homeobox is a 180 nucleotide sequence that codes for a 60 amino acid homeodomain in the encoded proteins. -Homeotic genes in Drosophila melanogaster encode genes (homeobox) that specify identity of body segments of the fly -An identical or very similar nucleotide sequence has been discovered in the homeotic genes of both vertebrates and invertebrates

What is the function of a gene (FOXP2) that may be involved in language acquisition?

A number of genes are apparently evolving faster in the human than in the chimpanzee or mouse. Among them are genes involved in defense against malaria and tuberculosis and one that regulates brain size The FOXP2 gene shows evidence of rapid change in the human lineage compared to other primates. The gene may be related to human speech; there are two amino acids found only in the human protein sequence -DNA sequences from both species encode the same two amino acids (in the FOXP2 gene) so these are not human-specific -Further research shows no evidence for selection for these two amino acids in the human lineage during the time frame relevant to language acquisition. However, several lines of evidence suggest that FOXP2 regulates genes that function in vocalization in vertebrates

natural selection

A process in which individuals that have certain inherited traits tend to survive and reproduce at higher rates than do other individuals because of those traits.

gene annotation

A process that uses three lines of evidence to identify a gene. Scientists aim to identify all protein coding genes in the sequence and ultimately their functions. -First computers search for patterns that indicate the presence of genes. This includes translational start and stop signals, RNA splicing sites and other signs, such as promoter sequences and mRNA -The second step is to obtain clues about the identities and functions. Software is used to compare the sequence of a protein to the products of known genes from other organisms. -The final step is to use RNA-seq or some other method to show that the relevant RNA is actually expressed from the proposed gene

hybrid zones

A region in which members of different species meet and mate, producing at least some offspring of mixed ancestry. -three possible outcomes over time for the populations involved in creating a hybrid zone: Reinforcement of barriers, fusion of species, or stability

adaptations

Adaptations are inherited characteristics of organisms that enhance their survival and reproduction in specific environments. -Darwin perceived that new species could arise from ancestral forms through gradual accumulation of adaptations -Darwin proposed natural selection as an explanation for adaptation

21. What is genomics? How does bioinformatics support genomic research?

An approach where, upon sequencing the genome of any species, scientists can study whole sets of genes and their interactions. The necessity of dealing with this ever-increasing flood of information has energized the field of bioinformatics, the application of computational methods to store and analyze biological data. -Scientists use bioinformatics to analyze genomes and their functions reference genome: a full sequence that best represents the genome of a species

autopolyploidy

An individual that has more than two chromosomes that are all derived from a single species is an autopolyploid. A tetraploid can produce fertile tetraploid offspring by self-pollinating or by mating with other tetraploids. In addition, the tetraploids are reproductively isolated from 2n plants of the original population because the triploid offspring of such unions have reduced fertility. Thus, in just one generation, autopolyploidy can generate reproductive isolation without any geographic separation.

How might a human gene microarray chip be of medical importance in cancer treatment?

Analyzing which genes are overexpressed or underexpressed in a particular cancer allows physicians to tailor patients' treatment to their unique genetic makeup and the specifics of their cancers. This approach has been used to characterize subsets of particular cancers, enabling more refined treatments.

Comparing Genomes Within a Species

As a species, humans have only existed for about 200,000 years and have low within-species genetic variation -Copy-number variants, SNPs, and other polymorphisms are useful genetic markers for studying human evolution -These variations are likely to play a role in complex diseases and disorders

Genetic variation levels

At the gene level, genetic variation is quantified by the percentage of heterozygous loci in a population At the molecular level, genetic variation is quantified by comparing the nucleotide sequences of two or more individuals Nucleotide variability rarely results in phenotypic variation -Most nucleotide differences occur within noncoding DNA segments (introns) -Variations in coding regions (exons) rarely change the amino acid sequence of the encoded protein -Phenotypic variation can result from environmental influences, as well as genetic differences. Only the genetically determined part of phenotypic variation can have evolutionary consequences

Balancing Selection

Balancing selection preserves variation at some loci by maintaining stable frequencies of two or more phenotypes Balancing selection includes: -Frequency-dependent selection: the fitness of a phenotype depends on how common it is in a population --For example, frequency-dependent selection results in approximately equal numbers of "right-mouthed" and "left-mouthed" scale-eating fish --Prey maintain both phenotypes by altering their behavior to defend against whichever is most common -Heterozygote advantage: If individuals who are heterozygous at a particular locus have greater fitness than do both kinds of homozygotes, they exhibit heterozygote advantage. In such a case, natural selection tends to maintain two or more alleles at that locus. --Natural selection will tend to maintain two or more alleles at that locus. For example, the deleterious sickle-cell allele is maintained at relatively high frequencies in some regions due to heterozygote advantage

Why is the amount of DNA variation among humans small compared to many other species?

Because the history of the human species is so short

metagenomics

DNA from an entire community of species (a metagenome) is collected from an environmental sample and sequenced -It can sequence the DNA of mixed microbial populations, which eliminates the need to culture each species separately in a lab.

history of life

Darwin viewed the history of life as a tree, with multiple branchings from a common trunk -Labeled branches represent groups of organisms living in the present day -Unlabeled branches represent extinct groups -A fork represents the most recent common ancestor of all lines of evolution branching from that point Large morphological gaps between related groups are explained by branching and extinction events -For example, living elephant species are similar because they split from a recent common ancestor

@ Descent with modification

Descent with modification by natural selection explains three broad observations: -The unity of life -The diversity of life -The ways organisms are suited to life in their environments By this view, all organisms are related by descent from a common ancestor that lived in the past. -Related organisms living in different habitats gradually accumulated diverse modifications to fit them to specific ways of life

Altering Gene Number or Position

Duplication of small segments of DNA, including genes, is a key potential source of genetic variation. Gene duplication occurs through errors in meiosis, slippage during DNA replication, or the activities of transposable elements. -If duplicated genes persist over generations, then mutations can accumulate, and new functions may arise -Increases in gene number likely played a major role in evolution

Tree thinking: information provided in an evolutionary tree

Each branch point represents the common ancestor of the two lineages diverging from that point. A hatch mark represents a homologous characteristic shared by all the groups to the right of the mark. -mammals and birds share a more recent common ancestor than do mammals and amphibians -homologies that evolved more recently are shared only within smaller groups -Evolutionary trees are diagrams that reflect hypotheses about the relationships among groups -Relatedness is determined by the recent common ancestor, not the proximity of groups on the tree -Evolutionary trees are made using many different data sets, including both anatomical and DNA sequence data

Biogeography

Evidence from biogeography, the scientific study of the geographic distribution of species, provides support for evolution. -Species distributions are influenced by continental drift, the gradual movement of Earth's landmasses -Understanding continental drift and modern species distribution helps predict when and where different groups evolved

What is evo-devo, and how does it relate to understanding the evolution of genomes?

Evo-devo is evolutionary developmental biology, which compares developmental processes of different multicellular organisms. With the advent of molecular techniques and the recent flood of genomic information, we are beginning to realize that the genomes of related species with strikingly different forms may have only minor differences in gene sequence or gene regulation. Discovering the molecular basis of these differences in turn help us understand the origins of the myriad diverse forms that cohabit this planet, thus informing our study of the evolution of life.

exon shuffling

Exon shuffling is the occasional mixing and matching of different exons (which often codes for a protein domain) either within a gene or between two different (nonallelic) genes owing to errors in meiotic recombinations -Errors in meiosis can result in an exon being duplicated on one chromosome and deleted from the homologous chromosome

S. aureus and soapberry bugs provide examples that highlight three key points about natural selection. Explain the three key ideas.

First, natural selection is a process of editing, not a creative mechanism. Second, in species that product new generations in short periods of time, evolution by natural selection can occur rapidly - in just a few years or decades. Third, natural selection depends on time and place. It favors those characteristics in a genetically variable population that provide an advantage in the current, local environment. -Natural selection does not create new traits; it selects for traits already present in the population

Gene Flow

Gene flow consists of the movement of alleles among populations and tends to reduce variation among populations over time Gene flow affects adaptation to local environments and can increase a population's fitness

Gene Pools and Allele Frequencies

Gene pool: All copies of every type of allele at every locus in all members of the population Fixed allele: All individuals are homozygous for that allele Geographically isolated populations rarely exchange genetic material If populations are not isolated, individuals still usually only breed with members of their own population

Sources of Genetic Variation

Genetic variation originates when new genes and alleles arise by mutation, gene duplication, or other processes. Sexual reproduction can produce genetic variation by recombining existing alleles

Genetic variation makes evolution possible

Genetic variation refers to the differences in genes or other DNA sequences among individuals, is a prerequisite for evolution by natural selection. One or more factors that cause evolution must be at work for a population to evolve. Natural selection can only act on variation with a genetic component

Evolution of Genes with Related Functions: The Human Globin Genes

Globin genes all evolved from a common ancestor globin gene that underwent duplication and divergence into the alpha globin and beta globin ancestral genes. Each of these genes was later duplicated several times, and the copies then diverged from each other in sequence, yielding the current family members. After the duplication events, the differences between the globin families arose from mutations that accumulated in the gene copies over many generations. -Subsequent duplications of these genes and random mutations gave rise to the present globin genes, which code for oxygen-binding proteins -The similarity in the amino acid sequences of the various globin proteins supports this model of gene duplication and mutation

Homeotic genes

Homeotic genes in animals are called Hox genes -The homeodomain is the part of the protein that binds to the DNA, where the protein functions as a transcription factor In addition to homeotic genes, many other developmental genes are highly conserved from species to species. Sometimes small changes in regulatory sequences of certain genes lead to major changes in body form -For example, variation in Hox gene expression controls variation in leg-bearing segments of crustaceans and insects -In other cases, genes with conserved sequences play different roles in different species

Explain how polyploidy could facilitate the evolution of genes.

In a polyploid organism, one set of genes can provide essential functions for the organism. The genes in one or more extra sets can diverge by accumulating mutations; these variations may persist if the organism carrying them survives and reproduces. In this way, genes with novel functions can evolve. As long as one copy of an essential gene is expressed, the divergence of another copy can lead to its encoded protein acting in a novel way, thereby changing the organism's phenotype. The outcome of this accumulation of mutations may eventually be the branching off of a new species.

Compare the DNA in bacterial genomes to the DNA in eukaryotic genomes with reference to function of the DNA, introns, length of genes, and nonprotein-coding DNA.

In all bacterial genomes studied so far, most of the DNA consists of genes for protein, tRNA, or rRNA; the small amount remaining consists mainly of non transcribed regulatory sequences, such as promoters. The sequence of nucleotides along a bacterial protein coding gene is not interrupted by introns. In eukaryotic genomes, most of the DNA either encodes protein nor is transcribed into RNA molecules of known function, and the DNA includes more complex regulatory sequences. In addition to introns, multicellular eukaryotes have a vast amount of non protein coding DNA between genes.

Sequences Related to Transposable Elements

In humans and other primates, a large portion of transposable element-related DNA consists of a family of similar sequences called Alu elements -Many Alu elements are transcribed into RNA molecules; some are thought to help regulate gene expression -The human genome also contains many sequences of a type of retrotransposon called LINE-1 (L1), which have a low rate of transposition and may affect chromatin structure

Hardy Weinberg equilibrium

In real populations, allele and genotype frequencies often do change over time. Such changes occur when one or more of the conditions for Hardy-Weinberg equilibrium are not met Conditions for equilibrium: 1. No mutations:The gene pool is modified if mutations occur or if entire genes are deleted or duplicated 2. Random mating: If individuals mate within a subset of the population, such as near neighborhoods or close relatives, random mixing of gametes does not occur and genotype frequencies change 3. No natural selection: Allele frequencies change when individuals with different genotypes show consistent differences in their survival or reproductive success. 4. Extremely large population size: In small populations, allele frequencies fluctuate by change over time (genetic drift) 5. No gene flow: By moving alleles into or out of populations, gene flow can alter allele frequencies

What Is Theoretical About Darwin's View of Life?

In science, a theory accounts for many observations and data, and attempts to explain and integrate a great variety of phenomena

How do prokaryotic genomes of the two domains Bacteria and Archaea compare to eukaryotic genomes?

In the completely sequenced group, about 137,500 are genomes of bacteria, and 1,200 are archaeal genomes. -Genomes of most bacteria and archaea range from 1 to 6 million base pairs (Mb) -Eukaryotic genomes tend to be larger -Most plants and animals have genomes greater than 100 Mb; humans have 3,000 Mb -Within each domain, there is no systematic relationship between genome size and phenotype and Number of genes is not correlated to genome size

@ From these observations, what two inferences did Darwin make?

Inference #1: Individuals with inherited traits that increase survival and reproduction in an environment tend to produce more offspring than other individuals Inference #2: The unequal ability of individuals to survive and reproduce will lead to the accumulation of favorable traits in the population over generations

Lamarck's Hypothesis of Evolution

Jean-Baptiste de Lamarck (1744-1829) proposed two principles to explain evolutionary change -Use and disuse: body parts used extensively become larger and stronger, unused parts deteriorate -Inheritance of acquired characteristics: modifications acquired in one's lifetime can be passed to offspring This mechanism is NOT supported by experimental evidence -Lamarck thought that evolution happens because organisms have an innate drive to become more complex. However, experiments and our understanding of genetics refutes this mechanism.

Alterations of Chromosome Structure

Large blocks of genes on human chromosome 16 are found on four mouse chromosomes. This indicates that the genes in each block (7, 8, 16, and 17)stayed together in both the human and mouse lineages since they diverged from a common ancestor. Comparative analysis between chromosomes of humans and six other mammalian species paints a hypothetical chromosomal evolutionary history. The rate of duplications and inversions seems to have accelerated about 100 million years ago. Chromosomal rearrangements are thought to contribute to the generation of new species

Multigene Families

Many eukaryotic genes are present in one copy per haploid set of chromosomes. The rest of the genes occur in multigene families, collections of two or more identical or very similar genes -multigene families of identical DNA sequences: Usually clustered tandemly and, with the notable exception of the genes for histone proteins, have RNAs as their final products. An example is the family of identical DNA sequences that each include the genes for three largest rNA molecules -multigene families of nonidentical genes: Genes that encode globins. One family, located on chromosome 16 in humans, encodes various forms of a globin. --The embryonic and fetal forms of hemoglobin have a higher affinity for oxygen than the adult forms, ensuring the efficient transfer of oxygen from mother to fetus.

Microevolution vs. Macroevolution

Microevolution is changes over time in allele frequencies in a population, while macroevolution is the broad pattern of evolution above the species level

Sexual Reproduction

Most genetic variation in sexually reproducing organisms results from recombination of alleles New combinations of existing alleles occur through three mechanisms: -Crossing over (exchange of genetic material between homologous chromosomes during prophase I of meiosis) -Independent assortment (random distribution of chromosomes into gametes during metaphase I of meiosis) -Fertilization (random combination of gametes)

How Transposable Elements Contribute to Genome Evolution

Multiple copies of similar transposable elements facilitate recombination, or crossing over, between different chromosomes -Insertion of transposable elements within a protein-coding sequence may block protein production. Insertion of transposable elements within a regulatory sequence may increase or decrease protein production -Transposable elements may carry a gene or groups of genes to a new position. Transposable elements may also create new sites for alternative splicing in an RNA transcript

Rapid Reproduction Why have the most effective treatments for HIV been drug "cocktails" rather than single-drug treatments?

Mutation rates are low in animals and plants, averaging about one in every 100,000 genes per generation -Prokaryotes have lower rates, but shorter generation times allow mutations to accumulate rapidly. Mutations can accumulate rapidly in viruses due to short generation times and rapid mutation rates It is less likely that a set of mutations that together confer resistance to all drugs will occur in a short time period.

Explain why there is such genetic diversity among African genomes when compared to European or Asian genomes.

Native africans have been evolving for longer than any migrant (non-african) population. -African genomes have higher genetic diversity than other genomes, suggesting these populations have been evolving longer than non-African populations

The Key Role of Natural Selection in Adaptive Evolution

Natural selection increases the frequencies of alleles that enhance survival and reproduction -Adaptive evolution results from an increase in the degree to which a species is well suited for life in its environment. Because the environment can change, adaptive evolution is a continuous process that varies from place to place

Formation of New Alleles

New alleles arise by mutation, change in the nucleotide sequence of DNA -"Heterozygote protection" maintains a pool of alleles that could be beneficial if the environment changes -In multicellular organisms, only mutations in cell lines that produce gametes are passed to offspring

allopolyploid speciation

Occurs when two different species interbreed and produce hybrid offspring. Most such hybrids are sterile because the set of chromosomes from one species cannot pair during meiosis with the set of chromosomes from the other species. However, an infertile hybrid may be able to propagate itself asexual. In subsequent generations, various mechanisms can change a sterile hybrid into a fertile polyploid called allopolyploid. The allopolyploids are fertile when mating with each other, but cannot interbreed with either parent species; thus they represent a new biological species. The new species has a diploid chromosome number equal to the sum of the diploid chromosome number of the two parent species.

Evolution of Genes with Novel Functions

One copy of a duplicated gene can undergo alterations that lead to a completely new function for the protein product. For example, the lysozyme gene was duplicated and evolved into the gene that encodes α-lactalbumin in mammals -Lysozyme is an enzyme that helps protect animals against bacterial infection -α-lactalbumin is a nonenzymatic protein that plays a role in milk production in mammals

Either-or characters

One type of variation is between "either-or" characters, and the other is when the character varies along a continuum. Characters that vary in this way are typically determined by a single gene locus, with different alleles producing distinct phenotypes. --For example, pea flowers are either purple or white In contrast, other phenotypic differences vary in gradations along a continuum. Such variation usually results from the influence of two or more genes on a single phenotypic character. In fact, many phenotypic characters are influenced by multiple genes. --For example, coat color in horses or height in humans

Why are the Galápagos Islands often cited as being critical to Darwin's development of the idea of descent with modification?

Organisms shared many characteristics, leading Darwin to perceive unity in life. He attributed the unity of life to the descent of all organisms from an ancestor that lived in the remote psat. He also thought that as the descendants of that ancestral organism lived in various habitats, they gradually accumulated diverse modifications that fit them to specific ways of life. Thus, Darwin thought of evolution as a process in which both descent and modification can be observed. -Darwin hypothesized that species from the mainland colonized and then diversified on the islands

Reduced hybrid fertility

Postzygotic Reproductive Barriers -Even if hybrids are vigorous, they may be sterile. If the chromosomes of the two parent species differ in number or structure, meiosis in the hybrids may fail to produce normal gametes. Since the infertile hybrids cannot produce offspring when they mate with either species, genes cannot flow freely between the species

Hybrid breakdown

Postzygotic Reproductive Barriers -Some first generation hybrids are viable and fertile, but when they mate with one another or with either parent species, the offspring are feeble or sterile

Reduced hybrid viability

Postzygotic Reproductive Barriers -The genes of different parent species ay interact in ways that impair the hybrid's development or survival in its environment

Behavioral isolation

Prezygotic Reproductive Barrier -Courtship rituals that attract mates and other behaviors unique to a species are effective reproductive barriers, even between closely related species

Mechanical isolation

Prezygotic Reproductive Barrier -Mating is attempted, but morphological differences prevent its successful completion

Temporal isolation

Prezygotic Reproductive Barrier -Species that breed during different times of the day, different seasons, or different years cannot mix their gametes

Gametic isolation

Prezygotic Reproductive Barrier -Sperm of one species may not be able to fertilize the eggs of another species. For instance, sperm may not be able to survive in the reproductive tract of females of the other species, or biochemical mechanisms may prevent the sperm from penetrating the membranes surrounding the other species' eggs.

Habitat isolation

Prezygotic Reproductive Barrier -Two species that occupy different habitats within the same area may encounter each other rarely, if at all

transposable elements

Prokaryotes and eukaryotes have stretches of DNA that can move from one location to another within the genome, called transposable elements -About 75% of human repetitive DNA is made up of transposable elements and the sequences related to them -A cut and paste transposon removes the element from the original site. A copy and paste transposon leaves a copy behind. -Transposons and retrotransposons comprise 20-50% of most mammalian genomes. They can move; the enzymes required for this movement may be encoded by any transposable element, including the one that is moving, Others are related sequences that have lost the ability to move altogether.

Proteomics and systems biology

Proteomics is an approach to studying large sets of proteins and their properties -The goal of scientists who study proteomics is to attempt similar systematic studies of sets of proteins and their properties from the scientific process resulting from sequencing genomes. -A proteome is the entire set of proteins expressed by a cell or group of cells Systems Biology - Biologists have begun to compile catalogs of genes and proteins and have begun to focus on their functional integration in biological systems

22. Evolution

Refers to the process by which species accumulate differences from their ancestors as they adapt to different environments over time -Darwin's phrase descent with modification Evolution can be viewed as both a pattern and a process -Pattern is revealed by scientific data showing that life has evolved over time -Process consists of the mechanisms that cause the pattern of change

Other Repetitive DNA, Including Simple Sequence DNA

Repetitive DNA accounts for about 14% of the human genome. About 5-6% of the human genome consists of duplication of long sequences of DNA from one location to another -In contrast, simple sequence DNA contains many copies of tandemly repeated short sequences -short tandem repeat (STR): A series of repeating units of 2 to 5 nucleotides --Simple sequence DNA makes up 3% of the human genome --It is common in centromeres and telomeres, where it probably plays structural roles in the chromosome

Reproductive isolation

Results when biological barriers impede members of two species from interbreeding and producing viable, fertile offspring. These barriers limit the formation of hybrids, offspring that result from interspecific mating -Reproductive isolation can be classified by whether factors act before or after fertilization -A mutation at a single locus can influence preference and hence contribute to reproductive isolation Prezygotic barriers: Block fertilization from occurring. Such barriers typically act in one of three ways: by impeding members of different species from attempting to mate, by preventing an attempted mating from being completed successfully, or by hindering fertilization if mating is completed successfully. Postzygotic barriers: If a sperm cell from one species overcomes prezygotic barriers and fertilizes an ovum from another species, a variety of postzygotic barriers (after the zygote) may contribute to reproductive isolation after the hybrid zygote is formed. Developmental errors may reduce survival among hybrid embryos. Or problems after birth may cause hybrids to be infertile or decrease their chance of surviving long enough to reproduce.

Describe how the chromosome banding pattern showing telomeres and centromeres may explain why there are different haploid chromosome numbers for humans (n = 23) and chimpanzees (n = 24).

Scientists have long known that sometime in the last 6 million years, when the ancestors of humans and chimpanzees diverged as species, the fusion of two ancestral chromosomes in the human line led to different haploid numbers for humans and chimpanzees. The banding patterns in stained chromosomes suggest that the ancestral versions of current chimpanzee chromosomes 12 and 13 fused end to end, forming chromosome 2 in an ancestor of the human lineage.

Give four reasons why natural selection cannot produce 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

Describe how analogous structures can arise and give an example.

Some australian marsupials have eutherian lookalikes with superficially similar adaptations. For instance, a forest dwelling Australian marsupial called the sugar glider is superficially very similar to flying squirrels, gliding eutherians that live in North American forests. But the sugar glider has many other characteristics that make it a marsupial, much more closely related to kangaroos and other Australian marsupials than to flying squirrels or other eutherians. Although they evolved independently from different ancestors, these two mammals have adapted to similar environments in similar ways. In such examples in which species share features because of convergent evolution, the resemblance is said to be analogous.

Modes of selection

Stabilizing: acts against both extreme phenotypes and favors intermediate variants. This mode of selection reduces variation and tends to maintain status quo for a particular phenotypic character. Directional: Occurs when conditions favor individuals exhibiting one extreme of a phenotypic range, thereby shifting a population's frequency curve for the phenotypic character in one or the other. Common when a population's environment changes or when members of a population migrate to new habitat. Disruptive: Occurs when conditions favor individuals at both extremes of a phenotypic range over individuals with intermediate phenotypes.

The Hardy-Weinberg Equation

The Hardy-Weinberg equation describes the expected genetic makeup for a population that is not evolving at a particular locus -If a population is not evolving, genotype and allele frequencies will be constant from generation to generation If the observed genetic makeup of the population differs from expectations under Hardy-Weinberg, then the population may be evolving -Mendelian segregation and recombination of alleles must also occur for frequencies to remain constant

Duplication, rearrangement, and mutation of DNA contribute to genome evolution

The earliest forms of life likely had only those genes necessary for survival and reproduction. The size of genomes has increased over evolutionary time, with the extra genetic material providing raw material for gene diversification.

How is the concept of biogeography supported by continental drift and the presence of endemic species?

The evolutionary lineages leading to endemic species began to diverge about 55 million years ago. By that time, the southernmost portion of Pangaea was breaking apart into what would eventually become South America, Australia, and Antarctica. This suggests that their ancestors had spread across southern Pangaea before it broke apart.

punctuated equilibria

The fossil record includes many episodes in which new species appear suddenly in a geologic stratum, persist essentially unchanged through several strata, and then disappear. The term punctuated equilibria is used to describe these periods of apparent stratus punctuated by sudden change. A punctuated pattern indicates that speciation occurs relatively rapidly -Rather than a punctuated pattern, other species appear to have changed gradually over time

The Fossil Record

The fossil record provides evidence of the extinction of species, the origin of new groups, and changes within groups over time -Fossils can document important transitions, such as the transition from land to sea in the ancestors of cetaceans -Fossil evidence shows that living cetaceans and even-toed ungulates are more different from each other than were earlier members of these groups

Explain the role of fossils in rock strata as a window to life in earlier times.

The fossils in a particular stratum provide a glimpse of some of the organisms that populated Earth at the time that layer formed. Later, erosion may carve through upper strata, revealing deeper strata that had been buried. -Many fossils are found in sedimentary rock, which appears in layers called strata -Fossils of extinct species can document the divergence of present day groups by filling in gaps between them

Convergent evolution

The independent evolution of similar, or analogous, features in distantly related groups (lineages) -Analogous traits arise not through common ancestry, but through independent adaptation to similar environments -For example, the sugar glider is an Australian marsupial that superficially resembles the flying squirrel, a North American eutherian -Similar problem, similar solution. Birds and bats both have wings that allow them to fly. Worms and snakes move similarly.

morphological and ecological species concept

The morphological species concept distinguishes a species by its structural features. It applies to sexual and asexual species and does not require information on the extent of gene flow. It relies on subjective criteria The ecological species concept defines a species by its ecological niche, the sum of its interactions with the nonliving and living parts of the environment It applies to sexual and asexual species and emphasizes the role of disruptive selection

What are two limitations of the biological species concept?

The number of species to which this concept can be usefully applied is limited. The biological species concept also does not apply to organisms that reproduce asexually at all or most of the time, such as prokaryotes. Furthermore, in the biological species concept, species are designated by the absence of gene flow. But there are many pairs of species that are morphologically and ecologically distinct, and yet gene flow occurs between them.

24. Speciation

The process by which one species splits into two species. Species: A group of populations whose members have the potential to interbreed in nature and produce viable, fertile offspring - but do not produce viable, fertile offspring with members of other such groups -The reduction or lack of gene flow required for the formation of new species

Natural selection, genetic drift, and gene flow can alter allele frequencies in a population

Three major factors alter allele frequencies directly and bring about most evolutionary change: -Natural Selection: differential success in survival and reproduction. Selection results in alleles being passed to the next generation in proportions that differ from those in the present generation. Natural selection can cause adaptive evolution, a process in which traits that enhance survival or reproduction increase in frequency over time -Genetic drift: a process in which chance events cause allele frequencies to fluctuate unpredictably from one generation to the next. Genetic drift tends to reduce genetic variation through the random loss of alleles and make populations more similar --The smaller the sample, the greater the chance of random deviation from a predicted result -Gene flow: The transfer of alleles into or out of a population due to the movement of fertile individuals or their gametes. Results in a random, nonadaptive change in allelic frequencies

In human evolution, the genes that appear to be evolving the fastest are those that code for transcription factors. Why does this make sense?

Transcription factors regulate gene expression and thus play a key role in orchestrating the overall genetic program.

Duplication and Divergence of Gene-Sized Regions of DNA

Unequal crossing over during prophase I of meiosis can result in one chromosome with a deletion and another with a duplication of a particular region. Transposable elements can provide sites for crossover between nonsister chromatids. Also, slippage can occur during DNA replication so that a part of the template is either skipped, or replicated twice

How is it possible for humans to have so few genes, in fact approximately the same number of genes as a nematode worm, and yet make so many proteins?

Vertebrate genomes can produce more than one polypeptide per gene because of alternative splicing of RNA transcripts. A typical human gene contains about ten exons, and an estimated 90% or more of these multi-exon genes are spliced in at least two different ways. -Humans and other mammals have the lowest gene density, or number of genes in a given length of DNA

Comparing Genomes

When comparing genomes, we find that the more similar in sequence the genes and genomes of two species are, the more closely related those species are in their evolutionary history. Highly conserved: Genes that remain similar in distantly related species -Bacteria, archaea, and eukaryotes diverged from each other between 2 and 4 billion years ago -Human and chimpanzee genomes differ by 1.2% at single base pairs and by 2.7% because of insertions and deletions

sexual selection

a process in which individuals with certain heritable traits are more likely to obtain mates than other individuals of the same sex -It can result in sexual dimorphism, a difference in secondary sexual characteristics between the sexes --Intrasexual selection: direct competition among individuals of one sex (often males) for mates of the opposite sex --Intersexual selection (mate choice) occurs when individuals of one sex (usually females) are choosy in selecting their mates. Female choice is often dependent on the showiness of the male's appearance or behavior. Though showiness can increase the likelihood of mating, it can also decrease the chances of survival -The "good genes" hypothesis proposes that females select males with traits that are related to their genetic quality or overall health. If true, then both the male trait and female preference for it should increase in frequency

differential reproductive success

differences in heritable traits can lead to differential reproductive success. This means that the individuals who have the necessary traits to promote survival in the current environment will leave the most offspring. An organism might have a trait that gives its offspring an advantage in escaping predators, obtaining food, or tolerating physical conditions. When such advantages increase the number of offspring that survive and reproduce, the traits that are favored will likely appear at a greater frequency in the next generation. Thus, over time, natural selection resulting from factors such as predators, lack of food, or adverse physical conditions can lead to an increase in the proportion of favorable traits in a population.

Describe what happens in each of these special types of genetic drift:

founder effect: When a few individuals become isolated from a larger population, this smaller group may establish a new population whose gene pool differs from the source population. Allele frequencies in the smaller founder population are different from those in the parent population bottleneck effect: A severe drop in population size due to a sudden change in the environment.The resulting gene pool may no longer be reflective of the original population's gene pool. If the population remains small, it may be further affected by genetic drift

Allopatric speciation

gene flow is interrupted when a population is divided into geographically isolated subpopulations. The gene pools of isolated populations may diverge through mutation, natural selection, and genetic drift. Reproductive isolation may arise as a by-product of genetic divergence -Intrinsic barriers to reproduction arise due to genetic change driven by processes including divergent selection and genetic drift -Reproductive barriers prevent interbreeding even if contact is restored between populations

Hardy-Weinberg equilibrium example

p2 + 2pq + q2 = 1 Let p = the frequency of A, the dominant allele and q = the frequency of a, the recessive allele. So, p2 = AA, q2 = aa, 2pq = Aa To calculate genotype frequencies, divide the number of individuals of each genotype by the total number of individuals in the population CRCR is 0.64 (320/500) CRCW is 0.32 (160/500) CWCW is 0.04 (20/500)

Noncoding DNA, found between genes, includes:

pseudogenes: Former genes that have accumulated mutations over a long time and no longer produce functional proteins. repetitive DNA: Consists of sequences that are present in multiple copies in the genome -Picture: types of DNA sequences in the human genome

Comparative embryology

reveals anatomical homologies not visible in adult organisms -For example, all vertebrate embryos have a post-anal tail and pharyngeal arches -The arches develop into structures with very different functions in adults from different vertebrate groups

Homology

similarity resulting from common ancestry, is another type of evidence for evolution Homologous structures are anatomical resemblances that represent variations on a structural theme present in a common ancestor -For example, the forelimbs of all mammals have the same arrangement of bones, but different functions Vesitgal structures: Remnants of features that served a function in the organism's ancestor. For example, snakes aose from ancestors with legs, and the skeleton of some snakes retain vestiges of the pelvis and leg bones of their ancestors. -Molecular homologies include the genetic code shared by all life and specific genes that are shared between vastly different organisms. In some species, homologous genes may acquire new functions, or lose function entirely. Similarities in such genes are evidence of inheritance from a common ancestor

Sympatric speciation

speciation occurs in populations that live in the same geographic area Sympatric speciation is less common than allopatric speciation -It occurs if gene flow is reduced by factors such as Polyploidy, Sexual selection, and Habitat differentiation (natural selection resulting from a switch in food source or habitat) -Mate choice based on male breeding coloration can act as a reproductive barrier that keeps the gene pool of two species separate. -When a subpopulation exploits a habitat or resource not used by the parent population.

23. Microevolution

the change in allele frequencies in a population over generations, is evolution at its smallest scale Three mechanisms cause allele frequency change: -Natural selection (adaptation to the environment) -Genetic drift (chance events alter allele frequencies) -Gene flow (transfer of alleles between populations) --Nonrandom mating can affect genotype frequencies, but not allele frequencies

Relative Fitness

the contribution an individual makes to the gene pool of the next generation relative to the contributions of other individuals -Selection favors certain genotypes by acting on the phenotypes of individuals -Although we often refer to the relative fitness of a genotype, the entity that is subjected to natural selection is the whole organism, not the underlying genotype. Thus, natural selection acts more directly on the phenotype than the genotype; it acts on the genotype indirectly, via how the genotype affects the phenotype.