bio evolution lectures 18-23 (quizlet 3)

Effects of Hox gene mutations

Example and a fruit fly and this specific Hox Gene called Ultrabithorax or Ubx Mutation of the Hox gene Ultrabithorax (Ubx) transforms the third thoracic segment (T3), which normally bears tiny structures called halteres, into a second thoracic segment (T2), which bears wings instead T3 is the third module of head to abdomen. As shown in A, T3 normally bears these tiny structures called halteres. But a mutation in Ubx changes T3 into a second thoracic segment (T2), which bears wings instead. So we now have a mutant fly that has 2 pairs of wings. As a result of a single mutation in ubx, the T3 was replaced by a second T2 segment A mutation in the Hox gene Antennapedia (Antp) replaces antennae with legs There are legs where the antenna should be this is another mutation in a Hox Gene that is a more extreme example. The mutation is in the gene antennapedia (antp), and it causes the mis-expression of the Antp protein in the cells that normally give rise to antennae, resulting in the replacement of antennas with legs. So these mutants literally grow legs on their heads

Evolution is not a scientific hypothesis because it is not testable: no possible observations could refute it

Facts are just a hypothesis in which we can have a very high confidence because of massive evidence in their favor and the absence of contradictory evidence Back in the years when natural selection was proposed by Darwin and Wallace, it was just a hypothesis. But evolution has now survived over 150 years of attempts at disproving it What type of evidence could refute evolution? Imagine finding a mammalian fossil at deeper stratigraphic layer than the origin of varied life. That would be evidence against evolution but there is no single contradiction in the fossil record about the timing in the origin of major groups

The fallacy of group selection (as originally conceived)

Fallacy of evolution of altruism via group selection (these original ideas are actually a fallacy): Do oysters have a high reproductive rate to ensure the survival of the species? Or do antelopes with sharp horns refrain from physical combat because that would lead to the species' extinction? Opposite to the natural selection theory! And as we know, natural selection is grounded on selfish principles

Adaptations for parasitism

(A) Common cuckoo (Cuculuscanorus)being fed by its foster parent (reedwarbler, Acrocephalusscirpaceus) Eggs of 6 species parasitized by the cuckoo = smaller than Cuckoo eggs laid in the corresponding host' nest We tend to think that parasitism only involves microorganisms, but the Cuckoo bird here is also a parasite On A (Eggs of 6 species parasitized by the cuckoo), we see how the common cuckoo is fed by its foster parent, the reed warbler On B, we have the eggs of 6 different species of birds that are parasitized by the cuckoo (on the left column) and the actual cuckoo eggs laid in the corresponding hosts nests (on the right column) The adaptation here is that the common cuckoo, which is one species, can change the color of the eggs the females laid depending on the host species they parasite 1. Adhesive Organ 2. Sense Organs Reduced 3. Digestive Tract Reduced/Lost (they absorb nutrients through the skin) 4. Body Wall Protection (biochemical defense system) 5. Fecundity Increased 6. Larval stages to facilitate passage from one host to another

Horizontal Gene Transfer (HGT)

(also, lateral gene transfer) transfer of genes between unrelated species Occasionally genes from other species are mixed into the gene pool Important to prokaryotes (antibiotic resistance) In eukaryotes, this usually occurs through hybridization between closely related species So genetic exchange also happens between distantly related organisms by HGT HGT is particularly important to prokaryotes like bacteria and archaea and is the most common way by which they acquire new genes (including those that confer antibiotic resistance) HGT Can vastly speed up adaptations since a new functional Gene is acquired in a single conjugation event, rather than waiting for evolution to happen via mutation, drift, and natural selection.

Irreducible complexity: complex adaptations

(such as wings, eyes, and biochemical pathways) could not have evolved gradually because the first stages would not have been adaptive Created by advocates of creationism and intelligent design

Gene families

Gaijin family is a set of loci that arose by duplication And that code for proteins that typically continue to have similar functions. Duplicated genes continue to have similar biochemical function Paralogs two or more genes that originated by duplication are said to be paralogs Some Gene families, such as the hemoglobin, have many paralogs created by several duplication events that are widely separated in time in the womb, oxygen comes from the mother's bloodstream. whereas in adults, lungs are involved. so different hemoglobins work during these different life stages and these different hemoglobins are simply copies of the same ancestral Gene with subsequent modification The figure shows the evolution of hemoglobin genes in different species of cod fish note that some species have more copies than others as noted by the squares in front of the tips in the phylogeny

The death of a Gene

A gene that is expressed only when a cell becomes committed to natural cell death (apoptosis). there are also many ways in which a gene can die. When a gene is duplicated, the new copy is often Dead on Arrival. The duplicate gene may not include the entire Gene, and even if it does, it often lacks the regulatory elements needed to express it at the right time and in the right place Gene Copies are often nonfunctional when a non-functional gene is fixed in the population, or a functional Gene becomes non-functional, the result is a genetic skeleton call a pseudogene Pseudogenes so the genomes of many species include many pseudogenes. For example, our own genome has almost as many pseudogenes as functional genes. although they serve no function, pseudogenes are useful two biologists as a sort of controlled natural experiment a parental Gene from which a pseudogene is originated continues to evolve under the forces of selection. But since the pseudogene does not produce a functioning product, it's therefore free from selection. so comparing the sequences of pseudogenes with those of their parental genes reveals that pseudogenes typically evolve much more quickly as we can see in the graph, most mutations to functioning genes reduce Fitness and are thus removed from the population by purifying selection (Selection against deleterious mutations). However, mutations in a pseudogene are selectively neutral and so they are free to drift to fixation

Methods in Evo-Devo: CRISPR-Cas9

A novel tool for developmental biologist is called crisper cas 9. it has been used to knock out the function of various Hox genes in the amphipod crustacean. Picture of wild type or control To the left we have the expression of Hox genes in a wild-type or control, with all segments (T4 to T8) in the expected order Picture of abdA Hox knocked out (deleted) via CRISPR-Cas To the right, what we see is you result after knocking out or deleting the abdA Hox gene from The genome. When this Gene is knocked out, the T6 T7 and T8 segments get replaced by T4 and T5 segments. This is not a natural mutant oh, this is a mutant created in the lab with this novel technique

Evolutionary arms race or escalation

A predator increases the capture of preys, and preys develop better defensive traits corresponding to the character of the predator Both traits are evolving in the same direction This may occur if the capture rate of the prey by the predator increases with the difference between the defensive trait of the prey species and a corresponding character in the predator Ex: cheetahs and gazelles, the selection by cheetahs (the predators) has resulted in the evolution of high speed in gazelles (the prey). Therefore, predators are also under selection for greater speed. . so the traits of both species evolve in one direction (which is also an example of a specific coevolution we saw earlier). These types of interactions can lead to the extinction of the victim or a stable point between both interacting parties During evolutionary arm races, some prey species have evolved defenses that can make them as dangerous to predators as predators are to prey For example: the rough-skinned newt (a salamander) has developed a neurotoxin (called tetrodotoxin or TTX), which provides a defense from predators Graph shows how levels of TTX varies among populations Populations of the garter snake (predator) that inhabit outside the range of the newt have no resistance to TTX. in contrast, sympatric populations that coexist and feed on the newts are resistant to TTX In this example, the prey's trait evolves in 1 direction, while the predators trait evolves to try and catch up with its prey

Evolution of genomes: Ultraconserved elements

A single gene can produce more than one protein another important aspect in the evolution of genomes are these so-called ultraconserved elements. So comparisons among the genome of distantly related species have also revealed small regions of non-coding DNA that are much more similar than the rest of the genome. So these ultraconserved elements are thought to be under strong purifying selection that constrains them from drifting apart So what we see in this graph is a comparison of a region of the genomes of the champ, The Mouse, and the chicken, highlighting in these Ultraconserved segments that show nearly identical DNA sequences across these diverse species. now the function of these regions is unclear, but it's believed to be regulatory... So in other words, switches that turn genes on and off

Aposematism differs from mimicry in that? A. Aposematism involves a warning signal, whereas mimicry is about one species imitating another species B. Mimicry is density dependent, whereas aposematism is not C. Aposematism is about one species imitating another species, whereas mimicry involves a warning signal D. Aposematism is density dependent, whereas mimicry is not

A. Aposematism involves a warning signal, whereas mimicry is about one species imitating another species

A mutation to the Hox gene Antennapedia in Drosophila causes: A. Legs to grow out of the fly's face B. Antenna to grow out of fly's face C. Legs to grow out of fly's trunk D. Antenna to grow out of fly's trunk

A. Legs to grow out of the fly's face

Which of these statements is NOT true about Hox genes? A. They are involved in regulation of color but not animal body plans B. Control the patterning of specific body structures C. The anterior-posterior identity of segments correlates with the arrangement of Hox genes in chromosomes D. Are highly conserved

A. They are involved in regulation of color but not animal body plans

mimicry

Ability of an animal to look like another more harmful animal, form of convergent evolution. Recap: under convergent evolution, 2 distantly related lineages evolve similar traits through different evolutionary paths With mimicry, a species mimics or resembles another distantly-related species This resemblance is only advantageous to the mimic species (not the model species) Ex: african swallowtail butterfly, which constitutes a single species, presents mimetic polymorphisms, so different populations have different color morphs Mimics = shown in middle row. Here, females have several color morphs that resemble their distasteful model in the top row with which they co-exist So predators that have consumed distasteful model species learn to avoid that particular coloration pattern or the mimic This adaptation (mimicry) is also frequency dependent as the abundance of any color morph increases the fitness. Frequency dependence decreases because predators can now associate the pattern with a tasty meal. So it only works out when the model species is much more common than the mimetic species Mimicry comes in 2 flavors -Batesian: a palatable (harmless) species (mimic) resembles an unpalatable (harmful) species (model) -Müllerian: mimic and model species are both unpalatable (harmful). Occurs when 2 or more unpalatable species are co-mimics. This happens because common phenotypes will be better recognized and avoided. Strategy here is to use fewer colors Ex of mullerian mimicry: an experiment is shown using Heliconius butterflies to test the effect of the abundance of the model species on the mimic forms. In this case, 2 color morphs of Heliconius cydno mimic 2 different species models: Heliconius sapho on the right and Heliconius eleuchia on the left. Here, the model species (eleuchia) is the most common at one locality whereas the other model species (sapho) is much more common at another locality. In both cases, the mimics that match the species that is most abundant locally have higher chances of survival

Shared Genes and the Evolution of Altruism: Hamilton's rule

According to W. Hamilton (Hamilton's rule), an allele will spread if the increase in indirect fitness outweighs the loss of direct fitness caused by the altruistic behavior Just to be clear, Hamilton's rule applies to all behaviors, not just altruism. rB>C. The principle that for natural selection to favor an altruistic act, the benefit to the recipient, devalued by the coefficient of relatedness, must exceed the cost to the altruist.

Altruistic behaviors do not evolve for the good of the species

Altruism cannot evolve via individual selection, because an altruistic trait reduces the fitness of the individual that carries it An altruistic genotype, among a set of non-altruistic genotypes, would rapidly decline in frequency (leaving fewer offspring) Conversely, a non-altruistic "cheater" genotype would increase in frequency rapidly

inversion

Another type Of evolutionary change in a karyotype is called chromosome inversions inversions are produced when a chromosome breaks at two places in the middle segment is then reinserted backwards. But if chromosomes with and without the inversion Have the same genetic content, what could possibly cause these inversions to spread in a species? There are several possible explanations What causes inversions to spread? Breakpoints can disrupt a gene or alter its expression, leading to occasional beneficial changes that can spread via positive selection Some inversions benefit from meiotic drive during recombination, forming inversion heterozygotes. When the inversion is heterozygous, so paired with a chromosome that lacks the inversion, It will get transmitted to the Gimme More than 50% of the Time, favoring the spread of inversion through the population Example of the effects of chromosome inversions in the evolution of this bird, the ruff Recombination is blocked in inverted regions of the chromosome The ruff (Philomachuspugnax) has three different male morphs that use different strategies to obtain mates. These morphs differ dramatically in plumage, behavior, and body size, representing alternative mating strategies. So these three different phenotypes are determined by a chromosome inversion that carries alleles that code for combinations a feather colors and reproductive hormones that determine the mating strategy for each of the morphs. Phenotypes are determined by a chromosome inversion that carries alleles that code for combinations of feather colors and reproductive hormones

Darwin: "if numerous gradations from a perfect and complex eye to one very imperfect and simple, each grade being useful to its possessor, can be shown to exist"

As we already know, darwin struggled to explain the complexity of the eye But then he noted that numerous gradations from a perfect and complex eye to one very imperfect and simple, each grade being useful to its possessor, can be shown to exist. And we now have evidence for the existence of functional eye intermediate across the diversity of animals

Recap on transcription and alternative splicing

As you may recall from the previous lecture, a single Gene can quickly evolve and produce more than one protein via alternative splicing during transcription A single gene can quickly evolve and produce more than one protein via alternative splicing Regulatory element (gene switch) = promoter → transcription → alternative splicing cuts out the introns and the exons come together → translation → formation of proteins Exon: protein-coding geneIntron: non-coding section Transcription factors The genes that control the rate of transcription of genetic information from DNA to messenger RNA, by binding to a specific DNA sequence = transcription factors In turn, this helps to regulate the expression of genes near that sequence In this way, transcription factors can produce upregulated or overexpressed genes and down regulated or under Expressed genes he mentioned in the last lecture that regulated genes are like switches that turn genes on and off. Then think of transcription factors as a dimmer switch that can regulate the brightness of the light. So upregulated transcription factors are like turning the dimmer switch up and downregulated transcription factors or like turning the dimmer switch down Upregulated: over-expressed Downregulated: under-expressed

What's a plausible hypothesis about the origin of transposable elements in our genome? A. Viral infections B. Endosymbiotic viruses C. Endosymbiotic bacteria D. Bacterial infections

B. Endosymbiotic viruses

Chromosome Evolution

Before the Advent of DNA sequencing Technologies in the late 20th century, much of what we knew about evolutionary genetics came from studying chromosomes ( and their shape) under the microscope. As you can see in the figure, species differ in the number of chromosomes substantially Species differ in their number of chromosomes karyotype refers to the number and structure of chromosomes

Evolution of cooperative interactions: cheaters are a problem! lab experiment

Blue = Mutant cheater cells (chtA locus) Orange = Wild-type non-cheater cells 2 types of cells: wild-type orange (non-cheater) and cheater cells in blue Blue cells are mutant for a single locus allied chtA In this, slime molds are maintained for multiple cycles of reproduction and selection under harsh conditions with limited food resources Result is that mutant cheater cells become concentrated in the cap and are thus more likely form reproductive spores cooperation collapses: mutant cheater cells become concentrated in the cap and thus are more likely to form reproductive spores. Over the course of 11 cycles, the frequency of selfish mutant cells increase, resulting in a collapse of cooperation among cells

modularity

Body plans of many organisms consist of modules

Our closest living relatives: chimpanzees and bonobos

Bonobos are a sexual species; chimps are more aggressive Chimps use tools Humans and chimps differ by less than 2% in the DNA sequences of protein-coding genes Bonobos Use sexual interactions, in both heterosexual and homosexual combinations, to resolve conflicts and to maintain bonds. Chimpanzees are much more aggressive and less sexual than bonobos. Champs can also use tools, which they learn to use by imitation chimpanzees have a great variety of vocalisations oh, but they do not use language in nature. Humans and chimps differ by less than 2% in the DNA sequences of protein-coding genes. The two species are so closely related that several loci we both share are polymorphic alleles that have persisted since our common ancestor because of bouncing selection and incomplete lineage sorting for example, the gene tree of humans for blood type shows that humans individuals with blood type A are closer to chimps with blood type A than to humans with blood type B. So that's just one gene tree of course, not the species tree, but it says a lot about how close we are to them

acquisition and loss of individualization of modules: mammal teeth

But we have on this side here is the acquisition and loss of individualization in mammal teeth. So the first thing is, what are the modules here? Well, the teeth obviously. Well each tooth is an individual structure, all teeth clearly share a common origin. Because we find multiple copies of a tooth, that means teeth are serial homologous features. They are repeated. (A): Haptodus, Mammal ancestor has uniform teeth (no individualization) In synaptic mammals, a fossil lineage, we can see that all teeth are uniform, very similar, so no individualization (B): elephant shrew, Teeth became individualized during the evolution of mammals but during evolution of modern mammals, including humans dog or this elephant shrew shown in the picture, teeth became individualized and differentiated into incisors, Canines, premolars, and molars. And all these serve different functions. (C): Dolphin, Dolphins have uniform teeth. They lost the individualization that was once gained during mammal evolution (no individualization) but this individualization of teeth was lost secondarily in some lineages like the dolphin, Which also have uniform teeth so no individualization

The easiest way in which a genome can produce different sets of proteins for different uses is via: A. Genetic drift B. Alternative splicing during DNA replication C. Alternative splicing during gene expression D. Mutation

C. Alternative splicing during gene expression

Which of these statements about mutualistic interactions is NOT true? A. A high prevalence of cheating genotypes can lead to the collapse of mutualistic interactions B. A cheating genotype can have a high fitness C. Cheating genotypes are always penalized by natural selection and therefore can never persist D. Cheating genotypes are observed in mutualistic interactions at both intra- and inter-specific levels

C. Cheating genotypes are always penalized by natural selection and therefore can never persist

Which of these statements about coevolution is true? A. Coevolution is a form of sexual selection B. Coevolution always involves mutualistic (+ +) interactions C. Coevolution can happen at different evolutionary scales, from macro- to micro-evolution D. Coevolution is the same as natural selection

C. Coevolution can happen at different evolutionary scales, from macro- to micro-evolution

The genetic toolkit: changes in gene expression

Changes in expression has allowed for differences in body plans within and among phyla, and for individualization of segments Sean Carroll referred to this as the genetic toolkit The genetic toolkit is shared widely among animals, and it contributes to evolutionary changes in the regulation of diverse genes with diverse developmental roles most of the morphological differences caused by Hox genes across species are due to changes in the expression of the genes that the Hox genes regulate. it is the gene expression of Hox genes that turns undifferentiated cells in the embryo into differentiated cells and juveniles and adults. The spatial expression of the genes has ultimately enabled arthropod Segments and their appendices to become differentiated, triggering individualization. So in other words, the differential turning on and off of the Hox genes is what causes the different segments in Drosophila to have different body structures. Sean carroll referred to this as the genetic toolkit the genetic toolkit is shared widely among animals, and contributes to evolutionary changes in the regulation of diverse genes with diverse developmental roles

Evolution of developmental pathways

Changes in expression of Bmp4 determines bill shape and size Darker areas shown by red arrows indicate higher gene expression of this gene (upregulation) This is another example at a much more shallow scale in The evolutionary continuum shown with the Galapagos finches. the enormous differences in Bill shape and size are determined by the differential gene expression of a single Gene is known as BMP4. so darker standing in the region, indicated by red arrows, shows higher gene expression or up regulation of BMP4 Genetic tool kits are deployed in different ways through molecular networks to produce what is known as Developmental Pathways. There are a great deal of Developmental Pathways, including signaling proteins, transcription factors, cis-regulatory elements and structural genes The genes that regulate function in hierarchies or networks termed developmental pathways or developmental circuits Developmental pathways include signaling proteins, transcription factors, cis-regulatory elements and structural genes Changes to developmental pathways, including differential transcription and gene co-option, are believed to underlie much of the phenotypic diversity seen in nature (Including the formation of major organs and limbs) So it is often the case that morphological variation within and among species are quads not just by changes in protein-coding sequences but also by changes in the Developmental Pathways , Such as differential expression

Natural selection in real time

Chart shows the results of the Framingham Heart Study, Which is the longest running study in medical history the data points or individual study between 1948 and 2008. It correlates cholesterol levels against Fitness, measured as lifetime reproductive success for each individual. And the results are shocking individuals with low total cholesterol of around 15 mg per liter had an average of just over three children and their lifetime those with high cholesterol levels of around 35 mg per liter had only two children so there is a strong directional selection favoring lower cholesterol levels acting as we speak on people in this country. Now will selection cause evolutionary change? Yes, as it turns out Heritability of total cholesterol is really high and estimated at 0.61. Thus we have the main ingredients needed 4 evolution of a quantitative trait: heritable variation, differential reproduction, and directional selection Cholesterol -US population (1948-2008)•15 mg/l: ~3 children; 35 mg/l: ~2 children High heritability (0.61) + directional selection = evolutionary change

de novo genes

Coding DNA sequences that originate from noncoding DNA. genes lacking homologs except in closely related species; thought to have evolved anew from intergenic DNA sequences It might seem unlikely that a new Gene could originated from DNA that previously had no function, but as unlikely as that may seem, Recent research has uncovered new genes in organisms ranging from yeast to even humans, That did indeed originate from non-coding DNA. these are called "de novo" genes a figure shown presents events in the birth of de novo genes A genetic alteration that is present for the first time in one family member as a result of a variant (or mutation) in a germ cell (egg or sperm) of one of the parents, or a variant that arises in the fertilized egg itself during early embryogenesis.

Aposematism and mimicry

Conspicuous colors are often used by prey to advertise their toxicity to predators. Mimicry can extend to behavioural and acoustic mimicry, while aposematic coloration can evolve secondary functions in signaling to competitors and potential mates.

The fastest way a genome can evolve to acquire a new function is via: A. Sexual selection B. Genetic drift C. Mutation D. Gene duplication

D. Gene duplication

If an specific trait grows at a faster rate compared to the complete body, the trait thus represents a case of: A. Progenesis B. Heterotopy C. Neoteny D. Positive allometry

D. Positive allometry

The hominin lineage

Darwin (1871): "...As these two species [gorilla and chimpanzee] are now man's nearest allies, it is somewhat more probable that our early progenitors lived on the African continent than elsewhere" in his book, The Descent of Man, published in 1871, Darwin wrote this quote and 50 years later, the first hominin fossils were found in South Africa. Now we know many hominin fossils that were discovered from the Africa savannas. The climate in this region is really dry, which is great for the formation of fossils. And, as pointed out before, we are really lucky to have all these fossils of hominins but this is not the case for other great apes that live in Green Forests where the climate for fossilization is not as good. Sahelanthropus(6-7 mya), Ardipithecus ramidus (4.5 mya), Australopithecus afarensis (3.5 mya), Homo habilis (2.6-1.4 mya), Homo erectus (1.9-0.2 mya), Homo sapiens (0.2 my-present)

Ardipithecus ramidus (4.5 mya)

Derived hominin feature: bipedal posture Ancestral ape feature: long arms and fingers Ancestral ape feature: opposable toe

Copy number variation (CNV)

Difference among individual organisms in the number of copies of any large DNA sequence (larger than 1000 bp). Refers to variation in gene structure involving copy number changes in a defined chromosomal region; could be in the form of a deletion where a copy is deleted or an addition (duplication) where an extra copy is added. ricardo: For example, the AMY1 locus in humans (saliva enzyme that breaks down starch) Low starch: ~5.4 copies High starch: ~6.7 copies As a chromosome with the new gene duplicate spreads through a population, there is a polymorphism in the number of copies that individuals carry This situation, called copy number variation or CNV, is found for instance at the AMY1 locus in humans so the gene codes for the enzyme amylase, which an en enzyme found in saliva that breaks down starch So individuals with more copies of the AMY1 locus have more amylase in their saliva and can digest starch more efficiently So the central african Biaka populations who are hunter gatherers with a diet low in starch typically have 4 or 5 copies of this gene. In contrast, japanese people whose rice-heavy diet has abundant starch typically have 6 to 8 copies of the gene (or more!)

Diversity of human populations

Differences in many traits, such as skin color, height, and facial bones, indicate that we are a very diverse species. But this diversity is only phenotypic... genetically, we are actually very similar In fact, the opposite happens with the chimp. They are not as different morphologically, but their genetic diversity is way higher than ours Humans: high phenotypic diversity; low genetic diversity Chimpanzee: low phenotypic diversity; high genetic diversity Genome comparisons of human populations from Africa, Asia and Europe: 12% of genomic differences attributed to each population 88% of genomic differences found within each population In other words, genomic differences are substantially higher within populations than among populations Striking phenotypic differences are adaptations. For example, light skin color of Europeans and East Asians is convergent. This convergence is the result of mutations at different loci adapted to limited sunlight at high latitudes When sunlight is limited, there is a deficiency in the production of vitamin D in individuals with darker skin color Darker skin color, on the other hand, provides protection from UV light in the tropics, thereby minimizing the risk of skin cancer. So light or dark skinned colorations are just adaptations to life at different latitudes

ecological character displacement

Divergence in response to competition between species

Altruistic behaviors and the fallacy of group selection

Do lemmings (Norway rodents) commit mass suicide to avoid overpopulation? (so "for the benefit of the species?") They do migrate in large groups when populations densities are too high and in doing so many may die So.. it's mass dispersal not mass suicide. Not migrating would mean even higher risk of death due to overpopulation! They are seeking, every selfish one of them, a less crowded place in which to live

Neofunctionalization (novel biological functions)

Duplicated genes can acquire novel biological functions, a process that is called "Neofunctionalization" an example is found in electric fishes All teleost fishes have duplicates of a sodium Channel Gene, which is expressed in muscles Sodium channel gene Paralog → The electric organ. in most teleost fishes, both genes are involved in triggering muscle contractions. But in two families of fishes, the knife fishes in South America in the elephant fishes in africa, one of the paralogs has independently evolved an entirely different function, which is the firing of the electric organ, a unique structure that enables these fishes to sense prey and to communicate with each other in the darkness Here is another example for my paper published last year. The researchers found that deep sea fish species have up to 38 copies of opsin genes which are involved in vision (humans only have three copies) Here, Multiple copies became specialized for vision in the darkness, as a very little or no light penetrates in the deep sea. Copy number in opsin genes enhances vision in the ocean depth

Red Queen Hypothesis (Leigh Van Valen)

Each species has to evolve as fast as possible just to survive because interacting species also continue to evolve "It takes all the running you can do, to keep in the same place" This running analogy may lead to the indefinite coexistence between enemies and victims, a switch by the enemy to a different victim species, or the extinction of the victim's populations

Homo habilis (2.6-1.4 mya)

Earliest species in our genus homo Homo habilis means handy man, and as the name suggests, it used tools Derived hominin feature: flatter face and large cranium (cranium substantially larger than that of Australopithecus and the face was a lot flatter) Derived hominin feature: human-like legs and feet Derived hominin feature:human-like hands Derived hominin feature:used tools

Evolutionary Developmental Biology

Eight genes in two Hox gene clusters -Antennapedia complex and the Bithoraxcomplex-that are part of the same family, and share developmental functions They regulate patterning along the anterior-posterior axes of the body of a fruit fly They are in the disophilia and are key in regulating the formation of segments along the main anterior-posterior axis in the body In the 1980's it was discovered that Hox genes exist in ALL animals It was learned that hox genes are not restricted to the fruit fly, but actually exist in all animals In vertebrates they are arranged in one cluster containing 13 genes This cluster has been duplicated four times (HoxA, HoxB, HoxC, and HoxD) Recall the previous lecture when he explained that Gene duplication and Neo functionalization is a main driver of evolution Segment-specific patterning functions of Hox genes in the vertebrate hindbrain and spinal cord in this diagram of a mouse embryo, do black horizontal lines or bars and indicate segmental patterns of expression in one of the gene clusters, the Hox B gene. do darker colors correspond to areas of high gene expression. Once again, we see a match between the order of the Hox genes in a chromosome and the Order of the structures in the body where these genes are expressed Probable evolution of the metazoan Hoxgene complex this diagram puts it all together in a phylogenetic context For the animal tree of life. So the vertical bars in the tree denote events of Gene duplication. and we see that from head to tail, the development of body structures is regulated by Hox gene following the same order in which they are arranged in the chromosomes. Gene duplications The Hox genes are expressed serially and their expression is highly correlated with the evolution of body plans. They are highly conserved among all living animals, which means that is we compare the DNA sequences of Hox genes Across different animal species oh, we will find very few differences. So this discovery of fundamental underlying similarities and developmental patterning systems of many different taxa raise two key questions... Similarities in the developmental patterns of many different taxa has raised two questions: -What is the basis of body plan differences among taxa? -How can conserved genetic factors play a role in those differences? in other words, If these Hox genes are so similar across the animal diversity, how can we explain their enormous morphological differences? The answer to this question lies in the genetic toolkit

So how do altruistic behaviors evolve?

Either the altruistic feature is not an adaptation at all, or it does provide a benefit to either the individual or the individual's genes Females of many species lay fewer eggs when population densities are high, but that's not to ensure a sufficient food supply for the good of the species What happens is that at high densities, when food is scarce, a female simply cannot form as many eggs, so her reduced fecundity may be a physiological constraint, not an adaptation

Character displacement in Anoles lizards (microevolutionary scales)

Evolution in real time: character displacement of a native species in Florida following invasion by a congener from Cuba Anoles lizards that coexist in the same location compete for food at other resources. What happens here is that small islands in florida that were invaded by the cuban anole during the last couple of decades, the florida native anole species underwent character displacement due to competition with the invader in just 3 years (20 generations) Displacement in the size of toepads happened in just 3 years or 20 generations The character that was displaced was the toepad, which makes sense because these structures are specialized for tree climbing. Essentially, the native species started climbing trees to avoid competition with this Cuban invader Notice that in control islands that lack of the invader species, which are denoted with white circles in the map, that toepads for the florida native species are much smaller compared to those in the invaded islands. This observation was based on both wild-caught individuals and in common garden experiments confirming that there's a genetic bases to the displacement, ruling out phenotypic plasticity as an explanation macroevolutionary scales: Similar eco-morphologies in different islands in the Caribbean Now, character displacement in the anole lizards in the Greater Antilles even extends to macro-evolutionary scales. In other words, speciation events are also involved here. So, each of the large islands in the region (cuba, hispaniola, jamaica, and puerto rico) includes a monophyletic radiation of species that have evolved within each island So within each island, different microhabitats (shown on left, such as tree crowns, twigs, trunks, and grass bushes) include different anole species with very different adaptive morphologies, showing how characters have become displaced over millions of years of evolution (so again, at large macroevolutionary scales) But it gets more interesting. These eco morphotypes originated in different islands independently, so the crown giant anole in Jamaica looks more similar to crown giant anole in Puerto Rico than to the trunk anole in Jamaica. Obviously, the phylogeny tells a different story hereto the morphology here, since all the species in Jamaica are more closely related to each other than to other species in other islands. So crown giants in different islands are the product of character displacement via convergent evolution, and this is one of the greatest examples that show that evolution can be deterministic. So imagine that a new island emerges in the Caribbean and it is then invaded by a trunk-ground species from Cuba. if we allow millions of years of evolution, we would expect to see a radiation of anoles in the new island that will include a tree crown species that evolved to be giant

Intelligent design (another anti-evoluntionary argument)

Evolution is far from perfect. It is so imperfect that we can actually calculate an intelligent design Why are the azuela genes in our genome in our genome? Genes that do absolutely nothing in humans. There are forces of the genes for every calling functional gene Imperfect evolution: 20 extra feet of recurrent laryngeal nerve in the giraffe's neck 2005 court case in the US: a judge ruled that intelligent design is not science (but rather, religious doctrine in disguise)

Uses and implications of evolutionary science

Evolutionary science not only attempts at explaining our origins, but it also has important practical implications in health science, food production, and other areas that can affect our lives This is exemplified by the famous cartoon by Garry Trudeau in which a patient who is diagnosed with TB asks a doctor if his condition is treatable. The doctor considers the options by asking if he is a creationist because, if that's the case, he can just describe the antibiotic streptomycin, which would have worked fine before humans started using antibiotics. But if the patient does believe in evolution, they need to consider that the original TB has not evolved into a strain that is resistant to multiple drugs and thus would prescribe instead the latest drug developed to treat TB. the patient finally asked "What are these new drugs like?" and the doctor responds "they are intelligent design"

The extreme adaptations

Has tiny blue light to make it look small Big red light to help them see but other organisms can't see it Enormous jaw with tremendous hinges Some deep sea fish have extendable stomachs

Heterochrony (process)

Hetero means different and chrono means time, so heterchrony is the process of evolutionary change in the timing or rate of developmental events In evolutionary developmental biology, heterochrony is any genetically controlled difference in the timing or duration of a developmental process in an organism compared to its ancestors or other organisms. This leads to changes in the size, shape, characteristics and even presence of certain organs and features. an evolutionary change in the timing or rate of developmental events

The hominin lineage: second wave of dispersal out of Africa (0.6 mya) by Homo heidelbergensis

Homo heidelbergensis is a direct descendant of homo ergaster This happened around 600,000 years ago Homo heidelbergensis gave rise to the popular Neanderthals in europe, and also to the species that is only known based on ancient DNA called the Denisovan Cranial capacity increases

Organismal Complexity vs. Genome Size

Homo sapiens: the human genome comprises 3.2 billion base pairs Pine: 23 billion base pairs (about 7 times more dna than humans have) By comparing humans to plants, we can see a rather surprising disconnect between our impression of the complexity of the organisms and the DNA that underlies these organisms Homo sapiens: 20,000 protein-coding genes Rice: 60,000 protein-coding genes Remember a lot of DNA is non-coding This highlights a surprising fact about life on earth: there is no simple relationship between our sense of the complexity of an organism and the size of its genome measured by the total content of DNA or the number of protein-coding genes

How does altruism evolve? Recap on kin selection

How do we explain worker ants that labor for the colony and do not reproduce, or birds that emit a warning cry when they see a predator approaching the flock? Kin selection: best understood from the "viewpoint" of a gene! An allele for altruistic behavior can increase in frequency in a population if the beneficiaries of the behavior are usually related to the individual performing it

The Evolution of Genes and Genomes, lecture 20 outline

How new genes originate Different fates of new genes How genes die How and why the number and structure of Chromosomes evolve Evolution of genome size and genome content

How humans differ from other apes

Human brains are 3x larger than the average primate brain a major difference between modern humans and living Apes is that we are fully bipedal the origin of bipedalism in our lineage led to important adjustments in our body plan, including changes to shape of the pelvis, an s-shaped vertebral column in the lumbar region, a forward relocation of the foramen magnum of the skull and other features by the time bipedality evolved, the African climate had become dryer and hominins inhabited open Savannah's instead of wet Forests. natural selection favored walking rather than climbing in this new environment. An erect posture may also have help in picking low-hanging fruits and running for hunting when hominins became runners, sweating was important for evaporative cooling. This probably selected for reduced hair, which is another remarkable feature of our species the zoologist and anthropologist desmond morris referred to humans as naked Apes. perhaps the most striking anatomical difference between humans and apes is the size of the human brain. Relative to body size, our brain is 3 times larger than the average primate brain, and five times larger than the average mammalian brain

Imbalance in a coevolutionary conflict

Imbalances can emerge in evolutionary conflicts Fruits of the Japanese camellia (Camellia japonica) have a much thicker pericarp in southern than northern Japan The rostrum of the camellia weevil (Curculio camelliae) is much longer in southern than in northern populations To the left of the dashed line, plants are effectively defended against the weevils, while to the right of the line the weevils can feed on the seeds

Source of ecological adaptations

Important ecological adaptations can also result from gene duplication Example: the monkey shown (the douc langur) lives on a diet that it mostly based on leaves. Like with cows, the leaves are fermented in the gut by symbiotic bacteria and the monkeys gain nutrition by digesting the bacteria. One of the enzymes that digests the bacteria is encoded by the RNAase 1B locus RNASE1B locus originated by gene duplication about 4 million years ago This new enzyme rapidly evolved nine amino acid changes, and those changes allowed the enzyme to work in the low pH environment of the monkeys gut that is needed to ferment the leaves Nine amino acid changes that allow the enzyme to work in the low-pH environment

Ancient and recent DNA: Humans, Denisovans and Neanderthals

In a past decade there has been many discoveries based on the ancient DNA about the history of denisovans, neanderthals, and modern humans by the groups of Svante Paabo in Germany and David Reich at Harvard Svante's group is the one that sequenced the Neanderthal genome based on a finger bone dated at 50 thousand years. They also discovered the Denisovans based on DNA obtained from a tiny bone We know nothing about the anatomy of Denisovans, all we have is the genetics for that species

The genetic toolkit and the evolution of novel characters: gene co-option

In addition to differential expression, another important genetic toolkit is gene co-option. Many Hox genes can also play multiple roles via co-option. Remember exaptation? a trait that has been co-opted to serve a new function Gene co-option: evolution of novel functions for pre-existing genes and developmental pathways. Developmental Pathways have often been co-opted for new functions. Gene co-option is probably responsible for the evolution of many novel morphological traits

Evolution of enemies and victims

Interactions between predator-prey, parasite-host, and herbivore-host plants These interactions can be unstable because enemies can extinguish or diminish their victim's population (ex: covid-19 and human host) Victims and enemies may coexist if their interactions are stabilized by ecological and evolutionary factors. For example: adaptations to escape or resist Some species have evolved extraordinary adaptations to capture prey, infect hosts, or escape predators For example, figure on left shows the larva of a parasitic trematode which migrates to the eyestalk of its intermediate host, a land snail. This causes a change in the coloration (and size) of the eyestalk and makes it more visible to the next host in the parasite's cycle (which is a snail-eating bird) On the right, we have the cryptic morphology of the katydids which have a remarkable resemblance to leaves, which helps this species to avoid predation extreme adaptations

evolution of competitive interactions

Interspecific competition: competition for resources across different species (if they use the same sort of resources) Species that use the exact same resources cannot coexist indefinitely, leading to one of them going extinct In this sense, competition may impose selection on the competing species, which will lead to a divergence in resource use. So species may evolve to use different types of foods Competition may lead to divergence and ecological character displacement!!!: Divergence in response to competition between species is called ecological character displacement. Example showing changes in the bill sizes of the Galapagos finches is correlated with the available resources or seeds of different sizes In A, the frequency of distributions of bill size overlap and the fitness is lower for the ones that overlap because of direct resource competition In B, selection against phenotypes that compete for the same resources may lead to divergent evolution and ultimately character displacement. So the character that is being displaced here is the size of the bill The bill depth of different species that co-exist in the same island diverge in response to the size and hardness of the seeds available to them

Many species have very similar embryos: can you tell which is the human, the mouse and the alligator?

Karl Ernst Von Baer: diverse vertebrate animals are very similar early in development (embryos); the characteristics that distinguish major vertebrate groups (e.g., mammals, reptiles, birds) are developed only at later stages (adults) Karl Ernst von Baer proposed a remarkable pattern about comparative animal development. By looking at the embryos of diverse vertebrate groups, von Baer noticed that they all look alike and that the main characteristics that distinguished them are developed only at later stages (look at image comparing embryos of human, mouse, and alligator... from L to R it goes alligator, human, mouse. By looking at image it is very difficult to tell which is which)

Language

Language is another remarkable tray of our species Originated as a result of social cooperation and accumulated knowledge It mediated social interactions and also enabled humans to transmit and receive information that was important in many other contexts, leading to an increase in language complexity Key adaptations: shape of larynx and tongue The tongue curves down into your throat to produce a particular Vocal Track that enables us to generate a remarkable diversity of sounds Language in 'Kanzi' -a bonobo Pic of cute monkey named Kanzi He was taught by Sue Savage to learn symbols by observation Kanzi Was able to associate over 200 different symbols with English words. The most remarkable thing is that he was able to create meaningful colorations of symbols for more complex communication. He couldn't talk but none the less this is remarkable

The human brain

Large brains: 3x larger than in other primates. This is the most remarkable physical trait of our species Adaptation by natural selection for living in large social groups Across species of monkeys and apes, there seems to be a strong correlation between the mean size of social groups and the relative size of the neocortex, what is the part of the brain that is most important to learning, memory, and recognition natural selection also probably favored larger brains that were more efficient at learning to function in complex environments. For example, while hunting

Natural selection in humans: past and present

Manhattan plot with genomes from European and Asian populations, including ancient DNA samples (8,500 years), so this is a historical plot We can see that most genes are fairly similar between different populations, But we can easily not the skyscrapers or outliers, hence the name Manhattan plot 12 genes showing strong adaptive evolution in human These are the 12 outliers, showing substantial differences across populations and thus reveal strong signals of adaptive evolution The first and most conspicuous signal is one of lactase persistence, Which means they continued activity of the enzyme lactase in adulthood. The majority of people in the world remain lactose intolerant as adults. Lactase persistence is associated with domestication of livestock (milk-producing animals) and consumption of dairy products Ancient DNA analysis have shown that mutations 4 lactase persistence originated and Europeans 4500 years ago for the first time The farther different populations are from Africa, the lower the genetic diversity and the greater the number of deleterious mutations the number of deleterious mutations in the human genome increases with a distance of a population from Southern Africa what we are seeing is successive waves of founder effects that lead to a reduction in genetic diversity associated with colonization events of different regions. And this happens because each time humans spread to an even more remote part of the planet, a small number of brave colonists set out, causing a series of genetic bottlenecks that increased the number farther from Africa they went so bottlenecks cause heterozygosity to be lost. variation declines with distance from Africa. Africans have the fewest deleterious mutations, while Europeans and Asians have more. people whose ancestors managed to spread all the way across Asia , the Bering Strait, and finally into the new world, are burdened with even more deleterious mutations

Exon shuffling

Mechanism for the evolution of new genes; in the process, coding sequences from different genes are brought together to generate a protein with a novel combination of domains. Mixtures of exons duplicated from genes with different functions can also generate new genes with new functions, which is a process called exon shuffling Duplicated from genes with different functions Yellow-emperor(Ymp) +Alcohol dehydrogenase (Adh) =The new Jingwei gene Ex: with the jingwei locus, which is found in only 2 species of Drosophila fruit flies. First 3 exons of this gene are duplicates of exons in the yellow emperor (or YMP gene) that are found in other species of Drosophila But the fourth exon is a duplicate of the entire alcohol dehydrogenase or ADH gene that became inserted into the YMP gene. So the new jinwei gene shows evidence of rapid evolution by positive selection after it originated about 2 mya

The evolutionary history of Homo sapiens

Mitochondrial DNA is inherited maternally, which is the technical term for saying that it is passed through mothers only Purpose of this: 1. To emphasize the complexity of the evolutionary history of humans We are an extremely mobile species. So, the typical barriers that cause allopatric speciation in other groups don't really work with us humans 2. With the genomic revolution in the last couple of decades, we have learned so many new things about human evolution and this is a rapidly changing field. for example, back in 2009 scientists were still debating whether humans and Neanderthals interbred. With the sequencing of the Neanderthal genome in 2010, we now know that not only did they interbreed, but that hybridization happened also in many different regions throughout the world

Evolution of cooperative interactions

Mutualism can evolve because it is directly beneficial to the actor Or it can evolve by reciprocity, based on repeated interactions between individuals The evolution of mutualism is not so obvious since individuals can "cheat" If a mutation for cheating has a high fitness, then it will spread rapidly resulting in the collapse of cooperation Cheating is about the effects on fitness, on the behavior. This is not to say that animals, let alone microbes or genes, can consciously plan their actions Mutualism and altruism are both cooperative behaviors

Cooperative Interactions

Mutualistic and altruistic interactions

Sahelanthropus (6-7 mya)

Oldest known hominin This fossil marks the minimum age for the split of our lineage and the chimp, dated at around 6 to 7 million years

Refuting anti evolutionary arguments

One of the arguments is that evolution is outside the realm of science because it cannot be observed We have seen many examples of evolution happening in real time before our eyes Remember the harbor experiment on the large p3s with different antibiotic concentrations or evolution of species that will be extinct in less than a decade as a result of competition with an invader Ex 2: Evolution cannot be observed: SARS-COV-2 phylogeny Tree here shows the evolution of the coronavirus based on data obtained from patients around the world from December through march. We can easily see how the virus has mutated through time Based on the genetic analyses, there is no doubt that the virus originated in china. Another argument: Evolution cannot be proved But nothing in science is ever actually proved. Only mathematical theorems can be absolutely proven

Gene duplications: an engine for evolutionary change

One of the most fundamental questions we can ask about evolution is how biological novelty originates... and the answer must lie partly with the origin of genes that have acquired new functions we now know that many new Gene functions have originated via Gene duplications. And this hypothesis was proposed by Susumu Ohno A hypothesis proposed by Susumu Ohno (Japanese-American geneticist) Gene duplications are the most common way that gives rise to new genes in eukaryotes The evolutionary change is that one copy can preserve the old function while the other copy can change and gain a new one In other words, this is Evolution's way of copy-pasting One copy can preserve the old function, while the other copy can change and gain a new one This is evolution's way of 'copy-pasting'

Practical applications of evolutionary science: Health and medicine (genetic diseases, cancer, infectious disease)

Only a few decades ago, antibiotics were considered wonder drugs because they work so well to cure diseases But many antibiotics are not less effective precisely because they have worked so well initially and because of their widespread use. So the golden age of antibiotics in the 60's was short-lived. During the past few decades, many strains of bacteria have evolved resistance to antibiotics Antibiotic resistance crisis: a dramatic example of evolution via natural selection An example of this is shown on the right with gonorrhea... in the 1960's, penicillin was able to control most cases of gonorrhea. But today, more than 24% of gonorrheal bacteria in the US are resistant to at least 1 antibiotic. And 98% if gonorrheal bacteria in southeast asia are resistant to penicillin. Infectious bacteria today are much harder to control than their predecessors Why do we need to get flu shots every year? Can't just one vaccine do the trick? No, because viruses evolve fast! Viruses are even worse as they tend to evolve much faster than bacterium... so that is why we need to get flu shots every year A single vaccine won't do the trick because the influenza virus has evolved so much over the course of a year, your immune system no longer recognizes the vaccine you got the previous year. And chances are the new coronavirus will become seasonal too Tracing the origins of HIV using phylogenetic analysesWe can also learn A silver lining in the evolution of virus is that the differences in their DNA or RNA sequences provide a way to trace their origins using phylogenetics. Ex: Transmitted to humans in Africa from a chimp HIV. according to the tree, chimpanzees were the original host of the HIV clade. Further analyses have shown that different lineages of HIV have arisen independently, by cross species transmission to humans (which probably happened via gorillas) Phylogenetic viruses have also been used in trial cases, ex: phylogenetic study led by SCC showed that a dentist in florida infected 6 of his patients with HIV Phylogenetic analyses showing that a Florida dentist infected patients with HIV All of the analysis conducted supported the existence of a dental plague, which suggests that the dentist's HIV strain is ancestral to those found in patients a, b, c, e, and g... but not in other patients such as f, d, and the controls Did the Florida dentist infect his patients with HIV? Yes, the HIV sequences from these patients in the top of the phylogenetic tree fall within the clade of HIV sequences found in the dentist

The phylogeny of living apes

Opposable toes from orangutan → gorilla → chimp then non-opposable toes in humans here we zoom into the phylogeny of living Apes. our closest living relative is a clade that consists of two species, the chimpanzee in the nearest sense of the word, and a bonobo, both of which are sometimes referred to as a chimpanzee in the broader sense of the word. the Divergence between homonyms and the chimpanzee lineage took place around 7 million years ago, which corresponds to the late miocene in the geologic scale. Hominins include many species see, as will be explained later. And with the exception of our own species, other hominins are extinct, including the neanderthal non-human Apes have feet that are like hands with opposable toes. Their thumbs are also opposable, but not as opposable as ours. African apes are highly social, and males are considerably larger than females, which is a consequence of sexual selection

Madagascar orchid → pollination?

Orchids are very diverse, both morphologically and in terms of numbers of species Phenotypic extreme represented by the nectar tube of the Madagascar orchid (shown in image) Based on the presence of this long spur, Darwin predicted that there should be a moth with an extremely long tongue that pollinates this flower This idea wasn't really accepted at the time, when flowers were conceived as a divine design of god Darwin suggested that the main adaptation of these long Spurs in the orchids was to attract insects and increase the probability of pollination 40 years after Darwin's death, the moth with the really long tongue was actually discovered (the Sphinx moth)

Gene Duplication: A key role in genome evolution

Pic shown of a phylogeny of mouse. The numbers beneath each branch in the phylogeny show the number of genes gained (+) or lost (-). The pie chart shows the fraction of genomes that have expanded, contracted, or not changed. And we can see that while chimps have largely experienced a contraction in their genome via gene losses, humans have instead undergone expansions via gene duplications

hybridization with Neanderthals and Denisovans according to genomics

Picture of this

Conflict between group and individual selection

Pink = Non-altruistic genotype(higher fitness) Blue = Altruistic genotype (lower fitness) A-"Group selection" fallacy Group selection favors the "altruistic" genotype Wynne-Edwards: Altruistic Behavior will evolve because group selection favors in (i.e., more "selfish" populations go extinct) B - Selfish genotypes prevail! The "selfish" genotype has a higher individual fitness Williams: Within-population selection favors the "selfish" allele and increases it more rapidly than whole-population selection can act, so the selfish allele will become fixed Here, we can see how the original theory on group selection A suggests that an altruistic genotype will spread, but as we know, that is not how natural selection operates B is what actually happens - the selfish genotype that is non-altruistic will have much higher fitness than the altruistic one and will therefore spread rapidly via natural selection

Two clusters of Hox genes: Bithorax and Antennapedia

Pioneering work by E. B. Lewis (1940s-1970s) on the Bithoraxcluster and by T. Kaufman (1970s-1980s) on the Antennapedia cluster They found that the genes in both clusters control the anterior-posterior identity of segments corresponding to their order on the chromosome they identified that the order of genes and both clusters in the chromosomes control the anterior posterior identity of segments in the same order

What about plants?

Plants also have homeotic genes that are master regulators of developmental processes Tomato (Solanaceae): MADS16 gene off in the fruit: no fruit envelop Ground cherry (Solanaceae): MADS16 gene on around the fruit (sepals): fruit envelop although we know much more about Developmental Pathways in animals than in plants, the same principles also apply here, consider these two species, the Tomato species in the ground cherry these belong in the same family Solanaceae In tomatoes, the MADS16 gene is only expressed in vegetative tissues but in ground cherries, The gene is also expressed in the sepals after pollination, which causes these flower parts to grow into a "balloon" that envelopes the fruit

Adaptations against herbivores

Plants can also protect themselves from herbivores by synthesizing a variety of secondary compounds Many of these compounds are toxic or repellant to animals, which results in the selection of some insects for chemical defenses These secondary chemicals provide a mechanism of defense for plants against herbivores Ex: common milkweed, which is genetically variable for latex production. Plants with great latex production have fewer herbivorous insects and higher fitness (shown by the seed production on the right compared to plants that produce less latex). So fitness of common milkweed is strongly affected by genetic variation in the production of latex, which reduces the abundance and impact of insects on the plant

The Birth of a Gene: Gene duplication

Principal mechanisms: 1. Unequal crossing over Recombination happens between different positions on chromosomes that are misaligned during meiosis Mispairing due to unequal crossing over Picture c: unequal crossing over → results: 2 copies (normal), 1 copy (deletion), 3 copies (duplication), 2 copies (normal) Recombination can lead to multiple extra copies or even fewer copies due to deletions 2. Replication slippage DNA polymerase loses its place and copies a segment of a chromosome twice, so the resulting chromosomes can carry a gene that is duplicated in tandem with the parental copy Replication slippage: errors during replication result in two copies in tandem of a gene Duplication mutation, a section of DNA on the duplicate chromosome is duplicated 3. Duplicated in tandem with the parental copy

Coevolution

Process by which two species evolve in response to changes in each other. The evolution of one species has been affected by the other, and vice versa. Reciprocal genetic changes in interacting species, owing to natural selection imposed by each on the other. "I can understand how a flower and a bee might slowly become, either simultaneously or one after the other, modified and adapted in the most perfect manner to each other, by the continued preservation of individuals presenting mutual and slightly favourable deviations of structure" (Darwin, 1859) This process of perfect adaptation, in Darwin's words, where the evolution of one species has been affected by the other (and vice versa): aka co-evolution!

Creationism and science

Public acceptance of evolution across countries: 2005 poll ask respondents if they thought evolution is true. A great majority of people in europe do not question the reality of evolution, (even religious people from countries like italy) Back in 2005, the united states ranked second lowest in public acceptance of evolution A more recent, 2018 poll shows that most U.S. adults (81%) believe in some form of evolution So things appear to be improving Now, the position of many religious people who do believe in evolution is that God established the natural laws (such as natural selection) and then let the universe to run on its own without further supernatural intervention

Allometric growth or allometry (pattern)

Refers to the differential rate of growth of different structures of an organism during its development Allometry is how an organism's features change relative to the size of its other features. In its narrowest sense, allometry refers to the different rates at which different organs grow. For instance, a male fiddler crab's display claw grows much faster than the rest of its body. Positive allometry (a>1), Isometric growth (no allometry, a=1), negative allometry (a<1, Y grows slowly relative to X, ex: head grows slowly relative to torso) In the plot to the left, we compare different features (say body size on the x which is the independent variable, and the other trait of interest in the y-axis, Such as head length, which is the dependent variable) so if the traits grow at a constant rate, such as the curves 1 and 2 in green and light green, then the growth is said to be isometric meaning there is no allometry, or there is constant growth but what is remarkable here is allometry, those are the blue and the red curves denoted with numbers 3 and 4. with the red curve we have positive allometry, in which the growth of the y variable happens at a faster rate than the independent x variable. In our example of head vs body size, positive allometry would result in adults having much larger heads in proportion to the size of their bodies compared to juveniles Negative allometry is the opposite. The girls of the head would be much slower than the rest of the body in our example. So adults would have much smaller heads in proportion to the size of their body compared to juveniles. In the picture on the right, we can see that the Beatles show positive allometry in their mandibles. So mandibles are much larger in proportion to body size in adults compared to juveniles Allometric growth is widespread and can also be seen in humans. We can see that heads, for example, show negative allometry sense they're much smaller in adults than juveniles after correcting for body size, what is the purpose of the images to the right

The Fate of a New Gene

Regardless of how new genes are bron, a new gene starts Its life as a single copy in the population. Figure shows different fates of gene duplicates Gene duplication mutations, or "dup" in the graph, produce chromosomes carrying an extra copy of locus A. copy number variation, or CNV, occurs when a duplicate is polymorphic. So in other words, chromosomes with different numbers of copies of locus A are present in the population. and some duplicates that become fixed retain their original function and serve to crank up production of the protein the gene produces. but a function duplicate that has become fixed can later be lost by a mutation that deletes it (so the "del" on the graph) or that renders it a pseudogene. A duplication can also acquire a mutation that leads to a new function. If this mutation becomes fixed, a gene family originates and Gene families are the next topic we will discuss

serial homology

Repeated modules have the same origin. Many of these modules are repeated leaning to duplicate organs in the body, which is this concept known as serial homology we learned before that homology means shared origin, so the term serial refers to the duplication of organs in the body.

How science works

Science is not about absolute truths; it accepts hypotheses provisionally and changes them in the face of convincing new evidence It is concerned only with testable hypotheses and thus depends on empirical studies subject to peer scrutiny (which can be verified and repeated by others) Creationism has none of the features of science (so it has no claim to be taught in science classrooms) Scientists have tested and falsified creationist claims: A worldwide flood once occurred The earth and all organisms are less than 10,000 years old (this claim about the age of the earth was actually refuted before the publication of Darwin's book) But science cannot reject the existence of Good, because it cannot even test it It is not testable, and therefore it cannot be falsified

Costs and benefits of interactions among individuals within a species

Several ways individuals in a species can interact, typically denoted with + or - signs, depending on the outcomes to the fitness of the individuals reactions. First sign denotes outcome of actor, second sign denotes outcome of recipient

individualization

Some homologous modules acquire their own identity. So some of these repeated modules acquire their own identity, which is a phenomenon that is further termed individualization

Repeated domains

Some proteins also have repeated domains that confer part of the function. For example, the sodium channel that is critical to the firing of vertebrate nerves has 4 domains with very similar structures 4 domains: two rounds of duplication of an ancestral gene These arose by 2 rounds of duplication of a gene in a remote ancestor that encoded for only a single domain

Types of coevolution:

Specific coevolution, Diffuse coevolution, Phylogenetic coevolution, Escape-and-radiate coevolution

Darwin suggested the existence of an animal capable of pollinate this species

Sphinx moth Uses its long tongue to feed on the nectar, and in the process it helps pollinate the orchid Darwin also observed that plants with shorter nectar spurs are pollinated by insects whose tongues are long enough to reach the nectar. His speculation was based on the principles of natural selection and genealogical relationships (look at quote below)

Hox genes and the dawn of modern Evo-Devo

The formation of modules and subsequent individualization during development leads us to this key cluster of genes called homeotic selector genes, or Hox genes for short. We can argue that the discovery of Hox genes gave rise to the field of evo-devo Hox genes are key in the origins of modules and individualization Between the 1940's and 1980's homeotic selector genes( Hoxgenes) were discovered in Drosophila Hox genes control the patterning of specific body structures Hox genes control the identity of segments along the anterior-posterior body axis of all metazoans Hox genes are members of the homeotic transcription factor family that play a key role in controlling the body plan along the cranio-caudal axis (also referred to as anterior-posterior), and specify segment identity of tissues within the embryo.

The evidence for evolution

The fossil record Phylogenetic and comparative studies, including developmental biology Genes and genomes Biogeography

developmental pathways or developmental circuits

The genes that regulate function in hierarchies or networks

lecture 20 Summary

The most common origin of new genes in eukaryotes is by gene duplication Most gene duplicates degenerate into nonfunctional pseudogenes. Some duplicates survive, however, and evolve to specialize in one of the functions of the original gene; or they can take on a new function Another important route to adaptation comes from changes in how genes are expressed Chromosome numbers change by fusion and fission. Inversions are also an important feature of the structural evolution of chromosomes Transposable elements, which are genetic parasites, are a major component of the noncoding DNA and account for much of the variation in genome size among species of eukaryotes

The origins of Homo sapiens (0.2 my-present)

The oldest fossil attributable to is 200,000 years old Average brain size increased throughout hominin history, and we have by far the largest brain So a remarkable increase in brain size There were also other changes in teeth, face, pelvis, hands, and feet Modern humans evolved from an ape-like ancestor, there is no scientific doubt about that a third wave of dispersal out of Africa This happened around 60,000 years ago Based on DNA analysis to estimate effective population size, it is estimated that only 2,000 individuals dispersed Out of Africa. These individuals were the ancestor of almost all the six million people living outside of Africa today humans colonized Europe, East Africa, and Australia between 60 to 40,000 years ago they walked from Siberia Into Alaska about 20,000 years ago when the sea level was well any Bering Strait was dry. It took them only eight thousand years to spread throughout North and South America. in less than 50,000 years, our species colonize the entire planet a mitochondrial gene tree of human populations mtDNAtree (matrilineal) Mitochondrial DNA only tells a fraction of the story, but it does tell a clean story Confirms close relationship with Neanderthals, Confirming the anatomical traits of the fossils Deepest branches in tree are from Africans (red) Non African humans share a common ancestor that is not shared by any Africans. So we all come from Africa, and the woman who carried that mitochondrion, also known as the mitochondrial eve ( a hypothetical ancestor that has nothing to do with the biblical Eve) about to happen is thought to have lived about 125,000 years ago Note that all mitochondrial lineage is outside Africa descended from just one branch of the African Gene tree

Practical applications of evolutionary science: Agriculture and natural resources

The the Irish Potato Famine: a case of missing genetic variation due to monoculture The irish in the 1800's planted a potato variety. Potatoes can be propagated vegetatively, so all the lumpers were actually clumps genetically identical to one another So this set the stage for human and economic brewing. When the deceased light hit the plantations, lack of genetic variation caused a collapse of the lumber on the lumber clonal variety (which could have been avoided in the first place growing genetically diverse potatoes) 1 in 8 irish people died of starvation in just 3 years Pest resistance and refugia Another common example is the evolution of pesticide resistance Pesticide insects have short duration times and large population sizes, which means they evolve weekly. What do farmers typically do to avoid pests? They spray, of course. But pests can evolve resistance to pesticides real fast because they have a very short generation time... So how can farmers slow the spread of resistant genes? Evolutionary theory actually provides a solution here by including isolated/free from pesticide areas where non-resistant insects can thrive. These isolated areas are called refugia In the absence of refugia, pesticide resistant beetles would eventually evolve and spread through their plantations. But keeping a refuge field without pesticides near fields planted with pesticide producing crops, both resistant and non-resistant beetles will be maintained. in this way, the gene pool preserves the non-resistant alleles And what happens here is that the alleles that are resistant are actually recessive. That means that the resistant allele can be masked by the dominant non-resistant allele. So if a resistant insect in the pesticide-producing field mates with a non-resistant insect from the refuge, all of the offspring will be non-resistant. In this way, there is a system below if beetles in the pesticide field continue mating with non-resistant beetles in the refuge, the final result is a low incidence of the pesticide resistant allele in the fields

Evolution: both fact and theory

The theory of evolution. Is it just a theory? It is a theory in the scientific sense, which is a coherent body of ideas that are well supported and confirmed by evidence and experimentation It is not a theory in the common sense, which is merely unsupported speculation Evolutionary theory interconnect ideas about the causes of evolution, genetic load, mutation, natural selection, and sexual selection Evolution is a theory in the same way gravitation and relativity are theories Evolutionary theory as we know it is considered a scientific fact It is a fact in the same way the Earth revolving around the sun is a fact Like other scientific theories evolution is also consider work in progress, since we don't yet know all the causes for it

Hox gene expression in Drosophila

There is an antennapedia complex and a bithorax complex Knocking out individual Hox genes in Drosophila causes homeotic transformations—in other words, one body part develops into another. A famous example is the Antennapedia mutant, in which legs develop on the fly's head instead of antennae. The figure shows a perfect match between the order of the Hox genes antennapedia and by thorax in the chromosome and the Order of segments in the body of a fly from head to abdomen along the anterior posterior axis.

Co-option of developmental pathways in the evolution of novelties: Hoxa & tetrapod limbs

This picture shows an example of co-option of Developmental Pathways involved in the evolution of tetrapod Limbs Ancestrally, Hox genes are expressed only along the anterior-posterior axis of the developing body. During Evolution, however, paired forelimbs and hind limbs involved in the novel gene expression by co-opting Hox genes 9 through 13. the picture below shows a zooming in into the expression of Hoxa and the evolution of the main bones of the forelimb and hindlimbs in vertebrates . so again, there is a match between Gene sequence and structure order in the body. But there's more. We can see how the humerus in the forelimb and the femur and the hind-limb (H and F in the top green panels) are essentially regulated by the same hox 9 and 10 genes. same thing for the radius and the tibia denoted by r&t in Orange/red. they are regulated mostly by hox 10. and finally, this is also a case With the metacarpals and metatarsals (MC and MT in light green) that are mostly regulated by Hox 12 and 13 that is why the bones in the forelimbs and hind limbs are so similar. They are homologous features regulated by the same genes. Note that we can see in dark blue the jeans that are upregulated and and light blue the ones that are down regulated. So this is how transcription factors work like the dimmer switches

Phylogenetic coevolution

Two lineages of hosts and parasites co-evolve for a long time so that speciation events produce similar (mirror) host-parasite phylogenies Ex: the association between insects and endosymbiotic bacteria that live in specialized aphid cells, supplying the essential amino acids to their hosts. So the phylogeny of the endosymbiotic bacteria is perfectly congruent with one of their aphid hosts. These completely congruent phylogenies suggest that the associations between the host and the parasite dates from the origin of the aphids, and the bacteria diverged with their hosts due to vertical transmission Remember, vertical transmission means through the ancestor-descendant paths, and that may be misleading here because of the horizontal arrangement of the phylogenies shown. So vertical here is along the horizontal axis since the trees are depicted horizontally

Specific coevolution

Two species evolve in response to each other(e.g., Cheetahs and gazelles or the Madagascar orchid and the sphinx moth)

Parasite-host coevolution

Water-flea example that shows the variation in parasite resistance of the water-flea (Daphnia) Daphnia, the host, produces eggs that can remain dormant in pond sediments for many years/decades and the eggs may harbor spores of their bacteria parasites. This is a great system because it allows for resurrection ecology studies Why is this called resurrection you may ask? What happens here is that dormant Daphnia eggs obtained from different layers in these ponds can be revived and hatched after many years What the graphs show is experimentally cross-infected Daphnia from different sediment layers or time periods (remember the deeper the layer, the older it is) So comparisons are made in the past (one year before), contemporary, and future (one year after) cross infections The study show that the bacteria were more successful at infecting contemporary (present) Daphnia. So in this case, Daphnia populations and their bacteria evolve in concert. The daphnia changed so that they were no longer as easily infected by older bacteria, and the bacteria changed being able to infect contemporary Daphnia

Evolution of Gene Expression

We have seen how a gene can evolve by mutation, therefore changing the coding sequence that alters the pterin made by the gene. There are also 2 key components to understand here. The genes code for certain proteins but there are also promoter and enhancer regions, which are switches that tell genes when are where to become active Genes are transcribed into proteins (transcripts) But there are also 'switches' that turn genes 'on' and 'off' These switches are regulatory regions, including both promoters and enhancers In other words, these switches turn genes on and off selection can also alter how often, when, and where a gene is expressed, how the transcript is sliced and processed, how the transcript is translated into a protein, and how it is deployed. So several mechanisms are involved here many evolutionary changes to expression of genes come from changes in the regulatory sites ( in other words, these switches). when we say a gene is expressed, what we mean is that it is on. of the many places in the genome that show evidence of adaptation, between 40% and 80% are regulatory (so the switches that turn genes on and off), while only 17% or the actual coding regions that encode for proteins this is shown on the pie chart on the right Changes in sites that bind transcription factors Alternative splicing patterns Epigenetic changes

Evolutionary Developmental Biology (Evo-Devo or EDB)

What role has development played in the history of life? development has played an important role in the history of life. So the field of Evo-devo or EDB integrates data from comparative embryology, or morphological Evolution, and developmental genetics with the goal of understanding the mechanisms by which development has evolved "Evo-Devo" (or EDB) seeks to understand the mechanisms by which development has evolved Biologists in the 1700s-1800s (G. Saint-Hilaire, E. von Baer, C. Darwin) were fascinated by the patterns of similarity and divergence in development among species Integration of developmental biology with evolution is recent Until recently, developmental biology was not integrated with evolution The difference in wing number between Diptera and Lepidoptera is due to differences in how Ubx regulates downstream genes Diptera(2 wings, 1 pair) Lepidoptera (4 wings, 2 pairs) The presence of either two wings in dipteran insects vs 4 wings in lepidopterans is due to differences in how the Hox gene Ubx regulates Downstream genes

Agricultural revolution

What's the most important technological advance in human history? Strong case for manipulating evolution via artificial selection Selective breeding wheat, cows and other plants and animals, humans gained access to abundant resources for the first time in history ca. 11,000 years ago Timeline of domestication of plants and animals in different regions Agriculture was developed independently at several places around the world this cradle of human civilization is the Fertile Crescent, which is highlighted in the map technological advances in the Fertile Crescent, such as the use of irrigation, writing, the wheel, the glass, all of which first emerged in Mesopotamia, were ultimately fueled by the Agricultural Revolution With the domestication of barley, wheat, peas, and lentils other key agricultural cradles include Mexico and Central America, where corn, cucumber, beans, and peppers were domesticated other crops domesticated are shown in the map

Whole genome duplication

Whole genome duplications are much more frequent in plants than in animals They occur when meiosis produces a gamete that carries the entire diploid genome rather than a haploid with just 1 copy of each pair of chromosomes If 2 of these gametes meet and fertilize each other, an offspring is produced that has 4 copies of each chromosome. This genetic result is called "tetraploidy" (tetra means 4, so 4 copies of the chromosomes) Occurs much more frequently in plants than in animals In some cases, the genomes duplicate via hybridization between different species (such as in pic of flowers shown) What we have in the pic is diploid species T, dubious and T. pratensis, hybridized and produced the tetraploid species T miscellus T dubious has also independently hybridized with the diploid T porrifolius to produce the tetraploid T mirus So the tetraploid has twice as many chromosomes as the 2 parent species 2 different examples of tetraploid species that have originated via hybridization between diploid species Many domesticated crop plants are also polyploid Recent events of polyploidy also have occurred during the domestication of many important crops of plants (such as wheat, coffee, and cotton). And this polyploidism has been ket in improving some of their economically valuable traits, such as fruit size and taste (ex: large strawberries we find in markets today are polyploid) 2n + 2n = 4n (tetraploid)

Australopithecus afarensis (3.5 mya)

Widely studied Ancestral ape feature: lower face projected far beyond eyes Ancestral ape feature: long arms Derived hominin feature:short fingers Derived hominin feature:loss of opposable toes Obviously also a bipedal species since, like most other hominins There are other species in the genus Australopithecus, such as A. africanus

scientific sense

a coherent body of ideas that are well supported and confirmed by evidence and experimentation

diffuse coevolution

a network of species undergoes reciprocal evolutionary change through natural selection. Several species are involved in the interaction and their effects are not independent resistance of a species to different species of parasites might be correlated (e.g., lichens, a three species interaction; limber pines, squirrels & Clark's nutcracker)

Selfish genes & kin selection... According to Dawkins, Hamilton, and others,

adaptive evolution occurs through the differential survival of competing genes, increasing the allele frequency of those alleles whose phenotypic trait effects successfully promote their own propagation Group selection is actually kin selection (or gene selection) Richard dawkins: book called the selfish gene

.Heterotopy (pattern)

an evolutionary change in the spatial position of a feature within an organism Hetero means different and topy means location, so the term referns to an evolutionary change in the spatial position of a feature within an organism. Pictures showing examples 1. Roots growing from stems. The vine has evolved exposed roots that grow from an aerial stem. 2. Entire plants growing from leaves we see entire plants growing from the leaves of this species called bryophyllum 3. Bone platelets developing in the skin the bottom two pictures show bone platelets developing in the skin of vertebrates, such as armadillos and crocodiles

Spiteful

both individuals are harmed - effect on actor and recipient - - Like in some male-male competition in sexual selection, sometimes those contests can result in -- interactions where both males become harmed

Paedomorphosis (pattern, an effect of heterochrony)

evolution of a juvenilized morphology. It can happen in two ways: neoteny or progensis One of the major effects of heterochrony, therefore it is a pattern (not a process) In Paedomorphosis, A species has a juvenilized morphology that is not observed among its close relatives. And this can happen in two ways Neoteny (process): retention of juvenile traits in adults due to delay in somatic development (growth) Progenesis(process): reproductive acceleration of development so that the juvenile becomes a sexually mature adult much faster than their close relatives More clear explanation: Species can change the timing of development compared to its close relatives. When that happens, a common effect is that a juvenile morphology can be observed in adults. And that happens because either the juveniles delays growth or accelerates sexual maturation. Now let's look at an example Patterns and processes in development: paedomorphosis and neoteny in axolotls Like most amphibians, salamanders undergo a metamorphosis from an aquatic juvenile to a terrestrial adult. We can see gills sticking out only in juveniles for respiration underwater but things are different in the Mexican axolotl. This species does not typically undergo metamorphosis, and what we see here is paedomorphosis: the evolution of a juvenilized morphology. So the retention of juvenile traits in adults by neoteny, which again is the result of a Slowdown in growth juvenile Tiger Salamander (aquatic larvae) → metamorphosis → Adult Tiger Salamander (terrestrial adult) Unlike most salamanders, the Mexican Axolotl does not typically undergo metamorphosis Adult Axolotl (no metamorphosis) This is paedomorphosis: evolution of a juvenilized morphology Retention of juvenile traits in adults are caused by neoteny: reduction of growth rate of somatic characters

so how did changes in a karyotype evolve? Although many questions are not yet answered, several patterns have emerged

fission and fusion, inversion

Escape-and-radiate coevolution

form of coevolution where a species evolves a defense against its enemies and is enabled to rapidly speciate into a diverse group. One lineage (a host/prey species) evolves a defense against enemies (parasite/predator) and is thereby enabled to radiate into diverse descendant species, to which different enemies may later adapt Multiple host/prey and predator/parasites species may be involved In this case, the predator or parasite did not evolve simultaneously with their host or prey

Evolution of Gene Expression: Alternative splicing

in eukaryotes, the production of proteins from DNA Gene regions involves splicing, which removes all segments of the message corresponding to the introns or the non-coding regions. But this slicing can also remove one or more segments that correspond to exons or the coding regions. So alternative splicing brings together different combinations of exons from the same gene. As a result, a single Gene can produce more than one protein A single gene can produce more than one protein So alternative splicing is a major mechanism used by eukaryotes to increase organismal complexity without increasing the size of their genomes it may be as important as amino acid changes in functional diversification of proteins Alternative splicing can evolve quickly Changes in alternative splicing can actually evolve quite rapidly. For example, about one-third of alternative splicing events are difference between the genes of humans and mice, while differences in their coding sequences have evolved only half as fast. So alternative splicing also contributes to phenotypic plasticity by changing the gene expression patterns on different environmental conditions without actual changes in the DNA sequence It can contribute to phenotypic plasticity Exons: protein-coding gene section Intron: non-coding gene section Promoter = Regulatory element (gene switch)

Mutualisms

interactions between species that benefits both species (+ + interactions) As we saw in the earlier lecture, mutualisms are ++ interactions. But this isn't limited to only individuals of the same species, mutualistic interactions can also happen between individuals of different species Mutualism (+ +) is best viewed as reciprocal exploitation. Selection favors genotypes that provide benefits to another species if this action yields benefits to the individual in return Thus the conditions that favor low virulence in parasites can also favor the evolution of mutualisms Mutualisms may be unstable if "cheating" is advantageous, or stable if it is individually advantageous for each partner to provide a benefit to the other Ex of that: graph shows how yucca moths lay eggs in yucca flowers. So the moths also pollinate the flowers, which is a reciprocal exploitation case in which each species obtains something from the other We have a phylogeny of the yucca family showing major evolutionary changes in which the mutualism first evolved in the ancestor of both the moth and the plant (that's where it says "yucca colonized") and later evolved twice in cheater moths. So mutualisms are not always stable over evolutionary time, as many species cheat. Cheaters that exploit their partner without paying the cost of providing a benefit in exchange is likely to have a selective advantage. So a genotype that cheats by exploiting its partner without paying the cost is likely to be advantageous But, selection also favors protected mechanisms such as punishment of cheaters to prevent overexploitation. So that way, selection will ultimately favor "honest" genotypes id the individual's genetic self-interest depends on the fitness of its host ...back to the Madagascar's orchid and the predicted sphinx The Madagascar sphinx clearly gets a benefit, but why would a very long nectar tube be advantageous to the plant? This trait forces the insects to press its head deeply into the flower and pick up and deposit pollen. So, there's an "ongoing race" in which the plant matches any elongation of the proboscis with an equal or greater elongation of the nectar tube In a similar example, this species of fly here gets nectar from this other flower. Chart B shows that flies with longer tongues tend to consume more nectar. Chart C shows that plants with longer floral tubes receive more pollen. So this confirms that the interaction produces an advantage to both the plant and the pollinators (mutualistic)

Evolution of Genome size and Content

let's look now at the evolution of genome size and content 98% of our genome does not code for a protein ( or other Gene as a product), as we can see here in the pie chart. therefore, only 2% of our genome is made up of coding sequences (exons) in other eukaryotic species, this fraction is actually larger (more than 98%). So many scientists think that the non-coding part of the genome is largely junk DNA that has no function to the organism "junk DNA" Where does all this noncoding DNA come from? the staggering diversity seen across the Tree of Life extends all the way to the genome level. As he explained at the beginning of the lecture, there is a huge disparity between the genome size and many different metrics of organismal complexity. Measuring complexity is a bit subjective here, but one useful metric can be the number of different tissues or type of tissues in a given organism. If we divide species into two major groups of life then plot the amount of DNA devoted to coding for proteins against the genomes total size, we see very interesting patterns. For instance, across viruses and prokaryotes oh, there is a nearly one-to-one relationship. So we see a pretty much linear relationship between genome size and number of protein-coding genes but in animals and plants, the correlation is much weaker. So a species with similar amounts of coding sequence can differ dramatically in the size of their genomes. So these patterns begin to make sense with a single key insight and that is that the genomes of most bacteria and viruses consist almost entirely of coding sequences. But in plants and animals, as we have seen, most of the DNA is non-coding. In humans, only 2% of the genome codes for proteins, while half of our genome is taken out by DNA parasites, which will be explained below (TEs) Genome size vs. coding sequences: -Viruses and prokaryotes: pretty much a linear relationship -Animals and plants: much weaker correlations

common sense

merely unsupported speculation

Karyotype

number and structure of chromosomes. A display of the chromosome pairs of a cell arranged by size and shape.

Homo erectus (1.9-0.2 mya)

so lived from 1.9 mya to 200,000 years ago! Derived hominin feature: much flatter face and large cranium 1000 cc cranium capacity Derived hominin feature: used more sophisticated tools and used and controlled fire Ancestor of Homo floresiensis(0.7 mya; Indonesia) Face becomes more vertical and jaw less projected Skull was rounded, and its face much less projected than earlier species, and its teeth were smaller Importantly, its cranial capacity was substantially larger at about 1,000 cc Homo erectus means upright man, And in many aspects it had the anatomy and behavior of modern humans Homo erectus was the first hominid to disperse Out of Africa around 2 million years ago Spread out into Europe and the Middle East There is a small amount of hominin fossils found in Indonesia called Homo floresiensis dated at 700,000 years ago It it Believed that homo erectus was the direct ancestor of Homo floresiensis Homo erectus was probably not our direct ancestor, We probably come from the lineage of another homo called Homo ergaster, which is shown inside the circle in the image

Transposable elements (TEs)

so what are these DNA parasites? These are transposable elements or TEs. they're also called transposons or jumping genes, and they're short sequences of DNA that occur in many copies across the genome Most common transposon in human genomes: Alu -300 bp long the most numerous TE in the human genome is called "Alu", and it is about 300 bp long. each of us has more than a million copies of Alu that together make up more than 10% of our genome, which are shown in the green fluorescent areas in the picture of the karyotype figure So Alu proliferates by making copies of itself. The DNA sequence is transcribed into RNA, which is then reversed-transcribed into DNA and inserted elsewhere in the genome. So Alu and other TEs are parasites that work at the molecular level. they will produce not to improve the fitness of their host, but simply because they can. Proliferates by making copies of itself (molecular parasites) Evolutionary origin The evolutionary origins of TEs is uncertain, but one plausible hypothesis is that they are modified viruses that evolved the ability to reproduce without leaving the cell. so, like viruses, transposable elements are usually bad news for the host Insertion of TE into the host genome can cause a mutation that disrupts a coding sequence or its proper expression. A second problem for the host is that two copies of a TE at different places in the genome can recombine, causing a chromosomal mutation. So host genome sub evolve several ways to fight against the spread of these TEs. while they often succeed, they are left with the aftermath of the battle. so we end up with these TEs that can no longer spread, but that still fill up much of the genome. So that is the current state of our own genome. our ancestors evolved ways to shut down most of the movement of the TEs. The figure shown shows that currently the activity of human transposons is much lower than it was in the past. Now occasionally, a human TE is able to reproduce, and when it does genetic diseases can result Modified viruses Currently the activity of human transposons is much lower than in the past

Selfish

the actor benefits but the recipient's is harmed + effect on actor, - effect on recipient, +-

Altruistic

the actor suffers but the recipient benefits + effect on recipient, - effect on actor, - +

Mutualistic

the fitness of both individuals is increased + effect on actor and recipient, ++

fission and fusion

the most common way by which the number of chromosomes change is when two chromosomes fuse (reducing the haploid chromosome number by 1) or when they undergo fission (increasing the number by 1). So humans have 23 pairs of chromosomes, but all other great apes have 24 pairs. What happened is that at some point Since our lineage split from that of chimps, two chromosomes fused. the mutant chromosome has spread to our species, resulting in the second largest chromosome in the human karyotype. We don't really know what cause fused chromosome to spread, it may have been a boost from positive selection, or the fused chromosome may have drifted to fixation Fusion: two chromosomes are joined Fission: one chromosome breaks into two

Development or ontogeny

the process by which a single undifferentiated cell transforms into a multicellular adult organism

T/F: Hamilton's rule states that an altruistic allele can spread as long as there's an indirect fitness gain that outweighs the loss in direct fitness caused by the altruistic behavior

true

t/f: There are no human races

true! Phenotypic variation is not discrete, it is a continuum (just like height. There aren't really any discrete traits that can differentiate races or populations) Larger genetic differences within than among populations Possible exception: Biaka hunter-gatherers of central Africa They are known as pygmy

t/f: The nature and the strength of the interaction between 2 species may vary depending on the genotype, environmental conditions, and other species with which those species interact

true! Ex: 2 populations of limber pines, whose cones vary depending on whether squirrels are present or absent In the presence of squirrels, the cones are better defended to reduce squirrel predation. But, these modifications are also less favorable for the Clark's nutcracker (a bird that the pine depends on for seed dispersal) The graph shown is a "morphospace" showing 2 major clusters of morphologies Populations on the right (green points) represent limber pines that adapted to resist seed-eating squirrels Left (red) shows populations that are better adapted for seed dispersal by the Clark's nutcracker in the absence of squirrels The results highlight the complexity of species interactions. In this way, selection may differ between populations resulting in a variety of coevolutionary forces

Aposematism

warning colorations that advertise defenses warning coloration, of coloration or markings) serving to warn or repel predators. Several species such as poisonous frogs in the tropics have bright colors to signal to a potential predator that they are distasteful or dangerous. Predators learn to avoid the distasteful color pattern Aposematism is beneficial to both the predator and the prey because it warns predator and protects prey However, aposematism is subject to frequency-dependence. If the frequency of the aposematic coloration is too low (so when poison frogs are too few or rare), predators will not learn to avoid the trait and thus it will not provide survival advantage Aposematism is exploited in Müllerian mimicry, where species with strong defences evolve to resemble one another. By mimicking similarly coloured species, the warning signal to predators is shared, causing them to learn more quickly at less of a cost.

Practical applications of evolutionary science: Human behavior (cognitive abilities, sexual orientation, culture)

we can also learn a lot about human behavior using evolutionary approaches For instance, in a study, researchers map lethal aggression behaviors onto a phylogenetic tree for mammals. We can see that most species of mammals lack lethal aggressive behaviors but humans and other primates have a strong genetic predisposition for lethal aggression Tracing the origins of lethal aggression in mammals Other aspects of behavior that can be studied using evolutionary research include sexual orientation Homosexual behavior has been reported in diverse animals, including more than 100 species of mammals. Sexual orientation is not chosen nor determined by childhood experiences. Instead, it appears to have an important genetic basis with a heritability of around 0.2 to 0.4. Why is there a genetic basis for homosexulaity if homosexuals are supposed to reproduce less than heterosexuals? The answer lies in the fact that there is little evidence of that throughout human history. Even today, many homosexual people do marry and have children. A genetic study found 2 chromosome regions associated with male sexual orientation. However, a more recent and larger study in Poland last year found no evidence of a gay gene, sugesting that homosexual heritiability has instead a polygeneic and an epigenetic bases, so many genes are associated Homosexual behavior in animals, no 'gay gene': massive stidy homes in on genetic basis of human sexuality