Exam 4 Evo Bio

Our particular primate family is called the .................................... What other species belong to our family?

Hominidae. Apes and humans, chimps (and bonobos are closer to humans than gorillas).

Because of fossils found in Dmanisi Republic of Georgia, traditional species known as Homo habilus, H. heidelbergensis, and H. erectus may now be recognized as being all ONE variable species known as .................................

Homo erectus

Which species is the first known to use fire?

Homo erectus

The Siberian traps is thought to be a geological feature for what event?

The mega volcano that lead to the massive eruption.

18: The fossil record shows various distinctions between background extinctions and mass extinctions. How do these histories of extinctions compare in the following aspects:

The vast majority of species that have ever lives have gone extinct, and the majority of these have not left descendants that survive today. We know of only a fraction of the extinct species, since we must rely on the imperfect fossil record.

-- What does prezygotic isolating mechanism mean? Give examples. Explain why they 'isolate'.

Prezygotic : Mating does not happen.Ex; Zygote is a fertilized egg. Frogs mate at different times. Bird sing different songs. Females choose males and males compete against each other. Females of one species prefers one song while others prefer different songs. Two trees separated by distance ( could result in speciation ). Easter and western spotted skunks separated by distance. Butterflies both live in same forest, but have different genitalia. Insect reproduction is a lock and key, so 1 species cannot mate with another.

21-1: Lets do some classification! The Order of animals that we belong to are the ...........................

Primates

Diagram what happens when a 2n is mated with a 4n. Why is the hybrid likely to be sterile?

2N x 4N 1N and 1N x 2N and 2N 3N :D Triploid may not survive and cannot reproduce it is sterile.

Lets review the costs of sexual reproduction. -- Sexual parents are ............ % related to their own offspring.

50% related.

What is the various geological and chemical evidence for this cause? What is found in the sediments laid down at the 'K-T boundary'? What is the large geological feature of the K-T event found in the Yucatan peninsula?

A crater over 100 miles in diameter that is not visible on surface, with layers or rock and soil over it. Discovered by gravitational anomaly over areas and you can see deep features in the ocean that was circular, age of creator was 65 myo. Unusual layer of clay at K-T that is found all over the world. In clay you see tiny glass beads that vaporized rock, because hit so hard, causing spherical glass beads. Iridium is a rare earth element, but this layer has a spike at high levels. Space rocks have high levels of Iridum and possibly came from space. Lots of soot, carbon particles, made from burnt plant matter (western hemisphere would be a big firestorm because of flash heat). Raining hot glass, fire, and global temps would drop because of the aerosols causing acid rain, increased C-2 and increased temperature.

What is the leading candidate for the cause of the end-Permian mass extinction? What is the major physical evidence for this event?

A massive volcanic eruption lasted approx 10 million years and the mega volcano was located in what is now called the Siberian Traps. Evidence includes large small marine animals with shells secreted CaC03 and little molluscs were everywhere, but at end of Permian were gone. At high altitudes, you'll find lava and volcanic ash spreading across 400 million cubic miles.

What is the phenetic species concept? What criteria is used for arguing for different species when using this concept?

A phenetic species concept; Quantifies character states in 'phenotype space' to find natural 'groups'. Phenetic definitions of species are important because they can be used for microbes, extinct species, animals, plants, anything. This is a more quantitative measure of proportions of individuals and lay out in a 3D space. Each individual in a specific place will have clusters to find a phenotypic grouping. Individuals are outliers so are not part of their species. This is used in a lot of extinct species to help find species of bacteria (using metabolic property stains).

-- A polymorphic species. The BSC would say these are ........................ The phenetic concept might say they are: ..............................

A species of catapillers in spring have camo called cat pins while in summer looks like a twig. They are found in the same tree, but mimic different parts. BSC would say these are the same species. Phenetic would say they are different species by biology. Technically they are the same species, but are polymorphic.

-- A network of interacting genes are expressed in the developing wings, and these genes become expressed in a 'bulls-eye' pattern and then they turn on genes for pigments --> an eye-spot pattern of color. My question is, what does this network of genes also do during development?

A well known network of regulatory genes is engrailed (cycle) hedgehog )- Distal less leading to limb growth. This is a positive feedback cycle that causes color patterns in butterflies. This projects as a flat color pattern on eye spots for butterflies. Turned genes into pigments, eye spots, that are legs. Distal less controls pigment and network genes thats good at making bulls eyes and now a network recruited in wings attached to pigments to create a bulls eye. This is an intro to developmental took kit. Pigment genes are co-option to make eye spots. (Hedgehog -> engrailed -> Distal less) all lead to pigmentation gene pathway.

16-1 : In embryos, cells are seen to differentiate. What does this mean?

All evidence says that these species descended from common ancestors, with homologous structures that went through different histories of divergent evolution. This must involve changes in development.

Allopatric speciation is... (in general terms). Recognize examples.

Allopatric speciation: A population is split by a physical barrier ans is probably the main way speciation happens. Ex; a mountain blocking gene flow, dispersal to isolated region aka natural selection won't work. If divided populations are large, then isolating mechanisms can be developed by natural selection. Millions of years ago, sea levels were higher, now a land bridge isolates populations and we see lots of separate species. Species (some in Atlantic others in pacific) closes relatives are across land bridge. Islands form and mainland animals come and drift. Grand canyon and ground squirrel populations.

List some of the characteristics that unite most primates.

Although essentially quadrupeds, apes are more erect than other primates. Apes often walk erect,tool use is well documented especially in chimps, and similar genetics.

In general, what is the relative number of HOX genes in a simple animal (like a jellyfish), when compared to an anatomically more complex animal like an insect, and then a very complex vertebrate?

Amount of HOX genes depends on amount of limbs, body parts, etc. Increase in body parts you have an increased number of HOX genes. aka an increase.

Organisms often have specializations where a body part shows accelerated growth to large size, or a body part slows their growth to stay a small size. This kind of heterochrony is called ................................

Another form of heterochrony is allometry: Change in the rate or amount of growth of one body part. Ex; Forelimb of bats have huge front limbs and continues to grow in womb. Mammals don't grow. Allometry can also be about decreased growth rate as well. Ex; t-rex, beetles head thing. D'arcy Thompson transformations - a lot of diversity revolves around proportion. Ex; was increasing Puffer fish proportions to make a Mola Mola.

What is significant about evolution of animals during the Cambrian? What sorts of animals appear at this time in the fossil record?

Appearance of most phylum of animals including segmented worms, chordates, etc

What is the evidence that bipedality evolved in the forested habitat? What is the 'ecological' evidence from the fossil record? What is the anatomical evidence from the early biped Ardipithecus?

Ardipithecus ramidus was thought to have diverged from humans and chimps approx 6 mya, that was no doubt an early biped with short broad pelvis with detectable sciatic notch and the pelvis appears that Ardi was able to walk erect with knees closer together to center of body, foramen magnem in a more forward position. Species lived in forested habitats with long arms that could swing from branches with long curved hands and short thumbs. Specialists from multitude of fields collected bones, soil, pollen, other fossils around the same location, layer of soil and Ardi was found with other forested species.

The rapid speciation of survivors after a mass extinction is a(n) .............................................

As in specialization on isolated island, we see a burst of specialization following mass extinctions. This patter is an adaptive radiation.

Now, lets go over the benefits of sexual reproduction. -- What is Muller's ratchet? What inevitably accumulates in ALL genomes of asexual populations?

Asexuals accumulate harmful alleles (the red dots) and cannot lose them. This is the Muller's ratchet.

Describe the origin of autopolyploidy. Constrast that with the more complicated scenario of allopolyploidy.

Autopolyploidy is where a single individual acquires duplicated chromosomes most likely caused by DNA replication without cell division. xxx -> IIIIII Allopolyploidy takes a couple steps where interspecies hybrid are close enough to where they ca breed (can be sterile). If they reproduced asexually then someone can produce a polyploid offspring an allopolyploid and they can be fully fertile. (Look in notebook)

n-- Local versus global extinction. n-- Effecting low, middle, and high levels of the food web versus effecting mainly the 'top' of the food web (large, dominant species). n-- Effecting a high % of species, versus effecting a low % of species.

Background extinctions are local and effect a low % of species. Species with shortest lifespan die out like species on the tops of food chain. Mass extinctions are brief extinctions, worldwide and throughout all species. They are distinctly different from background extinctions. They are global in reach, effects large # of species and a large % of species from top and bottom of food chains.

What is the biological species concept (BSC)? Be sure to be able to define this one!

Biological Species Concept (BSC); Species are groups of actual or potentially interbreeding populations which are reproductively isolated from other such groups. Ernst Mayr didn't make the concept, but made it important. It's all about sex. Either don't mate or do mate, but it is not successful. Limitations are with asexual species (bacteria) and cannot use this concept.

Besides whole genome sizes, we can also compare the relative numbers of working genes. Are there predictable differences in the numbers of genes when comparing, say, a protist, a plant, and an animal?

C-value paradox has been something that evolved, but remember that does not necessarily mean it was by natural selection. Extra DNA does not mean extra genes. Why does genome size vary? The first clue is that it does not particularly have to do with the numbers of genes.Within multicellular eukaryote, the number of genes are not that different aka there must be great differences in non-coding DNA.

Animal embryos soon make layers of cells called germ layers. -- What structures are made from ectoderm? -- What structures are made from mesoderm? -- What structures are made from endoderm?

Cell differentiation is determined progressively through various stages and events of early development. Fertilized egg or zygote is 1 cell. Then mitotic division which starts cell communication telling the location and what they will be called Morula (cluster of grapes). Then blastula (hollow ball of cells). Another event is gastrulation where some cells on the outside move inside and an embryo that is doing this is called gastrula (like gut). Now you have layers called germ layers or ectoderm (outer) that makes epidermis, nervous tissue, and is blue. Mesoderm (middle) that makes muscle, bone, blood, and is red. Endoderm (inner) that makes the inner lining of the gut and is yellow. After that you go into organogenesis or organ making.

Name a couple structures seen in ALL chordate embryos at their phylotypic stage. Can you think of some such structures that are developed, then lost in many chordate embryos? You developed some structures, only to lose them, for example

Chordate - phylum organ rudiments at phylotypic stage. Dorsal hollow neutral tube, post anal tail, pharyngeal pouches, somites, and notochord.

What happens to global temperatures if levels of CO2 rise?

Climate change can also threaten species. Increases in atmospheric C02 and Methane inc greenhouse gasses, trapping solar heat, and global temps increase having affects on species. As C02 goes up so does temperature. CO2 in past has increased and decreased in cycles. We know this by ice core samples that trap atmospheric gasses and fluctuations had in the past had an impact on the core sample. In long term, Co2 levels have changed dramatically. In Cambrian C02 was higher. In past C02 was way higher and so was temperature.

What is the C-value paradox? What is C-value in the 1st place?

Complexity of an organism does not predict genome size. Even within a group there can be huge differences in genome size. C-value; I am afraid the letter C stood for nothing more glamorous than 'constant', i.e., the amount of DNA that was characteristic of a particular genotype

Each homeotic (HOX) gene shares a domain called the ................................

Conserved region called a homeobox.

Sexual reproduction includes the special division known as meiosis. Meiosis 'scrambles' the combinations of genes in TWO different ways. What are they? (one is shown in the figure of meiosis in this chapter).

Crossing over, Independent assortment.

Current levels of CO2 Is about 350 parts per million. How does this compare to CO2 levels over the past several 100,000 years? How do these levels compare over the past several hundred million years?

Current levels compared to past several 100,000 years is the highest it has been. Compared to the past several hundred million years it is not even close to the highest the levels have been. Levels have been as high as 7000 parts per million.

There are species of plants and animals that are strictly asexual in reproduction. How successful is asexual reproduction in the long term among these species?

Dandelions, Hydras . Is not that successfulC for very long as Sexual are more suitable even thought it is strange.

Which of these can contribute to the reproductive isolation of populations, --> new species?

Deletion, duplication, translocation, inversions

Here are some chromosome rearrangements: deletion, duplication, inversion, translocation. Which of these is likely the source of new genes / new members of gene families?

Deletions and duplications occur together as a result of unequal crossing over. Duplications are especially important because they can accumulate mutations with a relaxed selection. Many become non-functioning pseudogenes. Others become new members of gene families.

Given two cells at different positions, explain how one cell comes to express a gene while the other cell does not express that gene. What do differences in cell--> cell signaling have to do with that? How about differences in transcription factors in the two cells?

Differences in transcription factors cause differences in transcription and so differences in cell differentiation. ex; The top gene is expressed, but the bottom one is not because of the transcription factors blocking the promoter. Differences in cell to cell signaling cause differences in transcription factors. ex: Bottom is father away from the signal so the gene doesn't get expressed.

What is anisogamy?

Different sized gametes And Polymorphism for male and female mating types for multiple allele types.

-- So, what combination of factors may have caused selection for bipedality in the early hominims?

Driven by combo of factors not seen in related primates including climate change, cooperative pair bonds (primates don't pair bond and females receptive when in estrus and males fight via intrasexual selection), humans had concealed ovulation fostering bonds and cooperative child rearing with fossil evidence. An obligation to move efficiently on the ground while carrying resources and young in cooperative families.

What is the chief function of the homeotic genes in the fruit fly Drosophila?

Drosophila homeotic genes are a gene family of related transcription factor proteins. Homeotic proteins control the identity of body segments in Drosophila.

How might a mutation in the gene coding region effect the gene (besides making it not work -- which it often does)?

Duplications lead to new genes. Mutations in gene coding region leading to change gene function.

Now we enter the world of homeotic genes, a.k.a., the 'HOX' genes. Bwa ha ha haaa. What kind of proteins do homeotic genes code for? (signaling, enzymes, transcription factors...?)

Each RNA contains an especially conserved region called a homeobox. The DNA homobox codes for a conserved region of the protein called a homeodomain. Homeodomain is a sequence of amino acids. Homeotic proteins act as transcription factors, bind to regulatory regions of other genes and control gene transcription. It is the homeodomain that binds most tightly to a target DNA sequence.

In terms of anisogamy, individuals that make small #s of large and expensive gametes are called ........................., and individuals who make large #s of tiny and cheap gametes are called .........................

Eggs; Sperm

On what continent do we see the first signs of symbolic thinking (art, etc.) in our species?

Earliest signs of our advanced thinking are in South Africa approx 80,000 ya with much better spears, carvings on bones, sea shells with holes (jewelry), and a Venus figure (possibly for ritual fertility symbol) . Art reveals complex and symbolic thinking.

What is a 'phylotypic stage' in general terms?

Early developmental stages look similar to each other in a phylum. Phylotypic stage - The stage that is very conserved in a phylum.

The old idea upright walking evolved on the open savannah plains is wrong. In what environment did upright walking evolve?

Early hominins lived in forested habitats.

A big question: Members of the genus Homo are also known by what COMMON NAME?

Early humans

What is more expensive to make per cell? -- eggs or sperm?

Egg

Briefly contrast the multiregional hypothesis and the out of Africa hypothesis.

Emergence of 'Anatomically Modern Humans' have 2 scenarios of origin of H. sapiens the Multiregional and Out-of-Africa hypothesis. Multiregional hypothesis - H. erectus migrates over Africa, Europe, and Asia begining 2 mya and H. sapiens evolves over this entire population, supported by natural selection and gene flow. This implies our lineage happened mya. Out-of-Africa hypothesis - H. sapiens emerges more recently in Africa, migrates into Europe and Asia, while other descendants of H. erectus die out. H. sapiens in Africa migrate out taking over older gene lines and we would expect our genetics would be younger and more recent.

We can credit this huge diversity of eukaryotes to a kind of developmental 'toolkit' for building diverse anatomies. Lets go over that toolkit. -- Name a cell structure component of the toolkit. What constraint did this resolve?

Eukaryote development, cell structure, genes amount to a tool kit that amounts to diversity.

--- Mutations in enhancers and silencers will have what effect on a gene? Can mutations in this area easily make new enhancers / silencers?

Eukaryote genes are modular meaning they have many upstream enhancers and silencers that are target for combinations of transcription factors. Mutations here lead to new gene expression patterns without changing the gene product.

-- The structure of eukaryote Eukaryote genes are modular meaning they have many upstream enhancers and silencers that are target for combinations of transcription factors. Mutations here lead to new gene expression patterns without changing the gene product. genes is 'modular', where changes can occur that causes a gene to work in new ways (and key thing here: the can still work).

Eukaryotes are modular (having regulatory genes). If mutant genes in the non regulatory region (yellow) mutation causes it to be an enhancer. Still have old regulatory region and gene is expressed in the old region, but now expressed elsewhere. Can make more than 1 protein from same gene via alternative proteins. If exons moved into a different gene, that protein now has extra part, but still in reading frame and will work. Eukaryote genes are modular like this: The gene Sonic hedgehog codes for a cell signaling protein and is expressed in a great variety of tissues, arms, legs, mammal hair, and bird feathers.

What is the evolutionary species concept? Is this concept especially good at recognizing diferent lineages that are different species versus just different local varieties within a species?

Evolutionary species concept ; A species is unique lineage with a shared evolutionary history. We would use the characters that build trees to also identify species. Good - Helps define species if you don't know a lot about biology (like if you have fossils), if we don't know about reproductive habitats (genetics can be used). Good concept to recognize different lineages that are different species. Bad - Have species of Magpies that look different and are found in different areas. Each bird has several different populations that live separately and each population might look different. Some species of Cicaiads that look the same from different states have different songs. Not a good concept for Regional pop/regional species/ local varieties within a species.

The neanderthals (Homo neanderthalis) seemed restricted and adapted to what sort of climate?

Evolved in Europe over last ice age and are cold adapted with robust body, broad nose, shorter limbs. Shorter limbs for more body heat, ate high meat diet going after big game using spears, lots of bone breaks, Broad nose to warm and humidify air with a larger surface area. Used spears, wore hide clothing, signs of burials with implements for afterlife. Neanderthals co-existed with N. African and European H. sapieins. Did we wipe them out? This is unknown.

--- What two things happen during meiosis that specifically increases diversity of gametes?

Exchange genes via sexual reproduction. Meiosis has independent assortment, crossing over (that leads to inversions, duplications, deletions, translocation).

-- Explain the differences in the relative reproductive success of females and males.

Females always reproduce while males do not have this guaranteed.

-- Why must females be 'choosy' about the males that they mate with?

Females must be choosy about their mates (because higher cost for gamete) and males must compete to be chosen. Females choose the males to give their young the best opportunity for survival. Selection pressure to choose wisely. Need the genes/brains to do so to judge males and be right. Fewer changes and make choices correctly what they're selecting for.

Why can polyploids become new species?

Fertile polyploids can be regarded as new species because they are reproductively isolated from the parent species.

What is the science called 'Evo Devo'? How are evolutionary changes inferred when we have no fossil record of embryos, and certainly no direct 'fossil' record of genes?

Field of evolutionary developmental biology. The basic approach is to compare genes controlling development between living species that represent primitive forms versus derived forms. The differences found are inferred to illustrations the genetic changes needed for the macro evolutionary change. Using living species to make inferences. Fishes fins to tetrapod legs. Look at gene differences to observe genetic changes.

How well does the BSC deal with organisms that do not reproduce sexually? How about organisms whose reproduction is not characterized? How about organisms that are extinct?

Finding patterns of gene flow is critical in defining species under the BSC. Each pop. has it's own gene pool (have particular set of alleles_. Populations physically separate, but have similar alleles, so they must have some "gene flow". Gene flow occurs or could occur between some populations. Use patterns of gene flow to assign species boundaries. BSC is not ideal for organisms that do not reproduce sexually, whose reproduction is not characterized, and for organisms that are extinct.

What major group of land vertebrates 'took over' the ecological niches left open by the end-Permian mass extinction?

Following the end of the Permian, the dinosaurs emerged during the Triassic to become the dominant vertebrates on land during the Jurassic and Cretaceous. Initially surviving species were small dinosaur precursors. Mammals evolved along side dinosaurs. 1 group of dinosaurs got feathers (Archaeopteryx) and started to become more bird like. First egg laying mammals were marsupials, then placental, early forms of primates and rodents.

Draw a simple tree that conveys the views of speciation according to a gradualist, and according to supporters of punctuated equilibrium.

Fossil record usually has gaps, and these are often substantial. Maybe change is gradual, ore resent, or very sudden. There is 2 schools of thought about how rapid speciation is over geological time. Phyletic gradualism - Small and incrimental changes or gradual. Darwin would favor. Gradualists point out evidence where fossil record is good. An early primate that had left a good fossil records and at the split showed morphological measurement. Another shelly plankton are great because they are numerous and see gradual changes of 1 species to the second. Snails that show good fossil records, from round to nobby to thwart predators.

-- Sister species (species that are very recently separated). The BSC would say these are ........................ The phenetic concept might say they are: ..............................

Fruit flys (Drosophila melanogaster and Drosophila simulans) are considered to be sister species or sister taxon that have been recently separated and are reproductively isolated. Phenetic would say they are grouped together. BSC would say they are separate because there is no gene flow so they are considered sexual so they apply to the BSC. One frog breeds sexually in spring, while another in summer, but are separate species, by BSC (because no gene flow). Phenetic would group together. One plant species is found in US and another in China. Are considered separate because of the distance (For Phenetic? can they breed?)

Give me an example of a chordate.

Fruit flys, Humans, pigs, chickens, turtles

Different cells express different genes. Lets go over some things about that. -- What are the proteins that bind to regulatory region DNA like enhancers and silencers? -- The enzyme RNA polymerase binds to what DNA region?

Gene expression is controlled by transcription factor proteins that bind to regulatory regions (enhancers, silencers) RNA polymerase binds to the promoter and the binding is controlled by transcription factor proteins.

What are homologous genes?

Gene families are a huge resource for evolutionary innovation. Family members are homologous to each other. Genes are similar in sequence, function, and came from common ancestor gene.

What is meant by the term colinearity here?

Genes are in the same order in chromosome and the linear order where the gene is expressed in the body. Arrangement of genes are in the same order in the chromosome as they are expressed in the body.

What is co-option of genes?

Genes coming under new control of other genes is called co-option.

What species was the first known to leave Africa, and populate Europe and Asia?

H. erectus were break out species. Oldest hominims found in Europe and Asia are considered to be H. erectus.

Homo erectus is credited for a number of 'firsts' in our history. This species is the first known to prepare food in what way?

H. eructus cranial sizes larger, but variable in size. Expanded repertoire of stone tools into "hand axe" where center of core rock used. Locations where rock is shapped into hand axe means H. erctus lived there with generations of older rocks meaning H.erectus lived in large encampments. Species used fire. Cooking improvements nutrient extraction of plants and meat. Allows continued selection for increased brain size allowing selection pressure for larger brains to exploit resources, tools, dominate groups better, wining conflicts, and being cleaver, but still has caloric restriction.

Explain the evidence that specifically supports the view that H. sapiens interbred with neanderthals. Just saying we lived alongside them, or that we share genes will not cut it! We live alongside and share genes with chimps, after all.

H. sapiens gradually moved through Europe and Asia etc. Earliest european modern humans found were often called 'Cro-Magnon' after discoveries in France. See cave paintings, combo diff rocks for diff uses, fish hooks, sewing, signature style carvings. Sequencing of Neanderthal DNA reveals that at least some Neanderthals interbred with non-African Homo sapiens. 1 to 4% of genome may be Neanderthal. Originally thought no interbreding because they were thought to be 2 different species. Sequence showed Shared genes in our DNA yes that came from same common Ancestors, but more importantly we only shared genes with Neanderthals where we lived with Neanderthals in Europe and Asia meaning they mated when the lived in the same areas.

Define Haldane's rule. When learning about the chromosomal basis of sexual determination, predict which kind of hybrid would have reduced fitness.

Haldane's rule: In many cases, interspecies hybrids show reduced fitness/sterile/death in one sex. This should be the heterogametic sex. Hetero/homo gametic sex; ex Human males XY so produce sperm X and Y aka heterogametic or make 2 kinds of sperm. Females XX and all eggs carry X so are homogametic in females. Why is hetero less fit? Best hint is about genes getting along. In hetero you have 1 X and Y so genes on X chromosome, won't get along with that copy. Male flies and Humans are hetero/less fit while female birds and butterflies are hetero/less fit.

Our sub-order are primates with dry noses, these are the .....................................

Haplorhines: include Tarsiers, monkeys, apes, and humans

What is a common trait shared by polyploid plants? Why might this give them a selective advantage in the wild?

Has bigger cells and organism is larger than diploid. Deeper roots for more water. Bigger seeds with more nutrients. Plants seem to be better at surviving and reproducing as polyploids and a high % of plants are polyploid &0% nonflowering and 40% flowering.

Give me examples of non-coding DNA that are still important for the organism (these ARE subjected to natural selection, b.t.w, so no all mutations in 'non-coding' DNA are neutral).

Heterochromatin includes ; Telomeres to preserve length of the chromosomes. Centromeres Regulatory regions aka enhancers, promoters, silencers

The homeobox of a HOX gene codes for a region of a protein that is specifically called a .............................

Homeodomain

When we compare genes that control development of tissues and organs and body dimensions across phyla, from worms, arthropods, molluscs, vertebrates, etc.., what do we find? Are they all really uniquely different, or are they strikingly similar to each other (homologous)?

Homeotic genes: HOX genes, a gene family similar in structure and function that code for transcription factor proteins. They make body parts different from others. All animals have genes homologous to the Drosophila homeotic genes and all are HOX genes.

Early humans that lived on the Indonesian island of Flores have given us a surprise. What is unusual about these humans? (there is more than one thing).

Homo floresiensis aka Hobbits, fossils found on an island in Indonesia that originally thought to be H. sapiens but a mutated/ dwarf or possibly all had a disease (unlikely, hard to find fossils and so many malformations is not coincidence) because of their small brain like a chimp and small jaw that says it is not H. sapiens. They had small brains, but made small tools. They lived with Homo. sapiens approx 12,000 ya.

Selfish DNA elements tend to increase their copy #, which probably reduces fitness of an organism by a small amount. Bacteria especially have very little selfish DNA --- most of their DNA is needed for something. Why might natural selection be able to minimize the amount of selfish DNA that they carry?

Huge populations means natural selection can act against small fitness differences and can select to minimize DNA to remove selfish DNA. The extra DNA has a small cost, but natural selection can detect this and prefers the genome to be smaller, so smaller organisms = smaller genome. Low drift because large population.

Consider an ecosystem in which various prey animals are kept in check by predators. If a new predator is introduced into an area, does this necessarily cause a decline in all potential prey animals?

Humans introduce change into these ecosystems leading to endangered and extinct species. Entry of new species not only effects those not adapted to them, but they can bring new diseases. The background extinctions may be due to similar events we see today: Movement causes new competition and new disease. Climate change has also occurred. Channel islands of California has species of unique endemic birds to the island including a lot of ground nesting birds. The birds had a natural predator and balance of power/ adaptions to predators. Humans introduced feral cats and rats driving birds to be highly threatened. In fossil records there will have a species of birds then some disappear, dropping to low levels. Fossil records show the birds are extinct even if only threatened, fossils show are extinct. One major predator was a fox, but humans brought pigs that escaped and formed wild populations. The pigs attracted their predators, the golden eagles which also ate foxes. In fossil record, you'd see eagles and pigs suddenly appear (could happen naturally). Foxes were previously keeping skunks in check, but have declined so increase skunk population. Humans brought diseases a species of amphibians are disappearing because humans introduced pathogenic fungus and native amphibians are not resistant. In places where humans have been for a while the fungus is there and amphibians are not affected.

What is significant about the Australopithecine known as Lucy?

Important Gracile Australopithicine fossil includes LUCY, an A. afarensis skeleton which, when discovered in 1970s proved that bipedalism came before brains as the brain was no bigger than a chimp, but walked upright. The Laetoli footprings are possibly also A. afarensis. Volcanic eruption deposited ash that left footprints once cooled showing big toe still offset.

21-2Who first proposed that humans evolved in Africa?

In 1871 Charles Darwin proposed that a) Humans (Homo sapiens) are primates and b) Humans evolved from apes, in Africa

Understand the concept of a ring species. There are, b.t.w., no good examples of this anymore! The salamanders described in class do not fit the concept as cleanly as once thought. Other examples of ring species (in birds, etc.) are also flawed in some ways as examples of what a ring species was supposed to be about.

In Parapatric speciation, there is a case of ring species. Here, the cline distributes varieties by divergent evolution in approximately a ring. Ex; Salimanders in Cali migrated down from the north and a natural barrier of high mountains and arid desert. They did not cross, so they split up with some in the forest and some in coast line while others in low lands. There are different sub species of salimanders and they can interbreed. The 2 extremes of the speciation do not breed, but their sub species can interbreed. In biology, a ring species is a connected series of neighbouring populations, each of which can interbreed with closely sited related populations, but for which there exist at least two "end" populations in the series, which are too distantly related to interbreed, though there is a potential gene flow between each "linked" population. Such non-breeding, though genetically connected, "end" populations may co-exist in the same region thus closing a "ring"

Name some cell activities that lie behind morphogenesis.

In eukaryotes, development of anatomy includes highly programmed cell activities; cell division, cell migration, differentiation. This process of generating anatomy = morphogenesis. Cell activities are controlled by genetic activities; differential gene expression and cell to cell signaling.

Here are two situations where identifying species can be problematical. Tell me what the BSC would say about them, versus what the phenetic species concept would say:

In extinct species, like dinosaurs, we do not know their patterns of gene flow, so cannot use BSC. Bacteria have gene flow at very low levels, but is still very difficult to asses. Phenetic species concept for extinct species and bactieria would simply use measurements of proportions of bones/ characteristics of metabolic processes/stains for bacteria, to graph and it will show clusters to where you find a phenotypic grouping to find species. Outliers would not be a part of that species grouping.

20 - Who was it that first proposed that sexual selection was a special kind of selection in many animals?

In his Origin of Species, Darwin argued that natural selection leads to traits for improved survival and reproduction. One area that was trouble for him is why should many species of animals have extraordinary ornamentation and behaviors that seem to reduce fitness? In his 2nd major book on evolution, The Descent of Man and Selection in Relation to Sex, Darwin makes his case for the reason of such traits. He argued there was a special case of natural selection called sexual selection.

Snakes effectively have a long thoracic region, with rib bearing vertebrae extending to just behind the skull, and rib bearing vertebrae also extending to the base of their tail. (this is for questions below but will talk about arthropods n'shit)

In most arthropods, Ultrabithorax and Abdominal A permits expression of Distal less, a gene that causes development of limbs. The arthropods have lots of appendages (legs) and Ubx and Abd-A control other genes permitting expression of distal less. In insects, Ubx and Abd-A repressed DII expression. This is a big reason why insects only have 6 legs. Ubx and Abd-A expressed in the same way in insects, but function is changes. Now they keep distal less from being expressed causing fewer legs = less weight, less energy, faster and can fly.

-- What is the function of the HOX genes that determine the extent of the thoracic region in snakes (and other vertebrates?

In vertebrates, cells expressing HOX c6-c8 form thoracic structures. The anterior limit of c6 and c8 sets the length of the neck. Ex; With HOX genes, different vertebrates have the same number of total vertebrates, but can have different number in the neck versus the trunk. Bird has a long neck with short trunk where mammals have 7 in neck and 12 in the trunk even though they have the similar total number of vertebrates. It causes vertebrae to grow in ribs. Bird stops early where mammals gene are expressed farther so the thoracic genes are expressed more. Snakes extend even farther.

Which of these can cause reduced fertility in heterozygotes?

Inversions - Heterozygotes for an inversion experience reduced fertility because of crossing over creating inviable chromosomes. In such a population when a homozygote for inversion appears fertility can be restored. This new variety may become a new species. Not sterile, but not fully fertile. Translocation - A piece of chromosome gets attached to another chromosome that is not homologous and has reduced fertility. Homozygotes can restore fertility and may turn into a new species.

LINES and SINES: Which are longer? Which contains the gene for transposase?

LINES (Long Interspersed Elements) - Have RvT. SINES (Short Interspersed Elements) - Lack RvT, but are endogenous RNA (like tRNA, rRNA) that are converted into DNA by RvT. Has transposase.

What was the leading factor in the cause of the K-T mass extinction?

Largely due to a 10 km meteor impact in what is now the Yucatan peninsula in central America.

Picture a homologous pair of chromosomes that are heterozygous for an inversion. Show me why crossing over within the inversion --> abnormal chromosomes and inviable gametes

Look at slide and notes.

When animals retain juvenile traits in their adult form, that is called ........................

Loss of adult form; Neoteny. Adults retaining juvenile morphology Axolotll. In the amphibian larva has gills then turn into adults that lives on land with no gills. Axolotl keep their gills, state of juvenile even though they can reproduce. Humans are sometimes described as 'neotenous apes', but its not that simple . Humans and chips have a big head, pushed in jaw, with a small face, but humans stay this way while chimps jaws push out and head gets smaller. Humans are Neotenous apes from the neck up.

--- What sometimes happens during meiosis that results in duplicated genes, adding members to expanding gene families?

Lots of sexual reproduction means meiosis, crossing over, independent assortment. All that means eukaryotes mix their mutations and regularly duplicate genes. Get diversity via mutation, but shuffles the genes and gets gene duplications creating gene families. Gene duplications create gene families.

Under intersexual selection, males must advertise the quality of their genes. Are they telling the truth in their advertising?

Males cannot lie about genes because the whole system would be messed up. Graph shows x= number of peacock eyes and Y the mean weight of male on day 84. Big showy tails males really do have better genes and have healthier chicks with higher survival rates.

-- Males are undergoing selection. What traits define 'fitness' in males?

Males need what females are looking for and need genes to make females look for them so males are obligated to display their traits ex; big antlers, large colorful tails, bright colors etc.

-- Explain the differences in the relative reproductive potential of females and males.

Males will have high productive potential by showing their traits that make them look successful/ advertise. Females just go look at shit.

What major group of land vertebrates 'took over' the ecological niches left open by the K-T mass extinction?

Mammals There is complication to the idea that the impact was the sole cause of this mass extinction because many groups, including dinosaurs, were in decline before the boundary.

The worst mass extinction of all time took place at the end of the ........................... period.

Mass extinctions, are distinctly different from back ground extinctions, are global in reach and effects large # of species and a large % of them. From both top and bottom of the food chains. The largest mass extinction was at the end of the Permian and was the greatest mass extinction on record with up 90% of species disappearing. Plankton, the base of the oceanic food web, was especially hit. Peak was not that high, but width lasted a long time. Diverse communities were decimated, especially the larger species of 'dominant' groups. Insects were also heavily affected and normally are not.

OK, now we look at a possible combination of factors that might select for bipedality in hominims. -- What is the ecological evidence that early forest living hominims might need to do a lot of walking on the ground?

Maybe they had to walk around while carrying things! a) Climate - lower rainfall and expansion of grasslands caused forests to break up. Populations had to travel from forest to forest. Climate went through a cooling with less rainfall, grasslands expanding, forests fragmented. b) There is a hint that this lineage formed with cooperative pair bonds between males and females. Different social structures that are different from other species. c) Primates do not pair bond. Females are receptive for mating when they are in estrus. Females not receptive to mating unless ovulating. d) Males must compete for females looking at size and canines as evidence of intrasexual selection. Males are built bigger for intraspecies conflict. e) Human mating system is based on concealed ovulation in females fostering long term pair bonds with cooperative child rearing. A consequence of this new fitness criteria would mean the old ways are lost. Females hide ovulation so males unsure when ovulating so this is thought to foster pair bonding and you raise offspring cooperatively with lots of carrying kids, food etc. Human teeth canines says they don't need large canines like chimps meaning no intrasexual selection. Males only 8% larger than females.

-- How does sexual reproduction disrupt inheritance of some favorable allele combinations?

Meiotic independent assortment will separate some favorable gene combinations.

-- Genetic 'age' of H. sapiens. Why does this favor the out-of-Africa hypothesis? -- Genetic diversity of different human populations in Africa versus Europe and Asia. Why does this say we are all Africans?

Mitochondrial (and genomic) DNA clearly shows that African genetic markers a) are more diverse and therefore older ( Indiginous Africans have more diverse genomic DNA making them older) b) are carried into European and then Asian populations ( DNA sequences that are African are found in Europeans).

How might a mutation in the gene regulatory region DNA effect the gene? Does this effect the function of the protein made by the gene?

Mutations in regulatory region leading to new gene expression patterns. Mutations in a gene coding region can lead to changes in gene function. Yes this effects the function of the protein made by the gene. Mutations in a regulatory region can lead to new gene expression patterns.

The species known as Homo heidelbergensis is traditionally considered to have produced what two other species? (we deal with current suspicions later).

New varieties appear in Africa and Europe which are traditionally considered to be a new species; H. heidelbergensis that produced Neanderthals (H. neanderthalis) and our lineage, H. sapiens (wise men).

Now lets talk about non-coding DNA. What is that?

Non-coding DNA : DNA that is not transcribed into functioning RNA aka extra DNA.

-- Recognize examples of character displacement. How can the traits of some hybrids --> reduced fitness, even if they are still fertile?

Once speciation has begun, character displacement can reinforce prezygotic isolation. ex; 2 snail species are reproductively isolated by distance, but now populations overlap, but they don't interbreed. When separate, they have similar penis size, but when overlap, penis length is different. Character displacement: Sorting out of certain trait because of different species that can cause speciation to happen. Hybrids of these species are not as fit/less successful. Seeing divergent evolution where they co-occur. Money flowers look different, but are really 2 genotypes. One red makes elongated red flower and hummingbirds like to pollinate (exclusively) because they like the shape and color. Pink flower is platform shape and bees like and pollinate these. (are these separate species or extreme differences?). Hybrid; Neither likes the flower, are less fit, pushing apart. AKA is in process of speciation. In Haldane's rule, interspecies hybrids show reduced fitness/ sterile/death in one sex aka the heterogametic sex.

Why can allopolyploids be fertile?

Once they reproduce asexually, you get an polyploidy called allopolyplid and they can be sexual towards other allopolyploids.

Any change in the rate of development, when compared between species, or between body parts, is called .......................

One pattern of evolutionary change that is often seen is heterochrony: any change in the rate of development in one system or another.

A biped human cannot outrun most quadruped mammals of comparable size. But we do have an advantage. What is it, and why?

Our bipedal walking (and running) is more energy efficient than being a quadrupedal. Not meant for speed, but good for distance. Ex; Walking is efficient and expends less energy than quad of same size. Benefits of being tall with center of gravity higher off the ground because walking uses muscles with support from bone. With the higher center of gravity you get assistance from gravity aiding the bone to propel/falling forward rear leg forward than your own energy using muscles. Quads also use gravity to assist but because COG is closer to ground they don't get a longer arch for gravity assistance in their strides.

21-3 Name ANY genus of hominin that is more 'primitive' than the genus Homo.

Our genus is Homo aka early humans. Earlier includes Australopithecus.

What easily preserved kind of TOOL can be found that tells us if a species is a member of the genus Homo?

Our genus is marked by a suite of characteristics; a) An increase in cranial size, edging out the Australopithecines. b) Definite regular use of stone tools bye Homo habilis aka handyman. Stone tools used to alter rock and use modified rock as a tool, not using core rocks but the flakes as we broke them off core rock and we know flakes used because flakes are worn, begining with Homo habilis with small brain and forward face.

What evidence overwhelmingly favors the out of Africa hypothesis? Explain the... -- Fossil evidence

Our species is considered an African descendant of H. heidelbergensis. Oldest possible fossils of H. sapiens are approx 190,000 yo in Africa and the oldest definite fossils of H. sapiens are approx 160,000 yo in Africa.

-- What seems to be the change in the HOX genes that caused this change in body body plan? (Don't worry about the specific names of the genes. I am just asking about the general change that occurred).

Over expression of HOX genes cause changes of the body plan.

Among the homologous genes, what are parologous genes? What are orthologous genes? What are (once again) pseudogenes?

Paralogous genes - Homologous genes within a species. Orthologous genes - Homologous genes across a species Pseudogenes - a mutated gene that no longer has a function and is not selected out.

Parapatric speciation is... (in general terms). Recognize examples.

Parapatric speciation: Where a population diverges along a 'cline; of environments. A population can spread over an area with a gradient of conditions called 'cline'. Environment at trees in low are different to higher elevation trees. Altitude, rainfall, temperature. Divergent evolution can lead to disruptive selection. If hybrids are less fit they might speciate . Resource partitioning can also lead to character displacement, because the hybrids are less fit (intermediate beaks suck). Galapagos finches show character displacement, they are considered to be separate species, but can hybrid, but are less fit. Beaks are similar sizes on separate island, but when together are different showing character displacement with recent speciation.

What eukaryote group is well known to have a high % of polyploid species?

Plants

-- What does postzygotic isolating mechanism mean? Give examples. Explain why they 'isolate'.

Postzygotic: They mate, but something goes wrong/ sterile. 2 species of cactus are unsuccessful at mating, chemistry is different. Lepard frog and picceru frog can breed together and sperm from one can encounter an egg from another, but there is a chemical differences. Post zygotic can cause chromosome rearrangements leading to sterile hybrids. Ex; Hybrids are sterile because chromosomes have inversions and translocations. Separately evolving genomes can become incompatible aka Haldane's rule. Look at picture in slide. Differences in chromosome number or structure is another postzygotic mechanism.

The eukaryote kingdoms are the animals, plants, fungi, and the protista. Which kingdom (if any) characteristically does NOT reproduce sexually?

Protista

Steven Jay Gould and Niles Eldridge used fossil evidence to support how speciation is sometimes seen in the fossil record called ...................................................

Punctuated equilibria - A history of stasis (no net change) and then speciation events (punctuation) that are rapid changes. Evidence of good fossil records. A fossil bed in ancient lake in Africa that had different species of snails you can see sudden new species with not a lot of intermediates. Little marine fossils (Britozoan) UNS 10 and UNS9 are both sudden new species with no intermediates. Thought of as controversial and not well described. Often described in a way of sudden big changes of species. Gould Focused on fossil record seeing allopatric speciation. Dispersal to isolated regions (not seen in fossils). Isolated species change (not seen in fossils) maybe by drift in species and get large enough in fossil record that it shows a sudden new species because of imperfect fossil record. Punctuated equilibria could just be ordinary speciation, recorded in a slightly imperfect fossil record.

-- The legs.

Quadrapeds back legs are more vertical in stance. Weight of the body is in the center and when walking upright the weight shifts back and forth that takes a lot of work to balance the weight as it is not in the center of gravity. Humans have longer legs with unique hip and knee joint angles that keeps the center of support in the center of gravity. Humans are more "knock kneed" meaning knees and femurs are closer together. Weight is close to center of support and center of gravity using the big toe to balance.

-- The pelvis.

Quadrapeds have narrow/elongated pelvis to hold powerful legs to give big surface area for powerful muscles int he back and legs. Vertically shortened, but broad pelvis. Humans are upright and don't need lots of muscle because energy is efficient. Pelvis is wider because it holds our guts weight, supports guts organs. Humans have greater sciatic notch in rear of pelvis that shows bipedalism.

-- The feet.

Quads feet are flatter. Walking on foot with an arch, and short, aligned toes. Transferring weight from heel to toe directs momentum forward. Humans have arch and toes that are short and point aiming forward. Toes project forward to push off with lots of momentum.

How do insertions of transposons compare between related groups of species?

Related species had retrotransposons inserted randomly and becasuse the animal has the same sequence then it must have happened from a common ancestor.

Butterflies and moths often have prominent "eye spots" of color on their wings, which have various uses. They can startle predators, misdirect bird predators to peck at the wings instead of the body, and they are sometimes used to recognize each other. Anyway...

Remember the modular nature of genes: a gene ca be expressed in new areas, while not changing their 'old' pattern and function.

Two examples of repeated DNA sequences are .................................. and .................................

Satellite DNA, VNTR, Transposons

What happens to male 'mollies' when they have an artificial sword added to their tails so that they resembled swordtail fish?

Scientists manipulated males to see what females do. A sword tail fish has a sword that females use to judge males immune system. Male Mollies do not have this sword and has one attached. The male Mollies are now more attractive/ successful. Augment the male beyond what is normal and he becomes even more attractive.

Identify cases of sexual selection that are intersexual selection.

Selection by one sex for traits in the opposite sex. Usually females choose males because of their traits. Intersexual selection - In this form of sexual selection, it is usually females that choose males based on traits. Here females assess males for the quality of their genes as the genes will be shared in her young. Females seem to have a sensory bias to select for ever more 'expensive; features in males, so males must spend energy to display gene quality and this only works if males are advertising truthfully about the fitness of their genes.

Identify cases of sexual selection that are intrasexual selection.

Selection within one sex because of competition for resources. Usually females choose a resource defended by the males. Intrasexual selection - Females choose a resource, and so males compete with each other to win and defend this resource. ex; Elephant seals fight on beach for land. Red winged black bird color is an aggression display and defends nesting area and entices females to the nest/ discourage other males from trying. Can change shoulder patches and this changes how successful the male is at keeping out other males. Males augmented for battle, antlers, silverback gorilla, big horns/ mandibles for beetles for combat.

What is a general definition of selfish DNA? Give examples of DNA structures that seem 'selfish'.

Selfish DNA; Junk DNA that that does not clearly do anything for the body. It's "using you" to continue to pass on its genes. Satellite DNA; tandemly repeated DNA sequences that range from a few to a couple dozen bases repeated over and over. Variable Number Tandem Repeats (VNTR), SINES (Short Interspersed Elements), LINES (Long Interspersed Elements), Viral DNA, Transposons (Transposable elements aka jumping genes).

-- What is the Fisher-Muller hypothesis?

Sex accelerates variation, finds beneficial gene combinations faster aka the Fisher-Muller hypothesis.

-- How does the rate of change in genetic variation compare between sexual and asexual populations?

Sex accelerates variation, finds beneficial gene combinations faster aka the Fisher-Muller hypothesis. Beneficial mutations in A, B, and C arise in 3 different individuals. The initial B mutation is lost, outcompeted by A. In an asexual population, there is no way to combine the A mutation in one individual with the B or C mutations in another. AB individuals arise only once the B mutation occurs in an A individual. In sexual population, outcrossing and recombination can bring together different beneficial mutations.

--- Meiosis is especially associated with organisms that have ..................... reproduction, where two individuals collaborate to reproduce.

Sexual

In the red queen hypothesis, it is predicted that sexual populations evolve faster than asexual populations. What is doing the 'selecting' in these different populations?

Sexual and asexual minnows were in environment in ponds in a desert. Sexual minnows do better in long run. They both are affected by a fungus (with very short germination time) and the fungi take it's toll. Evolutionary arms race starts. Asexual grows quickly, but plays the same hand of cards while sexual plays a different. What sorts of selective agents are known to correlate with selection for sexual reproduction? Disease, microbes, short generation time and post eukaryotes need to evolve quickly without short generation. Meiosis sexual reproduction.

Given a species with sexual and asexual forms, predict how the two kinds of reproduction will fare over time in the face of parasites and pathogens. Which will likely do better in the long run?

Sexual because they will start an evolutionary arms race to evolve faster than the parasites aka Red Queen Hypothesis. Parasite infects sexual and asexual snails. Sexual snails do better. In Alice, the red queen tells her to run fast just to stay where you are and eukaryotes evolve fast to continue to stay alive against pathogens.

-- What is the two-fold cost of sex? (This is really the 'cost of males'). Describe this in terms of relative reproduction rates of asexual versus sexual lineages

Sexual populations with males can grow only half as fast as asexual populations. A) Only females can reproduce. 2 to 4 to 8 B) Asexual so anyone can reproduce 4 to 8 to 16

19 - Be sure to understand the difference between sexual and asexual reproduction.

Sexual reproduction - Marked by meiosis. During Meiosis have 2 diploid parents set aside 2 gametes and divide cell by 2, chromosomes get scrambled via crossing over and independent assortment, results are gametes with half # of chromosomes and all gametes are genetically different. Then fertilize gametes, have diploid again with zygote. Asexual Reproduction - Very diverse, 1 common form is just mitosis where organisms arranged to make new organism by cloning. Taking cell and dividing to make daughter cell during reproduction cloning off another. Hydras and Dandelions do so.

This part is key -- we will here discuss the different factors that lead to sexual selection. Under sexual selection... -- Females are undergoing selection. What traits define 'fitness' in females? (this one is subtle).

Sexual reproduction tends to be anisogamy or different forms of gametes made by females and males. This means females and males experience different kinds of selection pressures Usually, its females that pay a higher cost/ gamete, than do males.

Selection for reproductive success over competitors is called .....................................

Sexual selection; Selection for reproductive success over others of the same sex. Males competing with other males for reproduction rights.

-- How does sexual reproduction eliminate harmful gene combinations?

Sexuals make new chromosome combinations during meiosis, purging harmful alleles in some chromosomes. Best chromosome in the population has two deleterious mutations, so a new chromosome with only one deleterious mutation is produced by recombination.

A eukaryote genome contains a diversity of sequence structures. Among these are the exons for genes that encode mRNA. This is a large / small part of the eukaryote genome (pick one).

Small part 1.5%

Eukaryotes seem to have a LOT of selfish DNA elements -- often well over 50% of their genome. Why might natural selection NOT be able to minimize the amount of selfish DNA that they carry? This may explain why the amounts of 'selfish' DNA is at high levels in eukaryotes in general, and in various species in particular.

Small populations cannot select against tiny differences in fitness because of drift. Selfish DNA enters some lineages and expands. Tiny differences in genome size cannot be selected against because of the small populations. Drift and fixation locks DNA because natural selection cannot select this out. This happens in tiny frequencies and reproduces to get more, then reproduce, get more etc. It is a Ratchet process because you can only go forward, but cannot go back. It has a trend of change, but no way to reverse it.

Most primate species have excellent color vision. Most primates are active in the day time, and they selectively feed on leaves and fruit. How might color vision be helpful here?

So you can see shit i dont know Traces of possible early primates are found in the late Cretaceous near the end of dinosaurs. Early primates definitely appear in the Tertiary after extinction of dinosaurs. Earliest primates seemed adapted to scurry around in trees and eat insects much like the primate cousins the tree shrews do today. Spreading over Africa, Europe, and Asia, are a variety of early forms of lemurs and moneys including old world and new world monkeys. Transitioning from old world monkeys are the ancestors of apes. These too range over Africa, Europe, and Asia. True apes will knuckle walk, modifications in hands and wrist to be able to do so. Our ancestors always walked on palms and we know this because we have no modifications. Proconsul africanus never walk on knuckles. These hominins then descended from ape like ancestors 6 mya. $

A group of more advanced hominims include members of the genus Australopithecus. What does their genus name mean?

Southern Ape extend approx 4 mya and have several species in 2 groups. Gracile Australopithicines have lighter build, rounder head, smaller teeth (though bigger than ours). Robust Australopithicines are today often put into a different genus; Paranthropus. Deep jaws and heavy "dish" shaped skulls for chewing plants. Suspected to go back to intrasexual selection.

Cooking food (with fire) may have had what effect on brain size? Explain carefully how cooking food could allow (not 'cause' -- allow) an increase in brain size. -- How expensive are large brains? Why does a diet of uncooked food restrict brain size? What sorts of selection pressures might exist that selects for larger brains (should diet allow it).

Species used fire. Cooking improvements nutrient extraction of plants and meat. Allows continued selection for increased brain size because cooking alters nutrients and food making it more available releasing restriction on brain size. This allows selection pressure for larger brains to exploit resources, tools, dominate groups better, wining conflicts, and being cleaver, but still has caloric restriction.

17: How reliable is it to use 'similarities' or 'differences' when trying to identify different species?

Species were thought of as "kinds" of animals/plants. It is an old idea looking for evidence. Can go by appearance, but doesn't always work. ex; Sagittaria is a form of plant that is effected by different environments. a norm of reaction. What about differences? Different is not necessarily different species. Dogs of different sizes are still same species same with humans. What about similarities? Not really. 2 types of birds live together, but don't interbreed. Toads live together, but dont interbreed either. What bout extinct species? We rely on if species can mate, but all we have is morphology. Fossils give us bones, shells, not soft tissue or color so we cannot determine their behavior. What about microbes like bacteria? Every time bacteria divides, it can be unique. Cell shape, change in characteristics and color in bacterial colonies. Color and culture can be altered via conditions so is every division a new species?

Primates with a wet, dog-like nose belong to the suborder ......................................

Strepsirrhines: Lemurs and lorises, are the least primate like. Note the moist muzzle.

Sympatric speciation is... (in general terms). Recognize examples.

Sympatric speciation; Speciation within the same geographic locality. This happens without separation. Something in the gene pool has genetic differences causing speciation over time. Ex; Large fresh water lakes have sister fish species and they speciated together. Adaptations to different environments, different parts of the lake, resource partitioning, breeding different times/ parts of the lake. The 2 fishes teeth are because of the diet they prefer. Hybrid have intermediate teeth and unable to eat well. Sympatric speciation does happen. Many seem to be from pre zygotic isolating mechanisms like mating times and mating preferences. ex; Fish females prefer males to have colors. Put orange light to mess up color and females mate with anyone, but hybrid is not viable child. Frogs using controlled environments can convince they're in their breeding time and will mate making hybrid that is not viable. Resource partitioning also causes speciation. Hawthorn flies are in incipient speciation aka separate species, but can still interbreed. Chromosome rearrangements/polyploidy is another form of speciation. 2 2n species mate making 4n hybrid that is sterile and allopolypolody.

What was the Cambrian explosion?

The Cambrian explosion is life's "big bang" ; Its a rapid appearance of new animals, predators and prey. Getting shells, hard parts, and it wasn't that sudden it was 40 myo. Why was it caused? Evolutionary arms race versus predators and prey, duplications of genes etc.

Describe the typical forms of animals known as the Ediacaran fauna that typified animal life during the late Precambrian.

The Ediacaran world in the Precambrian: soft, squishy animals. Towards the end of Precambrian you see small squishy animals in the ocean that are not fast or armored.

16-2: We start this with a remark that prokaryotes are still simple cells that basically look alike and are constrained to a small size and simple anatomy. Eukaryotes are wildly diverse. They can be single-celled, or multicellular. Large or small. They come in a huge variety of forms. On several different occasions they have evolved the ability to swim, walk, run, fly, and burrow. A few have evolved the ability to remember the past, to learn, and to have abstract thinking.

The discovery of conserved developmental genetics raises an important question: How do developed genes that are conserved across a phyla make all this diversity? Although bacteria dominate life on earth after billions of years they look similar and have failed certain 'economies of scale: which are exuberantly occupied by the eukaryotes. Why is that? Eukaryotes owe their diversity to what is called a developmental "toolkit". Modular in coding = introns and exons. Can shuffle exons to different gene and receiving gene can still work because is in reading frame. Can mutate DNA here and can make a new switch without effecting others. Switches tell where genes are expressed. Gene still expressed normal pattern ,but also in a new place. (this is on worksheet)

Adaptations for upright walking requires global modifications of anatomy. Describe how the following areas are modified and why. -- The skull.

The foramen magnum opening is very forward, under the skull that causes upright body position for bipedal walking.

There are 8 different homeotic genes in Drosophila. How is their arrangement on a chromosome similar to the 'order' of their expression from the head to the tail of the embryo?

The homeotic genes are clustered together, and arranged colinear in their expression pattern.

What is a common explanation for why phylotypic stages have a conserved anatomy. It has to do with interactions between genes that control development. That is a strong hint.

The phylotypic stage is likely there because of developmental stages, genes interacting with genes in this period where gens are cross reacting. Genes need genes and it is difficult to change a gene. Any mutation during the cross reacting will create a bottle neck in the flow of development and is most likely fatal. Likely a developmental constraint. Many genes x-interact.

What major group of land vertebrates famously died out at the K-T mass extinction? What are the surviving descendants of these charismatic vertebrates?

The rein of the dinosaurs ends 65 mya at the Cretaceous-Tertiary (K-T mass extinction except for birds). 50% of terrestrial species and 70% of marine species.

If male versus female roles under sexual selection are reversed, it is because of what circumstance?

The roles of sexual selection are sometimes reversed,where males have a high cost and females are under sexual selection. Falarope birds. Males build nest and raise chicks and females lay eggs, more colorful, and leave. Female convinces the male to allow to lay eggs so has displays color/genome on body.

How do volcanoes change in our atmosphere --> acid rain and (indirectly) a decline of atmospheric O2?

The volcano spewed aerosols that reduced sunlight dimming the sun and initially had a global cooling. Massive slow release of C02 and S02 created acid rain and dramatic global warming. Low sunlight and acid rain caused a loss of photosynthesis that and microbial decay lead to decline in 02. The most heavily affected species include plankton, but also larger species that can not 'hunker down', or required lots of resources. Fungi took over. Most affected are photosynthetic species aka plankton, and species that eat them. Species that can't hibernate or burrow.

15 - Is there generally a difference in the amounts of DNA when comparing the genome sizes of viruses --> prokaryotes --> eukaryotes?

There is a increase in genome

Eukaryotes can differ dramatically in complexity (#s of cells, behavior, etc.). Are there predictable differences in the sizes of genomes when comparing, say, a protist, a plant, and an animal?

There is no trend in eukaryotic genomes size with complexity. This is called the c-value paradox.

--- If an exon is 'shuffled' to a new gene, what can happen to that receiving gene? Why does its protein still function, and not suffer a serious frame-shift mutation?

They always have introns mean that exons can be 'alternatively spliced' leading to different proteins. Exons can be shuffled leading to other genes. Results in new components of proteins. Eukaryote genes are rather plastic they can be viably changed into new genes and new functions. Can be changed in various viable ways to make good proteins.

-- Describe how reproduction adds to the toolkit. Lets see...

They host prokaryotes (mitochondria and chloroplast) that free them from an old surface area/volume problem letting them become multi cellular and larger.

The phrase 'humans evolved from apes' is technically wrong. Explain why this is so

Today, we consider it technically wrong to say "we descended from apes". Why? Ape refers to specific modern species. We instead say "Humans and apes share a common ancestor: Apes knuckle walked and we never did. Paleontologists first decided that we came from Europe or Asia because there were fossils being found there and it wasn't until the late 1940's that the filed began to accept older fossils that were found in Africa all along. ex; Taung chlild. The filed of human paleontology is peppered with a history where major ideas are revised ex; old and wrong ; Human origin in Europe and Asia. New and right; Human origin in Africa. Old and wrong; Upright walking evolved on the open savannah. New; Early hominins lived in forested habitats. Old and wrong; Upright walking driven by increased brain size. New; Upright 1st, big brains later.

Describe how most active transposable elements copy themselves, and insert into genomes. What enzyme do they use that is also found in some viruses?

Transposable elements (jumping genes) - Most are mutated and no longer jump. Most are retrotransposons (jumping genes with reverse transcriptase) and they code for, or were converted by, Reverse Transcriptase (RvT). Many were viruses. Most are mutated and no longer jump and sit there for millions of years. They enter a cell and use RvT to convert RNA to DNA to then insert the double stranded DNA into the genome. Also, there are other proteins from virus genome that can get into the germ line cells passed on in sperm and egg and get fixed.

-- The vertebral column.

Trunk with separate thoracic and lumbar curvature with not just one arch. There are 2 curvatures that makes the impact on the spine while walking lessen as this subtly flexes/bends and cousions the blow. A natural spring. Quadrapeds hold weight in the hands and front of their legs with 1 large curvature because it distributes the load to the front and back feet evenly.

Another old idea is that upright walking evolved alongside enlargement of the brain. What evolved FIRST?

Upright walking did not co-evolve with larger brains. We were walking first. Our ancestors also never knuckle walked. That is a derived trait among apes.

What repeated DNA sequence is used in DNA fingerprinting?

Variable Number Tandem Repeats VNTR

What sorts of imbalances happen today that causes species to be threatened, or to go to extinction? Describe in terms of competition for resources, predator-prey relations, and resistance to disease.

We can study causes of background extinction by looking at modern examples. Species adapt to their physical and biotic environments. Resource partitioning; Species adapt by partitioning resources ex water is limited so plants have shallow roots and take water from the surface, medium roots, and deep roots. If all were the same would all compete for same resource. Predator prey relations; Predators go after prey and prey have defenses. Disease resistance; Microbes go to host and prey have defenses/ disease resistance.

We are erect-walking primates, so our tribe is the .................................... How many species belong to this tribe today?

We evolved from erect walking hominids so our tribe is called Hominina. Our species is the last of our tribe. There were other species of erect walking hominins.

When we compare HOX genes across species, from invertebrates --> vertebrates, what do we find that is comparable about them?

We find Orthologous homologous genes across species. These are a sequence that is conserved across a species meaning it is important for function of that protein.

If cells from two parents are selected to fuse to make high variation offspring, what combination of cells provides the greatest overall fitness?

Why are there males? There will be a direct relationship between zygote size and fitness, but an inverse relationship between gamete size and abundance (bigger is rarer because they cost more) . Big zygotes are more fit. Males make small gametes, but are more abundant and they ensure a high portion of eggs get fertilized. Use anisogamy or different sized gametes. 1 makes a lot of small gametes and another a big egg to have a high fitness, healthy and common zygote.

Once species start to become reproductively isolated, they can (sometimes) stay isolated and not merge as one species again because of certain isolating mechanisms.

Why don't species merge back into 1 species? Actually, they probably can early on, but isolating mechanisms make it less and less likely. Some mechanisms are good at making separate species while others begin the process of new species.

Are species that have a broad distribution at a high / low risk for extinction? (pick one).

Y axis shows how widespread a species are and how much of a risk factor this is or a factor of risk of extinction due to range. Values above 0 show a correlation between broad range and low extinction. Most of the time species having a broad range have low risk of extinction. If value is around 0 there is no correlation between broad range and low extinction meaning if the species is threatened and in one local area, then it's all threatened. Broad range does not help with mass extinctions.

-- What is the evidence that early hominims (represented by Ardipithecus) had a radical shift in their social structure? What was this possible shift in social structure?

f) Ardipithecus( and other early hominins) have less sexual dimorphism and smaller canines - evidence that old sexual selection regime was lost, perhaps replaced by pair bonds and cooperative family living. Ardi cainines are smaller (intermediate) and suggest no intrasexual selection in humans.

How might non-division cause a cell to change from 2n --> 4n?

xx -> iiii BAM

Draw some chromosomes that represent the chromosomes in a diploid (2n) cell. Draw the same set of chromosomes as you might find them in a tetraploid (4n) cell.

xx xx xx Diploid xxxx xxxx xxxx Tetraploid