Evolution Final Review PDF

## Quiz 6: Why Do Organisms Reproduce Sexually? ### Paradoxical In A Lot Of Ways - Costs to reproduce sexually - makes more sense for organisms to reproduce asexually - Ultimately sexual reproduction is better ### Why Do The Benefits Of Sexual Reproduction Outweigh The Costs Of Asexual Repro...

## Quiz 6: Why Do Organisms Reproduce Sexually? ### Paradoxical In A Lot Of Ways - Costs to reproduce sexually - makes more sense for organisms to reproduce asexually - Ultimately sexual reproduction is better ### Why Do The Benefits Of Sexual Reproduction Outweigh The Costs Of Asexual Reproduction? - Most species in the tree of life reproduce sexually - The sharing of genetic material and the opportunity for recombination - Recombination is a key idea associated with sexual reproduction ### "Twiggy" Phylogenetic Distribution Of Asexuality - Asexual lineages spontaneously appear in the tree of life - lizards are one example where asexual lineages spontaneously pop up - in almost all cases they are short lived and sometimes have an advantage over sexually reproducing, they eventually disappear - Striking pattern across the tree of life - some asexual lineages today, tend to have very recently evolved - sometimes we say that asexual reproduction has a “twiggy" phylogenetic distribution - we find it only at the tips of the tree of life ### Types Of Asexual Reproduction - Apomictic Parthenogenesis - Quite a few different forms of asexual reproduction - **Classic Form - Apomictic Parthenogenesis** - happens in Whiptail lizards and sometimes in New Zealand Mud Snails - standard diploid genome set, cells undergo mitosis, and instead of meiosis, they form eggs - no reduction in copy number, just a direct copy of all of the genetic material from the mother to the offspring - in those Whiptail lizards, there's no males in those lineages - mud snails have a mixture of sexual females and males and asexual females - one reason they have so much attention is because we can do experimental tests on the costs and benefits of reproduction and compare ### Gynogenesis - Similar to Apomictic Parthenogenesis on a cellular level - Still have one diploid cell in the mother, undergo mitosis, forms direct genetic copies and eggs - Interesting thing about Gynogenesis, and this is powerful evidence for the recent evolution of asexual reproduction: - females in these species must still mate with the male; the presence of sperm is what stimulates mitosis and the formation of eggs; even though the genetic material from the male is never incorporating into the offspring genomes. - This is because these species arose relatively recently in sexually reproducing ancestors. - Also, interesting because it puts a constraint on this, if you're an asexual female from one of these types of lineages, you must be sympatric - found in the same place as males of the sexually producing closely related species) - in a sense, females from gynogenesis lineages steal sperm from males of closely related sexually reproducing species to stimulate egg production. ### Hybridogenesis - Small fish do a lot of weird things, as do amphibians, but theses are independent evolutions - These two species are not at all closely related! - However, they have evolved the same mode of reproduction - The wild thing is that the offspring in these lineages are diploid - Adult females are diploid, and they have genetic material from both mother and father - But, when females of this lineage go to reproduce, instead of undergoing the usual process, they keep genomes separate and kick out the male genome, and only make eggs from the female genome - All the females of this lineage are diploid! But, only passing along the maternal genome in their lineage. - Maternal = A - Paternal = B - So, we have this unbroken lineage of A genomes - There are some male versions of asexual reproduction, where sperm goes into the eggs and kick out the maternal genome - So, males steal eggs from closely related sexually producing lineages - This isn’t just one mode, it’s not just one thing that happens at the cellular level - It’s happen repeatedly in different ways across the tree of life ### Sexual Reproduction - **Classic meiosis^** - When meiosis happens, we get a reduction in copy number; so, if you have diploid adults, they form haploid gametes - Haploid gametes have some genetic material from both parents - Shuffling around of genes; which turns out to be a key idea that differentiates sexual and asexual reproduction - We often think of bacterial as being clonal, and reproducing asexually - An extreme case of Horizontal Gene Transfer, we have the movement of genes all the way across species boundaries - We get a lot of movement of DNA between individuals as as well, through these different mechanisms that bacteria has. - transduction, conjugation, transformation - Even though there's not a process of two cells coming together in order to form daughter cells in prokaryotes, still get DNA transferred and still get recombination. - Those are the key things associated with sexual reproduction, and we are going to consider this form of reproduction in prokaryotes still falls under sexual reproduction category - There's an exchange of genetic material and there's recombination – shuffling of genes. ### Why Might Sexual Reproduction Be Selected Against By Natural Selection? What Are Some Costs? - "Twiggy" distribution of asexuality, in short term, there are obvious benefits to reproducing sexually, and so another way to think about this is that there are costs to reproducing asexually. ### The Cost Of Sex - Two Fold Reproductive Cost Due To Anisogamy - 1st cost, the one most associated with sexual reproduction: The Two-fold Reproductive Cost due to Anisogamy - Anisogamy: the gametes from male and females have different levels of investing - the idea that females are materially investing a lot in producing eggs - Males are investing relatively little in producing sperm - Unequal investment in gametes between the two sexes - easiest to think about this in a simple case where we don’t have any parental care (certainly not parental care) - Fusion between egg and sperm – production of new offspring – offspring is left to try to survive and grow on its own. - Imagine that every female has enough sort of energetic resources available to be able to produce two offspring - Sort of an extreme case: imagine a sexual female produces exactly two offspring, in order for reproduction to continue it would have to be both males and females sexually reproducing lineage – turns out evolution selects for parents to invest equally in the two sexes – interesting theory shows why parents should invest equally in the two sexes - Female can only produce two offspring. - A male and a female – which means there is only 1 female in the next generation so they go on to produce offspring - that female can only produce 1 female and 1 male - So that population never actually grows in size - Can contrast that in the case where we have an asexual female that does not need to produce male in order for reproduction to happen in the next generation. - An asexual female can produce two daughters, each of whom can go on. - Easy to think about in a setting where every female can only produce two offspring (easiest to understand why it's called two-fold cost) - Same general principle applies: if asexual females don't have to invest in producing males, and those males aren't materially investing in producing the next generation, then an asexual lineage is going to be able to increase much faster than a sexual lineage - Intrinsic rate of reproduction – in ecology we often use r to refer to that? – way to increase population size is going to be a lot bigger in an asexual lineage ### The Costs Of Sex - Experimental Evidence For The Two Fold Cost - Not very many systems where you can do this experimental tests - Not very many species where you can have both sexual and asexual reproduction – that's why they received so much attention - Classic experiments and studies done on them in the mid-late 1990s - classic study with experimental evolution of mud snails over the course of a few generations - they maintained these for a year - they started off at equal frequencies of all 3 types of snails (males, sexually reproducing females, & asexually reproducing females) - equal frequencies of the two types of females, but the sexually reproducing females had equal access to males for mating - started all of these replicants, they had 14 different replicants - started all of these populations off with 1/3 females then just let them go, let them reproduce, and they maintained those colonies over time - even over the course of 1 year, they got a radical increase in asexual females across all these replicants. - nice experimental demonstration of the principle we just talked about - a lot of theoretical and empirical evidence ### The Costs Of Sex - Can Break Up Favorable Gene Combination - When recombination occurs, it can break up favorable gene combinations of traits - Monkey flowers have 2 different types of populations (inland-hot, dry & coastal-cool, moist environments) - these two environments don't just select for 1 trait they select for a whole bunch of traits that have to work together - What do we say happened to these lineages to make sure it was going to stay together? - We have these inversion event that can reverse the order of the genes - if we locked up all those genes together and formed a supergene - contained all of the traits that those coastal genes need to do well and prevents recombination from shuffling those traits - that allows both of the lineages to do better - If you have a set of well adapted traits, in general recombination is going to mix those up and reduce offspring fitness - unless they get locked up in inversion like this or unless there’s some kind of mechanism to stop recombination ### The Costs Of Sex - Mate Searching Can Be Costly - Other thing is if you're a sexually reproducing individual, there is a time and energy cost associated with mate searching, which is going out in the environment and finding a mate. - requires you to spend energy and in many cases poses them to predators more often than normal - Example from water beetles where females remain in contact with males who are mating....probability of that female being attacked by a predator - when females - probability depending on what size male she mates with - if she mates with a smaller male, she has greater chances of being attacked by a predator - larger male, less chance of getting attacked. - Idea that females choose mates based on probability ..... - Key Idea: is that the very act of going out and finding a mate has costs ### The Costs Of Sex - Sexually Transmitted Diseases and Parasites - Mating requires organisms coming into contact with other individuals which increases the probability of disease transmission and there are some parasites and pathogens that have been adapted to being transmitted during sexual encounters in all kinds of different organisms - not only increases the energetic cost and the probability of predation but also increases the probability of disease transmission and the cost associated with it - What might sexual reproduction be selected for by natural selection? - What are some benefits? - the benefits of sex (or costs of asexuality) - Muller's Ratchet and Mutational Load ### Mutational Mode - Every generation and every organism has new mutations that their parents did not. - Those mutations that are deleterious (harmful) – overall effect on the genome is the mutational load - Red circles = deleterious mutations - Red genome has only one least loaded class - Minimum number of mutations has increased in both A and B - Both drift and mutation can cause this to happen - Offspring themselves carry new deleterious mutations - A shows mutation - B shows drift - Minimum # of mutations across the population is going up - Key idea of a ratchet can only turn in one direction - Without recombination, mutational load can only go up – no way without mutation to go backwards - We all have new deleterious mutations - It has been estimated that each human carries 2-3 new deleterious mutations in their genome that are not present in their parents - Clicks of the ratchet do not require fixation events – so much accumulation of mutations that the population simply can't exist. - If mutations keep accumulating in the genome, the population cannot keep going. - Twiggy distributions - One important thing to distinguish is the ratchet turning and the mutation fixing in a population. - 1 circle across all genomes in a population. - Mutational load thinks horizontally – how many mutations are in each genome (does not have to be the same one in each genome) ### Recombination Unclicks The Ratchet - The benefit to sexually reproducing lineages is that they can go backwards - You can get new genomes that have few deleterious mutations than the genome before. - Key idea: genomes in the parental generation do not have the same deleterious mutations - Gone from a population that all had 2 deleterious mutations to all populations having at least 1 ### Recombination Facilitates Faster Adaptation - The Fisher-Muller Hypothesis - In Muller's ratchet we are talking about deleterious mutations and how we don't want them together - Recombination is important for bring together beneficial mutations into the same genome - X axis is time - Y axis is meant to represent a bunch of individuals in the population - ABC represent different possible mutations - By chance each of those occurs (adaptive alleles) - selection starts to favor all of them - What happens when A B and C get to high frequencies in this asexually reproducing population? - No way to bring them together, they start to compete with each other, called Clonal Interference (interfering because they are beneficial, but they cannot all be in one genome) - asexual reproduction cannot have recombination - Maybe by chance A goes to fixation, and gets rid of B and C - They could be in totally different parts of the genome - Makes the process much slower. - Sexual reproduction removes the barrier (process of interference) - As they increase in frequency, the first-time individuals A and B meet they could reproduce a super genome - Sexual reproduction can have recombination so they can have AB or ABC, etc. ### Testing The Benefits Of Sex: Experimental Evolution With Yeast - Did a study where they populated yeast productions - Red lines represent mutations that spontaneously occurred as deleterious (reduced fitness) - Don’t fix in the sexual population, but they do start to increase in frequency. - Hitchhiking also occurs for deleterious parts of the genome - Beneficial – blue - Deleterious- red - Asexual lines go to fixation, still gaining beneficial mutations, but dragging along the harmful ones, which increases mutation load ### Adapting To Changing Circumstances - Bet Hedging - If the environment might change, but an organism doesn’t know how, it could be beneficial to produce many different types of offspring. - Offspring that are produced by a given parent are more genetically variation in a sexual population - Asexual populations – offspring is just like the parents, if there's climate change; producing variable offspring is more beneficial ### The Red Queen: Outrunning Parasites - Host parasite interactions are very important for how we think about the benefits of sexual reproduction - The most important kind of coevolution that occurs - Looking at frequency of hosts - Do well with resisting parasites that are around. - Clone can produce more offspring than the sexual individuals - As asexual lineage starts to increase in frequency, there is super strong selection that become good at - now not beneficial to be a clone, tend to be selected outside of the population. - The process of constant coevolution - Constantly running just to stay In the same place - Constantly evolving just to not get outdone but another being - Adaptive immune systems bc we cannot keep up with parasites ### Tests with New Zealand Snails - Need organisms that only differ in their mode of replication - Has been useful – given a lot of insights - If entirely sexually reproducing – half male half female - Asexual – all female - Surveyed snails for parasites - Most sexual reproduction found in populations with the most parasites ### What Is Sexual Selection? - A process that "depends on the advantage which certain individuals have over other individuals of the same sex and species in exclusive relation to reproduction” - C Darwin - Fitness has to do with genetic contributions made for future generations ### Variance In Mating Success - Most species, males are not limited in terms of reproductive opportunities, but females are - Males have more variants in reproductive success - Varies a lot among species - Certain males dominate territories - Some individuals by virtue of having access to more reproductive opportunities ### Types of Sexual Selection - **Intersexual Selection (female choice)** - Between 2 sexes - mate choice - Bright colors, dancing birds, mating calls - Dancing birds- male trying to do fancy dance – scaring off female – males also have iridescent colors - Males and females look and behave differently – sexual dimorphism - same = sexually monomorphic ### Models Of Mate Choice Evolution - **A. Direct Benefits** - Females directly gain from certain mates - Sexual Cannibalism in Australian Redback Spiders - Some species bring food items to mate; others mate and then act as food source themself - Resources, territories, or nests - **B. Good Genes** - Female choose mates that can provide their offspring with favorable traits - One favorable trait is resistance to parasites - How might females assess males to find the right ones? - Parasites are really important - Male displays are meant to show their ability to be healthy in the face of parasitism - Idea is that males are showing off - showing their ability to produce traits that are costly - Classic example widow birds with really long tails. - Top graph shows relationship between body conditions - Better body conditions – less parasites - Worse body conditions more parasites - Researchers have artificially cut the birds tails and looked at who did better - Body conditions are both going down - Control tailed males are paying a steeper cost - Trait is costly and an accurate description of male health - honest signal - Trait has to be an honest indicator. - **C. Runaway** - If: - Some females in a pop'n have a preference for extreme males, while other females choose randomly - The female preference is heritable - The preferred male trait is heritable - Then: - The trait and preference will become associated - Some males will have higher fitness just because an arbitrary female preference existed. - A positive feedback loop ends up driving male traits and female preference to high frequency. - Genetic association becomes established - Not an indicator of genetic quality - Called runaway because of the positive feedback loop because you can keep going until you get some extreme – really hard to verify. - **D. Sensory Bias** - Female become attuned to picking out the red berries -All birds are blue - One day red dot appears on a male - Female is already attracted to red dot, so she will become attracted to the male with the red dot - Genetics are better, he just is prefered - Female guppies prefer males with orange spots - They also like orange fruits that fall in their streams ### Tungara Frogs: A Case Study In Mate Choice - Choruses in frog species -a lot of males calling in the same place - Common in central and south America - Calling to attract females – auditory cues since it's at night - Calls got more frequent over time –got competitive. - can't constantly call be lose energy and attract predators - More clicking sounds at the end 2-part call –(wine & chuck parts of the call) - They can add different numbers of chucks ### Tungara Call Structure - 2-part call: whine (higher pitch) & chuck - Females prefer calls with chucks & calls with more chucks ### Why do females like chucks? - Researchers surveyed a bunch of closely related species, and which ones produce chucks - They estimated that the use of chucks in calls in a synapomorphy (evolved from one the the common ancestors) - Female preference for chuck probably evolved earlier than the chuck - Female preference must precede the male trait - This confirms that prediction - Female auditory systems are extra attracted by the sound ### Tungara Calls Vary In Chucking - Males will only turn on chucks and extra chucks when they have to (aka when there's competition) ... they may not want to waste energy or attract predators - Why don't tungara males try to be as “sexy" as they can whenever they call? ### Sexual and Natural Selection Can Often Conflict - Species of bats that are specialized at finding Tungara frogs and have an easier time locating the male frogs when producing chucks - Highlights things that are favored by sexual selection by not natural selection - Other physical traits like long tails – they cannot adapt that – tail length will be determined by balance in natural selection and sexual selection - Parasitic blood sucking flies also find frogs easier with hearing the chuck sounds - Intrasexual Selection (male-male competition) - Direct competition between members of the same sex - Classic example is deer antlers - Males lose calcium in bones and the rest of the body in order to have antlers - Many species shed them in order to not pay the cost during competition and mating - Beetles mate in open spots in the rainforest where there's been a tree downfall and there's a sunny spot, male beetles will fight for access to those territories because females like to congregate in the sunny spots – pseudoscorpions on their backs are also fighting simultaneously - Weapons of beetles have evolved ### Intrasexual Selection - Cuckoldry - Some traits are very straightforward – those in direct combat - Some are not as straightforward - Sneaker and satellite are a type of Intrasexual selection that selection for cuckoldry. - Cuckoldry – 3 different types of males. - Parental - Big and showy; trying to attract females to come and fertilize, territorial - Sneaker – maintains a small size, hide in vegetation nearby, wait for a female to lay eggs in a parent male nest, and sneaks in and tries to fertilize as many as possible - Satellite - parental males don't run them off because they don't recognize them ### Sperm Removal - Seed beetles – lots of spikes - Various physical aspects to their genitalia – actively trying to remove sperm before they deposit sperm - Morphological characteristic is the length of ventral genital spines in relation to fertilization success ### Stages of Sexual Selection - **Precopulatory** (all previous examples) - Taking place before the act of mating occurs - **Postcopulatory** (sperm storage) - Female can mate with multiple males then decide which she wants to keep - Intrasexual - Can be adaptations in the sperm itself (male – male competition, taking place within the morphology of sperm) - Positive correlation with body weight and testes weight - Intersexual - Behaviors that can occur post fertilization. - Males tap females and somehow related to female choice - Relation between number of tapping sequences and fertilization. ### 4 General Categories Of Mate Choice In Evolution - **Direct Benefits:** territory; sexual cannibalism - **Good Genes:** quality of genes; a trait that can only show if a male is healthy (honest signals) - **Runaway:** some preference that arises for some reason; usually think about extreme phenotypes (really long tail) once that preference arises gives males with extreme traits higher fitness, so their offspring will carry the gene preference (linkage disequilibrium between the traits); end up in positive feedback loop- can end up benefiting female offspring - **Sensory Bias:** Different sensory systems in different species might be tune to different things based on natural selection; idea is that there is some preference for some kinds of signals ### Sexual Conflict - Unless male-female pairings are monogamous over the course of a lifetime, male and female mating interests may be different - This results in sexual conflict - Males may seek to force female investment in their offspring, at the expense of her other offspring - In many species where male and female species are not monogamous... - May be the case is that male fitness may be maximized if whoever they mated with that year... - Overall fitness over the course of a lifetime can lead to different interests in different mating seasons ### Sexual Conflict In Drosophila - In drosophila males produce extra proteins that are deposited in females during insemination costly to females from a health perspective even though it increase the chance of fertilizing the eggs - Coevolution where male proteins are trying to maximize fertilization of female eggs and females have proteins that are counteracting - Took away benefit of accessory proteins: females defenses against accessory proteins went down - Then brought the females back to mating with males with accessory proteins – females had shorter life expectancies ### Sexual Conflict In Ducks - In some duck species, up to 1/3 of matings may be forced, but they result in only 3% of offspring. - Duck penises have, in some cases, evolved to be exceptionally long. And are shaped like corkscrews - Female ducks have corkscrew oviducts, but they spiral in the opposite direction. - Seems to limit the ability of unwanted males to deposit sperm - Classic work done of ducks in terms of sexual conflict - The idea is that in many species male and female reproductive systems are not aligned - There's been coevolution in male genitalia - Female ducks have evolved counter defenses and are able to control the mating opportunities - Males and females do not have perfectly aligned fitness. - Males may try and force females to allow them to have access to certain reproductive activities or to invest in their fertilization. ### Humans As Primates - Nearly all apes remaining are found in Africa - We in particular sit in the highlighted portion of the ape phylogeny ### Interbreeding And Introgression - A lot of introgression, essentially the same thing as horizontal gene transfer – except with sexual reproduction - Species tend to be mostly reproductive isolated units - There is still a flow of genetic material across species boundaries ### Our Closest Extant Relatives - Last common ancestor of orangutans and gorillas was about 20 million years ago [based on a combo of fossils and data] - Our last common ancestor of us, chimps, and bonobos was about 7 million years ago - Chimps and bonobos are the closest living relatives - We are most likely to see gene trees that don't match the species tree (incomplete lineage sorting) when there are short intervals of time in between speciation events ### Incomplete Lineage Sorting - Not every gene tree matches the species tree ### Testing The Evolutionary Hypothesis Of Common Ancestry - Less about finding who our closest relatives are and more about finding evidence about them. - If we were to estimate ancestral chromosome number, we may see unique reduction in chromosome number along the lineage leading to modern humans. - Chromosomes can break apart and fuse together. - General idea is that we have two ancestral chromosomes that fuse together. - We should see evidence of a pseudogene that used to function on the chromosome - Testable prediction: If these organisms share common ancestry, the human genome must contain a fused chromosome. - The marks of that fusion must appear in one of the human chromosomes - Turns out this pseudogene is exactly what we see - Just a draft of the sequence - Now today we have an extremely detail draft/view of the structure of our genome. - When folks first assembled the structure of our genome they found exactly what they hoped to find. ### Our Closest Extinct Relatives? Sahelanthropus tchadensis (aka Toumai) - Our closest relative that ever existed are no longer living. - known as hominins some lineage that branched off of our ancestral lineage. - All species known as hominins are more closely related to us than any other species. - Fairly close relative around the time that we last shared a common ancestor with chimpanzees ^ pic ### Ardipithecus ramidus (4.4 MYA) - Ardi - is pretty clearly a hominin - Shows some evidence of put hominin like features some anatomical adaptations for walking, and some for climbing - Most other apes are arborical (live in trees) have adaptations for climbing - We have evidence for much of the body – enough to draw a lot of inferences ### Gracile Australopithecines And Kenyanthropus - Theses are clearly hominins more closely related to us - 2 1/2 to 4 MYA - In many cases, there only only be a skull, tooth, or jaw to draw conclusions - Paleontologists try an ask about how measurements of those body parts relate to other species - Recognize that there were several of these lineages and many share features that we associate with us as modern humans ### Australopithecus afarensis footprints is ash (3.6 MYA) - These are two sets of footprints Australopithecus afarensis, shortly after volcanic eruption there was ash on the ground and then it rained and left footprints of adult and child footprints ### Robust Australopithecines - Paranthropus - Not only were there many other hominin lineages in the past, but they also have different morphologies and have left no living descendants - Key idea is that the process of hominin evolution is not linear, the same way the overall tree of life is a process of diversification, many of them have gone extinct, we are the only living hominin species left today. ### Key Characteristic Is The Skull Morphology – Massive Jaw And Teeth – Needed This To Chew The Tough Foods They Were Chewing - Clear adaptations that are very similar to us, even within our our genus there has been remarkable differences ### Early Homo - Most recent genus in our species is obviously us ### Homo Naledi - Paleoanthropologists all women team who did this discovery – recovered hundreds of bones from at least 15 different individuals - Controversial proposal - Full collection of bones that they found - Experts formed teams depending on who specialized in what bones - They all examined and came to conclusions then brought their ideas together - This species came close enough to us and became known as homo naledi - May have branched off very early in our genus about 2 MYA - Bones are dating just to a few hundred thousand years ago – this branch existed for a long time nearly 2 million years – and lasted close to a time that we evolved in Africa for the first time ### Homo floresiensis - Interesting discovery of another fairly close relative of homo – fossils of species found on the islands of Indonesia - Very short and small compared to modern humans – they lived until about 40 thousand years ago – may have overlapped with modern humans - Shrinking on islands is common – bc of restricted resources – matches what we see in other species- island dwarfism ### Humans & Other Hominins - Early lineages that are possibly early hominin - Archaic hominins definitely more closely related to us but have many features associated with other apes like climbing - Megadonts – hominins that diversified and... - Our time here has been much shorter on earth than many other lineages only about 300 thousand years so far - Bottom- different genus in our species - The idea that we are the only hominin lineage here on earth is a very recent thing (about 40 thousand years ago) ### Early Hominin Movements - Just genus homo – all hominin species originated in Africa. - but find early lineages outside of Africa – approaching 2 MYA - found quite far away much smaller population sizes but yet they still moved huge distances away - first wave out of Africa was called homo erectus ### Major Innovations - Adaptations for walking bipedally - Changes in jaw and tooth structure - Changes in cranial structure - Early hominins were probably using tools to butcher meats - In the species that we think of as most closely related to us most changes are enlarged cranial size (major feature of evolution in hominin species) ### Increases In Cranial Capacity - There’s been a steady increase of cranial size through time ### Evolution of Bipedalism - Australopithecus afarensis - A lot more changes in these species - Different features in the body labeled if they were more adaptive for walking or climbing - Homo erectus very well adapted to walking long distances - Ongoing area of research for the evolution of bipedalism was because of climate because of less rainfall and climate change from rainforest to more savannah like forest - For individuals to just find food fitness benefit for walking instead of climbing ### Closest Relatives - **Neanderthals** - 400-40 kya - Much of Eurasia - Among our very closest relatives are Neanderthals. - Evidence as early as 400 thousand years ago -up to 40 thousand years ago - Covered much of Eurasia – colder climates - Very very close relatives to us but they have wider body structure wider rib cage but generally shorter and stockier ### Evolution Of Homo Sapiens - Age of modern humans as early as 300 thousand years ago in modern Africa - About 100ish thousand years ago we began dispersing out of Africa. - Still unpacking now through genomics – can use our own genomes to construct our patterns of dispersal - Probably multiple waves of migration (probably not strictly linear) probably waves in and out of Africa. - Around 40-50 thousand years ago see us moving into Europe - Modern humans have lived in Australia for quite a while. - Northern dispersals are somewhat more recent. - Timing of Neanderthals extinction was probably not accidental - Not until 16 ish thousand years ago humans moved into North America (definitely the most recent dispersal) - Footprints of giant sloths in north America and footprints of human children inside the footprints of the giant sloths (somewhere in new Mexico) - Humans probably crosses when the sea levels were lower – modern humans traveled the coast to avoid glaciers (migrated before glaciers disappeared) ### Human Genetic Diversity - X axis - Distance from East Africa (using Africa as reference because it's probably where we originated) - Y axis – is heterozygosity - Less genetic diversity, the further we go away from East Africa (serial Founder events) - Most founder events in southern Africa – genetic diversity matches those very closely - Dispersal into Oceania was distinct from the dispersal into the Americas - Sequenced full genomes – represents the most genetically diverse population on earth because there has been NO founder events - unique kinds of mutations show this pattern ### Deep Coalescence Times - Most Of The Rest Of Humans Khoe-San - If we think about human populations as a phylogenetic tree, the very bottom of the tree is all non- African populations - Bottom graph is the coalescence time - Blue dot represents most populations today (MRCA) - Coalescence time just in the Khoe-San population is more than 50% older - Genetic diversity is not equally distributed among human populations ### Human Genetic Diversity - Looking for ancestors that all come from the same part of Europe - Taking a lot of variation in data and compressing it down into 2 dimensions and squashed it down - Figure on the left made with no information about geography – only info about genetic diversity - But using genetic diversity they almost perfectly made a geographical map - For much of human history, movement was relatively slow - Genetic drift happened independently in human populations ### Gene Flow From Neanderthals - Turns out we do have connections - Movement of neanderthals to us as we moved out of Africa - All nonafrican populations carry some sort of Neanderthal DNA - African populations do not ### Humans And Denisovans - Bones that didn't match modern humans or neanderthals, low and behold they were from a totally new hominin species (found about 15 years ago) - Became known as denisovans - We find connections mostly in Polynesian populations - This implies that this was not a unique species – they were a widespread population that moved across Asia. - Neanderthal - Denisovan - Unclassified - More evidence and more genomes to find Neanderthals, Denisovan, and other ### Multiple Episodes Of Introgression - Archaic Sequence (Probably) Selected FOR in Other Regions - Immune Related Genes - Some genes are immune related genes – having extra alleles in our genomes gives us increased fitness because we have more genetic variation to work with. - Genes from Neanderthals that remain in modern humans may be important in these phenotypes: - Skin and keratin production - Resistance to ultraviolet radiation - Immune genes - Modern human health conditions may have come about because of introgression. - Types of genes where we see archaic ancestry. ### Tibetans Get High-Altitude Edge From Extinct Denisovans' Genes - Epas1 gene super adaptive to good oxygen levels at high altitude levels - Bones found from Denisovan in Tibet – neanderthals and denisovans were sister lineages. - Allele being selected for because of some benefit - EPAS1 came from Denisovan ancestry - example of local adaptation - Other classic example of Local Adaptation: - milk tolerance – lacta