Session 2: Theory Behind Evolution II

00:00:07.06 Hi.
00:00:08.06 My name is Uma Ramakrishnan and I'm an associate professor at the National Centre for Biological
00:00:12.22 Sciences in Bangalore, India.
00:00:15.18 This is a research institute where we study biology, and I've come all the way from there
00:00:20.17 to tell you a little bit about biogeography and the work that we do on understanding biodiversity
00:00:27.12 in the Indian subcontinent.
00:00:29.13 So, anywhere you live, if you look outside your window, you'll see many different species.
00:00:35.06 This is biodiversity.
00:00:36.06 And as humans we're fascinated by biodiversity.
00:00:40.16 And biogeography actually is a field which studies the distribution of species and biodiversity
00:00:47.03 across space.
00:00:48.10 And, you know... you know immediately, even as a child, that certain places have more
00:00:56.10 species than others, the species in a particular place seem to be similar, and so on.
00:01:01.05 You observe these things almost naturally.
00:01:04.05 And this is basically how we measure biodiversity and how we study it.
00:01:08.09 We try and quantify biodiversity and look at why places have more biodiversity than
00:01:14.08 do others.
00:01:15.15 So, how do we quantify biodiversity?
00:01:18.11 How do we actually use mathematical ways to study patterns of biodiversity, statistical
00:01:24.19 ways, across the world?
00:01:27.09 So, the first thing we do is we actually count the number of species, right?
00:01:33.09 This is something which has often been controversial in biology.
00:01:36.11 How do we know what is a species?
00:01:38.05 A taxonomist... as humans, we have this desire to put things in boxes and say, this is one
00:01:44.19 species, this is another... and in some cases this might be relatively easy.
00:01:49.03 For example, with apes, you know, the gibbon... gibbons look very different from gorillas
00:01:55.20 and chimpanzees and modern humans.
00:01:57.15 And when we look at their DNA there are several of these differences which are reflected,
00:02:03.01 allowing us to build a phylogenetic tree.
00:02:05.08 We heard about this also, for example, in Scott Edwards' talk.
00:02:09.21 So, this allows us to understand that there are multiple species of apes which look different
00:02:16.24 and are genetically different, distinct, as well.
00:02:20.10 This may not always be the case.
00:02:22.14 For example, this really beautiful examples of a ring species, salamanders in California.
00:02:30.03 It shows you, here, that across their distribution these different salamanders look slightly
00:02:36.08 different and yet similar, right?
00:02:38.04 So, here, speciation or these different species are along a continuum, right?
00:02:44.05 They look slightly different... one looks slightly different from the other and so on.
00:02:48.19 So, it's not always easy to classify species, but, overall, we use various tools: morphology,
00:02:55.19 how species and individuals... how individuals in a population look; genetics, how different
00:03:00.20 or similar their DNA is; and it could be several other forms of behavior -- do they have similar
00:03:06.12 songs, if they're birds, and so on -- and we use all of these bits of information to
00:03:11.19 make an informed guess about whether we think sets of individuals are distinct species or
00:03:17.10 not.
00:03:18.10 For the sake of correctness, I should tell you that the biological species concept proposed
00:03:23.06 by Ernst...
00:03:24.06 Ernst Mayr is what we accept, and this suggests that a species is a group of individuals that
00:03:29.14 can and do interbreed with each other in nature.
00:03:32.11 So, not if you put them together in a zoo, but in nature you do find them interbreeding.
00:03:38.10 And, as we said, species could look similar or different, but at some point we take a
00:03:44.14 call and we say, okay, this is a species and these two populations are not distinct enough
00:03:49.08 to be a species.
00:03:50.17 So, once we have catalogued species -- that's the first thing we have to do, these are our
00:03:55.07 primary data -- we measure biodiversity in units of species.
00:04:00.23 So, how do species actually evolve?
00:04:04.03 I mean, we said, okay, they look different or, you know, they're genetically different.
00:04:09.06 Well, this has also been a field of extensive study in evolutionary biology and you made
00:04:13.16 have seen a talk as part of this series by Hopi Hoekstra, who's actually trying to understand
00:04:18.01 how these differences between how species look/evolve from a genetic perspective, right?
00:04:24.03 Adaptation from a DNA level.
00:04:26.19 But this picture, here, shows you a really simple kind of theoretical idea of speciation.
00:04:33.09 So, the most basic is allopatry, over here, where you can see that there's two pop...
00:04:39.03 there's a population and suddenly, potentially, there's a barrier between two parts of this
00:04:45.03 population, maybe a road came up or there was a... a... a, you know, a rift or something
00:04:50.01 like that, a river.
00:04:52.00 And now, individuals on either side of this barrier develop different adaptations or they
00:04:59.16 become different.
00:05:01.13 And so, when they meet again, say, when this barrier disappears, they don't interbreed
00:05:05.23 with each other.
00:05:06.23 So, this has now resulted in the creation of two species from what was a single population,
00:05:12.24 right?
00:05:13.24 So, this is a case of allopatric speciation, and often what we see most commonly in nature.
00:05:21.13 On the other hand, speciation could theoretically also be sympatric, where you have a new, for
00:05:27.14 some reason, change...
00:05:30.12 ecological change, maybe, or adaptation... of some individuals in one of this... in this
00:05:35.16 population, and this results in differentiation and, over time, these differences became...
00:05:42.05 become so large that these two populations do not interbreed.
00:05:47.06 An example for this is the [unknown] flies, or the apple flies, and the Hawthorn flies,
00:05:53.00 which lay their eggs on different fruits.
00:05:55.23 Apple and Hawthorn [flies] are just coexisting, so they're sympatric, these flies, and yet,
00:06:02.11 you know, they do become... could become different species.
00:06:05.01 There are kinds of shades and grades of these two examples, where you could have speciation
00:06:10.13 in peripatry or parapatry, a creation of a new niche or a certain kind of budding off
00:06:16.24 of a set of individuals and so on, a range expansion.
00:06:21.06 But, basically, the mechanisms are somewhere between sympatry and allopatry.
00:06:26.21 While these are nice examples from a theoretical, hot perspective, what do we know about speciation?
00:06:34.06 So, early on, Dodd did experiments with Drosophila where, you know, different populations of
00:06:41.00 flies were given two different kinds of food and, over time, these two flies... fly populations
00:06:49.23 became differentiated and then they developed mating preferences, so flies from population
00:06:56.16 1 didn't want to mate with flies from population 2 and vice versa.
00:07:00.23 So, this is very important because it shows that not only did they become different, they
00:07:06.17 developed reproductive preferences and, potentially, reproductive isolation -- what's most important
00:07:13.04 for the lack of gene flow of mating, in the end, between two species.
00:07:18.00 So, now I'll go... we go back to biogeography, which is basically the distribution of species
00:07:26.14 on our planet, right?
00:07:28.08 So, how do we actually study this?
00:07:30.17 In a sense, it's one of those... the most basic things.
00:07:34.04 Even before people thought about DNA or evolution, a lot of naturalists walked all over the world
00:07:41.19 and did surveys and catalogued interesting things about biodiversity.
00:07:47.17 Alexander von Humboldt was one of these people and he basically did a lot of explorations
00:07:54.10 and studies in South America, and this beautiful illustration he has of this mountain, Chimborazo,
00:08:02.13 in South America, which is a volcanic mountain, which goes really high -- 6200 or so meters
00:08:09.03 -- he shows that, actually, as you go up the mountain, the ecological environment changes
00:08:14.15 dramatically.
00:08:15.15 So, you can see, for example, at the top of this mountain, you have snow, right?
00:08:19.20 And that's not there at the bottom of the mountain; it doesn't seem to be covered with
00:08:24.06 snow at all.
00:08:25.11 So, what Humboldt did was he also catalogued the plants at the... along this mountain.
00:08:32.13 He was a botanist and he said, well, it seems to be that there are very different species,
00:08:37.09 very different sets of species, which occur across this mountain, and this famous and
00:08:41.20 really beautiful illustration he made kind of shows this, shows the community of plants
00:08:46.24 associated with these environmental gradients.
00:08:50.17 And so, Humboldt thought early on that ecology, or differences in habitat, might be important
00:08:57.06 to determine where species are distributed.
00:09:02.03 The father of evolutionary biology, Darwin, also had contributions to thinking about biogeography.
00:09:08.01 So, Darwin, as you know, went on this really long voyage across the world on the Beagle.
00:09:15.21 And he... while he was going on this voyage, he thought about all the species present along
00:09:21.11 this route.
00:09:22.11 And he actually happened to go to South America and then later to the Galapagos Islands, and
00:09:28.21 when he did that he noticed something really interesting.
00:09:31.17 He saw many birds on the Galapagos Islands.
00:09:34.08 They look similar to the ones he'd seen on the mainland and yet different, right?
00:09:39.06 So, Darwin realized that, potentially, the species that occur in a location may be there
00:09:45.16 because of history, because they're colonizing from somewhere close by, and so the finches
00:09:51.19 are similar to those on the mainland and yet they're different.
00:09:59.04 Most interestingly, also, Alfred Russel Wallace, around the same time as Darwin... he was a
00:10:05.03 codiscoverer of the theory of natural selection with Darwin, they chanced upon the idea together,
00:10:10.01 in the same ti... not together, but the same... at similar times... was also a very avid explorer
00:10:16.13 and he also studied distributions of species across the world.
00:10:22.01 And what he did was he actually realized that certain sets of species seemed to be most
00:10:28.20 similar to each other and these sets of species seemed to occur in similar locations, okay?
00:10:34.24 So, he tried to group the species in the world into bins, in a sense, not just one species
00:10:41.21 but sets of species.
00:10:43.06 And he, for example, suggested that all of the Orient, which is Southeast Asia and India,
00:10:50.11 was one biogeographic zone or grouping.
00:10:55.06 And it's interesting to note that, very recently, in 2013, Holt and other authors actually kind
00:11:01.15 of reevaluated Wallace's ideas of these biogeographic zones based on modern DNA phylogeny.
00:11:09.10 So, Alfred Russel Wallace and Darwin are pre-DNA -- they didn't know anything about, you know,
00:11:15.10 the kind of hereditary material that we know so much about today, which we use to study
00:11:19.20 evolution.
00:11:21.03 And they also found very similar results to what Wallace had found so many years ago.
00:11:28.24 So, now we can look, then... we are looking with modern tools of GIS and DNA and so on,
00:11:37.12 and we can now look at biodiversity and ask questions in biogeography.
00:11:42.12 And this actually shows you a distribution of vertebrate species across the world, and
00:11:48.19 you can see immediately, anyone can see, that some areas have more diversity than others,
00:11:55.12 and this tends to be in the tropics.
00:11:57.12 So, of course, here, the colder colors or blues are areas with lower numbers of species
00:12:03.02 and the warmer reds are regions with higher numbers of species.
00:12:08.06 What I'm also going to try and convince you is that if you actually were to plot onto
00:12:13.12 this map mountain rangers, you would see that mountain ranges tend to correlate with areas
00:12:20.04 where there are high species, and we'll come back to this in a little bit.
00:12:25.01 There's other ways to look at species, right?
00:12:28.00 You can just count all of them, but you can also ask whether some places have more restricted-range
00:12:34.22 species, or higher endemism.
00:12:36.24 Do some places have more special species, which are not found anywhere else?
00:12:41.09 This is also an important thing for us to understand when thinking about biog... biogeography
00:12:46.12 and biodiversity.
00:12:47.12 So, we can quantify this by quantifying endemism, or how restricted a species' range is to a
00:12:54.12 geographic location.
00:12:57.05 And when we do this, again, we find, you know, really interesting patterns.
00:13:01.00 We find, for example, superimposing our mountains, again, that endemism, or special species,
00:13:07.23 tend to be found also in areas where there are mountains and, very interestingly, also
00:13:14.18 on islands, okay?
00:13:16.14 So, islands, mountains, and the tropics seem to be important for presence of species.
00:13:25.07 So, how do we actually study why there's more biodiversity in a particular location?
00:13:30.14 So, okay... so, why may there be more species in a particular place?
00:13:34.12 Well, clearly there's more speciation there.
00:13:38.03 Maybe there's less extinction.
00:13:39.20 Speciation increases the number of species while extinction might decrease the number
00:13:44.00 of species.
00:13:45.00 So, clearly, the balance or diversification... the balance between speciation and extinction
00:13:51.12 must be high.
00:13:52.12 There must be a net positive rate or diversification.
00:13:56.08 And we can actually quantify speciation rate and extinction by looking at phylogenies.
00:14:02.09 And so, in this paper, Rolland et al tried to do this, and what we did was they contrasted
00:14:08.16 the net accumulation of biodiversity, or diversification, amongst the tropics and amongst the temperate
00:14:16.01 regions.
00:14:17.10 And what you can see here, in this really beautiful graph is, if you look at speciation,
00:14:23.04 it's higher in the tropics, extinction seems to be much higher in the temperate regions,
00:14:30.06 and so, overall, on an average, it appears like diversification -- that's net diversification
00:14:36.07 over there -- is much higher in the tropics.
00:14:39.05 So, this suggests that the tropics are cradles of diversity, which means that new species
00:14:48.12 are being created here, right?
00:14:50.12 They're also museums -- there's less extinction, so they retain these species over longer periods
00:14:56.18 of time.
00:14:57.18 So, because they're both cradles and museums, tropic regions, overall, tend to have higher
00:15:03.05 biodiversity.
00:15:04.05 Islands, as we pointed out earlier, are also a really interesting case.
00:15:10.00 This is a very interesting figure from a review, a recent review, by Losos and Ricklefs, where
00:15:15.24 they actually suggest a model for how something like this may happen.
00:15:20.07 They basically verbalized what Darwin thought those many years ago, that you may have a
00:15:25.10 finch which moves from the mainland onto one island.
00:15:29.23 These islands are different and so it manages to disperse to all these islands over time.
00:15:35.10 And then, slowly, these finches or birds maybe differentiate over time, they become adapted
00:15:42.23 to the conditions on that particular island.
00:15:46.04 And then, maybe, if there's further speciation in allopatry, you have recolonization of these
00:15:52.23 different birds across these different islands, now, and further speciation.
00:15:56.23 So, islands are really nice because they're actually models to study speciation.
00:16:02.12 So, because they're small and they're in the ocean, environmental conditions can vary very
00:16:08.01 dramatically on islands, and any of you who've been to an island know it's suddenly raining
00:16:12.15 or suddenly there's a storm, so it's... they're very easy to see environmental changes on.
00:16:18.17 At the same time, because there are many islands, often, in a sea, there are natural barriers
00:16:24.15 which exist between islands, so we can clearly see a role for history -- there's a mainland
00:16:30.13 close by -- ecology -- differences between islands or within an island -- and things
00:16:36.22 like dispersal, right, where differences can actually come based on islands across space.
00:16:42.15 So, let's look at a couple of examples of speciation and its study on islands.
00:16:48.23 So, you know, one of the most biodiverse islands we have in the world is Madagascar.
00:16:56.15 It's a really interesting place because it has a very unique set of species found nowhere
00:17:01.21 else.
00:17:02.21 And I show you, here, a map of... of... a picture of birds -- these are called vangas
00:17:11.03 -- and these have diversified on Madagascar.
00:17:12.23 So, you can see, below, there, there's a map which shows the different kind of ecological
00:17:18.22 conditions or habitats within Madagascar.
00:17:21.12 And, here, you can see a phylogeny, a DNA-based tree, of all these birds, which allows us
00:17:28.02 to infer who evolved from whom, and who colonized which environment first, and so on.
00:17:34.12 And so here we can see an example of ecological speciation, right?
00:17:39.21 Diversification of these birds into different niches, different habitats on this island
00:17:45.23 of Madagascar.
00:17:46.23 And, actually, if you look at Madagascar, there's also incredibly rich vertebrate diversity,
00:17:55.01 in terms of reptiles and amphibians, and these maps on this side actually show you those
00:18:01.06 types of diversity.
00:18:02.09 They show you where there are more or less species, and you can see, for example, that
00:18:07.09 diversity tends to be high in some environments -- higher that, say, in other.
00:18:11.23 So, wetter environments, which you can see below, actually tend to have higher diversity
00:18:16.13 than drier environments.
00:18:17.17 So, again, examples of ecologically driven speciation within an island, and a place with
00:18:24.13 high biodiversity.
00:18:27.11 On the other hand, you can also have geographic examples of speciation.
00:18:31.05 So, here we see these insects on the Hawaiian island chain.
00:18:37.07 So, the nice thing about the Hawaiian island chain is the different islands have different
00:18:42.12 ages, right?
00:18:43.21 So, the oldest island is Kauai and the youngest island is Hawaii, and you can look and see
00:18:52.07 this, also, in the phylogeny.
00:18:54.00 So, for example, the authors have very nicely colored these islands in different colors
00:19:01.04 and the insects found on those islands are in the phylogeny in the same color.
00:19:05.16 So, if you look down, for example, you can see... you can this order, you can see green,
00:19:11.03 orange, purple, blue, and red, right?
00:19:15.17 So, in terms of time, the oldest island is green and then there's orange and then there's
00:19:21.22 purple and then there's blue and then there's red.
00:19:24.09 And you can see that reflected in the phylogenetic tree as well.
00:19:28.11 So, speciation has progressed with time and you have these different islands being colonized
00:19:34.17 and these different species diverging across the Hawaiian island chain.
00:19:39.12 So, lineages, or sets of individuals which are closer together from a DNA perspective,
00:19:45.22 are related on an island, younger lineages are on younger islands, and genetic data kind
00:19:51.16 of helps us explore the history of speciation on these islands.
00:19:56.24 So, now...
00:19:59.08 I've been kind of alternating between mountains and islands, slipping in the fact that mountain
00:20:04.21 ranges have high biodiversity.
00:20:06.21 Why was I doing this?
00:20:08.05 Well, it turns out as Humboldt showed us, and this is an example from the U.S., the
00:20:15.22 Southwest, mountains also have "islands", they have habitat islands.
00:20:21.06 As you go up a mountain, you can see that the habitat or the ecology actually changes
00:20:27.00 -- higher parts of the mountain are different than the lower parts of the mountain.
00:20:32.09 And so you might imagine that, ecologically, species would become adapted to live in these
00:20:38.10 specialized environments.
00:20:40.13 And then, if you looked at the mountain range, that's like a set of islands, kind of like
00:20:45.17 Hawaii in a sense, right?
00:20:48.00 So, it might be interesting to try and explore patterns of speciation, or the accumulation
00:20:53.15 of biodiversity, in mountain chains.
00:20:57.07 And this is what I'm going to talk to you about in terms of our research, but the best
00:21:00.20 part of it all is the history of this speciation is actually written in the DNA of these species,
00:21:07.19 of the populations which actually live on these islands.
00:21:11.11 A way to look at their past is through sequencing their DNA.
00:21:15.23 Umm... this is also important; it's not just fun.
00:21:19.12 But, uhh... you know, our existence as humans is critically dependent on biodiversity.
00:21:25.09 There are many studies which show us, now, that human well-being, not just from an aesthetic
00:21:31.03 perspective, but in terms of our ecosystem services and many, many things, is critically
00:21:35.21 dependent on biodiversity, and this allows us to really prioritize studying areas of
00:21:42.18 high biodiversity.
00:21:44.05 It's important to us; it's not just interesting.
00:21:47.16 And these can be classified globally as biodiversity hotspots, not just regions where there is
00:21:53.15 higher... high biodiversity, but also regions where there are threats to this biodiversity.
00:21:59.10 And two of the regions I'm going to talk to you about today happen to be biodiversity
00:22:03.07 hotspots -- the Western Ghats, which is in India and Southern India, and the Himalayas,
00:22:09.03 which is the in the northern part of Asia.
00:22:10.23 So, uhh...
00:22:12.00 I guess what I'm trying to say is that, you know, we're really interested in understanding
00:22:16.06 biodiversity, but it's also critically important from a conservation perspective.
00:22:20.11 This understanding, we hope, will help us to think about how we can save these species
00:22:26.02 in the future.
00:22:27.02 So, I'll just summarize and uhh... kind of give a leap into our research questions, which
00:22:32.17 I'm going to talk about in the next part of this talk.
00:22:36.09 Biodiversity is higher in the tropics, in mountain ranges, and in islands, and the barriers
00:22:42.12 which cause allopatric speciation, or the creation of biodiversity, could be physical
00:22:47.07 or ecological.
00:22:49.19 But what still remains for us to explore is whether what's driving speciation is really
00:22:56.02 different or the same in various locations across the world.
00:23:00.01 And you saw, for example, that study... you know... from Madagascar on vangas, right?
00:23:07.19 It's a particular type of bird.
00:23:10.02 But you could also think about this from the perspective of all the species which live
00:23:14.06 in a location.
00:23:15.15 Do they all respond similarly to these different barriers or changes in ecology?
00:23:22.07 How generalizable are these patterns?
00:23:24.22 How important are physical differences?
00:23:26.07 Are they more important to some species versus others, or not?
00:23:30.21 And this is what I'm going to talk about in the next talk.
00:23:34.02 Thank you.

00:00:07.10 Hi, I'm Sarah Tishkoff.
00:00:08.23 I'm a professor at the University of Pennsylvania
00:00:11.02 in the Departments of Biology and Genetics,
00:00:13.24 and today I'm gonna tell you about my research
00:00:15.18 on African integrative genomics,
00:00:17.29 and implications for human origins and disease.
00:00:21.17 So in Part 1, I'm gonna tell you a bit about
00:00:23.24 human evolutionary history,
00:00:25.24 and what the implications are of that
00:00:27.20 on the patterns of genomic variation
00:00:29.18 that we see in populations today.
00:00:34.05 So I want to start by talking about some of the
00:00:35.26 key challenges in human genomics research.
00:00:38.19 And the first one is to characterize
00:00:40.27 the immense array of genomic and phenotypic diversity
00:00:44.29 across ethnically diverse human populations.
00:00:48.14 Secondly, to understand what the evolutionary processes are
00:00:51.16 that are generating and maintaining that variation.
00:00:54.14 And third, to better understand how
00:00:56.04 gene-gene, gene-protein, and gene-environment interactions
00:00:58.28 contribute to phenotypic variability.
00:01:01.27 So first let's start with the evolutionary history
00:01:05.00 of the hominin lineage
00:01:06.26 that's leading to modern humans,
00:01:10.13 which begins around the time that we
00:01:12.03 diverged from our closest genetic relative
00:01:14.04 the Chimpanzee,
00:01:15.18 sometime between 5-7 million years ago.
00:01:18.14 So shown here are some of the fossils
00:01:20.07 from the different species
00:01:22.17 preceding anatomically modern humans.
00:01:25.16 In blue are shown fossils from the oldest lineages,
00:01:30.06 and in fact one of the oldest is Sahelanthropus,
00:01:34.10 which has been dated to at least 7 million years ago,
00:01:37.29 and there's some debate about whether it even
00:01:39.14 belongs on the hominid lineage
00:01:41.09 or if it actually preceded the Chimpanzee and human divergence.
00:01:45.26 After that, in green,
00:01:47.14 we see the Australopithecus genus.
00:01:50.14 In yellow, we see Paranthropus genus.
00:01:54.09 In orange, we have the genus Homo
00:01:56.24 and the species proceeding anatomically modern humans
00:02:01.13 is Homo erectus, dated to about 2 million years ago.
00:02:06.14 And then we have the origins of
00:02:08.15 Homo neanderthalensis
00:02:11.02 and of anatomically modern humans.
00:02:13.24 Neanderthals are thought to have originated
00:02:16.00 somewhere between 300,000-400,000 years ago,
00:02:19.12 and modern humans originated
00:02:20.27 approximately 200,000 years ago.
00:02:24.03 Here's one of the best examples
00:02:26.11 of Australopithecus afarensis.
00:02:29.07 This was a set of fossils that was
00:02:31.24 discovered in the 1970's by Johanson and Gray,
00:02:36.02 named Lucy,
00:02:38.00 and Lucy was about...
00:02:41.04 she lived about 3.2 million years ago.
00:02:43.29 She was very small, only about 3 feet tall,
00:02:46.13 she had a very small brain,
00:02:48.07 and she was bipedal.
00:02:49.27 And being bipedal, in fact,
00:02:51.07 is one of the characteristics of the hominin lineage.
00:02:57.12 And, interestingly,
00:02:59.17 there have been some fossilized footprints
00:03:01.21 identified in Tanzania,
00:03:03.24 and we can see from these that there
00:03:06.08 appears to have been a mother,
00:03:08.27 from the species Australopithecus afarensis,
00:03:12.08 and she was holding the hands of her child.
00:03:14.29 And they must have been walking
00:03:16.15 in ash from recent volcanic activity,
00:03:20.06 and then that ash hardened and preserved these footprints
00:03:23.06 so that we can see them today,
00:03:24.21 and we can clearly see that they were bipedal.
00:03:29.08 So the species preceding modern humans
00:03:31.28 is called Homo erectus.
00:03:33.24 Homo erectus evolved around 2 million years ago,
00:03:39.02 and then after the origin of Homo erectus in Africa,
00:03:42.24 Homo erectus spread across Eurasia
00:03:47.17 and, indeed, shown here are some of the
00:03:49.21 oldest fossils of Homo erectus,
00:03:52.18 dated to as early as 1.9 million years ago (MYA) in Indonesia.
00:04:00.15 And this species was very successful,
00:04:03.14 lasting to as recently as 25,000 years ago
00:04:06.17 in Southeast Asia.
00:04:09.08 A very interesting recent finding was
00:04:11.20 a set of fossils identified on the island of Flores,
00:04:14.26 which is within Indonesia,
00:04:17.25 and these fossils actually show some characteristics
00:04:21.22 that look very similar to Homo erectus,
00:04:24.19 and for that reason it was proposed that
00:04:27.09 this species may have directly evolved
00:04:30.23 from a Homo erectus ancestor
00:04:33.20 that arrived on that island
00:04:36.07 about 1 million years ago
00:04:37.28 and then evolved in isolation.
00:04:39.25 And two of the very unique features of this species
00:04:42.17 is that they were very short, so again,
00:04:46.01 about the same size as Lucy, around 3 feet tall,
00:04:50.15 and secondly, that they had tiny brains.
00:04:53.14 And there's been a lot of debate about
00:04:55.01 whether this is an adaptation or in fact a pathology,
00:04:58.09 and there's still a lot of research being done,
00:05:01.03 but what was clear is that there were multiple species
00:05:04.01 outside of Africa
00:05:05.29 within the past 2 million years.
00:05:08.20 So now let's move on to the origins of
00:05:10.15 Homo neanderthalensis and Homo sapiens.
00:05:13.12 There's some question about the species preceding
00:05:16.28 Neanderthal and Homo sapiens.
00:05:19.17 Some say that it was heidelbergensis,
00:05:22.04 but there's debate about that.
00:05:24.15 However, what is clear is that the Neanderthals species
00:05:28.10 arose somewhere within the past 300,000-400,000 years,
00:05:32.15 and Homo sapiens arose within the past 200,000 years.
00:05:38.04 And this is a fossil from Neanderthals,
00:05:40.29 we can see a few features such as
00:05:44.02 the double arched and very wide brow ridges,
00:05:47.08 a broad nose,
00:05:48.28 a very large brain size,
00:05:50.27 and a retromolar space,
00:05:52.21 and in fact these species were very robust.
00:05:55.16 The males would have been over 6 feet tall,
00:05:57.15 they had very big bones,
00:05:59.19 and they had rather big brains.
00:06:02.20 In fact, here are some reconstructions of Neanderthal.
00:06:06.28 We have the old reconstruction
00:06:09.03 and then the more recent one as well.
00:06:12.11 So, anatomically modern humans, Homo sapiens sapiens,
00:06:16.06 arose approximately 200,000 years ago.
00:06:19.02 In fact, here these red dots
00:06:21.09 are representing locations where fossils have been found
00:06:24.11 of anatomically modern humans,
00:06:26.27 and the oldest fossil is
00:06:28.22 dated to around 150,000-195,000 years ago,
00:06:32.19 in Southern Ethiopia.
00:06:36.23 We also see evidence of early modern human behavior
00:06:40.10 dated to 70,000 years ago,
00:06:42.11 or even as old as 120,000 years ago,
00:06:45.16 in caves in south Africa
00:06:47.13 and also some from east Africa as well.
00:06:51.05 So after modern humans arose in Africa within the past 200,000 years,
00:06:55.08 one or a few small groups of individuals
00:06:57.25 migrated across the rest of the globe
00:07:00.11 within the past 50,000-100,000 years.
00:07:03.23 Indeed, we think that Europeans...
00:07:07.15 there were no people in Europe, actually,
00:07:09.06 until about 40,000 years ago,
00:07:11.13 and then modern humans crossed the Bering Straits
00:07:14.15 and went into the Americas
00:07:16.28 within the past 30,000 years.
00:07:19.05 The earliest migration event was actually into Australo-Melanesia,
00:07:23.11 dated to about 40,000-60,000 years ago.
00:07:26.14 And then we have much more recent migration events,
00:07:29.03 such as into the Pacific Islands,
00:07:31.12 within the past few thousand years.
00:07:34.11 Now, interestingly,
00:07:36.16 when modern humans migrated out of Africa
00:07:39.08 within the past 50,000-100,000 years,
00:07:42.05 they would have run into Neanderthals,
00:07:44.10 in fact they overlapped in their distribution.
00:07:47.08 So shown here is the distribution of Neanderthals,
00:07:50.22 and the modern humans who lived at that time
00:07:52.25 were referred to as Cro-Magnon,
00:07:55.17 and in fact we did not see anatomically modern humans
00:07:59.09 in this region, in Europe, until about 40,000 years ago.
00:08:03.03 They would have been in the Middle East a little bit earlier,
00:08:05.23 but it appears they overlapped
00:08:08.18 for about at least 10,000 years with Neanderthals.
00:08:12.13 And as we'll discuss later,
00:08:13.27 there is some evidence that there could have been actual admixture
00:08:17.05 between Neanderthal and anatomically modern humans
00:08:20.18 during that time.
00:08:22.26 So now I want to discuss the evolutionary forces
00:08:25.27 that influence the patterns of genetic variation
00:08:28.08 that we see today.
00:08:30.04 And these include mutation,
00:08:32.14 genetic drift,
00:08:33.29 migration,
00:08:35.09 and natural selection.
00:08:37.16 So let's first introduce some terminology.
00:08:40.05 The gene pool refers to the set of all genomes
00:08:42.25 in a specified population,
00:08:44.10 and here we have an example from a population of warthogs.
00:08:47.22 So where we have at a single genetic locus
00:08:51.03 two alleles, big B or little b,
00:08:54.17 and here's an example of an individual
00:08:56.11 who is homozygous for the big B allele,
00:08:59.07 and an individual homozygous for the little b allele,
00:09:02.12 and here's an individual who is heterozygous
00:09:05.08 for big B and little b.
00:09:07.12 And together, the set of alleles in that population
00:09:10.19 represents the gene pool.
00:09:13.28 So when we are doing population genetics analyses,
00:09:16.25 we can't actually go out and look at every genotype
00:09:21.00 for every individual in the population,
00:09:23.14 that would be unfeasible.
00:09:25.13 So what we typically do is to
00:09:26.23 infer frequencies by estimating them
00:09:30.10 from a random sample.
00:09:32.25 So in population genetics
00:09:35.01 generation, each new individual
00:09:37.16 is viewed as drawing from a set of gametes
00:09:39.20 with alternative alleles,
00:09:41.08 so let's use an example here
00:09:43.01 in which we have a set of marbles in a bowl.
00:09:46.05 And initially, we have a distribution of
00:09:51.26 60 of the white marbles
00:09:54.13 relative to 40 of the green marbles,
00:09:56.27 and these, the white and the green,
00:09:58.08 are representing different alleles.
00:10:00.14 So let's say that we're gonna pick...
00:10:02.04 we're gonna reach into this bag
00:10:04.04 and we're gonna randomly draw out
00:10:06.09 another hundred of these marbles.
00:10:09.01 And now in the next generation
00:10:10.26 we have 80 of the white and we have 20 of the green.
00:10:15.02 We're gonna reach back in,
00:10:16.01 we're gonna grab another set of a hundred,
00:10:18.09 and now in the next generation
00:10:20.15 we have 100 of the white alleles and 0 of the green.
00:10:26.08 And this is a demonstration of
00:10:27.15 how we get changes in allele frequency over time.
00:10:31.25 Allele frequencies will also change over time
00:10:34.23 due to genetic drift,
00:10:36.21 which is defined as random fluctuations
00:10:39.01 of allele frequencies from generation to generation,
00:10:42.03 simply due to chance.
00:10:44.19 So as we see, sometimes things could happen,
00:10:47.16 like these bugs are getting squashed,
00:10:50.00 and that's gonna change, perhaps,
00:10:52.07 the allele frequency in the next generation.
00:10:55.19 Here's another example from some lady bugs,
00:10:58.23 and we can see that, perhaps,
00:11:01.03 in the next generation, just by chance,
00:11:03.10 we're gonna see more of these ladybugs
00:11:04.29 with the dark colors,
00:11:06.12 or we might see more that are with the medium colors and dots.
00:11:10.16 And the fact is that drift is just an inevitable fact of life.
00:11:16.15 I also want to define what we mean by neutral evolution.
00:11:20.08 So we define a selectively neutral allele
00:11:22.10 as one that does not affect reproductive fitness of individuals
00:11:25.20 who carry that allele,
00:11:27.20 so it's frequency in the population
00:11:29.25 changes by chance or genetic drift alone.
00:11:32.18 And here we have an example:
00:11:35.04 this is just a substitution
00:11:37.22 in the third position of the codon,
00:11:41.02 and when we have substitutions
00:11:44.09 of nucleotides in the third position,
00:11:46.20 very typically they result in a silent or synonymous change.
00:11:51.05 So here there's been a substitution,
00:11:53.00 but there's no change in the amino acid;
00:11:55.02 it remains as valine.
00:11:57.26 So the rate at which genetic drift occurs
00:12:00.01 is going to inversely proportional to the population size, N,
00:12:03.23 and it's going to be very fast in small populations.
00:12:06.27 And here's an example that we can look at
00:12:08.23 based on computer simulation.
00:12:11.20 So let's assume here that we're looking at a single locus
00:12:15.15 and it has two alleles
00:12:18.06 that are at 50% frequency each,
00:12:21.25 as we can see here.
00:12:23.22 We have a sample size of 25,
00:12:27.06 and we're going to do the simulation
00:12:29.03 over 80 generations.
00:12:31.14 Now, each of these lines here
00:12:34.03 represents a different simulation,
00:12:36.27 and what we can see is that
00:12:38.23 over time alleles are either going to
00:12:44.02 be lost from the population
00:12:46.08 or they're going to reach fixation,
00:12:48.17 which means that they go to 100% frequency.
00:12:52.10 And the rate at which this occurs
00:12:54.00 is going to depend on the sample size.
00:12:56.09 So in a small sample it's gonna be very rapid,
00:12:59.19 but in this example where we have a larger sample, now N=300,
00:13:03.26 you can see that it just takes more time.
00:13:05.23 There's not as much genetic drift occurring.
00:13:08.19 Now, the end result is gonna be the same,
00:13:10.15 it just takes more time.
00:13:14.09 The change in allele frequency also is going to depend
00:13:17.27 on the initial allele frequencies.
00:13:19.20 So in this particular case,
00:13:21.05 we've now changed the starting frequency:
00:13:23.20 it's not 50%, it's now 10%.
00:13:27.06 And you can see that there's much more
00:13:29.28 probability of loss of the allele in this case,
00:13:34.11 and here we have just one of the alleles reaching fixation.
00:13:42.08 So again, in this particular case,
00:13:44.05 about 1 out of 10 will eventually become fixed,
00:13:47.14 or reach 100% frequency.
00:13:51.09 Now here's an example from a large population.
00:13:54.01 It'll take longer for this to occur,
00:13:56.02 but the proportion of alleles are gonna be
00:13:58.12 roughly the same,
00:13:59.29 so again roughly 1 out of 10 will go to fixation,
00:14:03.06 it's just gonna take longer.
00:14:05.16 Other important terms in population genetics
00:14:07.26 are bottleneck and founder effects,
00:14:10.08 and this is because genetic drift
00:14:11.23 has a large effect on allele frequencies
00:14:14.10 when a population originates
00:14:16.05 via a small number of people from a larger population.
00:14:19.16 So here we have an example of a bottleneck,
00:14:22.10 and what a bottleneck means is that
00:14:24.01 there's been a decrease in population size
00:14:26.21 at some time in the past.
00:14:28.14 So you can think of it as a population crash.
00:14:31.10 And what happens when the population is very small,
00:14:34.28 you're going to have a higher rate of genetic drift,
00:14:37.12 and we can see here that these alleles,
00:14:39.20 which are represented by the different colors,
00:14:42.00 have shifted from what we're seeing
00:14:44.18 back at this earlier time.
00:14:46.25 Now we go through the bottleneck,
00:14:48.19 and now we're seeing predominantly
00:14:50.07 these white and black alleles.
00:14:53.09 Another example we can look at is a founder event,
00:14:57.20 which is sort of a special case of a bottleneck event.
00:15:00.11 And in this case it's where a population, a small population,
00:15:05.03 breaks off from the larger population,
00:15:07.25 and again there's going to be increased genetic drift
00:15:10.26 in this initially small population
00:15:13.12 and here, by chance,
00:15:15.05 we just happened to see more of these dark blue
00:15:18.12 and light blue alleles.
00:15:21.09 The pattern of variation that we see
00:15:22.23 in the human genome
00:15:24.09 is also dependent on the effective population size,
00:15:27.17 which we distinguish as capital N sub e.
00:15:32.10 And the definition of the effective population size
00:15:35.10 is the number of breeding individuals in a population.
00:15:38.19 So estimates of Ne
00:15:40.17 are most strongly influenced by population sizes
00:15:43.07 when they're at their smallest,
00:15:45.10 and it could take many generations
00:15:47.02 to recover from a bottleneck event.
00:15:49.11 So estimates of Ne in modern populations
00:15:51.21 reflect the size of the population
00:15:53.20 prior to population expansion.
00:15:56.22 Pretty consistently, studies of nuclear sequence diversity in humans
00:16:00.24 have estimated an effective population size
00:16:03.15 of about 10,000.
00:16:05.19 Now, by contrast, if we look at Chimpanzees,
00:16:08.29 the estimate is closer to 35,000.
00:16:12.14 And so what that means is that
00:16:14.01 humans have undergone a bottleneck
00:16:16.18 sometime during their evolutionary history.
00:16:19.22 So the pattern of genomic variation
00:16:21.25 that we see in modern populations today
00:16:24.00 is a reflection of our evolutionary and demographic history.
00:16:27.14 So how much do we differ?
00:16:29.17 Well, identical twins
00:16:31.27 have no differences at the nucleotide level.
00:16:35.06 If we compare unrelated humans,
00:16:36.29 we differ at about 1 out of 1,000 nucleotide sites.
00:16:41.12 And if we compare humans to our closest genetic relative, the Chimpanzee,
00:16:45.02 we differ at about 1 out of 100 sites.
00:16:47.29 So, as a whole, our species is very similar,
00:16:50.27 and that simply reflects our recent common ancestry
00:16:54.05 from Africa within the past 100,000 years.
00:16:57.06 But when you consider that there are
00:16:58.27 over 3 billion DNA bases in the genome,
00:17:02.02 that results in 3 million differences
00:17:04.16 between each pair of genomes,
00:17:06.05 more than enough to generate the diversity
00:17:08.29 that will make each of us unique.
00:17:12.02 Now I want to introduce a statistic
00:17:14.13 that we typically use to look at how much variation
00:17:17.06 there is among populations,
00:17:20.01 and this is referred to as an Fst statistic.
00:17:24.00 And it's simply looking at the proportion of genetic variation
00:17:27.03 that is within populations,
00:17:29.06 relative to that which is between populations.
00:17:32.18 Fst can be measured based upon heterozygosity,
00:17:37.20 and heterozygosity is simply a measure of genetic variation,
00:17:41.26 which is very simply calculated as
00:17:44.15 1 minus the sum of the allele frequencies squared.
00:17:49.09 And so once we calculate
00:17:51.26 the heterozygosity for each locus,
00:17:53.29 we can look at the average,
00:17:55.23 and we can look at the average within a subpopulation,
00:17:58.03 or in the total combined population.
00:18:00.29 Now, just as an example,
00:18:03.15 if we were to see here that
00:18:06.22 in the case of Fst = 1,
00:18:09.12 it means that there is no overlap at all in the allele frequencies.
00:18:13.15 So we can see that in population 1 they have all A's,
00:18:16.13 and in population 2 they have all B's.
00:18:19.15 And in the case of Fst = 0,
00:18:22.18 there is complete similarity,
00:18:26.08 so here we see exactly the same number
00:18:28.13 of A alleles and exactly the same number of B alleles.
00:18:32.01 And then here's an intermediate case
00:18:33.29 where we have about 0.11, 11%,
00:18:39.07 showing that there's just a small amount of differentiation
00:18:43.04 between these two populations.
00:18:46.09 So what do we see in humans?
00:18:47.29 Well, the average Fst between human populations
00:18:51.04 is about 15%,
00:18:53.15 and what that means is that the majority of genetic variation
00:18:56.04 is found within a population,
00:18:59.07 and only about 15% of the genetic diversity
00:19:02.08 differs between populations.
00:19:04.23 Again, this is reflecting our recent common ancestry in Africa,
00:19:09.00 within the past 50,000-100,000 years.
00:19:14.13 Now, interestingly,
00:19:16.09 if we were to do this calculation from Chimpanzee populations,
00:19:19.08 we see that the value is around 32%,
00:19:22.15 so there's actually a lot more differentiation
00:19:25.04 among Chimpanzee populations
00:19:27.07 than among human populations,
00:19:29.18 again reflecting our overall close genetic similarity to each other.
00:19:36.19 So I now want to talk about the
00:19:38.04 different sources of DNA that we use
00:19:40.04 to reconstruct human evolutionary history.
00:19:43.01 One source of DNA is
00:19:45.29 that which is present in the nuclear genome
00:19:48.06 that's located in the nucleus of the cell.
00:19:51.03 And there's another type of genome
00:19:53.20 which is present in the mitochondria of the cell,
00:19:56.15 and the mitochondria is the energy-producing organelle.
00:20:02.13 So what is the difference between these different genomes?
00:20:06.03 Well, the nuclear genome
00:20:08.09 consists of 22 autosomal pairs of chromosomes
00:20:12.26 and then the sex chromosomes,
00:20:14.15 XX for females and XY for males.
00:20:17.27 The nuclear genome is about 3.4 billion bases in size,
00:20:22.02 and it consists of about 20,000 coding genes.
00:20:25.10 It's inherited from both parents,
00:20:27.21 but it also undergoes extensive recombination each generation.
00:20:32.07 But, one of the reasons it's useful is that there's
00:20:34.18 so many different locations where we can study variation,
00:20:38.08 given that there are 3 billion nucleotides,
00:20:41.02 it's just a little bit more difficult to trace them back
00:20:43.29 to a single common ancestor.
00:20:46.20 By contrast, the mitochondria DNA genome
00:20:50.21 is very small, it's only about 16,000 nucleotides in size,
00:20:55.14 and it's circular,
00:20:57.17 and it's passed on only through the maternal lineage.
00:21:00.19 There's also no recombination
00:21:02.17 and it has a very high mutation rate.
00:21:05.00 All of these features make it very useful
00:21:07.01 for tracing evolutionary history.
00:21:09.27 So let me give you another example of what I'm referring to.
00:21:13.12 The mitochondrial DNA is inherited through the maternal lineage,
00:21:17.05 whereas the nuclear DNA is inherited from both parents.
00:21:22.08 So if we were to trace back from a present day individual,
00:21:25.26 they will have inherited their nuclear genome
00:21:28.20 from their parents,
00:21:30.17 their parents would have inherited from their set of parents,
00:21:33.28 and then their set of parents, and so on.
00:21:36.15 So we can trace it back to a large number of ancestors.
00:21:39.16 But by contrast, if we're tracing back mitochondrial DNA lineages,
00:21:44.00 we can see that they're only passed on
00:21:46.25 through the maternal lineage,
00:21:49.10 so they're essentially inherited from a single lineage.
00:21:52.03 We can trace them back to a single common female ancestor,
00:21:56.01 and that's why they're been very useful
00:21:57.29 for human evolutionary genetics studies.
00:22:00.21 So for example, if we were to consider
00:22:02.26 these dots to be mitochondrial DNA lineages,
00:22:06.20 and let's start at generation 11 at the bottom,
00:22:10.12 shown by the red dots,
00:22:12.06 and imagine those are different mitochondrial DNA sequences
00:22:15.00 from different individuals.
00:22:17.10 At some time in the past, these two individuals, for example,
00:22:22.06 coalesced back to a common ancestor,
00:22:24.26 and then this group coalesces back to a common ancestor here,
00:22:29.29 and ultimately they all coalesce back
00:22:32.20 to a single common ancestor.
00:22:35.03 Now, in the popular literature,
00:22:36.22 the single common ancestor for mitochondrial DNA
00:22:39.04 is often referred to as "mitochondrial Eve",
00:22:42.21 but one thing to remember is that
00:22:45.17 Eve was not alone, she lived within a population,
00:22:49.06 as we can see here by the other colors.
00:22:51.22 But those lineages just never made it
00:22:54.22 down to the present day.
00:22:57.25 So this is a phylogenetic tree
00:23:00.11 constructed by sequencing mitochondrial DNA
00:23:03.10 whole genome lineages
00:23:05.02 from ethnically diverse individuals.
00:23:07.19 So each individual actually represents
00:23:10.29 a branch on this tree,
00:23:13.02 and if two individuals are very closely related to each other,
00:23:16.05 they'll be very close to each other
00:23:19.01 in the tree.
00:23:21.03 So one of the first things you can see
00:23:22.19 using Chimpanzee as an outgroup
00:23:25.01 is that all modern human lineages
00:23:27.25 coalesce at about 170,000 years ago,
00:23:31.12 and so that corresponds very well with the
00:23:33.05 time of origin of anatomically modern humans.
00:23:36.23 So another thing that we can see is that
00:23:39.25 all of the oldest genetic lineages
00:23:42.26 are from African individuals.
00:23:45.22 We can also see that
00:23:48.12 the very oldest lineages
00:23:50.15 are from the San and the Mbuti pygmy hunter-gatherers,
00:23:54.28 and then the more recent lineages
00:23:57.13 are from non-African populations.
00:24:00.01 And that is a pattern that's very consistent
00:24:02.17 with the model of a recent African origin
00:24:05.12 of modern humans.
00:24:07.23 Now, another way that we can compare mitochondrial DNA sequences
00:24:11.21 is to simply count up the number of sites
00:24:14.04 at which they differ when we compare any pair of sequences.
00:24:17.23 And when we do this,
00:24:19.09 we observe that
00:24:22.11 any two African lineages will differ from each other
00:24:25.03 at many more sites than any two non-African lineages.
00:24:29.06 And again, that means that there has been more time
00:24:32.02 for variation to accumulate in Africa,
00:24:34.16 and is consistent with an African origin
00:24:37.08 of modern humans.
00:24:39.20 When we sequence the mitochondrial DNA lineages,
00:24:42.21 we can classify them as haplotypes,
00:24:45.10 and those haplotypes belong to
00:24:47.16 larger subsets of haplogroups.
00:24:50.01 You can think of a haplotype as simply
00:24:52.14 the arrangement of genetic variants along a chromosome,
00:24:55.19 or in the case of the mitochondrial DNA
00:24:57.22 there's just a single genome,
00:24:59.14 so it's really just the different nucleotide differences
00:25:02.27 amongst different mitochondrial DNA lineages.
00:25:06.24 And one of the first things that you can note is that
00:25:09.26 there are different haplogroups
00:25:11.29 in different regions of the world.
00:25:13.19 So here are some that seem to be pretty specific to Africa,
00:25:16.20 but are also present in some regions
00:25:18.20 where there may have been some gene flow
00:25:20.20 from Africa.
00:25:22.21 Then we have others that may be more common in Europe,
00:25:25.12 or in east Asia,
00:25:28.18 or in the Americas.
00:25:30.19 And for that reason,
00:25:32.11 mitochondrial DNA can be very useful for
00:25:34.11 tracing recent human migration events.
00:25:38.13 Now, by contrast,
00:25:40.02 the Y chromosome is also inherited with no recombination,
00:25:45.14 and so it can also be very useful for tracing back
00:25:48.01 through the male lineages.
00:25:50.16 And here is a phylogeny constructed from Y chromosome variation,
00:25:55.07 and as with the mitochondrial DNA,
00:25:58.08 what we see is that the oldest lineages
00:26:01.19 are specific to Africans,
00:26:04.02 and the more recent lineages
00:26:06.05 are found predominantly in Non-Africans,
00:26:08.13 although we do see some in Africans as well.
00:26:11.25 Again, this is consistent with the recent African origin of modern humans.
00:26:18.14 We can also look at Y chromosome haplogroups,
00:26:22.09 and one of the things that's a little bit different
00:26:24.04 is you can see that they're a bit more differentiated
00:26:26.16 between geographic regions.
00:26:29.03 So for example,
00:26:30.24 here we just see haplogroups that are in blue,
00:26:34.04 and we see very distinct haplogroups
00:26:36.20 in the Americas, shown in purple.
00:26:39.26 And one of the reasons for that may have to do with
00:26:43.08 sex-biased migration,
00:26:46.01 that you may have, for example,
00:26:47.16 one male traveling long distances.
00:26:50.06 And it may also have to do with patterns of mating structure.
00:26:54.20 So for example, in some populations or ethnic groups,
00:26:57.23 you may have one male who has many different wives,
00:27:01.05 and because of that the effective population size of the Y chromosome
00:27:07.01 is actually smaller than the mitochondrial DNA,
00:27:09.28 and we tend to get more genetic differentiation
00:27:12.27 around the world.
00:27:15.07 So now I want to talk about analyses of ancient DNA,
00:27:18.27 for example, in this case from Neanderthal,
00:27:22.12 and these are some images of scientists
00:27:25.20 working on a Neanderthal fossil.
00:27:29.10 And this type of analysis is very challenging
00:27:32.01 for a number of reasons.
00:27:33.25 One is that DNA which is that old,
00:27:38.04 on the order of say 30,000 years old
00:27:40.10 to even 100,000 years old,
00:27:42.06 is going to be highly degraded,
00:27:44.24 and if there's any contamination
00:27:46.25 with modern human DNA,
00:27:49.02 that is much more likely to amplify
00:27:51.19 than the old degraded DNA
00:27:54.01 from the archaic species,
00:27:56.21 so one has to be extremely careful when analyzing this DNA.
00:28:01.03 Now, more recently,
00:28:02.24 there was a pinky finger bone
00:28:05.07 identified in a cave in Siberia
00:28:07.22 from a region called Denisova,
00:28:10.11 so it's referred to as the Denisova
00:28:13.21 or Denisovan genome.
00:28:16.11 Here I'm presenting a phylogenetic tree
00:28:18.29 based on mitochondrial DNA variation
00:28:21.24 comparing modern humans, shown in blue here,
00:28:26.09 to Neanderthals shown in red,
00:28:29.01 and the Denisova individual shown in yellow.
00:28:32.23 And what we can see is that the
00:28:34.17 time to most recent common ancestry in humans,
00:28:37.08 as we've already discussed,
00:28:39.00 is about 200,000 years ago.
00:28:41.13 The time to most recent common ancestry
00:28:43.14 between humans and Neanderthals
00:28:46.01 is about 500,000 years ago,
00:28:48.13 for the mitochondrial DNA lineages.
00:28:51.03 And the time to most recent common ancestry
00:28:53.20 with the Denisova mitochondrial lineages
00:28:57.08 is about 1 million years ago.
00:29:00.05 So this is demonstrating a couple of things.
00:29:02.20 From the mitochondrial DNA perspective,
00:29:05.07 there's no evidence of any admixture
00:29:07.13 with anatomically modern humans.
00:29:10.02 The Neanderthal sequences are clearly
00:29:12.18 very distinct from modern humans.
00:29:14.28 It's also showing you that there was another species, Denisova,
00:29:18.15 that appears to be distinct from the Neanderthals,
00:29:21.07 and they diverge even earlier than Neanderthals
00:29:24.09 from modern humans.
00:29:26.21 So if we were to compare pairwise nucleotide diversity,
00:29:31.01 for example,
00:29:33.02 among anatomically modern humans shown in blue,
00:29:35.24 you can see that there's not a lot of diversity,
00:29:38.15 as expected considering that
00:29:40.13 we all have a very recent common ancestry.
00:29:43.04 If you compare the modern human mitochondrial genomes to Neanderthal,
00:29:48.03 you can see that they're more divergent,
00:29:50.07 as expected, given that the mitochondrial DNA lineage
00:29:54.04 diverged about 500,000 years ago.
00:29:57.02 If we compare to the
00:29:59.03 Denisovan mitochondrial DNA lineage,
00:30:01.10 they're even more divergent.
00:30:04.04 And then if we compare to Chimpanzee,
00:30:06.14 of course as expected,
00:30:08.11 given that they diverged at least 5 million years ago,
00:30:11.14 they are the most different in terms of sequence variation.
00:30:15.13 Now, several years ago
00:30:18.13 there was a draft sequence produced of
00:30:21.20 the Neanderthal genome using next-generation sequencing technology.
00:30:25.25 And this was an absolutely amazing feat,
00:30:28.17 but at the time they had very low coverage,
00:30:31.07 meaning that any particular region of the genome
00:30:33.19 was sequenced only about once or twice.
00:30:36.20 Now, more recently,
00:30:38.07 as the technology has improved,
00:30:40.05 they've gotten much better coverage of the Neanderthal sequence,
00:30:43.04 and quite recently they now have a 30-fold coverage,
00:30:46.22 meaning that on average most sites
00:30:49.03 will have sequenced 30 times.
00:30:51.22 And so you'll have a much better accuracy
00:30:54.23 when determining nucleotide variation.
00:31:01.07 So, when the Neanderthal genome
00:31:03.25 was compared to the human genome,
00:31:06.11 what you can do is first
00:31:08.10 look at how much divergence has occurred
00:31:11.02 since modern humans differentiated from Chimpanzees
00:31:15.10 within the past 6.5 million years.
00:31:18.12 And you can look at the divergence
00:31:20.24 that has occurred specifically in the human lineage
00:31:24.06 since they diverged from Neanderthal,
00:31:26.21 and they've only accumulated
00:31:29.07 about 8% of this total divergence.
00:31:34.08 And so the estimate of the time of population divergence
00:31:38.06 between humans and Neanderthals
00:31:40.15 is about 400,000 years ago.
00:31:43.09 Furthermore, it has been estimated that
00:31:45.24 there may have been a small amount of admixture
00:31:48.16 between Neanderthals and anatomically modern humans,
00:31:52.01 as shown by this red arrow here.
00:31:54.18 So the estimated amount of admixture is about 1-2%,
00:32:00.15 of the modern human genome,
00:32:02.17 may be of Neanderthal ancestry.
00:32:05.03 But what is of interest is to note that
00:32:07.24 this is only present in Non-Africans.
00:32:10.13 It is not present in African genomes.
00:32:13.05 And so what we can infer from that is
00:32:15.16 that this admixture event probably occurred
00:32:18.25 before modern humans spread across the globe.
00:32:22.01 It may have occurred, for example, in the Middle East,
00:32:24.28 and that's why we're seeing it present in all Non-Africans,
00:32:29.18 and we don't see it at all in Africans.
00:32:32.15 Now, more recently, there has been
00:32:34.22 whole genome sequencing of the Denisovan individual,
00:32:39.20 and what that has shown is that
00:32:42.09 the Denisovan species, or this individual,
00:32:45.15 appears to have diverged from modern day humans
00:32:48.13 around 800,000 years ago,
00:32:51.09 consistent with what we saw from the mitochondrial DNA.
00:32:55.21 They also observed low levels of heterozygosity in Denisova,
00:32:59.21 suggesting that they may have had
00:33:01.19 a small population size.
00:33:04.06 Additionally, when a phylogenetic tree
00:33:07.24 was constructed from the nuclear DNA variation,
00:33:11.13 they could see that the modern humans
00:33:15.11 tend to cluster together,
00:33:17.09 and as we expect they're divergent
00:33:19.01 from the Denisova and the Neanderthals.
00:33:21.29 The Neanderthals tend to cluster together,
00:33:24.06 so they're clearly divergent from Denisova.
00:33:27.03 But what's interesting is if you look at how much
00:33:31.01 variation there is amongst the modern humans,
00:33:34.11 as indicated by the length of these lineages,
00:33:38.06 and then you compare that to Neanderthals,
00:33:40.14 which have very short branches.
00:33:43.06 What that suggests is
00:33:44.28 that there was not a lot of genetic variation
00:33:47.09 amongst the Neanderthals,
00:33:49.23 and therefore they may have undergone a bottleneck,
00:33:52.11 so they might have undergone a population crash
00:33:54.20 at some point in the past.
00:33:57.07 So in summary,
00:33:59.04 what we can see is that
00:34:01.23 Homo erectus left Africa
00:34:04.05 within the past 2 million years,
00:34:06.28 and spread throughout Eurasia,
00:34:09.09 giving rise, possibly,
00:34:11.09 to species like Homo floresiensis,
00:34:14.17 and surviving until quite recently,
00:34:17.12 as recently as around 25,000 years ago.
00:34:20.28 Then we have other species like Neanderthal and Denisovans,
00:34:27.02 who may have originated from a different species,
00:34:30.07 such as heidelbergensis,
00:34:33.10 and they differentiated sometime
00:34:36.12 around 600,000 or 700,000 years ago in the case of Denisova,
00:34:39.29 or in Neanderthals around 400,000 years ago.
00:34:43.05 And then we have the modern human lineage,
00:34:46.11 Homo sapiens,
00:34:49.00 which arose around 200,000 years ago
00:34:51.07 and spread out of Africa.
00:34:53.21 And when they did so,
00:34:55.02 they would have encountered these other species,
00:34:57.09 and there may have then been low levels of gene flow.
00:35:01.20 And in fact for the case of the Denisovan genome,
00:35:03.23 it appears that the gene flow
00:35:05.26 was predominantly with populations from Oceania,
00:35:10.01 implying that this admixture
00:35:12.17 may have occurred in a different location and a different time.
00:35:16.00 Now, we still don't know exactly
00:35:18.05 how much admixture there may have been
00:35:20.12 between archaic species
00:35:22.23 and modern humans in Africa,
00:35:25.01 but there's some preliminary data suggesting that
00:35:27.10 this has occurred there as well.
00:35:29.14 The problem is that the fossils don't preserve as well in Africa,
00:35:32.19 so we don't have any DNA sequences
00:35:34.26 from archaic lineages in Africa at this point.
00:35:40.01 So in conclusion,
00:35:41.18 Africa has the most genetic diversity in the world.
00:35:44.15 Human dispersions out of Africa
00:35:46.11 populated the entire world,
00:35:48.15 and we are the last of a series of hominin dispersal events
00:35:51.14 out of Africa.

00:07.3 Hi. I'm Liz Hadly.
00:09.2 I'm a professor at Stanford University,
00:11.2 and I'm here to tell you about some of the work
00:13.1 that my lab and I have been working on
00:16.2 for the last several decades.
00:18.1 So, by training, I'm a paleontologist,
00:20.2 which means that I go back in time
00:22.2 and study how different animals have been affected
00:25.2 by changing environments of the past.
00:28.1 Those environmental changes include climate change,
00:30.1 they include volcanic eruptions,
00:31.3 and they include dispersal between continents.
00:34.2 What I'm here to tell you about today is that,
00:36.1 increasingly,
00:37.2 I've learned that what's happening on the planet now
00:40.0 is essentially equivalent
00:42.1 to the kinds of changes that I've been looking at
00:44.1 in the fossil record.
00:46.2 The biggest reason why these things are happening
00:48.3 is that the world population is enormous,
00:51.3 and it's continuing to grow.
00:54.3 If we manage somehow to hold our population
00:58.1 to just replacing every man and woman
01:00.3 with another man and woman,
01:02.2 we will still reach 9 billion people
01:06.2 by the year 2045,
01:08.3 and that means trouble for other animals
01:11.2 on the planet.
01:13.0 As a matter of fact, world population growth
01:15.0 has really contributed to our colonization of the planet.
01:19.1 As humans expanded out of Africa
01:21.2 somewhere between 100 and 200 thousand years ago,
01:24.1 they colonized Australia,
01:26.2 they colonized Asia,
01:28.0 they colonized Europe,
01:29.1 and, last of all, they colonized the Americas.
01:32.0 So, by about 13 thousand years ago,
01:34.1 humans had reached every continent
01:38.1 except Antarctica.
01:40.3 So, this expansion was also tied to
01:44.1 extinctions of large animals,
01:46.2 so we call this the late Pleistocene megafaunal extinction,
01:49.3 and in addition to the loss of these animals, for example,
01:53.1 all of which were present in North America
01:56.1 until about 10 thousand years ago,
01:59.0 there was also a climate warming event.
02:01.2 So, not only the expansion of humans,
02:03.2 but also this climate change
02:05.2 that happened at the same time...
02:07.2 it turns out those are exactly the same two features
02:10.0 that are affecting the planet today.
02:13.1 Humans, in fact, have been killing,
02:14.3 deliberately killing, wildlife for thousands of years,
02:19.2 and through that and the expansion out of Africa,
02:22.3 it turns out that every continent
02:24.2 lost their large animals, not just North America.
02:27.2 What you see here are bar graphs of just the number of species
02:30.0 in different size categories
02:31.2 #NAME?
02:34.1 and over here are the larger animals --
02:36.2 and Africa is really the only continent that has maintained
02:39.1 most of the large animals, like we see these elephants today,
02:41.2 whereas in North America and the other continents
02:44.1 lost their megafauna, lost their large animals.
02:47.2 These elephants now are threatened with extinction as well.
02:51.2 They have a gestation time of 22 months
02:54.0 and, on average,
02:56.1 one elephant is killed every 15 minutes.
02:58.2 There is no way that this large,
03:01.1 slow metabolism animal
03:03.1 could actually keep up with the deliberate
03:06.1 slaughter of these animals.
03:08.2 We're much, much better
03:10.2 at killing wildlife. As a matter of fact, we specialize in going after the very last
03:16.1 of some of these exquisite animals.
03:19.2 So, among about 5500 mammal species,
03:22.2 almost a quarter of them are threatened,
03:25.1 and most of them are threatened deliberately with hunting,
03:28.2 but there's more than that.
03:30.2 Humans, it turns out, have commensal animals
03:33.3 -- our cows, horses, and sheep --
03:35.3 are actually...
03:37.2 they dominate the biomass of the planet.
03:39.2 So, these are to scale in terms of the number of individuals
03:42.2 and their body mass,
03:44.1 so you see humans here and our livestock and pets.
03:47.0 Wild animals, on the other hand,
03:48.3 have just a tiny proportion of the total biomass
03:52.1 that dominates the planet today,
03:55.1 so that means there's little room for these wild animals,
03:58.1 because we consume most of the energy
04:01.3 on the planet.
04:03.3 The other thing that's happening is climate is changing.
04:06.2 So, this is a diagram of climate change
04:09.2 over the last 5 million years,
04:11.2 and you'll not they're changing scales as we go here
04:13.1 -- this is in millions of years and then thousands of years,
04:16.2 and then just the number of years before the present,
04:18.2 and then we finally move into the future over here.
04:21.0 So, what you'll see is that, in the last 5 million years,
04:23.3 the climates we're about ready to experience,
04:26.2 within the next 50-100 years,
04:28.3 are warmer than anything we've experienced
04:32.0 in our lifetime as a species,
04:34.1 and that any of the mammal species, for example,
04:37.0 that we're used to interacting with on the planet
04:39.0 have experienced in their lifetimes.
04:41.2 As a matter of fact, in the western US alone,
04:44.0 wildfires have doubled in frequency since 1988,
04:48.1 putting many people at risk for losing their homes.
04:55.1 Climate is also contributing to actual biome shifts.
04:57.3 This is a particular X-ray image
05:00.2 of the area around Pinnacles National Park,
05:02.3 showing that the trees that are standing there right now
05:06.2 are threatened with death in the near future
05:10.0 #NAME?
05:12.3 and blue, here, are the only healthy trees in this particular environment.
05:16.1 So in just a few years,
05:18.2 we're seeing a major shift
05:20.3 in where trees are present
05:22.2 and where trees are not present on the landscape,
05:24.2 simply because of climate,
05:26.3 and then the interaction between climate and things like
05:30.0 beetles, in particular, for trees.
05:32.2 We've lost a tremendous amount of forest cover.
05:36.2 The rate of loss has slowed down,
05:38.2 but that really doesn't matter in some ways,
05:41.2 because we've lost
05:44.3 a vast amount of many of these forests
05:47.1 in just the last 14 years
05:51.0 around the world.
05:54.0 Humans, in fact, are really good at causing habitat loss.
05:57.1 We can do this...
05:58.2 basically go out...
06:00.0 this is like hunting for trees...
06:01.1 we go out and we just take them down.
06:04.2 We transform ecosystems in radical ways.
06:07.2 This is an image of what
06:09.3 New York used to look like before we actually
06:12.2 built up the city
06:14.2 next to what the place looks like now.
06:15.2 And clearly there's no way for biodiversity,
06:18.1 at least most biodiversity,
06:20.1 to thrive in an environment that's so human-dominated.
06:24.1 In fact, if you look at the sum total of the terrestrial land on the planet,
06:28.2 we have used and coopted about 51% of the land
06:32.2 area just for our use,
06:34.1 mostly for production of food for ourselves
06:36.2 and our commensal animals.
06:38.3 If you look at this, you'll see that the only places
06:41.1 that we haven't really occupied
06:44.1 and we haven't transformed
06:46.0 are the hard to reach places
06:47.2 -- the Sahara Desert, the Congo,
06:49.2 the Amazon,
06:51.0 two of the places that have the largest
06:54.2 tropical forests left in the planet --
06:56.1 and the boreal forests and the tundra region.
06:59.2 So we've taken all the easily farmable land in the world.
07:03.2 Now, we need to basically farm this land we already have co-opted
07:08.0 more efficiently
07:10.1 in order to feed the coming mouths.
07:13.2 One of the things that matters a lot
07:15.2 when you think about how much of the land
07:17.3 we've actually changed on the planet
07:20.2 is that just by this simple rule,
07:22.2 this is one of the fundamental rules in ecology,
07:25.2 is that the number of species
07:28.1 is a function of the size of the place they occupy.
07:31.3 This is a rule of island biogeography,
07:34.2 and so here what we see across the x axis
07:36.2 is the size of the island,
07:38.1 these are the islands in the Caribbean,
07:40.2 and then number of species on the y axis,
07:43.0 and so the larger the island is
07:45.3 the more species are found on the island.
07:49.3 More area means more species.
07:52.2 Here you see an image
07:55.0 for different continents on the planet
07:56.3 and the number of amphibians.
07:58.1 So, even on a continental scale,
08:00.3 we're finding that larger areas
08:03.2 mean more species.
08:06.2 So, when you look at the amount of land
08:09.1 we've actually set aside to be protected on the planet,
08:12.3 it amounts to only 13% of our land surface.
08:15.2 So, even though we've co-opted
08:18.2 the function of 51%,
08:20.1 we've only actively set aside 13% of this to be protected,
08:24.1 and areas like Yellowstone National Park,
08:26.1 the world's first national park,
08:28.1 as you can see,
08:30.1 are isolated from all the other protected areas in North America.
08:35.2 So what these patches mean
08:38.0 is that we don't have a lot of connectivity
08:40.2 between our protected areas.
08:43.2 That exacerbates our attempts at conservation,
08:46.3 because animals like to move
08:49.1 to deal with different environments.
08:51.1 As the climates change,
08:52.2 they like to move to novel environments.
08:54.2 This is Yellowstone National Park,
08:57.1 seen from Earth Observatory,
08:59.1 and what you see is a nice long line there
09:02.1 showing you the division between
09:04.1 the forest service land on the west
09:06.2 and national park land on the east.
09:09.3 And what you'll see is clear-cutting
09:15.2 defines, now, the western border of Yellowstone National Park.
09:17.1 This is true for many of the protected areas of the world.
09:20.3 There's not a lot of buffer
09:23.1 for the animals that want to move away from Yellowstone
09:25.2 to a part of the landscape
09:28.1 that they can adjust to.
09:31.1 It's not just the transformation of habitat
09:34.0 that matters either;
09:35.2 it's that our transportation system itself
09:38.2 has disrupted a lot of these corridors of connection.
09:41.2 This slide, which is really spectacular
09:44.1 at showing how much of the landscape
09:46.3 we cut up with our transportation,
09:49.2 shows that...
09:51.2 in green you see the global roads,
09:53.3 you see in yellow our urban areas,
09:56.0 in blue you see our shipping routes,
09:58.2 and in white you see our air networks.
10:01.1 So it's not just on land,
10:03.0 it's not just what we've kind of transformed in terms of deforestation...
10:06.1 it's the roads we've built,
10:07.2 it's the number of ships we send across the ocean,
10:10.2 and it's the number of planes that fly in the sky,
10:12.3 all of which interrupt and threaten
10:16.2 animals that need to move across this landscape.
10:20.0 Species move to follow their habitats
10:22.2 and they've done this in the past.
10:24.1 This is in fact one of the first signs
10:26.2 of adjusting to climate that we see,
10:28.3 and the black dots, here, you see,
10:30.3 are data from the Pleistocene,
10:32.2 showing that these animals used to be present
10:36.2 greater than 10 thousand years ago,
10:38.0 somewhere between 10 and 20 thousand years ago,
10:39.2 at these parts of North America,
10:41.3 and as climates warmed
10:44.2 at the end of the Pleistocene
10:46.3 into what we call the Holocene,
10:48.1 which is the last 10 thousand years,
10:49.2 this species, the Northern Bog Lemming,
10:51.2 moved to the north,
10:53.3 and now you see its range occupying
10:56.2 the orange part of this figure.
10:58.2 So these species just responded
11:01.0 by moving pole-ward as climates changed.
11:03.2 This is a very typical response
11:06.0 among animals of the world,
11:07.2 that they move pole-ward as climates warm
11:10.0 and they move equator-ward as climates cool.
11:13.3 In fact, species are already moving north today.
11:16.3 There are examples of species
11:19.2 interacting with species that they don't normally see,
11:22.2 so southern species
11:24.2 are now starting to encounter species
11:27.1 from northern boreal forest or tundra regions,
11:29.1 and there are really interesting
11:32.1 and sometimes not very positive interactions
11:35.1 that result from those interactions.
11:37.1 They create new ecosystems.
11:39.1 So, these are animals just doing what they need to do
11:43.0 and challenging us, too,
11:44.2 in thinking about what is natural, what is pristine,
11:47.2 and what we should expect in the future.
11:50.1 So, I already said that animals are on the move
11:53.1 and what that means is that
11:55.2 they need to find areas that they can colonize,
11:57.3 where they can live.
12:00.1 And it turns out that this fundamental rule of island biogeography,
12:03.2 that includes more...
12:05.2 larger area means larger number of species...
12:08.1 it also includes a concept of connectivity.
12:11.2 So, the closer these islands or these populations
12:15.0 are to each other,
12:16.1 the more likely they are to maintain more species.
12:18.3 So, what you see across the x axis
12:20.3 is the number of species present,
12:22.3 and this is the rate of extinction shown in red
12:26.3 and immigration, shown in blue.
12:28.1 And so when the populations
12:31.3 are far from the mainland,
12:33.1 there are many fewer species
12:35.1 that can be maintained,
12:36.1 and when they're close to another population
12:40.0 they can maintain more species.
12:41.3 Likewise, when the island area is small,
12:44.1 it maintains very few species
12:46.2 compared to when the islands are large.
12:48.3 So it's this equilibrium,
12:51.0 it's this balance between these rates
12:52.2 that really matters,
12:54.3 and we have to think about this in moving into the future.
12:58.1 So really what that means is biodiversity
13:01.1 is threatened even in protected areas,
13:03.2 and it's threatened surely by overexploitation,
13:05.2 by hunting, deliberate poaching,
13:08.0 but it is also threatened by ecosystem transformation.
13:11.2 Protected areas don't preserve entire ecosystems,
13:15.0 and so the transformation of what's happening outside the protected areas
13:18.1 matters to the species that live within it.
13:21.1 Novel species are interacting with disease
13:25.0 and bringing new diseases into places
13:27.1 that they haven't yet been because they are responding to climate change
13:30.2 and other sources of environmental transformation,
13:33.3 and that means that the connectivity between these protected areas
13:39.0 is very important.
13:40.1 So, finally, the thing that's really pushing all of this is climate change,
13:43.3 and that's what's very important
13:46.1 to consider going into the future.
13:48.2 Now, one of the things that happens as populations
13:51.1 get fragmented
13:53.1 is that their population size, the animals' population size,
13:56.2 starts to decline.
13:58.3 And extinction, the loss of a species forever on the plant,
14:01.2 is just when population size goes to zero.
14:04.2 So, here we see amphibians, birds, mammals,
14:07.2 and many other species,
14:09.2 and these are all animals that are threatened somehow with extinction.
14:13.0 There are animals shown in black
14:14.2 that are completely extinct in the wild.
14:16.3 There are animals shown in these warmer colors
14:19.2 that show different kinds of threats to their systems,
14:23.0 whether they're facing eminent extinction
14:25.1 or whether their populations are threatened.
14:28.2 And so, all this is to show is that
14:31.3 there are many animals, many... over...
14:34.2 you know, thousands of animals that are threatened with extinction
14:37.3 because of population demise.
14:41.0 In fact, global population numbers of wildlife
14:45.0 are 50% of what they were
14:47.1 just in 1970,
14:49.1 so animals of all types
14:51.1 -- birds, fish, reptiles, and mammals --
14:54.0 are showing really large declines
14:56.2 in the number of populations
14:58.2 that are on the planet,
15:00.2 just the number of individuals of these species
15:03.1 have declined by half.
15:06.0 I want to give you an example of what this means.
15:08.1 So, this is the Iberian lynx,
15:10.1 it's found in Spain, and this animal, in 1900,
15:13.1 was occupying most of Spain.
15:15.2 And you can see its demise through the '60s, the '80s,
15:18.1 and in 2010 there are two populations remaining,
15:24.0 one with 73 individuals and the other with 173 individuals.
15:28.2 So, not only have we lost populations,
15:31.1 and clearly we've lost individuals,
15:33.0 we're just down to a couple hundred of these lynx.
15:36.2 And what does that mean?
15:38.1 It means that they've gone through what we call a population bottleneck,
15:42.1 and I'll explain what that means to the species in just a second.
15:46.1 In particular, what we see is that as population size declines,
15:50.2 so, as we decrease population size,
15:53.2 we actually decrease genetic diversity as well,
15:56.2 and so in general the larger the population is
16:00.0 the more genetic diversity will be maintained in that population.
16:03.2 And why do we care about population diversity?
16:06.3 We care about population diversity
16:08.2 because that's the toolkit that species have
16:11.2 to move into the future.
16:13.2 So, if we... you know,
16:15.1 if we kind of look at this in a little simulated model, here,
16:18.3 if you think of every one of these marbles,
16:20.2 these different colored marbles,
16:22.2 as some sort of a...
16:24.2 different kinds of a...
16:26.1 a genotype of some sort,
16:28.2 we start with a lot of genetic diversity
16:30.1 and then you just grab a few of these marbles,
16:32.3 you're going to get a bottleneck.
16:35.2 There's no way you can get all of this diversity
16:37.2 if you decrease the number of marbles
16:39.1 that you've pulled out of the system.
16:40.2 That's called a bottleneck.
16:42.3 You can recover, you can recover in numbers.
16:45.1 You can actually start reproduction
16:47.1 of this particular hypothetical species,
16:51.0 but you can't recover the initial genetic diversity,
16:53.1 because it takes so long,
16:55.1 in evolutionary time,
16:56.2 to accumulate.
16:58.0 So not only are numbers of individuals important,
17:00.3 but it's important to retain those individuals
17:02.3 as long as possible
17:05.1 to maintain genetic diversity.
17:07.1 Genetic diversity is a toolkit for adaptation.
17:11.2 Here's a great example.
17:13.1 These are the wolves of Isle Royale.
17:15.1 They've been studied for over 50 years,
17:17.1 it's the longest study of a predator-prey system
17:20.1 that we know about.
17:22.0 Wolves colonized this island
17:24.2 in Lake Superior in the 1940s
17:27.2 and they bounced around,
17:28.2 there's a pretty close relationship
17:30.2 between wolves and their moose prey,
17:32.3 where there's kind of a dynamic between the two of them.
17:37.2 There's been some severe winter declines in moose
17:41.1 and then that affects the wolves in some way.
17:44.1 There's been a particular canine parvovirus
17:47.1 that caused a large crash in the number of wolves,
17:49.2 and every one of these diamonds
17:51.2 shows you that there was a winter bridge to the mainland
17:55.1 that wolves could colonize across,
17:57.2 and so the population
18:00.3 was continually being rescued.
18:02.3 You see now that there aren't very many of these colonization events
18:06.3 and in fact the wolves are in decline.
18:11.2 And not only are they in decline,
18:13.1 but because they are losing their genetic diversity,
18:17.2 abnormalities in this population
18:20.0 have increased dramatically.
18:22.0 So, for example, these particular abnormalities
18:25.1 in their spinal column...
18:27.0 in Isle Royale, their incidence is about 1 in every 3,
18:31.2 and in a normal population
18:34.0 it would just be about 1%.
18:36.1 What this means is...
18:38.1 you can see in this last wolf here, of these three...
18:41.0 these are the last three wolves remaining on Isle Royale as of 2015,
18:46.1 and this last wolf has a shortened tail,
18:49.1 it's slightly twisted,
18:51.1 and his back... he looks like he has scoliosis.
18:53.2 They think that this is the pup of these two, this pair,
18:56.3 but these are the last three left,
18:58.3 and clearly this wolf has been affected by inbreeding.
19:04.2 So, there is this possibility
19:08.2 to rescue populations
19:10.2 by bringing in some kind of new individuals
19:13.2 to a population,
19:15.0 and that indeed is what happened to the Florida puma.
19:16.2 So, in the mid-1990s,
19:20.3 puma were brought in from Texas,
19:23.3 and what you see in terms of the population size,
19:25.2 which was on decline,
19:27.2 is that they basically started breeding more frequently,
19:30.2 and so the population really bounced up in individuals,
19:34.1 but there was also a rescue of genetic variation.
19:37.3 The eight Texas puma...
19:40.3 you see before this time,
19:43.0 there's hardly any variation,
19:45.2 and after that time there's an enormous increase
19:48.2 in the amount of genetic variation in this population,
19:51.2 suggesting that there's been genetic rescue
19:54.1 just by adding eight individuals
19:56.2 from another healthier population.
20:00.0 Small populations, then,
20:02.1 to kind of summarize this part,
20:04.1 small populations
20:06.2 tend to result in inbreeding, and so...
20:09.1 and the reason is because it brings out
20:12.0 the recessive deleterious genotypes.
20:15.3 In this case, you'll see this lineage
20:19.1 showing this recessive allele
20:21.1 that doesn't get expressed in the offspring
20:24.1 because there's always this dominant allele,
20:26.3 this large A,
20:28.2 that is overprinting it.
20:31.1 When there's inbreeding,
20:33.0 you have the opportunity to produce an individual
20:36.2 that has both of these recessive alleles,
20:39.0 and what that means is that
20:40.3 these deleterious phenotypes
20:43.0 then become expressed.
20:45.3 Okay, so what are these recessive deleterious alleles?
20:49.2 What do they result in?
20:50.2 What's the problem with inbreeding?
20:52.2 It turns out that inbreeding creates
20:56.1 a pretty typical list of problems with many animals:
21:00.0 their faces aren't symmetrical;
21:02.2 they have reduced fertility,
21:04.1 and this is true both in terms of the number of offspring that they produce
21:11.0 and also whether their sperm are even viable;
21:12.3 there are many genetic disorders, including Down's syndrome,
21:14.2 that show up in animals;
21:16.3 they have a much lower birth rate;
21:18.1 higher infant mortality;
21:20.3 and because they have a slowed growth rate,
21:23.1 they also reach a much smaller adult size;
21:26.2 and then most importantly, perhaps,
21:28.2 in this changing world
21:30.1 is that they really lose a lot of their abilities
21:33.0 to respond with their immune system.
21:36.0 So, I want to point out...
21:38.0 here is an example in tigers,
21:40.1 these are white tigers...
21:42.2 white tigers, for those of you who don't know,
21:44.1 white tigers are not Siberian
21:45.2 -- they look like they should be,
21:47.1 they have this white coat --
21:48.2 it turns out they're completed created in zoos.
21:51.1 White tigers are actually Bengal tigers,
21:53.2 they're from India,
21:55.1 and they've been highly inbred in zoos
21:57.1 because people like white tigers.
21:59.2 But it turns out the white coat
22:01.2 is also associated with the same gene
22:06.0 that creates cross-eyes in the individuals,
22:10.0 so it crosses the optic nerve,
22:12.2 and so every white tiger that you see
22:15.1 is cross-eyed.
22:16.3 And you can see this other tiger, here,
22:18.3 with a severely misformed face and a very asymmetrical face,
22:23.0 he has a cleft palate,
22:24.3 he has a lot of problems.
22:26.1 This animal could not survive in the wild.
22:30.1 So, to conclude,
22:32.2 I just want to really underscore that
22:35.1 humans dominate the planet.
22:37.3 Populations of wild animals and species of animals
22:40.3 are threatened with extinction --
22:43.1 they're in decline.
22:44.2 What does that matter?
22:46.1 Why does that matter?
22:48.0 Declining populations lose genetic diversity.
22:50.2 They're more likely to lose all those tools
22:53.1 that they need to adapt to whatever the future
22:56.0 is bringing to us.
22:57.2 And then, importantly,
22:59.2 the connectivity between these populations,
23:02.1 the ability for these animals to move
23:04.2 and find a new home,
23:06.2 is increasingly getting more and more difficult.
23:09.1 That's critical for their survival.
23:12.1 So, what I want to do is conclude
23:14.2 by saying thank you to all of
23:17.1 the former and current members of my lab,
23:18.3 all of my collaborators,
23:20.1 the funding agencies I've had through the years,
23:21.3 and Stanford University.