Bio 102 quiz 1 preparation

2 Billion Years Unchanged

A 2.3 billion year old bacterial fossil was found in the deep ocean off the coast of Australia. When this fossil is compared to a 1.8 billion year old fossil and the same kind of bacteria living today in the deep ocean, they find the bacteria is unchanged. Why has this bacteria not evolved? The fossils studied date back to a period known as the Great Oxidation Event, which occurred when oxygen levels surged on Earth between 2.2 billion and 2.4 billion years ago. During this time, there was also a large rise in sulfate and nitrate levels, which provided all the nutrition the sulfur bacteria needed to survive and reproduce. The environment inside these deep-sea rocks hasn't changed since then, so there has been no need for the organisms to adapt, the researchers said.

The Uncertain Conservation of Hybrids

A case in point: In the 1950s, a pair of California bait dealers from the Salinas Valley, seeking to expand their business, hopped into a pickup truck and took off to central Texas and New Mexico. They brought back barred tiger salamanders, which could grow to more than double the size of California's native tiger salamander. The new species quickly proved to be good for the local fishermen but bad for the local ecosystem: The introduced salamanders mated with the natives, creating a hybrid breed that could outcompete its parent species. Soon the California tiger salamander found itself in danger of being wiped out entirely, and it remains a threatened species today. Such examples illustrate why hybrids have generally been disqualified from protection by conservationists: Hybrids are thought to degrade the gene pools of their parent generations and pose a threat to biodiversity. This exclusion seems particularly valid when the interbreeding is caused by human actions, as was the case with the California tiger salamander and, in more recent news, the lionfish devastating the Caribbean. "In a conservation context, hybridization is usually seen as negative simply because the mantra of conservational biology is to protect species and lineages as they evolve, on the landscape they evolved in," said Bradley Shaffer, a conservation biologist at the University of California, Los Angeles. Introduce foreign species from a different part of the world, and the consequences can be devastating even if the lineage of the invasive species is swallowed up by hybrids. But preventing hybridization altogether can also have negative repercussions. As the work being done by Mallet, Arnold, Eizirik and the Grants (among others) has shown, when interbreeding between geographically neighboring species happens naturally, it can help species adapt to new threats. "When [hybridization is] a creative evolutionary force, conservation policies that retain that process are important and should come to the forefront," Shaffer said. So although hybridization shouldn't be introduced into threatened or endangered populations artificially, it shouldn't necessarily be prevented when it happens on its own. And being a hybrid shouldn't rule out protection under conservation laws, according to Mallet and other researchers who see hybridization as natural and evolutionarily important. "If you continually prevent hybridization, this could be a problem," Mallet said. Many experts therefore believe that the Endangered Species Act and other legislation are outdated and in need of revision. "I want to help move our discussions of conservation into the genomic era, where [hybridization] is now found to be far more prevalent than we ever thought or imagined," said Bridgett vonHoldt, an evolutionary biologist at Princeton. "Our policies need to be more flexible and inclusive." Take the various species of wolves that roam North America. Gray wolves, Mexican wolves, red wolves and eastern wolves, all endangered, were once treated as distinct species. Recent genomic evidence, however, points to the likelihood that red and eastern wolves are in fact hybrids of gray wolves and coyotes. Given the murky area hybrids occupy when it comes to conservation policy, this finding called into question their protected status and complicated biologists' understanding of their ecological role in the evolutionary history of gray wolves. Determining the best course of action in conservation when so many factors are unknown or unclear is an exceedingly difficult task, and one that experts have yet to resolve. Nuances in the environment and genomic history of a given hybrid species, according to Shaffer, call for nuances in how to approach their conservation. "It's a balancing act," Mallet said.

Determination of blood type is an example of which of the following? A. Codominance B. Epistasis C. Incomplete dominance D. Mendelian genetics

A. Codominance

The offspring of two species may not be fit for the environment of either of it's parents. They would not survive long. This prevents gene flow between the two species. What type of reproductive barrier is this? A. Reduced hybrid viability B. Reduced hybrid fertility C. Hybrid breakdown

A. Reduced hybrid viability

A population of snails is separated into 2 populations by a flood which results in the formation of a new stream. As time goes by, the 2 populations diverge genetically because they no longer exchange genes. What type of speciation might this lead to? A. allopatric B. sympatric C. not enough information to tell

A. allopaatric

The Biological Species Concept

Although supporting data as detailed and as thoroughly analyzed as Eizirik's is rare, the underlying idea that hybridization contributes to species development is by no means new. Biologists have known since the 1930s that hybridization occurs frequently in plants (it's documented in about 25 percent of flowering plant species in the U.K. alone) and plays an important role in their evolution. In fact, it was a pair of botanists who, in 1938, coined the phrase "introgressive hybridization," or introgression, to describe the pattern of hybridization and gene flow they saw in their studies. Imagine members of two species—let's call them A and B—that cross to produce 50-50 hybrid offspring with equal shares of genes from each parent. Then picture those hybrids crossing back to breed with members of species A, and assume that their offspring do the same. Many generations later, nature is left with organisms from species A whose genomes have retained a few genes from species B. Studies have demonstrated that this process could yield entirely new plant species as well. But animal species seemed more discrete, at least for a while. Most zoologists supported the biological species concept proposed in 1942 by the legendary biologist Ernst Mayr, who was one of the architects of the modern synthesis, the version of evolution theory that combined Darwin's natural selection with the science of genetics. Mayr's biological species concept was based on reproductive isolation: A species was defined as a population that could not or did not breed with other populations. Even when exceptions to that rule started to emerge in the 1970s, many biologists considered hybridization to be too rare to be important in animals. "We had a blinkered attitude," said James Mallet, an evolutionary biologist at Harvard University. Today, he added, saying that such hybridizations don't affect reconstructions of evolutionary history or "that this wasn't useful in adaptive evolution—that's no longer tenable." This is especially true now that computational and genomic tools prove just how prolific introgression is—even in our own species. Since 2009, studies have revealed that approximately 50,000 to 60,000 years ago, some modern humans spreading out of Africa interbred with Neanderthals; they later did so with another ancestral human group, the Denisovans, as well. The children in both cases went on to mate with other modern humans, passing the genes they acquired down to us. At present, researchers estimate that some populations have inherited 1 to 2 percent of their DNA from Neanderthals, and up to 6 percent of it from Denisovans—fractions that amount to hundreds of genes. In 2012, Mallet and his colleagues showed a large amount of gene flow between two hybridizing species of Heliconius butterfly. The following year, they determined that approximately 40 percent of the genes in one species had come from the other. Mallet's team is now working with another pair of butterfly species that exchange even more of their genes: something like 98 percent, he said. Only the remaining 2 percent of the genome carries the information that separates the species and reflects their "true" evolutionary trajectory. A similar blurring of species lines has already been found in malaria-carrying mosquitoes of the Anopheles genus. Other types of organisms, from fish and birds to wolves and sheep, experience their share of introgression, too. "The boundaries between species are now known to be less rigid than previously thought," said Peter Grant, an evolutionary biologist at Princeton University who, along with his fellow Princeton biologist (and wife) Rosemary Grant, has been studying the evolution of Galápagos finches for decades. "Phylogenetic reconstructions depict treelike patterns as if there is a clear barrier between species that arises instantaneously and is never breached. This may be misleading." Arnold concurred. "It's a web of life," he said, "rather than a simple bifurcating tree of life." That also means it's more necessary than ever before to examine the entire genome, and not just selected genes, to understand a species' evolutionary relationships and generate the correct phylogeny. And even that might not be enough. "It may well be," Mallet said, "that some actual evolutionary patterns are still completely irrecoverable."

Sex-Linked Genes

Any gene located on a sex chromosome is called a sex-linked gene. Most sex-linked genes are found on the X chromosome. Red-green colorblindness is a common human sex-linked disorder and caused by a malfunction of light-sensitive cells in the eyes.

How many species of giraffe are there? A. 1 B. 4 C. 5 D. 10

B. 4

The hybrid that the Grants' studied in the Galapagos called "Big Bird" represents a new species of finch. A. true B. false

B. False

What percentage of the offspring would you predict to be homozygous recessive? 0% 25% 50% 100%

C. 50 %

What percentage of the offspring would you predict to show the dominant trait? 0% 25% 50% 100%

C. 50 %

One of these snakes lives on land and the other in water. What type of reproductive isolation is this? A. Temporal B. Gametic C. Habitat D. Behavioral

C. Habitat

Charles Darwin

Charles Darwin published On the Origin of Species in 1859 but he wasn't the first to propose the concept that all life evolved from a common ancestor. Darwin's own grandfather has expressed this idea. But Charles Darwin was the first to publish a hypothesis for the mechanism by which evolution occurs: natural selection.

behavioral isolation

Courtship rituals and other behaviors unique to a species. You have to do the dance right in order to be recognized as the right species in order to mate. Watch the video of the blue-footed booby here.

According to the article "Uptown Mice are Different from Downtown Mice" what is one trait that city mice seem to be evolving that other mice aren't? a. Development of larger brains. b. Mutations that result in more offspring. c. Adaptation to warmer environments. d. Genetic mutations that help them neutralize toxic metals in soil.

D.

Which of the following traits is determined by Medelian genetics? A. Hair color B. Eye color C. Height D. Eye shape

D. Eye shape

natural selection

Darwin's evidence for natural selection came in part from his study of finches in the Galapagos Islands. He observed about 15 species of finches found only on these islands. The primary difference between each species is the shape and size of their beaks which are highly adapted to different food sources. The shape and size of the beak are adapted for different food sources. Darwin concluded, ""Seeing this gradation and diversity of structure in one small, intimately related group of birds, one might really fancy that from an original paucity of birds in this archipelago, one species had been taken and modified for different ends." Darwin hypothesized that each of these finch species descended from a common ancestor. This helped him form his ideas about natural selection. In 2004, molecular analysis of the development of beak structure found a small change in expression of a protein results in the diversity of beak shape.

Family Pedigrees

Dominant traits are not necessarily normal or more common. Wild-type traits are those seen most often in nature and not necessarily specified by dominant alleles.

Homologies

Even distantly related species that descended from a common ancestor often share a trait inherited from that ancestor that has been modified based on the evolution of the different species with that trait. For example, as shown above, frogs, rabbits, lizards, and birds all share a common ancestor, Eusthenopteron. This species had an appendage with three bones: a humerus, radius, and ulna. All the descendants of this species (frog, rabbit, lizard, and bird) share this trait though it has been modified due to different natural selection pressures.

Role of evolution

Evolution also plays a role in how effectively we can grow crops to feed the world's population.

Misconceptions 2

Evolution has, unfortunately, been used to justify the oppression of one group over another by saying that "the strongest survive." But that isn't what Darwin argued. He said: "It is not the strongest of the species that survives, nor the most intelligent that survives. It is the one that is most adaptable to change." 65 million years ago, a catastrophic event killed off most of the life on earth, including the dinosaurs. Small rodent-like creatures survived and gave rise to today's mammals. These rodents weren't smarter than dinosaurs and they certainly weren't stronger. But they were better adapted to the new environmental conditions. Evolution the effect of environmental change on populations through the mechanism of natural selection.

Misconception 3

Evolving to a super-organism •Evolution is not a progression to a perfect, super-organism. The characteristics that make a species well-adapted to the environment will change as the environment changes.

Reproductive isolation as a by-product of selection

For example, isolated populations of mosquitofish have evolved reproductive isolation as a result of selection under different levels of predation. Populations in high predation have a thicker, larger tail to allow for faster swimming. It turns out that male mosquitofish in high predation also have evolved longer, bonier genitalia which allow for mating faster. Being able to mate faster reduces the risk of predation.

Restless Genes Make Themselves Felt

Genomic studies can't create a complete picture of the introgressive movements of genes. Whenever one species inherits genes from another, the outcome can be either deleterious, neutral or adaptive. Natural selection tends to weed out the first, although some of the genes we have inherited from Neanderthals, for example, may be involved in disorders such as diabetes, obesity or depression. Neutral introgressed regions drift, so it's possible for them to remain in the genome for very long periods of time without having an observable effect. But it's the beneficial introgressions that particularly fascinate researchers. Take the Neanderthal and Denisovan DNA again: Those genes have allowed people to adapt to the harsh environs of places like the Tibetan plateau, protecting them against the harmful effects of high altitudes and low oxygen saturation, which in nonlocals can cause stroke, miscarriage and other health risks. Variants from interbreeding with archaic humans have also conferred immunity to certain infections and made skin and hair pigmentation more suitable for Eurasian climes. Mallet's butterflies, too, reflect evidence of adaptive hybridization, particularly with traits involved in mimicry and predator avoidance. Researchers had observed that although most Heliconius species had highly divergent wing coloration and patterning, some bore a striking resemblance to one another. The researchers believed that these species had independently converged on these traits, but it turns out that's only partially correct. Mallet and others have found that introgression was also responsible. The same goes for Galápagos finches: Pieces of their genomes that control for features including beak size and shape were shared through hybridization. Once again, parallel evolution can't explain everything. For these effects to occur, the rate of hybridization can be—and most likely is—very small. For Mallet's almost entirely hybridized butterflies, "the occasional trickle of one hybrid mating every 1,000 normal matings is sufficient to completely homogenize genes between the species," he said. "That's pretty exciting." As these patterns of introgression have become more and more predominant in the scientific literature, researchers have set out to uncover their evolutionary consequences. These go beyond the fact that speciation tends to be a much more gradual process than it's often made out to be. "Diversification, adaptation and adaptive evolution really do seem to be driven quite often by genes moving around," Arnold said. The research done by Eizirik and his team makes a compelling case for this. Around the time when the gene introgressions they analyzed occurred, the populations of all five Panthera species are estimated to have declined, likely due to climate changes. The smaller a population is, the greater the probability that a harmful mutation will get affixed to its genome. Perhaps the gene flow found between the different species, then, rescued them from extinction, providing adaptive mutations and "patching" deleterious ones. "This kind of infusion of genetic mutations is so large that it can cause really rapid evolution," Arnold said. And the process doesn't end with speeding up evolution in a single species. Adaptive introgression can in turn contribute significantly to adaptive radiation, a process by which one species rapidly diversifies into a large variety of types, which then form new lineages that continue to adapt independently. The textbook case can be found in the great lakes of East Africa, which are home to hundreds upon hundreds of cichlid species, a type of fish that diversified in explosive bursts (on the evolutionary timescale) from common ancestors, largely in response to climatic and tectonic shifts in their environment. Today, cichlids vary widely in form, behavior and ecology—thanks in large part to introgressive hybridization. Biologists will need many more years to understand the full importance of hybridization to evolution. For example, Arnold wants to see further investigations like the ones that have been done on the finches in the Galápagos and the wolves of Yellowstone National Park: behavioral, metabolic and other analyses that will reveal how much of introgression is adaptive and how much is deleterious or neutral—as well as whether adaptive introgression affects only particular kinds of genes, or if it acts in a more widespread manner. Unfortunately, for conservationists and others challenged with managing the diversity of imperiled species, the absence of satisfactory answers poses more immediate problems. They must often weigh the value of protecting wild hybrid populations against the harm hybrids can do to established species, including the ones from which they emerged.

Mendel

Gregor Mendel is considered the father of genetics for his work on patterns of inheritance. Mendel's research was based on the question: Why do offspring resemble their parents? •Remember, this was before we had any concept of genes, DNA, or cellular reproduction. Yet he carried out experiments to answer this question and found certain patterns that became the basis for our laws of genetics. Mendel used pea plants for his experiments and followed the above traits. He purposefully crossed plants with specific traits to determine how often that trait was passed on.

Hybrid breakdown

Hybrid breakdown: Some first-generation hybrids are fertile, but when they mate with each other or with either parent species, offspring of the next generation are feeble or sterile

What ligers, grolar bears, and mules show scientists about evolution

IN 2006, A hunter shot what he thought was a polar bear in the Northwest Territories of Canada. Closer examination, however, revealed brown patches on its white fur, uncharacteristically long claws and a slightly hunched back. The creature was in fact a hybrid, its mother a polar bear, its father a grizzly. Although this cross was known to be possible—the two species had mated in captivity before—this was the first documented case found in the wild. Since then, it has become clear that this was not an isolated incident. Conservationists and others worry that if climate change continues to drive grizzly bears into polar bear territory, such interbreeding will become more common and will devastate the polar bear population. Some have even proposed killing the hybrids in an effort to conserve the species. But grizzlies and polar bears, as it turns out, have been mating since the species diverged hundreds of thousands of years ago. Polar bear genomes have retained mitochondrial DNA from ancient grizzly bears, and grizzlies have inherited genes from hybridizing with polar bears. "People worry that if they interbreed, polar bears will lose their beautiful white coats," said Michael Arnold, an evolutionary biologist at the University of Georgia. "But the truth is these organisms have not been looking entirely like themselves for a long time now." "If this mixing is a common natural event," he warned, "then killing hybrids to prevent them from mixing with the 'pure' parent genomes is not a management technique we should do lightly." In fact, it may be that the genetic variation introduced by this kind of hybridization could save the polar bears, whose survival in the face of rising temperatures and melting ice may hinge on their ability to adapt to a rockier, less frozen habitat. Taking in some genes from grizzly bears is highly likely to be adaptive for polar bears, Arnold said, even though the results "won't look exactly like a polar bear." Controversies like this one underscore the possibility that the bad reputation of naturally occurring hybrids is not entirely justified. Historically, hybrids have often been associated with the sterile or unfit offspring of maladaptive crossings (such as the mule, born of a female horse and a male donkey). Naturalists have traditionally viewed hybridization in the wild as a kind of irrelevant, mostly rare, dead-end fluke. If hybrids aren't viable or fertile or common, how could they have much influence on evolution? But as genomic studies provide new insights into how species evolve, biologists are now seeing that, surprisingly often, hybrids play a vital role in fortifying species and helping them take on useful genes from close relatives. In short, maladaptive pairings don't tell the full story of interbreeding. The genetic transfer that takes place between organisms while their lineages are diverging has a hand in the emergence of adaptive traits and in the creation of new species altogether. According to Arnold, not only is it common for newly emerging species to reacquire genes through hybrid populations, "but it's probably the most common way evolution proceeds, whether you're talking about viruses, plants, bacteria or animals."

Fossil Distribution

In general, older fossils are deeper in the earth and younger fossils are shallower and closer to the surface. If we have a hypothesis that one species descended from another, we can predict where we would be likely to find their fossils in the fossil record. This allows scientists to test their ideas about evolutionary descent. As our knowledge of the fossil record increases, we work out the possible order of descent along with the other techniques such as homologies and intermediate traits

Incomplete Dominance in Plants and People

In incomplete dominance, F1 hybrids have an appearance between the phenotypes of the two parents

The Mutant Genes behind the Black Death

In other organisms, speciation can be influenced by larger numbers of genes and gene interactions Yersinia pestis required a gene for a single protein to cause pneumonic plague

Sympatric ("Same Country") Speciation

In sympatric speciation, speciation takes place in geographically overlapping populations

Mitosis Cell Cycle

Interphase Prophase Metaphase Anaphase Telephase/Cytokinesis

Giraffe genetic secret: Four species of tallest mammal identified

It is a famous, gentle giant of the African savannah, but the giraffe's genetics have just revealed that there is not one species, but four. Giraffes have previously been recognised to be a single species divided into several sub-species. But this latest study of their DNA suggests that four groups of giraffes have not cross-bred and exchanged genetic material for millions of years. This is a clear indication that they have evolved into distinct species. The study published in the journal Current Biology has rewritten the biology of Earth's tallest mammal. The scientists say their findings could inform the conservation efforts for all four species of giraffe. Conservation was the catalyst for this genetic research; the Giraffe Conservation Foundation asked the team to carry out genetic analysis of giraffes in Namibia. The foundation wanted to understand the genetic differences between different giraffe populations, to see how the animals might be affected if different subspecies were mixed together when animals were moved into protected areas. What we found then, says Axel Janke, a geneticist at the Senckenberg Biodiversity and Climate Research Centre, who led the research, "was that the sub-species were genetically very different and separate. "I'd never seen that in a population study [of a species] before." This initial study examined what is known as mitochondrial DNA - a packet of DNA within every cell's "engine". This is useful for population genetics - it can be easily isolated and contains lots of known variants that can track relatedness. But mitochondrial DNA is not part of the code that builds an animal, so Dr Janke decided to examine and compare parts of that code - the nuclear DNA. "It turned out, he told BBC News, that, for example, "the whole clade of northern giraffes was very different from reticulated giraffes." "Our findings indicated four distinct species." Those four species include: southern giraffe (Giraffa giraffa), Masai giraffe (G. tippelskirchi), reticulated giraffe (G. reticulata) northern giraffe (G. camelopardalis), which includes the Nubian giraffe (G. c. camelopardalis) as a distinct but related subspecies. While giraffes had always been thought to be of one species, Dr Janke likened the difference between one species and another - in terms of their genetic code - to that of a Polar bear compared with a brown bear. This suggests that each species is adapted for a specific environment or diet - a question that is the subject of his team's next research project. Neglected by science Matthew Cobb, professor of zoology at the University of Manchester explained that the "four groups of giraffes had "been separated for 1-2 million years, with no evidence of genes being exchanged between them". "This is an important finding that will enable conservation biologists to target their efforts and, perhaps, to come up with new conservation approaches in captivity or in the wild, based on the genetic similarities and differences between these groups," Professor Cobb told BBC News. Dr Janke commented: "We've clearly completely forgotten what a giraffe is." He added that conservation programmes focused on specific species - understanding an animal's life, behaviour and habitat, to inform how it can be protected in the wild. In the last 15 years, the population of giraffes has declined by 40% - there are now an estimated 90,000 individuals in the wild. But, as a single species, they are classified by the International Union for the Conservation of Nature as of Least Concern. Now, it is clear that each of these four newly classified species could be faring very differently. It's important to raise awareness for conservation, said Dr Janke, "to protect his beautiful animal of which we know so little."

Giraffes

It was long thought that there was only one species of giraffe. Recent research has found there are actually 4 species: Southern giraffe, Masai giraffe, reticulated giraffe, northern giraffe. No hybrids between these species have been discovered in the wild. Over the past 30 years giraffe numbers have dropped to about 90,000 individuals from about 150,000. Right now there are only about 4,750 northern giraffes and 8,700 reticulated giraffes.

monohybrid crosses

Mendel developed four hypotheses from the monohybrid cross, listed here using modern terminology (including "gene" instead of "heritable factor"). 1. The alternative versions of genes are called alleles. 2. For each inherited character, an organism inherits two alleles, one from each parent. An organism is homozygous for that gene if both alleles are identical. An organism is heterozygous for that gene if the alleles are different. 3. If two alleles of an inherited pair differ, then one determines the organism's appearance and is called the dominant allele and the other has no noticeable effect on the organism's appearance and is called the recessive allele. This explains Mendel's results. Purple flowers were dominant and white flowers were recessive. We use letters to represent the allele combination present. A capital letter represents the dominant allele while a lower case letter represents the recessive allele. 4. Gametes carry only one allele for each inherited character. The two alleles for a character segregate (separate) from each other during the production of gametes. This statement is called the law of segregation. An organism begins cellular division with two copies of each gene. To prepare for reproduction, they produce gametes (eggs and sperm) that each have only one copy which is assigned randomly. Phenotype: the outward manifestation of the genes (the physical appearance) Genotype: the actual alleles that determine the phenotype. Flower color is the phenotype The alleles present are the genotype and are represented by these letters. Capital for the dominant trait and lower case for the recessive trait. Parents that only have dominant alleles for a trait can only pass on the dominant allele. Parents with only recessive alleles can only pass on the recessive allele to offspring. So when Mendel crossed purple flowers with white flowers, the offspring all received a dominant allele from one parent and a recessive allele from the other parent.

mechanical isolation

Morphological differences can prevent successful completion of mating or in other words, the parts don't fit. In the Japanese Euhadra snails, having the same direction of shell spiral allows them to reach each other to mate. If their shell spiral is different, they can't reach the parts needed to mate. Japanese Euhadra snails, the direction of shell spiral affects mating

Lions and Tigers and Jaguars, Oh My!

Most recently, signatures of hybridization have turned up in studies on the evolution of the jaguar. In a paper published last month in Science Advances, a team of researchers from institutions spanning seven countries examined the genomes of the five members of the Panthera genus, often called the "big cats": lions, leopards, tigers, jaguars and snow leopards. The scientists sequenced the genomes of the jaguar and leopard for the first time and compared them with the already existing genomes for the other three species, finding more than 13,000 genes that were shared across all five. This information helped them construct a phylogenetic tree (in essence, a family tree for species) to describe how the different animals diverged from a common ancestor approximately 4.6 million years ago. One of the group's leaders, Eduardo Eizirik, a biologist and ecologist at the Pontifical Catholic University of Rio Grande do Sul in Brazil, has dedicated the past 15 years to studying the jaguar. As he and his colleagues mapped its genome, they combed it for genes that could have been responsible for adaptations like the animal's large head and strong jaw, which likely evolved to accommodate a diet of armored reptiles—allowing the jaguar to crush through alligator skin or turtle shells, for instance—after an extinction event that wiped out most large mammalian prey. Some of these adaptations, however, may not have originated in the jaguar lineage at all. Eizirik's team found evidence of many crossings between the different Panthera species. In one case, two genes found in the jaguar pointed to a past hybridization with the lion, which would have occurred after their phylogenetic paths had forked. Both genes turned out to be involved in optic nerve formation; Eizirik speculated that the genes encoded an improvement in vision the jaguars needed or could exploit. For whatever reasons, natural selection favored the lion's genes, which took the place of those the jaguar originally had for that trait. Such hybridization illustrates why the Eizirik group's delineation of the Panthera evolutionary tree is so noteworthy. "The bottom line is that this has all become more complex," Eizirik said. "Species eventually do become separated, but it's not as immediate as people would frequently say." He added, "The genomes we studied reflected this mosaic of histories."

Uptown vs. Downtown Mice

Munshi-South never anticipated that he would study evolution in New York City's parks. He began his career as a biologist traipsing after elephants, parrots, and snakes in the jungles of Africa and Borneo. He was particularly interested in how logging and drilling for oil forced animals to adapt to a changing landscape. In 2007, however, he accepted an attractive assistant professorship at Baruch College, which meant moving to NYC. Despite trading the rainforest for skyscrapers and rivers of asphalt, he was determined to continue studying wild animals. What began as a few exploratory trips with a lone undergraduate to capture mice in Central Park turned into several long-term research projects. It's been a fascinating, learn-as-you-go adventure, with more drama than you might expect. One time, in a patch of forest on the Brooklyn-Queens border, the police accosted Munshi-South and his colleagues, guns drawn. A passerby had apparently mistaken some of their equipment — jugs of ethanol and a blue tarp — for the accoutrement of a mobile drug lab. Biologists now recognize Munshi-South as a pioneer of an emerging science that sees the city itself as a major engine of evolution. "Evolution can happen much more rapidly in cities than had been appreciated," Munshi-South says. Creatures change with their environment. A group of finches swept onto an unfamiliar island by a storm; pine trees routinely ravaged by lightning-sparked fires; freshwater fish faced with a prolonged period of drought — generation by generation, each must adapt to nature's vicissitudes. But some of the greatest pressures to evolve exist in places where nature appears to have been all but evicted. How New York City has changed the white-footed mouse is a perfect example. Before the 1700s, the white-footed mouse (Peromyscus leucopus) roamed the vast woodlands that once covered the five boroughs. New York City's expansion sliced up that native habitat into scattered fragments of greenery, isolating numerous groups of mice, who fear the open roads and highways and stick to much safer areas thick with foliage. Such geographic isolation drives evolution and can even cleave a single species in two. To find evidence of such adaptation, Harris, Munshi-South, and their colleagues have been catching mice in NYC's remaining islands of wilderness and taking snips of their tails, from which they extract DNA. They have discovered that segregated populations of this one species have diverged onto different evolutionary paths. The mice have become so genetically distinct from one another that if you show Munshi-South a DNA sequence randomly selected from a white-footed mouse in NYC, he can tell you where it lives. At the same time, city mice as a whole also seem to be evolving new traits that mice from rural areas outside the city lack: genetic mutations that may help them neutralize toxic metals in polluted soil, for example, or speed up their sperm in response to the intense sexual competition in their overcrowded metropolitan homes. The city has likely been a catalyst for more explicit changes in the mice as well — that's what Munshi-South and his collaborators are searching for next. In the city's parks, where there is still plenty of shrubbery, the mice tend to be more acrobatic, sprinting along logs and vaulting over tangled vines. In the suburbs, where deer strip away much of the vegetation, mice mostly scurry over flat ground. Munshi-South predicts that after enough generations, the length of the mice's tailbones and limbs might have shifted to suit these different styles of locomotion, something the researchers can demonstrate by meticulously measuring enough of their skeletons. In a separate study, Dimech is investigating bacteria that live inside the rodents' gut and are known to increase the production of T cells, an indispensable legion of immune system warriors. The demographics of gut bacteria shift depending on diet and lifestyle, so Dimech suspects that mice from urban, suburban, and rural areas will have different numbers of these immune-boosting bacteria, which will in turn alter their health. Mice aren't the only creature that have endured the city's evolutionary pressures: In another series of studies, Munshi-South and an ecologist with the city's Parks and Recreation Department, Ellen Pehek, have focused on the dusky salamander (Desmognathus fuscus), a native amphibian that hadn't been observed in the city for decades. Their investigation started after Pehek found a curious research note from 1945 detailing the discovery of 11 dusky salamanders "under rocks lying in and adjacent to several small springs" located on "the bluffs overlooking the Harlem River, between 181st and 190th Sts." When Pehek visited the same spot in 2005 and again in 2010, she was amazed to discover that the salamanders were still living and breeding there. Ecologists now know that these salamanders cling to a handful of places around New York City where clean water seeps from the ground. Their future is highly tenuous, however. Based on surveys and genetic analysis, Pehek and Munshi-South have learned that each of the scattered salamander populations is so small, inbred, and homogenous that it likely lacks the genetic diversity required to keep adapting. Unless the city establishes protected areas for the salamanders, boosting their numbers, they may soon go extinct. I find Munshi-South checking traps at the bottom of the hill. A handful are flipped on their sides or tossed a short distance from their flags. "Sometimes you get just one raccoon that messes with all of them," he says. He shows me a trap with warped metal. "They chew the corners." The edge of the park is bordered by a thin strip of turf grass and an adjacent sidewalk. "So this is what's called an edge effect," Munshi-South said. "There's all this sunlight right at the edge, so it dries out and you get a lot of invasive plants like vines. But just before the edge, it tends to be pretty dense bush that the mice like. We have trapped here before with good success." I looked past the sidewalk to Harlem River Drive, where cars roared past with terrifying speed. After checking more traps, we rendezvous with Dimech and Harris halfway up the hill. The day's search has yielded five mice in total — only half of what they wanted, but the researchers are used to disappointment and unpredictability. "The trap success is usually anywhere from 7 percent to like 50, depending on the site and time of year," Munshi-South says. As the weather cooled this fall, the researchers headed inside to begin analyzing their findings, a process that will extend well into the spring. This year, they hope to add rats and coyotes to their evolutionary menagerie. Munshi-South suspects that, like white-footed mice, geographically segregated populations of NYC rats have become genetically distinct from one another — possibly on a block-by-block level — and that all the efforts to poison and deter rats may also have steered their evolution, selecting for rodents that are more resilient. Other scientists are beginning to enter the field as well: "It's really starting to catch on," Munshi-South says. At Barnard, Rebecca Calissi is preparing to study how city life changes the brains and immune systems of pigeons. Researchers in Australia recently discovered that golden-orb-weaving spiders living in cities have evolved bigger bodies and larger ovaries for increased reproductive capacity. And biologists in the Netherlands have learned that birds in urban areas sing at a higher pitch to be heard above all the hustle and bustle. Eventually, this new generation of urban ecologists hopes to learn something fundamental about evolution by comparing the way urbanization puts pressure on animals to adapt around the globe. "What we really want to understand," Munshi-South says, "is whether this is happening independently in cities all across the world in idiosyncratic ways. Or are we creating urban environments that more or less drive species to evolve along roughly the same paths? In other words, is there a syndrome?"

Sex determination in humans

Nearly all mammals have a pair of sex chromosomes designated X and Y. Males have an X and Y. Females have XX.

Misconceptions 1

One misconception that circulates about evolution is that man evolved from monkeys. To many, this idea seems absurd both because man and monkeys seem so different and because monkeys still exist. (Have you ever heard "If man evolved from monkeys, why are there still monkeys?") This is a misconception for two reasons: 1.Man did not evolve from monkeys. We do, however, share a common ancestor. Man and monkeys are different branches of the same line. 2.Even if man had evolved from monkeys (which they didn't), monkeys could still exist as a species. We'll talk later about how species come to be, a process called speciation, and how two distinct species can arise from one population.

Intermediate traites

Pakicetus (below left), is described as an early ancestor to modern whales. Although pakicetids were land mammals, it is clear that they are related to whales and dolphins based on a number of specializations of the ear, relating to hearing. The skull shown here displays nostrils at the front of the skull A skull of the gray whale that roams the seas today (below right) has its nostrils placed at the top of its skull. It would appear from these two specimens that the position of the nostril has changed over time and thus we would expect to see intermediate forms. Note that the nostril placement in Aetiocetus is intermediate between the ancestral form Pakicetus and the modern gray whale — an excellent example of a transitional form in the fossil record! •This is one example of making a prediction of what we should find if our

Fossils snarl mammalian roots

Part of the reason mammalian origins are so tough to pin down is because there is no one characteristic, or set of characteristics, than can be used to infer relationships across the class. Further complicating matters is that early mammalian evolution was likely rife with homoplasies—trait similarities that evolved independently, rather than by descent from a common ancestor.

Genetics

Patterns of Inheritance

Postzygotic barriers

Postzygotic barriers prevent the hybrid zygote from developing into a viable, fertile adult Reduced hybrid viability Reduced hybrid fertility Hybrid breakdown

Reduced hybrid fertility

Reduced hybrid fertility: Even if hybrids are fit, they may be sterile

Reduced hybrid viability

Reduced hybrid viability: Hybrids not as fit for the environment or are frail A hybrid of two species may not be fit for the environment of either of it's parents. They would not survive long. This prevents gene flow between the two species.

Reproductive isolation

Reproductive isolation is the existence of biological factors (barriers) that impede two species from producing viable, fertile offspring

Allopatric ("Different Country") Speciation

Separate populations may evolve independently through mutation, natural selection, and genetic drift Reproductive isolation may arise as a by-product of genetic divergence

Evolution Connection:The Advantages of Sex

Sexual reproduction may convey an evolutionary advantage by speeding adaptation to a changing environment or allowing a population to more easily rid itself of harmful genes.

Sexual Selection

Sexual selection can drive sympatric speciation Sexual selection for mates of different colors has likely contributed to speciation in cichlid fish in Lake Victoria For example, pollution in Lake Victoria has reduced the ability of female cichlids to distinguish males of different species

Cellular reproduction

Somatic cells: any cells other than reproductive cells produced through mitosis Sexual cells: cells for reproduction such as eggs or sperm produced through meiosis

Misconception 4

Some say there is disagreement among scientists about evolution •However, by most estimates 99.9% of scientists accept the theory of evolution. While 99.9% of scientists accept evolution, there is still active research questions about the evolutionary record and how evolution occurs in real-time. The article shown here ("Fossils Snarl Mammalian Roots" which is posted in the course content folder) shows how new discoveries from the fossil record add to what we know. This new evidence is then incorporated into our body of knowledge and is used to inform new research. This information allows us to ask questions that can then be confirmed or rejected as evidence is found. So while scientists may "argue" about evolution, the evidence so far has confirmed our fundamental understanding of the theory of evolution

Speciation types

Speciation can be described as allopatric or sympatric depending on if the two populations are overlapping.

Studying the Genetics of Speciation

Speciation can occur rapidly or slowly and can result from changes in few or many genes Many questions remain concerning how long it takes for new species to form, or how many genes need to differ between species Depending on the species in question, speciation might require change in a single gene or many genes For example, in Japanese Euhadra snails, the direction of shell spiral affects mating and is controlled by a single gene

Speciation

Speciation, the origin of new species, is at the focal point of evolutionary theory

gametic isolation

Sperm of one species may not be able to fertilize eggs of another species In sea urchins, the protein bindin is how the sperm of a species recognizes the egg of the same species. Large overlapping populations of different species of sea urchin all release their eggs and sperm into the water but bindin allows this species to find only the eggs of it's own species.

limitations of biological species concept

The biological species concept cannot be applied to fossils or asexual organisms (including all prokaryotes) The biological species concept emphasizes absence of gene flow However, gene flow can occur between distinct species For example, grizzly bears and polar bears can mate to produce "grolar bears"

The Biological Species Concept

The biological species concept states that a species is a group of populations whose members have the potential to interbreed in nature and produce viable, fertile offspring; they do not breed successfully with members of other populations Gene flow between populations holds a species together genetically

Chromosomal Basis of Inheritance

The chromosome theory of inheritance states that genes are located at specific positions (loci) on chromosomes and the behavior of chromosomes during meiosis and fertilization accounts for inheritance patterns. It is chromosomes that undergo segregation and independent assortment during meiosis and account for Mendel's laws.

Watching Bacteria Evolve, With Predictable Results

The experiment was carried out by Joao Xavier of Memorial Sloan-Kettering Cancer Center and his colleagues. They studied a common species of bacteria called Pseudomonas aeruginosa. These microbes live pretty much everywhere — in dirt, in water, on our skin. Under certain conditions, they also invade our bodies and cause dangerous infections. People with cystic fibrosis, for example, can get P. aeruginosa infections in their lungs, which are often impossible to eradicate. To better understand the biology of this pathogen, Dr. Xavier began to study how it searches for food. In a process called swarming, the bacteria spray out gooey molecules that form a slippery carpet; they can then slither over it by whipping their tails, devouring food they encounter along the way. "I just wondered why nobody had filmed them before, because the pattern is so striking," said Dr. Xavier. He dropped a few hundred microbes in the middle of a petri dish laced with sugar and switched on a camera overhead. To better understand how the bacteria swarm, Dr. Xavier and his colleagues allowed them to evolve. They seeded petri dishes with a few hundred microbes and gave them a day to swarm and reproduce. The next day, they drew a small sample of the bacteria from the dishes and used them to seed new ones. The scientists reasoned that, with each generation, new mutations would arise from time to time. If a mutation helped bacteria thrive in this new environment, it might become more common because of natural selection. And so it did. Within a few days, the evolution of the bacteria took a dramatic turn. The bacteria became 25 percent faster than their ancestors — Dr. Xavier dubbed them "hyperswarmers." A movie of hyperswarmers starkly illustrates how different they had become, able to fill up the entire dish. "We thought, 'Something weird has happened,'" said Dr. Xavier. The hyperswarmers emerged in three lines of bacteria overseen by Dr. Xavier's post-doctoral researcher Dave van Ditmarsch. Dr. Xavier and another lab member, Jen Oyler, each ran the experiment again. "I wanted to make sure this wasn't just due to Dave's magic fingers," said Dr. Xavier. But no matter who applied their fingers to the task, the result was the same. Out of 27 lines of bacteria, 27 evolved into hyperswarmers. When the scientists put the hyperswarmers under a microscope, they could see what had changed. An ordinary P. aeruginosa sports a single tail. The hyperswarmers had evolved so that they had as many as half a dozen tails. Those extra tails gave the bacteria more speed. To determine how the bacteria had gained their tails, Dr. Xavier and his colleagues sequenced the DNA of 24 lines of hyperswarmers. In 24 out of 24 cases, they discovered that they have gained a mutation in the same gene, called FleN. FleN encodes a protein that controls other genes involved in building tails. Somehow — Dr. Xavier doesn't yet know how — the mutations cause FleN to produce a multitude of tails, all of which are fully functional. Using their many tails, the hyperswarmers were able to get out in front of ordinary bacteria and reach fresh food first. They could then reproduce faster, leaving behind more offspring. As a result, each population of the bacteria rapidly turned into pure hyperswarmers. Hyperswarmers evolved so reliably in Dr. Xavier's experiments that he began to wonder why they had never been seen before. He speculated that, in his lab, the bacteria gained an ability to swim fast at the expense of some other trait that they need in nature. Swarming, after all, is not the only essential task that P. aeruginosa must carry out. When the bacteria find a place that's good for settling down, they anchor themselves to a surface — on a leaf, for example, or inside a human lung. They form a rubber sheet known as a biofilm. Dr. Xavier and his colleagues found that the hyperswarmers are bad at making biofilms on their own. They then mixed hyperswarmers with normal bacteria and allowed the two types of microbes to make biofilms together. When the biofilm formed, the scientists tallied up how many bacteria in it were ordinary microbes and how many were hyperswarmers. In a video showing the 3-D structure of one of these biofilms, the ordinary bacteria win, and the hyperswarmers have practically gone extinct — confirming that the ability to make microfilms is more important to the bacteria's survival than being speedier consumers of food. Dr. Xavier's discovery could help doctors who are struggling to fight P. aeruginosa. In hospitals around the world, the bacteria are evolving resistance to many antibiotics, and biofilms provide some of their protection by acting like a shield. If scientists could find a way to coax ordinary P. aeruginosa to behave more like hyperswarmers, they might lose their ability to make biofilms. But Dr. Xavier's research also provides a scientific thrill in itself: the chance to see evolution in action — over and over again. And if there's one thing Dr. Xavier can now be sure of, it's that his bacteria will end up as hyperswarmers, thanks to mutations to the same gene. "In this case, it could be that there are only a few solutions in the evolutionary space," he said.

habitat isolation

These two snakes are isolated by their habitat. One lives on land and the other lives in water. They will not encounter one another and therefore won't try to mate. This prevent gene flow between these two species.

Antibiotic resistance

They consists of only a single cell,their total biomass is greater that of all plants and animals combined. Although you have 10 times more bacterial cells inside of you, than your body has human cells. Many of these bacteria is harmless or even beneficial helping digestion and immunity. The problem is not with the antibiotics but the bacteria, they were made to fight and the reason lies in Darwin's theory of natural selection. Individual bacteria can undergo random mutations. Many of these mutations are harmful or useless. One comes along that gives its organism an edge in survival and for bacteria mutation making it resistant to certain antibiotic gives quite the edge. As the non-resistant bacteria are killed off (hospitals), there is more room and resources for the resistant ones to thrive passing along only the mutated genes that help them do so. Reproduction isn't the only way to do this. Some can release their DNA upon death to be picked up by other bacteria, while others use method called conjugation-connecting through pili to share their genes. Over time, the resistant genes proliferate, creating entire strains of resistant super bacteria. In some bacteria its already happened. For instance, some strands of staphylococcus aureus which causes everything from skin infections to pneumonia and sepsis have developed in MRSA becoming resistant to beta-lactam antiobitotics like penicillin, methicillin, and oxacillin. Thigs to a gene that replaces the protein, beta-lactams normally target and bind to, MRSA can keep making its cell walls unimpeded. Other super bacteria like salmonella even sometimes produces enzymes like beta-lactams that break down antibiotic attackers before they can do any damage and E-coli, a diverse group of bacteria that contains strains that cause diarrhea and kidney failure can prevent the function of antibiotics. like quinolones by actively booting any invaders that manage to enter the cell. Phage therapy such as using vaccines to prevent infections. Most importantly, curbing the excessive and and unnecessary use of antibiotics such as for minor infections that can resolve on their own. as well as changing medical practice to prevent hospital infections. In the war against super bacteria, deescalation may sometimes work better than an evolutionary arms race.

Bacterial Evolution

To better understand how the bacteria swarm, Dr. Xavier and his colleagues allowed them to evolve. They seeded petri dishes with a few hundred microbes and gave them a day to swarm and reproduce. The next day, they drew a small sample of the bacteria from the dishes and used them to seed new ones. The scientists reasoned that, with each generation, new mutations would arise from time to time. If a mutation helped bacteria thrive in this new environment, it might become more common because of natural selection. And so it did. Within a few days, the evolution of the bacteria took a dramatic turn. The bacteria became 25 percent faster than their ancestors — Dr. Xavier dubbed them "hyperswarmers." A movie of hyperswarmers starkly illustrates how different they had become, able to fill up the entire dish.

temporal isolation

When two species have different mating seasons, even if they encounter each other, they will not try to mate. This also prevents gene flow and keeps these two species separate.

Genetic Recombination: Crossing Over

separate linked alleles, produce gametes with recombinant gametes, and produce offspring with recombinant phenotypes.

antibiotic resistance

the evolution of populations of pathogenic bacteria that antibiotics are unable to kill

Evidence for evolution

•The fossil record provides snapshots of the past that, when assembled, illustrate a panorama of evolutionary change over the past four billion years. The picture may be smudged in places and may have bits missing, but fossil evidence clearly shows that life is old and has changed over time. •Fossils or organisms that show the intermediate states between an ancestral form and that of its descendants are referred to as transitional forms. There are numerous examples of transitional forms in the fossil record, providing an abundance of evidence for change over time.