BIODIVERSITY Evolution Part 2 So far we

BIODIVERSITY Evolution Part 2

So far we have emphasized that life is an interesting form of chemistry. This helps understand its role in transforming the biosphere. But the most obvious feature of life is the staggering DIVERSITY of its many forms We will examine this diversity from the two main perspectives 1. Evolution 2. Ecology

In order to make sense of this vast diversity, we look for ways to classify it, to simplify Looking closer at this diversity, various patterns emerge.

One natural classification scheme is to arrange organisms into groups that look the same. This is the approach of traditional taxonomy. This approach leads naturally to a study of evolution - evolutionary relatedness and organismal adaptation (form and function). That is, organisms will look the same for two main reasons – they are closely related, and/or they express similar functional “designs”

For example, butterflies, birds and bats all fly and they all look similar because of the wings. But looking closer, there are big differences too, so they are classified as separate groups (there are many different kinds within each group)

Another natural classification scheme comes from noticing that some organisms tend to live together in the same places (and not in others) – that life is organized into natural “communities” of diverse organisms. This leads to the study of ecology, the logic of how different organisms interact and coexist.

For example, major ecosystem types called biomes (deserts, rainforests etc. ) have characteristic organisms and are found distributed in different places on the earth 3 -5/3 -6

And the distribution of biomes is closely related to the distribution of climates. 12 -2

Taxonomy – the classification of life Both evolution and ecology are important dimensions of the multidimensional problem of understanding biodiversity. But before we could think about understanding, a huge effort had to be expended in collecting and grouping organisms into logical classes. All human cultures have developed systems for classifying life The system used by our culture was established by Carolus Linnaeus in the 1700 s in Sweden. http: //www. ucmp. berkeley. edu/history/linnaeus. html

The Linnaean System This system is based on the idea that life is separated into distinct species that can be classified into a nested, or hierarchical, increasingly inclusive set of groups. Ultimately, each species is given a distinctive binomial – a two word name referring to the species and the group to which it belongs (this is called “binomial nomenclature”) This is similar to our method of naming people, family name and individual name e. g. Jimmy Page Leopard- Panthera pardus Genus – Panthera Species - pardus

Panthera onca (jaguar) Panthera pardus (leopard) Panthera tigris (tiger) Panthera uncia (snow leopard) Panthera leo (lion) http: //home. globalcrossing. net/~brendel/index. html

And now, more BIOLOGY In The News!

Sunday, Mar. 01, 2009 Indonesian tiger catchers race against time By ZAKKI HAKIM - Associated Press Writer SUNGAI GELAM, Indonesia -Indonesia's tiger catchers have a double job - protecting humans from tigers, and tigers from humans. The elite teams of rangers and conservationists rush to the scene every time villagers report attacks or sightings of critically endangered Sumatran tigers. First, they calm the people. And then, if there are signs the animal is nearby, they return with steel cage traps, live bait, heatsensitive cameras and other equipment to capture the magnificent beasts. This time Sartono, who at 40 has spent nearly half his life in the job, arrives with his six-member squad at a remote oil palm plantation in Sungai Gelam district, 375 miles west of the capital, Jakarta, knowing they'll have to act fast. Three people have been killed in less than a week. Sartono knows if he and his team cannot put a quick end to the killing spree, residents will shoot or poison the Sumatran tiger, which is already on the brink of extinction because of rapid deforestation, poaching and clashes with humans.

There are only around 250 of the cats left in the wild, compared to about 1, 000 in the 1970 s, according to the World Wildlife Fund, meaning the Panthera tigris sumatrae could become the first large predator to go extinct in the 21 st century. For the next few days, they hike beneath the equatorial sun, their clothes soaked in sweat, in search of clues, while other team members interview witnesses and check out rumors of more attacks and sightings. Finally, they have one of their own. On a scorching Sunday afternoon, an adult tiger charges out of dense jungle brush and then suddenly retreats into the shrubbery. Slowly, as Sartono aims his cocked rifle at the trembling bushes, the squad walks backward. "I was afraid, who wouldn't be!" the veteran tiger catcher later says with an uneasy laugh. "We might have experience, but we don't have superpowers!"

The squad finally snags her. When they pull up in their green pickup truck on day eight, they find a tigress six feet long - excluding the tail crouched in the trap. First she is calm, then she explodes, growling and throwing her 180 -pound body against the steel bars. "Easy, easy, we're here to save you, " whispers Nurazman Nurdin of the Nature Conservation Agency, as the crew carefully approach the tigress, which has since been named Salma. For the tiger catchers it is a tense but thrilling moment. For villagers - who have locked themselves up after dark, shuttered stores, and canceled prayers in the mosque from dusk to dawn - it is a relief. Though some support plans to relocate the animal into a jungle far away, others wish the rangers would just shoot it. Many worry there may be more tigers out there. They are right. Three more people have been mauled to death in the same area since the capture, all of them illegal loggers. Since those attacks took place within the cats' habitat, there are no immediate plans to catch or relocate them.

The men on the tiger team said it was disturbing - and rare - that Salma ate one of the victim's remains. Normally, Sumatran tigers avoid humans, but if they do kill a man, they usually leave the corpse untouched. The tiger catchers saw the unusual behavior as a sign of how desperately hungry the tigress must have been. "There's no place for its prey to live here, all the land has been converted into oil palm plantations, " said Nurdin, the Nature Conservation Agency official, as he surveyed churnedup wasteland neat rows of trees. "You can't expect tigers to become vegetarians, " Nurdin said. "They need meat and humans trespassing their territory are relatively easy targets. " As their name suggests, these tigers can only be found in the wild on Sumatra island. Their habitat is disappearing at an alarming rate, with 667, 000 acres of lowland forests being cleared annually, mostly for palm oil, which is used in cosmetics and candy but also to make "clean-burning" fuel for markets in the U. S. and Europe. Other culprits are loggers and mining companies, whose projects limit mating grounds, leave remaining tiger populations isolated and scattered, and chase off the majestic cats' prey.

On average, five to 10 Sumatran tigers have been killed every year since 1998, the report said. "At this rate, they will soon be extinct, " said Hariyo Wibisono of Harimaukita, an alliance that coordinates 15 state agencies and tiger conservation groups. Sometimes the animals are killed by frightened villagers, other times by poachers who sell their carcasses for trophies or to supply a growing demand for tiger bones in traditional medicine. A poacher can get $3, 300 for a dead tiger - what some people in this impoverished nation of 235 million make in a year - but Nurdin said trafficking operations are almost impossible to crack because they involve syndicates. "Only the well-connected would dare to buy such things, " he said, noting that the last person they caught trying to sell a carcass was a soldier.

At the present rate of deforestation, there will eventually be no safe place to release the captured tigers. So international wildlife experts are working with the government to come up with a 10 -year conservation strategy. They want palm oil and other companies to either help monitor the activity of tigers on their property or, better yet, put aside some land as a sanctuary for wildlife. Panthera tigris sumatrae "For years, we fought against land conversion, but it did not work, " said Wibisono, of the tiger conservation alliance. "We had to try a different approach. "

Jim Corbett “Man-eaters of Kumaon” and other books “A man-eating tiger is a tiger that has been compelled, through stress of circumstances beyond its control, to adopt a diet alien to it. The stress of circumstances is, in nine out of ten cases, wounds, and in the tenth case old age. ” “There is , however, one point on which I am convinced that all sportsmen … will agree with me, and that is that a tiger is a large-hearted gentleman with boundless courage and that when he is exterminated – and exterminated he will be unless public opinion rallies in his support – India will be the poorer, having lost the finest of her fauna. ” -from the Author’s Note

As we were saying -The Linnaean System This system is based on the idea that life is separated into distinct species that can be classified into a nested, or hierarchical, increasingly inclusive set of groups. Ultimately, each species is given a distinctive binomial – a two word name referring to the species and the group to which it belongs (this is called “binomial nomenclature”) This is similar to our method of naming people, family name and individual name e. g. Jimmy Page Leopard- Panthera pardus Genus – Panthera Species - pardus

The Linnaean System Some interesting examples of species names (NY Times Feb 20 2005): Bittium (mollusk) has a related genus Ittibittium Ba humbugi (snail) Insects: Heerz tooya Apopyllus now Pieza pi, Pieza rhea, Pieza deresistans Phthireia relativitae For more check this out: http: //home. earthlink. net/~misaak/taxonomy. html Updated link - http: //www. curioustaxonomy. net/

And now, more BIOLOGY In The News!

Saturday, Feb. 28, 2009 Indonesia's psychedelic fish named a new species By ROBIN Mc. DOWELL - Associated Press Writer JAKARTA, Indonesia A funky, psychedelic fish that bounces on the ocean floor like a rubber ball has been classified as a new species, a scientific journal reported. The frogfish - which has a swirl of tan and peach zebra stripes that extend from its aqua eyes to its tail - was initially discovered by scuba diving instructors working for a tour operator a year ago in shallow waters off Ambon island in eastern Indonesia. The fish - which the University of Washington professor has named "psychedelica" - is a member of the antennariid genus, Histiophryne, and like other frogfish, has fins on both sides of its body that have evolved to be leg-like. But it has several behavioral traits not previously known to the others, Pietsch wrote. Each time the fish strike the seabed, for instance, they push off with their fins and expel water from tiny gill openings to jet themselves forward. That, and an off-centered tail, causes them to bounce around in a bizarre, chaotic manner.

The fish, which has a gelatinous fist-sized body covered with thick folds of skin that protect it from sharp-edged corals, also has a flat face with eyes directed forward, like humans, and a huge, yawning mouth. Mark Erdman, a senior adviser to the Conservation International's marine program, said Thursday it was an exciting discovery. "I think people thought frogfishes were relatively well known and to get a new one like this is really quite spectacular. . It's a stunning animal, " he said, adding that the fish's stripes were probably intended to mimic coral. "It also speaks to the tremendous diversity in this region and to fact that there are still a lot of unknowns here - in Indonesia and in the Coral Triangle in general. " Ques – so what is the correct binomial for this species?

The Linnaean System Hierarchical classification is totally natural for us – although the “ideal” system of classification can be elusive Music groups English Rock Bands Led Zeppelin Jimmy Page Dec. 10, 2007

Stairway to Heaven (R. Plant & J. Page) There's a lady who's sure All that glitters is gold And she's buying a stairway to heaven. When she gets there she knows If the stores are all closed With a word she can get what she came for. Ooh, ooh, and she's buying a stairway to heaven. There's a sign on the wall But she wants to be sure cause you know sometimes words have two meanings. In a tree by the brook There's a songbird who sings, Sometimes all of our thoughts are misgiven. Ooh, it makes me wonder, Ooh, it makes me wonder.

There's a feeling I get When I look to the west, And my spirit is crying for leaving. In my thoughts I have seen Rings of smoke through the trees, And the voices of those who stand looking. Ooh, it makes me wonder, If there's a bustle in your hedgerow Ooh, it really makes me wonder. Don't be alarmed now, Its just a spring clean for the May Queen. And its whispered that soon Yes, there are two paths you can go by If we all call the tune Then the piper will lead us to reason. But in the long run There's still time to change the road you're And a new day will dawn on. For those who stand long And the forests will echo with laughter. And it makes me wonder. Your head is humming and it won’t go In case you don't know, The piper’s calling you to join him, Dear lady, can you hear the wind blow, And did you know Your stairway lies on the whispering wind

And as we wind on down the road Our shadows taller than our soul. There walks a lady we all know Who shines white light and wants to show How everything still turns to gold. And if you listen very hard The tune will come to you at last. When all are one and one is all To be a rock and not to roll. And she's buying a stairway to heaven.

The Linnaean System The Linnaean system uses a particular set of levels that has been modified over time – genus, family, order, etc.

The Tree of Life The Linnaean system was developed before ideas about evolution and the relatedness of all life, yet it is consistent with that view (and inspired it) and has remained in wide use The evolutionary view adds an historical component – that the species we see today derive by a process of speciation (separation of one species into two over time), creating a “family tree” of ancestral and descendant species These relationships are usually depicted as a branching tree, or phylogeny (or “phylogenetic tree”) The Y-axis is time – down is longer into the past, branching implies speciation events

The Tree of Life The hierarchical branch “clusters” correspond to the taxonomic levels This is a “rough” correspondence but overall traditional taxonomy has been an excellent guide to modern phylogenetic reconstruction

The Tree of Life Phylogenetics – determining these trees for taxonomic groups is a very active area of research. The ultimate goal is to construct the complete family tree of life, and to make this the basis of our taxonomic system. You can find out the current status of this effort at http: //tolweb. org/tree/phylogeny. html The basic idea of this approach is to classify species by their various characteristics, or traits, and to identify which traits are newer and which older. Traits that are relatively older are called ancestral, more recently evolved are called derived.

The Tree of Life This style of reasoning is essentially the same as traditional taxonomy

The Tree of Life The current explosion in tree of life research has been fueled by our new knowledge about gene (and protein) sequences. This is essentially an entirely new and extremely precise array of species traits from which detailed phylogenies can be constructed – independently of traditional observable traits. This independence creates a welcome check on traditional taxonomy. So far it has mostly confirmed the traditional approach, but in some cases has provided interesting new insights.

The Tree of Life For example, traditionally reptiles and birds are separated into different classes: Reptilia and Aves But the genetic evidence suggests that crocodiles, traditionally considered reptiles, are really closer to birds than to other reptiles. Reptilia Aves Naturally, there is a lot of discussion about how to sort this out What would you suggest?

The Tree of Life Here are some of the contenders – is your solution here?

http: //www. eidnesfurs. com/index. html

How can a gene sequence be used to create a phylogenetic tree? What is a gene sequence? Recall: Gene expression is the protein production machinery of a cell’s biochemistry. Proteins are used in various ways, but especially in the form of enzymes, that catalyze reactions – they regulate what reactions happen when – that is, they control everything. What is a protein? - a long chain molecule, or polymer, a chain of small organic molecules amino acids (20 different types), that when assembled, folds itself into a 3 -dimensional shape that can catalyze a reaction.

The final protein structure is determined by the sequence of amino acids in the protein polymer.

What controls the amino acid sequence of a protein? The DNA molecule is also a long chain of simpler organic molecules (“nucleic acids”) that contains the protein sequence in coded form, using the genetic code This molecule can be copied, keeping the sequence intact The genetic code is not a simple one-for-one code because there are only four different nucleic acids (A, T, G, C) to code for 20 amino acids.

It is a “triplet code” – every three nucleic acids code for each subsequent amino acid DNA sequence becomes a protein sequence There is an intermediate step involving an RNA sequence

The genetic code As far as we know, the code is pretty arbitrary – could have been different and still work fine Yet, all species use the same genetic code, supporting idea of a common origin of all life

The DNA stores the sequence information for all the proteins needed by the organism A “gene” is a particular DNA sequence that codes for a particular protein “Gene expression” is this conversion – protein production. Which genes are “turned on” when Gene expression is responsive to the environment (internal and external) Since enzymes regulate biochemistry, including gene expression, the regulation of gene expression is the ultimate controller

And now, more BIOLOGY In The News!

Friday, Feb. 27, 2009 Gene therapy might regrow teeth By Lauran Neergaard - Associated Press WASHINGTON — Ever wonder why sharks get several rows of teeth and people get only one? Some geneticists did, and their discovery could spur work to help adults grow new teeth when their own wear out. A single gene appears to be in charge, preventing additional tooth formation in species destined for a limited set. When the scientists bred mice that lacked that gene, the rodents developed extra teeth next to their first molars — backups like sharks and other non-mammals grow, University of Rochester scientists reported Thursday. If scientists knew exactly what triggers a new tooth to grow in the first place, it's possible they could switch that early-in-life process on again during adulthood to regenerate teeth. Also intriguing: All the mice born without this gene, called Osr 2, had cleft palates severe enough to kill. So better understanding of this gene might play a role in efforts to prevent that birth defect, the Rochester team reported in the journal Science.

Think of the Osr 2 gene as a control switch, a kind of gene that turns on and off the downstream actions of other genes and proteins. The Osr 2 gene works in concert with two other genes to make sure budding teeth form in the right spot, said lead researcher Dr. Rulang Jiang, a geneticist at Rochester's Center for Oral Biology. "It's almost a self-generating propagation of the signal" that leads to one tooth after another forming all in a row, he explained. Knocking that molecular pathway out of whack causes either missing or extra teeth to result, Jiang showed in a series of mouse experiments. 'It's exciting. We've got a clue what to do, ' said Dr. Songtao Shi of the University of Southern California School of Dentistry, who said the Rochester discovery will help his own research into how to grow a new tooth from scratch.

Saturday, Dec. 26, 2009 UK researcher helps develop Ruppy, a glowing dog By Cheryl Truman, Herald Leader Ruppy, a genetically engineered beagle that glows, lives in Korea, but he's creating a stir at the University of Kentucky. The fluorescent canine, infused with a gene from a sea anemone and known as the world's first transgenic dog, isn't really a single animal. Even in broad daylight, this is a dog of a different color: You can see it in the red flush of the pads on the bottoms of his feet. Why a red flush? Because researchers needed a trait that would be visible immediately. A color change in a puppy does just that.

Initially there were three "Ruppy" puppies — short for ruby puppy— all beagles, part of a project that UK fertility researcher Chemyong Jay Ko was involved with at Seoul University in South Korea. Now, Ko says, there are several groups of cloned Ruppys — maybe 30. Ko is emphatic that the latter-day Ruppys not be called offspring or siblings or even the next generation of transgenic puppyhood: They're clones, he says, and clones do not follow the standard order of beagle family trees. Ko, who came to UK as a post-doctoral student in 1998, says he spends several weeks a year in Korea working with the research team that developed Ruppy. In 2005, Snuppy, a cloned Afghan hound, was introduced. Ko then contacted the researchers and became involved in the research that resulted in Ruppy. This new proof-of-principle experiment should open the door for transgenic dog models of human disease, says Ko. "The next step for us is to generate a true disease model, " he says. His lab hopes to knock out a specific oestrogen receptor in dogs to understand the hormone's effects on fertility.

Ruppy is almost too cute to be thought of as a research subject. There are two ways of looking at this: You can think, as Ko does, that the development of a glowing beagle is a step forward in genetic science that points the way to all manner of advances — from commercial development of dogs bred with specific traits, such as green eyes, or developing a gene that could address a specific disease, to changes in the way researchers collect blood for research. [He says that dogs have a lot more blood than a lab mouse. Further, he says that lab technology has evolved to allow for a nearly painless withdrawal of blood. ] The other way to look at the moral implications of Ruppy raises questions about whethere's a difference between exhausting a supply of lab mice and keeping dogs for experiments. Where in the mammalian line the difference comes, where humans start to look at animals as companions and defend their welfare rather than writing them off as commodities is difficult to say. But the idea of tinkering with dogs strikes some as far more awful than making Glo Fish, which are available at many pet stores. The genetically altered fish are available in "Starfire Red, " "Electric Green, " and "Sunburst Orange, " although sale of the designer fish has been banned in California.

[Ko] professes some amazement in dealing with the aftermath of the announcement of Ruppy's existence. Network news has been in touch. Animal-rights activists are posting on The New York Times Web site, where Ruppy made the Times magazine's list of the top ideas of 2009, and the Ruppy project has been kicked around on various blogs. "You can make thousands of kinds of transgenic animals, " Ko says. Sara Rosenthal, director of the UK Program for Bioethics, says that humans tend to assign greater moral worth to larger animals and those who resemble us. Nonetheless, she notes, even primates such as chimpanzees are used in research because such research spares human suffering; to humans, and in research circles, that is the most unsettling research. "We use animals because we find that animals are in service to reduce the number of humans" that have to be used for medical advances, Rosenthal says. "The ethical justification for using animals in research has to be very strong. "Some medical advances, such as the discovery of insulin in 1921, would not have been possible without using dogs in research, Rosenthal said.

Genes are third key ingredient, or resource, in the recipe for life – information 1. Energy 2. Materials 3. Information encoded in the sequences of DNA can be thought of as a kind of knowledge, often referred to as a library This information has accumulated over the billions of years of life’s history on earth. It is reasonable to think of it as a natural resource, built into the structure of living organisms.

The differences between organisms are due to differences in their genes Each species carries genes that are unique to that species – unique information

DNA sequences can be used to create phylogenies by assuming that the more similar the gene sequences, the more closely related the species are What is the logic behind this assumption? Reptilia Aves

What is the logic behind this assumption? 1. All life arose from a single common ancestor 2. Organisms differ primarily in their genes 3. Given 1 & 2, the current diversity must have resulted from a diversification of the genetic makeup of organisms. 4. The diversification was one step at a time – biochemistry is too complicated to change radically 5. The more time has elapsed since lineages diverged, the more steps have been taken Interestingly, these assumptions don’t require any specific knowledge about gene function – it even applies to genes that have no known function (silent or “junk” DNA)

Some genes have changed very little, and can help compare very distant relatives (here a segment of r. RNA) Human . . . GCGGTAATTCCAGCTCCAATAGCGTATATTAAAGTTGCTGCAGTT. . . Yeast . . . GCGGTAATTCCAGCTCCAATAGCGTATATTAAAGTTGTTGCAGTT. . . Corn . . . GCGGTAATTCCAGCTCCAATAGCGTATATTTAAGTTGTTGCAGTT. . . Escherichia coli . . . GCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGT. . . Methanococcus sp. . GCGGTAATACCGACGGCCCGAGTGGTAGCCACTCTTATTGGGCCT. . . Some regions change very fast – what would they reveal? http: //www. bact. wisc. edu/Bact 303/Phylogeny

This work has led to a detailed “big picture” view of the tree of life, including the establishment of the “Three Domain” concept Also, much fine detailed study of evolutionary changes within-species

End Evolution part 2