Friday, February 29, 2008

Toucans

If you want a challenge then try to complete the Toucan exercise using all 16 birds plus you now get 3 outgroup examples (the last 3 with whiskers). I've added the file with the bird pictures to the links at the top right. As you can see some of the birds that look the most similar are already grouped into the same genus. Don't let that distract you, these may, or may not, be appropriate. I'll have a crack at this so let me know if you want to compare Toucan phylogenies....

Thursday, February 28, 2008

Lichens in space

During the European Space agency's 2005 Foton mission lichens were exposed to space for 15 days. They had to endure a wide range of harsh conditions: a vacuum; wide fluctuations of temperature; the complete spectrum of solar UV light; and bombarded with cosmic radiation. If we were living in a comic book then the lichens would have returned with super powers but here in the real world most people were surprised to find the lichens merely survived. They appeared totally dormant whilst in space but soon revived back on earth.

One conclusion of this experiment is that it appears likely that lichens may be able to survive on the surface of Mars.
Although the Martian atmosphere is very thin, it is filled with carbon dioxide, which is necessary for ’photosynthesis. However, long term survival and growth may be prevented by the low oxygen levels in the Martian atmosphere.

Woof

As we have mentioned several times Darwin was a very smart and perceptive guy. But when it came to dogs even Darwin underestimated the power of selection (here artificial selection rather than natural selection). Darwin thought that the current array of dog breeds must have been descended from a number of different wild canine species such as such as jackals, coyotes and wolves. We now know this is not the case and all 350+ distinct breeds are, in fact, descended from one species, the grey wolf. This raises the question of just where all the variety in dogs came from.

A paper in Genome Research by Matthew Webster of Trinity College Dublin, Ireland, and colleagues at Uppsala University in Sweden has proposed an explanation. They analysed the complete mitochondrial DNA genome in 14 dogs, six wolves, and three coyotes. This data suggests that mutations in the canine genome have played a bigger role in dog evolution than previously thought. Natural selection usually weeds out mutations in wild species if they offer no survival advantage. But if that pressure is removed, these mutations will get passed on. This provided dog breeders with a wide inventory of traits in the DNA to exploit. Others disagree, Webster et al. only studied mutations in mitochondrial DNA, which tends to accumulate more quickly than in nuclear DNA which forms the largest part of the genome. Far fewer mutations may have occurred in genes in the nucleus compared with mitochondria. Much of the variation we see in dogs may have to do with pre-existing variation from the ancestral wolf-dog population.

Wednesday, February 27, 2008

Humongous Fungus

If you'd like to read a little more about the original humongous fungus there's a really interesting article by Tom Volk, first published in Inoculum in 2002, a decade after the discovery of the fungus. You can read the article online here. The fungus they discovered, an individual Armillaria bulbosa, aka the honey mushroom, was conservatively estimated to be at least 1500 years old and weigh around 100 tons - making it one of the largest and oldest living organisms.

I learned lots of fascinating trivia from this article:

The project was actually an offshoot of a grant from the Department of Defense, which funded a project to study the possible biological effects of ELF (Extra Low Frequency) stations in the Upper Peninsula of Michigan. These ELF stations were built to communicate underground with ocean-going submarines in time of war.

They sampled for the fungus by 'baiting' with tongue depressors. The fungal mycelium quickly colonized the wood sticks.

They were not looking for a large fungus, or even trying to measure the size of any fungus. The project was originally to look at how mitochondrial DNA was inherited in fungi in nature.

When news of the 'giant fungus' broke in the press CNN wanted someone to go out into the woods and wave from the fungus so they could get an aerial picture of the humongous fungus.

Even better, a Japanese businessman called and wanted to build a boardwalk around the humongous fungus and charge people to view the 'pulsating mass of fungus'.

Tuesday, February 26, 2008

Hox

The problem with introductory biology is sometimes you have 2 minutes to try and introduce something that has gone rapidly from an interesting observation to a whole area of biology. The hox genes are a good example of this. For an overview of the topic you should read this posting at the Pharyngula blog entitled 'A brief overview of Hox genes'. You'd be surprised how much we know about how to build a fly.

Evolution practical

Please read this document before class on Thursday. You will then use this methodology to construct cladograms for two groups. One, major plant groups, where you know the answer but constructing the data matrix will be a useful review, and the other where the answer is totally unknown. If some of you can bring your textbook to class that might be useful too.

Monday, February 25, 2008

Beatrix versus the Botanists

When I was a sophomore at college in England I spent a summer working at the Freshwater Biological Association in the English Lake District. The cottage I stayed in was in a tiny village called Far Sawrey. Just down the road is the village of Near Sawrey which contains a small 17th century farm house where Beatrix Potter spent most of her later years, and where she wrote and set her many Peter Rabbit books.

Having mentioned it in class I thought I'd see if I could find out whether Beatrix Potter was happy in her later life or whether she resented being excluded from the male dominated scientific community. Thanks to the wonders of the internet I found a highly relevant book and, even better, the relevant chapter is available online as a sample chapter.

Chapter 1 of Liaisons of Life, Beatrix versus the Botanists, by Tom Wakeford describes Beatrix Potter's encounters with the scientific establishment. Fascinating reading and a picture of science at the turn of the century. Beatrix Potter was facing an uphill battle, not just as a woman in science but also in proposing lichens as a symbiotic and mutualistic association. James Crombie, a prominent English naturalist said:

"A useful and invigorating parasitism —who ever before heard of such a thing?"

and he described the relationship as:

"an unnatural union between a captive algal damsel and a tyrant fungal master."

After her aborted scientific career and her successful career as a children's author Beatrix Potter went on to a third, and equally successful career as a sheep breeder and conservationist in the English Lake District.

Sunday, February 24, 2008

Pictures from Lotus Land

I've uploaded lots of pictures from Lotusland onto Facebook. 


Enjoy!

Saturday, February 23, 2008

Pictures?

If you took any good pictures of plants at Lotusland then send me your best shots and I'll post them here for everyone to see.

Diamonds of the kitchen

Lots of newspapers, including the Santa Barbara New-Press, picked up an an AP story today about the decline in the truffle harvest in Europe. Suspicion seems to rest on climate change but the article has the usual array of interesting truffle facts.

Specially trained dogs sniff and dig them out, and are rewarded with doggy treats. Pigs — bigger, hungrier and harder to manage — have largely fallen out of favor.

Friday, February 22, 2008

Lotusland

Don't forget, we meet in the small lot behind the CCS building at 9.30 tomorrow (Saturday 23rd). Our tour is from 10-1 so we will be back shortly after 1. Current forecast is that it will possibly be dry in the morning tomorrow and rain in the afternoon so we may luck out - but you should bring something in case it rains.

Thursday, February 21, 2008

Chytridiomycota

Until recently the Chytridiomycota were thought to be mostly detritivores, living on dead material, but at least one species is pathogenic. The species of Chytridiomycota, or Chytrid fungi, that is killing amphibians worldwide is Batrachochytrium dendrobatidis.

Work carried out at UC Berkeley and published in PNAS last year now suggests that the fungus may end up playing a bigger role in the frog's demise than previously thought because of the pathogen's ability to spread over long distances and possibly persist in the environment as a consequence of sexual reproduction. A study of the genetics of the fungus provided the first evidence of genetic recombination in B. dendrobatidis, which results in multiple, related genotypes and suggests that sexual reproduction is occurring - even though spores have not been discovered.

This work was carried out in the Briggs lab in Integrative Biology in association with the Taylor lab in Plant and Microbial Biology and is part of a larger project on chytridiomycosis (the disease caused by B. dendrobatidis) and the mountain yellow-legged frog led by Cheryl Briggs, UC Berkeley associate professor of integrative biology. Cherie has now moved to UCSB so there is an opportunity to get involved in this research if it interests you.

Wednesday, February 20, 2008

Cultural Evolution

A study published in PNAS yesterday shows that the process of natural selection can act on human culture as well as on genes. Stanford researchers showed that traits affecting survival and reproduction evolve at a different rate than other cultural attributes.

Using functional and symbolic design features for Polynesian canoes, we show that natural selection apparently slows the evolution of functional structures, whereas symbolic designs differentiate more rapidly. This finding indicates that cultural change, like genetic evolution, can follow theoretically derived patterns.

Nina Jablonski, chair of the Anthropology Department at Pennsylvania State University, said "This paper is revolutionary in its approach … one of the most significant papers to be written in anthropology in the last 20 years."

Tuesday, February 19, 2008

Pestilence wort

Commonly known as bog rhubarb, devil’s hat, pestilence wort or, simply, common butterbur, Petasites hybridus is native to Europe and northern Asia (though it is now established in some areas of North America). It is primarily found in areas with wet soil, like many other Petasites species.

A favorite Botany site is the Botany photo of the day from the University of British Columbia Botanical Garden. They always seem to have some new interesting plant fact with some great photographs

Plants may not have the cute behavior of animals but they are sure good at staying still while people photograph them. Well, except when it's windy....

There are lots of interesting photographs and stories at this site. If you are familiar with the cork oak outside UCSB library (at the corner of the library nearest the bike path) you might be interested to see how a harvested cork oak looks. They only harvest the cork every decade but the harvest from a single tree can be up to a tonne!

Note the taxonomic index on the right hand side of the page which allows you to jump straight to pictures of mosses, ferns, liverworts, plants and insects etc etc.

Monday, February 18, 2008

Beelzebufo

Artist's impression of the Beelzebufo frog. Scientists, who unearthed the 70-million-year-old fossil in Madagascar, said it would have had a body length of about 40cm (16 inches) and weighed about 4kg (10lb).

A team from UCL and Stony Brook University, New York, have discovered a fossil of a giant dinosaur-eating frog in Madagascar, giving weight to the theory that the island off Africa’s east coast was once linked to India and South America.

You can read a fairly good report on the BBC website but there were numerous other press reports today. Everybody seems to love the picture.

Oh man, what's not to love about this story? It's a giant frog, it's got one of the best scientific names I think I've ever come across and there's a beautiful artists reconstruction. Does it remind anyone else of hypno-toad?

Sunday, February 17, 2008

Male Killer

A really nice story from UC Berkeley last year shows natural selection in action and illustrates the Red Queen principle.

Wolbachia is a is a genus of inherited bacterium that infects a high proportion of all insects. They are the world's most common parasitic microbes and often lead to the death of males.

Over only 10 generations that spanned less than a year, the proportion of males of the Hypolimnas bolina butterfly on the South Pacific island of Savaii jumped from 1 percent of the population to about 39 percent. The researchers considered this a stunning comeback and credited it to the rise of a suppressor gene that holds in check the Wolbachia bacteria, which is passed down from the mother and selectively kills males before they have a chance to hatch.

"To my knowledge, this is the fastest evolutionary change that has ever been observed. This study shows that when a population experiences very intense selective pressures, such as an extremely skewed sex ratio, evolution can happen very fast."
Sylvain Charlat

The fieldwork for this study was carried out on two South Pacific Islands and the researchers were based out of UC Berkeley's Richard B. Gump South Pacific Research Station on the island of Moorea in French Polynesia. I mention this because although the field station is run by Berkeley, UC Santa Barbara runs the Moorea Coral Reef Long Term Ecological Research Program and there are plenty of opportunities to get involved in this research if that is where your interests take you.

Friday, February 15, 2008

Gene flow

The growing global appetite for cheap farmed salmon is imperiling wild fish populations across the planet, scientists warn. The first worldwide assessment of the impact of cultivated salmon on wild stocks found that where native populations encounter salmon farms, the numbers of wild fish crash, on average, by more than 50 percent.

The farmed
fish spread diseases and parasites to wild salmon. Some cultivated escapees also interbreed with the native fish, reducing the ability of their offspring to survive, researchers say.

Outbreeding depression and gene flow in action. From a paper in PLOS this week (paper and summary) as reported on by National Geographic. If you go to the National Geographic website you should check out the blood squirting lizard....

Thursday, February 14, 2008

UC

Todays visit to CCBER reminded me to remind me that as CCS students you are also UCSB students (well duh) but you are also UC students. The combined resources of the UC system are tremendous, and are potentially available to you as UC students.

Berkeley, for example, has a tremendous set of museums and has much of their data online and searchable already.

In another lifetime I worked on some websites at Berkeley and one of them had a table of all the departments, research groups and museums studying ecology and environmental change in California. This may be useful link to bookmark if you ever need museum data. Although I notice it's already out of date since I think I did most of the work in 2004 or 2005 and since then CCBER has replaced the Museum of Systematics and Ecology at UCSB. There are also pages of links to field sites, field stations, state agencies and much more.

For those who enjoy very slight coincidences (everyone, right?). I just finished reading 'Anthrax: The Investigation of a Deadly Outbreak' about the Sverdlovsk anthrax leak, an incident where spores of anthrax were accidentally released from a military facility in the city of Sverdlovsk in the former Soviet Union in 1979. The ensuing outbreak of the disease resulted in 94 people becoming infected, 64 of whom died over a period of six weeks. The outbreak was denied by the Soviet Union for decades. Prior to communist rule Sverdlovsk was known as Yekaterinburg. In fact it has reverted to this name again today. Having gone my whole life without ever hearing of this town it seemed a coincidence to hear that was where Katherine Essau was from.

Wednesday, February 13, 2008

Information request

It has come to the attention of those in the college admissions office that postings at the College Confidential website contain a lack of information, and some misinformation, about the CCS program. Whilst it would be inappropriate for me to post there (actually I don't even know if that's true as long as I didn't misrepresent my affiliation) I think it is appropriate for me to encourage you to post there if you want to help CCS attract the right sort of people and the right sort of people to be attracted to CCS.
UPDATE: a number of CCS students have already risen to the task. There is now a thread for CCS itself which would be an appropriate place to add comments if you have anything to add.

Tuesday, February 12, 2008

Deep Green

Page from Darwin's notebooks around July 1837 showing his first known sketch of an evolutionary tree.

There are a number of useful resources on the web to help you understand the relationship between the different plant groups and explore their diversity.

The Tree of Life is a collaborative project that provides information about the diversity of organisms on Earth, their evolutionary history and their characteristics. The link above takes you to the main page or you can skip directly to the green plants.

The Green Plant Phylogeny Research Group (Deep Green) is a group that coordinates research into the phylogeny of the green plants. Their website contains a useful hyperbolic tree. Hyperbolic trees are one way to display complex trees clearly. I posted a link to the hyperbolic trees earlier when we talked about phylogenies.

The Green Tree of Life aims to resolve the primary pattern of evolutionary diversification among green plants. An overview of the results to date can be seen in this poster.

Monday, February 11, 2008

Fossil poop

As we cover more material there is more to choose to blog about but it sometimes gets hard to know whether to add something now or wait until later. However since I inevitably forget to post later I think it is better to post now as long as it's sort of relevant.

This story includes plants, insects, climate change, fossils and herbivory. Accordng to a study of 5000 fossil leaves a period of increasing temperature 55 million years ago led to a huge increase in the percent of plants that were being attacked. This is thought to be because insects do better and plants are more nutritious as it gets warmer. This study could obviously have implications for the global change we are currently seeing.

More info on algae

http://www.mbari.org/staff/conn/botany/greens/anna/default.htm


This is a great website with information about algae. I found it while trying to figure out where in the heck a thin leafy green algae like "sea lettuce" (Ulva/Enteromorpha) hid its reproductive structures or cells, especially since both gametophyte and sporophyte life stages look so similar. Check it out. There are even recipes!


You can choose to "enter Enteromorpha" if you dare, by clicking here:
http://www.mbari.org/staff/conn/botany/greens/Ram/enter.htm

Sunday, February 10, 2008

Digital Biology

Researchers have rebuilt an entire genome from scratch, they report online today in Science. Although the team has yet to demonstrate that this DNA can substitute for the real thing, the work paves the way for customized bacteria that could efficiently produce drugs, biofuels, and other molecules useful to humankind.

I mentioned this briefly in class for some reason. It might be more MCDB1A material but it's amazing stuff. Here's the news article from Science where they published the study and an article from Wired magazine that reveals what Venter's 'watermarks' are.

With the help of what he calls "digital biology," he can begin to redesign life.

Saturday, February 9, 2008

Anthropocene

Although the term has been in use by some scientists for a while there have been some recent papers calling for formal recognition of the term 'Anthropocene' to describe a new geological epoch that began with the industrial revolution. The Anthropocene epoch would thus mark the peiod where humans became a predominant geophysical force. There are popular articles in the last couple of weeks about this from the Christian Science Monitor and the BBC.

Friday, February 8, 2008

Vicariance versus Dispersal

Vincenzo stumped me with a question about how you distinguish vicariance (what I termed the dumb bell model) from dispersal (the peripheral isolate model) as mechanisms for allopatric speciation using phylogenetic data.

It turns out the answer is quite simple but that I'd been thinking too specifically. We just need to think outside the box for a moment and consider using phylogenies for groups other than the one we might be specifically studying.

A vicariance event will affect many different taxa and leave similarities in their cladograms. For example the breakup of Gondwana caused deep divisions in the cladograms of many groups representing the now separated continents. These similar cladograms are 'congruent'. Lack of congruence in cladograms is better explained by dispersal. Obviously this only works on a larger scale. I thought this page explained it all quite clearly.

Thursday, February 7, 2008

Next Thursday 2/14 we will visit the Cheadle Center for Biodiversity and Ecological Restoration. You can find information and directions at their website. We will meet there at 10.00 am and you should allow 10-15 minutes if you are walking over there - although that is naturally dependent on where you are walking from......

What plants crave....


From what they are now calling a 'cult' movie, Idiocracy. Based on the politically incorrect question of what would happen if unintelligent people outbreed intelligent people, creating a future society which is a few sandwiches short of a full picnic. Which I guess makes it slightly relevant to our class. Plus, you now know what plants crave.

Wednesday, February 6, 2008

Red Versus Blue


I looked up both the red and blue footed booby after class today, and then a sketch idea appeared in my head. So here's my sketch. I tried to make the birds reasonably accurate, using photo references for both species. Hooray for silly seabirds!

Tuesday, February 5, 2008

Preble's jumping mouse

The Preble's meadow jumping mouse (Zapus hudsonius preblei) is a small mouse, about three inches long, but with a six-inch long tail. They get their name from the fact they can use their large hind legs to jump 18 inches into the air. The mouse is not a distinct species but is on the endangered species list because it is recognized as a distinct subspecies.

For some years the mouse, found in Colorado and Wyoming, has been on the federal endangered species list. Its declining numbers are probably due to habitat loss and much of the remaining mouse habitat is also under threat. Its preferred habitat is a narrow band of land along the eastern edge of the Rocky Mountains that is being keenly eyed by developers.

A subspecies, by definition, differs morphologically from members of other subspecies of the species. Subspecies may, in some cases, be on their way to forming full species. In other cases they may not ever form separate species but will contain important genetic variation. Although the endangered species act preserves both species and 'subspecies' there is no clear definition of how distinct a 'subspecies' has to be before it deserves separate protection. In the current case opinions are sharply divided over whether the Preble's Jumping Mouse is distinct enough from the more common Bear Lodge meadow mouse. The story was summarized by the Jackson Hole Star Tribune when the US Fish and Wildlife Service convened a panel of scientists to review the evidence. A google search on the mouse will show the history of the debate.

This may sound like a small academic debate but it could have important outcomes for how the endangered species act is interpreted in the future. Genetic data is becoming increasingly important in deciding what is a valid subspecies but there are no guidelines for how much genetic difference is required between two populations for them to be considered different subspecies.

There are a lot of issues here, some of which we touched on and some of which we will touch on in the ecology section. It is important to realize that we may not currently have enough information to make these decisions.

Blue footed booby


The narration is annoying but the film is clear. I think the narrator is joking about the red footed booby but they do exist. Getty images have a nice video here.

Spots 'n stripes

If you check Wikipedia you'll see there are a number of Zebra crosses, collectively known as Zebroids:

Zebra (stallion) + horse (mare): zorse, zebra mule, zebrule or golden zebra
Zebra (stallion) + pony (mare): zony
Zebra (stallion) + Shetland pony (mare): zetland
Zebra (stallion) + any ass species (jenny): zebrass
Zebra (stallion) + donkey (jenny): zedonk, zeedonk, zonkey, zebronkey, zebadonk
Zebra (mare) + donkey (sire): zebrinny
Zebra (mare) + horse (stallion): hebra

Apparently they were mentioned by Darwin: in the Origin of Speies he refers to four coloured drawings of hybrids between the ass and zebra. These crosses are usually sterile. The Zorse article has some comments on genetics:

Zebras, donkeys, and horses are all members of the family equus -- equines. Equines can be crossbred to produce hybrids. They are all slightly different in genetic makeup, but still all equines. That is, horses have 64 chromosomes, zebra have between 44 and 62 (depending on species). Zorses can be male or female, but are sterile since their chromosome count is 63.

Just in case you think I get all my information from Wikipedia I'll also refer you to the wonderfully named International Zebra-Zorse-Zonkey Assocation. Lots of information and pictures and even a Zonkey for sale. Where else but at the Spots 'n Stripes Ranch in California. I didn't know I wanted a Zonkey, but now I do.

Monday, February 4, 2008

Look around you!


This should serve as a handy summary of our lecture on Prokaryotes.
The only thing I miss about England is the TV, satire has been raised to an art form here.

Sunday, February 3, 2008

Rabbit-sized 'shrew' discovered

A little out of sequence for our lectures but New Scientist has a report this week on a new species of giant elephant shrew found in Tanzania.

Friday, February 1, 2008

High-performing males have underachieving daughters

An interesting article in Nature last year, summarized in New Scientist here, described how, in red-deer, successful fathers tend to have unsuccessful daughters. In contrast male deer that carried genes that led to greater success in daughters were less successful themselves. This provides an interesting insight into the so called 'battle of the sexes' and may help explain why some genetic variation is maintained in sexual species. The nature article is available as a pdf file here.