Sunday, October 31, 2010

Man and Nature

This video from VBS TV was linked to on BoingBoing last week and I thought I'd save it for Halloween. The video is more sad than creepy but it does make you think about man's relationship with nature.

The Aokigahara Forest is the most popular site for suicides in Japan. After the novel Kuroi Jukai was published, in which a young lover commits suicide in the forest, people started taking their own lives there at a rate of 50 to 100 deaths a year. The site holds so many bodies that the Yakuza pays homeless people to sneak into the forest and rob the corpses. The authorities sweep for bodies only on an annual basis, as the forest sits at the base of Mt. Fuji and is too dense to patrol more frequently.

Apart from hundreds of corpses what is it that makes a place creepy? I think there is something about a relatively dense forest of similar trees with little in the way of topography that ties into some primitive fear of getting lost in the woods. Like in the Blair Witch Project or that great episode of the Sopranos where Paulie and Christopher get lost in the New Jersey Pine Barrens.
Happy Halloween.

Discussion Question 7 (Tools) comments due Nov 2nd

Choose a recent large development project, such as a dam, sewage treatment plant, shopping mall, highway, or housing development, and examine some of the costs and benefits of the project in terms of biological diversity, economic prosperity, or human health. Who pays the cost and who receives the benefits?

Discussion Question 8 (Tools) comments due Nov 2nd

How do traditional (or rural) societies use and value biological diversity? What is the relative importance of biological diversity in both traditional and modern societies? How do these societies value biodiversity knowledge?

Discussion Question 9 (Tools) comments due Nov 2nd

Traditional economists have argued that the marketplace will determine species protection. By this they mean that exploited species will be reduced only to the point where extraction costs equal revenue. It also implies that by giving economic value to species it is more likely that people and governments will protect them. Government regulation is seen as an unnecessary intrusion. Think of positive and negative aspects of this free market approach to conservation.

Saturday, October 30, 2010

More frogs than you can shake a stick at

A good piece of advice I heard once was that a scientific paper is not, and should not be written as, a murder mystery. ie. don't wait until the last page to reveal your conclusions.  I remembered that when I saw the title of this 2009 PNAS paper on Madagascar's amphibian biodiversity: Vast underestimation of Madagascar's biodiversity evidenced by an integrative amphibian inventory.
Amphibians are in decline worldwide. However, their patterns of diversity, especially in the tropics, are not well understood, mainly because of incomplete information on taxonomy and distribution. We assess morphological, bioacoustic, and genetic variation of Madagascar's amphibians, one of the first near-complete taxon samplings from a biodiversity hotspot. Based on DNA sequences of 2,850 specimens sampled from over 170 localities, our analyses reveal an extreme proportion of amphibian diversity, projecting an almost 2-fold increase in species numbers from the currently described 244 species to a minimum of 373 and up to 465.
Our results suggest that in Madagascar the spatial pattern of amphibian richness and endemism must be revisited, and current habitat destruction may be affecting more species than previously thought, in amphibians as well as in other animal groups. This case study suggests that worldwide tropical amphibian diversity is probably underestimated at an unprecedented level and stresses the need for integrated taxonomic surveys as a basis for prioritizing conservation efforts within biodiversity hotspots.

Friday, October 29, 2010

The million dollar bed

This bed is for sale in China for a million dollars. It's not my taste but that's not really the point. What is the point? That we are sacrificing Madagascar's unique forests for expensive furniture and the demand for that furniture is being fueled by China's economic growth.

The Environmental Investigation Agency recently published a major report on the global trade in rare woods from Madagascar. It's well worth taking a look at it. A point they make several times is that very little of the money remains in Madagascar - less than 1% of the wood's final value even remains in the country and only a small fraction of that will remain with the poorest people.

Since Halloween is right around the corner here's the Satanic leaf tailed Gecko (Uroplatus phantasticus). Leaf tailed geckos are only found on Madagascar and The World Wide Fund lists all the Leaf tailed geckos on their "Top ten most wanted species" list of animals threatened by illegal wildlife trade.

Thursday, October 28, 2010


We'll talk more about Madagascar in the next class but if you are interested in biology it is hard not to be interested in just why Madagascar has such a high number of endemic species.

The simplest explanation would be that after Gondwana broke apart and Madagascar separated from Africa 120 million years ago the isolation led to evolution and allopatric speciation. The problem though is that lemurs and some other groups had not yet evolved on the African continent 120 million years ago. We think much of Madagascar's animal population began arriving much later, sometime after 65 million years ago - and subsequently speciated from these original colonists. This raises the very interesting question of how they got there. Did they cross a causeway or land bridge that now no longer exists, did they swim or 'raft' on vegetation?

A paper in Science earlier this year provides evidence supporting the rafting hypothesis: Mammalian biodiversity on Madagascar controlled by ocean currents
There's a nice editorial summary too: Biogeography: Washed up in Madagascar

How, when and from where did Madagascar's unique mammalian fauna originate? The idea that the ancestors of that fauna rafted from Africa finds support in innovative simulations of ancient ocean currents.

Which explains why there are no elephants on Madagascar. A rat on a bunch of sticks and vegetation swept out to sea surviving for a few days is not hard to believe. Even a lemur ancestor on a tree swept downriver and out to sea in a storm. But an elephant? It's an amusing image but simply not likely.

As an aside it is perhaps an indication of one of the problems of conservation that a Google Image search on one of the most photogenic and unique places on earth brings up page after page of pictures of an animated movie.

Wednesday, October 27, 2010

Good news, bad news (but mainly bad news)

On Tuesday the academic journal Science released an assessment of the survival chances of the world's vertebrates. 

Using data for 25,780 species categorized on the International Union for Conservation of Nature (IUCN) Red List, we present an assessment of the status of the world’s vertebrates. One-fifth of species are classified as Threatened, and we show that this figure is increasing: On average, 52 species of mammals, birds and amphibians move one category closer to extinction each year. However, this overall pattern conceals the impact of conservation successes, and we show that the rate of deterioration would have been at least one-fifth as much again in the absence of these. Nonetheless, current conservation efforts remain insufficient to offset the main drivers of biodiversity loss in these groups: agricultural expansion, logging, overexploitation, and invasive alien species.

For some popular reports see:
Fifty species move closer to extinction every year, report says in the LA Times
Biodiversity study sounds an extinction alert (for things with spines) in the Christian Science Monitor
and Conservation offers hope for biodiversity decline at

Tuesday, October 26, 2010


Avenue of the Baobabs, an area near Morondava protected since 2007, is all that remains of a once thick forest cleared for farmland. Growing 80 feet (24 meters) or more, baobabs are valued for fruit and bark.

Can you imagine a whole forest of these trees? We'll be talking about Madagascar a bit in the next lecture and National Geographic has an article about this unique country in this month's edition. For those not taking a trip to the dentist or a grandparents house, you can read it online: Madagascar's Pierced Heart

The island’s geographic isolation created a wonderland of biological richness. Now population pressures and political turmoil speed the plunder of its rosewood, minerals, and gems.

Don't miss the photo gallery. Go read the article, it's very well written and the photographs are, as usual, amazing. It makes me feel bad for letting my subscription to National Geographic lapse. And very pessimistic for the future of Madagascar.

Domoic acid and HABs

The California Department of Public Health (CDPH) issued a warning to avoid eating locally harvested shellfish due to high levels of domoic acid. This toxin largely affects seabirds and marine mammals, since their primary food source, shellfish, bioaccumulates the toxin in their tissue. Domoic acid is a neurotoxin that naturally occurs in microalgae blooms, also known as harmful algal blooms (HABs). However, the blooms are becoming more frequent likely due to increasing coastal nutrient inputs (largely agricultural run-off). Here is a great fact sheet for reference.

Monday, October 25, 2010

Generally exaggerated

I was updating a figure for the next lecture and came across this chart from an annual poll conducted by the Gallup organization. (See the post below and the comment.)

It's very depressing but as the evidence of global climate change accumulates there has been a very large swing in the US and almost 50% of people think the problem is being exaggerated.

We've changed the pH of the ocean. The freaking ocean.

Coral death

Reefs of Pulau Weh; before, during and after the bleaching event. (a) April 18, 2009 ; (b) May 31, 2010; and (c) July 26, 2010.  Photo credit (left to right): R. Graham, N. Fadli, Y. Herdiana. 

International marine scientists say that a huge coral death which has struck Southeast Asian and Indian Ocean reefs over recent months has highlighted the urgency of controlling global carbon emissions.

Many reefs are dead or dying across the Indian Ocean and into the Coral Triangle following a bleaching event that extends from the Seychelles in the west to Sulawesi and the Philippines in the east and include reefs in Sri Lanka, Burma, Thailand, Malaysia, Singapore, and many sites in western and eastern Indonesia.

“It is certainly the worst coral die-off we have seen since 1998.  It may prove to be the worst such event known to science,” says Dr Andrew Baird of the ARC Centre of Excellence for Coral Reef Studies and James Cook Universities. “So far around 80 percent of Acropora colonies and 50 per cent of colonies from other species have died since the outbreak began in May this year.”

For the full press release from the Australian Research Council Center of Excellence for Coral Reef Studies see - Worst coral death strikes at SE Asia 10/19/10.

Sunday, October 24, 2010


This blog has a number of functions. It's a place for me to post some follow ups to lecture, a place for me to post some recent relevant research and a place for me to post articles of interest and amusement. It also sometimes serves as a place for me to rant.

I was in Las Vegas this weekend. A visit of such monumentally depressing experiences I have not yet recovered. Anyway, in this monument to excess, a monument that takes excess and then raises it to a higher power of excess than you even imagined existed, it is just petty and annoying to see the constant greenwashing. Sure, keep your lights on 24/7 and produce a lush oasis in the desert but as long as my coffee cup sleeve is 40% post consumer content and my towels are only washed every other day the earth will be okay.

The University of Oregon maintains a Greenwashing Index if you are interested in this type of thing.

Friday, October 22, 2010

In denial again.

Climate change is such an overwhelming problem that I can almost understand this response - Let's just pretend it isn't happening. That is exactly the response of a staggering 95% of the Republican senate candidates.

With one exception, none of the Republicans running for the Senate — including the 20 or so with a serious chance of winning — accept the scientific consensus that humans are largely responsible for global warming. 

This was the topic of an editorial in the New York Times last weekend: In Climate Denial, Again

Interestingly this situation is fairly unique to the US. Conservative parties in Europe may disagree on the actions to be taken but do not deny the reality of the situation. It makes me think of the quote attributed to Daniel Moynihan (pictured):

Everyone is entitled to his own opinion, but not to his own facts.

Thursday, October 21, 2010

No bad birds

When discussing alien and invasive species it is very easy to slip over into thinking that some species are just bad. Whilst there are some species that are rather widely problematic every species is also native somewhere. In its native range attitudes towards it are often very different. Take that most trashy of the trash birds the European starling. Even Fox news hate the starling (I suspect they particularly dislike it because it's from Europe).

But when I came across this video I thought the spooky smoke monster starling flock looked familiar. Here it is with a rather different narration from its European home. This second video is a bit slow to get going but don't miss the section starting at about 3:20. Amazing.

Wednesday, October 20, 2010


California Invasive Plant Council is a nonprofit organization formed in 1992 to address one of California's top environmental threats. They run courses, maintain an inventory of the state's invasive plants and also, and probably most conspicuously, publish leaflets as part of their 'Don't Plant a Pest Program'. You can download them all from their website, or click here for a pdf version of their central coast version.

Certified Wildlife Habitats

My sister took this photo and sent it to me the other day to ask if I knew about Certified Wildlife Habitats... and I didn't until I googled it! Have you heard about this before? I thought I would pass it on to see what everyone thought about this... very interesting!

Tuesday, October 19, 2010

Catch Shares

Article in Science Science 19 September 2008: Vol. 321. pp. 1678 - 1681 by Christopher Costello, Steven D. Gaines, John Lynham. Can catch shares prevent fisheries collapse?

Recent reports suggest that most of the world's commercial fisheries could collapse within decades. Although poor fisheries governance is often implicated, evaluation of solutions remains rare. Bioeconomic theory and case studies suggest that rights-based catch shares can provide individual incentives for sustainable harvest that is less prone to collapse. To test whether catch-share fishery reforms achieve these hypothetical benefits, we have compiled a global database of fisheries institutions and catch statistics in 11,135 fisheries from 1950 to 2003. Implementation of catch shares halts, and even reverses, the global trend toward widespread collapse. Institutional change has the potential for greatly altering the future of global fisheries.

Science also had a news story on this article.

Monday, October 18, 2010


"Lady's Slipper Orchid" (Cypripedium parviflorum var. makasin) 

The Victorians coined the phrase Orchidelirium to describe an obsession with collecting orchids that seemed to grip certain people. A number of relatively high profile cases in recent years suggest the condition did not die with the hooped skirt and the handlebar mustache.

  • Dr. Sian Lim was caught at Heathrow Airport in June 2004 with more then 100 endangered orchids. Lim, employed by an English drug company, appears to have collected the plants in Borneo, Indonesia and his native Malaysia.
  • A 41-year-old Fort Lauderdale, Florida resident made his initial appearance today in United States Magistrate's Court in Miami after being charged by a federal grand jury, sitting in Miami, in connection with the illegal importation of more than 1,400 orchid plants from the Republic of the Philippines in February 2005.
  • George Norris, 66, a resident of Spring, Texas, pled guilty in Miami federal District Court in connection with a conspiracy to smuggle into the U.S. protected orchid specimens, including specimens of the genus Phragmipedium, commonly known as Tropical lady's slipper orchids. All species of orchid are protected under the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES), a treaty to which the U.S. and Peru, along with over 160 other nations, are parties. 
Susan Orlean's book The Orchid Thief: A True Story of Beauty and Obsession centers on south Florida and John Laroche a charismatic schemer once convicted of attempting to take endangered orchids from the Fakahatchee swamp, a state preserve.  Laroche sums up the obsession that drives him and so many others:
I really have to watch myself, especially around plants. Even now, just being here, I still get that collector feeling. You know what I mean. I'll see something and then suddenly I get that feeling. It's like I can't just have something--I have to have it and learn about it and grow it and sell it and master it and have a million of it.

Sunday, October 17, 2010

Island Scrub Jay

On the front page of the California section in today's Sunday edition of the LA Times is an article about the Island Scrub Jay found only Santa Cruz Island.

There are several interesting connections to the class. First, this is a nice example of a 'rare' species that is locally somewhat abundant but has a very restricted geographic range (a narrow endemic).

Second, this is a somewhat unusual example of steps being taken to protect a species before it is endangered:

The rare jay is not officially endangered but could be in peril: Biologists working in Channel Islands National Park worry that it's easy pickings for the West Nile virus, which could swiftly wipe out the species once infected mosquitoes or birds cross the Santa Barbara Channel.

"It's imprudent to think it's not going to happen," said Scott Morrison, director of conservation science for the Nature Conservancy in California. "It's just a matter of time."

Working on and off for more than a year, a crew has been laboriously trapping jays one by one and inoculating them with a vaccine produced — initially for condors — by the Centers for Disease Control. By next spring, the crew on Santa Cruz will have given the needle to about 250 birds — enough, they hope, to form a disease-resistant core if West Nile takes out all the rest.

Saturday, October 16, 2010

Weekend bring down

Slow Loris loves getting tickled but he's pissed off about the impact of the pet trade on his endangered species. This video went viral a year or so back but the emphasis was, naturally, on the cuteness of the slow loris rather than the conservation implications of the pet trade.

The BBC article linked to above claims that a slow loris will cost you between $1,500 and $4,500 in Japan. It would be interesting to know if this changed following the uplisting from Appendix 2 to Appendix 1 within the Convention on International Trade in Endangered Species (CITES).I'd look into it but the article was just too depressing. Sorry for harshing your weekend buzz.

Friday, October 15, 2010

The only good sheep....

The sale of 'Trophy Tags' has been an important source of revenue for the conservation of animals like bighorn sheep. In a typical year the auction of just twenty permits at the Foundation for North American Wild Sheep’s annual convention  will raise over $2 million - ninety percent of which goes to wildlife agencies for wild sheep management, herd restoration and research.

However, this practice leaves even some hunters uneasy:
Trophy Tag Auctions Bad Business.

We might not need to read about yet another example of hunters assuming the role of their own worst enemy in the war to save our hunting tradition, but I can’t resist writing about this one.
Here in the New West, we’ve had at least three recent headliners about our state wildlife agencies and conservation organizations condoning and even promoting the practice of the super-rich paying obscene amounts of money to buy big game licenses. Does this practice really promote the future of hunting or give it another self-inflicted black eye? 

It was interesting to check out some of the comments on the two articles referred to in the post. Hunters clearly come in many forms.

I do not have a problem with hunting for food, if that is how you choose to eat. I do have a problem with hunting culture and trophy hunting. It is stupid to hunt mature, healthy adults (it is a shame these are referred to as Trophies) since this depletes the gene pool of the most successful traits in the population. It is equally a shame the kill shot photos that are taken after the animal is killed. This shows utter disrespect to life and the spirit that was taken from animal. It used to be that deep reverence and honor was considered for the animal. The act of the hunt was also sacred. We need hunting policy that really serves conservation and is not an arm of hunting culture.

Thursday, October 14, 2010

Discussion Question 4 (Primary Threats)

Why is habitat degradation the greatest threat to biodiversity?

Discussion Question 5 (Primary Threats)

Learn about a well known endangered species, such as the koala bear, the right whale, or the cheetah. Why are these particular species vulnerable to extinction? Use the IUCN criteria (IUCN 2001) to determine the appropriate conservation category for one or more species.

Discussion Question 6 (Primary Threats)

Control of invasive species may involve searching for specialized natural enemies, parasites, or predators of that species within its original range and releasing such organisms in an attempt to control the invasive species at the new location, For example, an attempt is currently underway to control exotic purple loosestrife in North America by releasing several European beetle species that eat the plant in its home area. As another example, biologists are talking about introducing an exotic fungus into Hawaii to eliminate the invasive Puerto Rican coqui frog. What if these biological control agents begin to attach native species rather than their intended host? How might such a consequence be predicted and avoided? Consider the biological, economic, and ethical issues involved in a decision to institute a biological control program.


The intriguing cod-in-a-coffin picture I used today comes from an item in the Smithsonian National Museum of American History. In particular it is part of the 'Commercial Fishers: Atlantic Cod' section of their 'On the Water' exhibition.

It was made by fisherman Dan Murphy of Dunville, Newfoundland. Made in response to Canada’s moratorium on cod fishing, Murphy sold these items at local flea markets and from his home. This folk art cod-in-a-coffin, carved from wood and lined with fabric, represents the death of many Newfoundlanders’ livelihood. The fishing ban was declared on July 2, 1992, in an attempt to replenish the distressed levels of North Atlantic cod.
The moratorium was extended indefinitely in 1993, giving jobless fishers little hope for a return to their way of life. According to a 2007 study, the North Atlantic cod population was estimated to be at one percent of its 1977 numbers.

European fishermen in the 1500’s reported the Gulf of Maine waters so thick with cod that a man could walk to shore on their backs.

Wednesday, October 13, 2010

More cowbird

All the cowbird hate has got me thinking about the unpopular cowbird. Not only are they frequently blamed for songbird declines (even though the root cause is habitat change) but they appear to be generally unpopular birds due to their ubiquitous nature (bird watchers like rare birds), dull plumage and parasitic behavior. Cowbirds are an example of what many bird watchers consider to be 'Trash birds'.

'However, before we discuss how to lure these lovelies, let's consider what most birdwatchers agree are the "trash" birds: grackles, starlings, and cowbirds.'
Article on Birdwatching forum

'I have designed a feeder with only one perch on it. When a cowbird lands on it, I push a button and an electrical current surges through.... Everytime I zap a cowbird, a nestful of beautiful baby songbirds gets their wings'.
Readers comment on Birdwatching forum 

Is parasitism an ecosystem disservice (kills beautiful baby songbirds) or an ecosystem service (may be important in regulating the populations of beautiful songbirds)? 

For some cowbird love check out Cowbirds in Love - a daily comic about sad things, happy things, science, philosophy and occasionally obligate brood parisitism.

Biology without borders... one backyard at a time

Just out today in Nature, there are a few of pieces that are highly relevant to last week's discussion.

There is an editorial that highlights the upcoming global summit on biodiversity in Nagoya, Japan, which will be focusing on the agendas of the international Convention on Biological Diversity. The piece ends with:

"The global picture is gloomy. But if each country can empower the citizens and international research communities that focus on local threats, using the tools of all the sciences, there could be movement rather than paralysis."

Also, check out this comment written by David E. Schindel. He is the executive secretary of the Consortium for the Barcode of Life, an international initiative devoted to developing DNA barcoding as a global standard for the identification of biological species, established in 2004 with 200 Member Organizations from 50 countries. It operates from a Secretariat Office located in the Smithsonian Institution's National Museum of Natural History in Washington, DC.

And, there is a news article "Biodiversity hope faces extinction: Upcoming meeting will set out global conservation targets." which provides more detailed information on the meeting.

Tuesday, October 12, 2010

Cowbird traps

Thanks to Texas Parks and Wildlife's 'Cowbird Trapping Guide' I now know much more about cowbird trapping. Q and A below inspired by their pamphlet.

Q - Why would I want to trap cowbirds?
A - Throughout North America songbird numbers are declining. While there is no one single reason for this decline, one major contributing factor is the spread of the brown-headed cowbird. It is not feasible to eliminate grain fields and suburban yards, or remove all grazing animals from the landscape to control parasitism by cowbirds. Therefore, trapping of cowbirds to reduce their numbers becomes an important option to consider if we are to prevent declines in songbird populations.

Q - How do I attract cowbirds to my trap?
A - Cowbirds are gregarious - add a dozen live cowbirds to your trap.

Q - I don't have any cowbirds how do I get started?
A - Add some grain, place it in cowbird habitat and be patient.

Q - Can I build my own trap?
A - Why yes you can with these easy to follow instructions for a 6' x 8' portable trap.

Q - How do I kill the cowbirds?
A - Quickly and humanely.

Q - No really, how do I kill the birds?
A - Cervical dislocation: Hold top of neck between thumb and forefinger, grab head with other hand, turn and lift until you feel the cervical vertebrae detach from the head.

Q - Doesn't the cowbird have as much right to live as the songbirds?
A - Did we mention that this means we don't need to remove cattle or restore habitat?

Rather than removing cattle in order to reduce parasitism, the members of the Central Texas Cattlemen’s Association and Texas Parks and Wildlife Department have found that parasitism rates can be reduced in Black-capped vireos by using the cattle to attract cowbirds into traps located near the cattle.

Monday, October 11, 2010

Bee Colony Collapse update

Many of you have probably heard of 'Bee Colony Collapse Disorder' - the somewhat mysterious decline in bee populations worldwide.

Research published in PLoS this week (Iridovirus and Microsporidian Linked to Honey Bee Colony Decline)
suggests the bees may be suffering from both an insect virus and a fungus and it may be the combination that is proving especially lethal

The insect virus is closely related to another virus that wiped out bee populations 20 years ago in India.

Though an association between exposure and death was found, scientists don't yet know if the two pathogens cause Colony Collapse Disorder or whether Colony Collapse Disorder colonies are more likely to succumb to the two pathogens.

The next part of the research project, is to isolate the virus from infected bees.
Once we isolate and identify the virus, we will have a way of monitoring it,” one of the authors, Shan Bilimoria, a professor and molecular virologist at Texas Tech, said. “It is easier to fight the problem if we know what the culprit is.

Since many of our agricultural crops are bee pollinated this is one ecosystem service that people are very concerned about.

As an aside, and on the remote chance that anybody has read this far, I was amused to go to the Texas Tech homepage to see their press release on this research to find a headline you won't find anytime soon on the UCSB homepage:
Meat Judging Team wins Eastern National Contest. Does UCSB even have a meat judging team?


Sunday, October 10, 2010

Salmon Run

Each year Patagonia sponsor a 5k race called the Salmon Run along the Ventura River and the proceeds from entry and raffle tickets go to a local environmental organization. Last year the beneficiary was the Matilija Coalition, a program started by the Ventura County Chapter of the Surfrider Foundation to focus attention on the removal of Matilija Dam. This year the beneficiary is the Environmental Defense Center which protects and enhances the local environment through education, advocacy, and legal action. The race is on November 7th - further details at their website.

Comment limit

I didn't realize there was a limit on the comment size in the Blog but apparently there is - 4,096 characters. This comes about from some flaw in the code (Google makes mistakes?) that meant that comments above that size were undeletable. Going for the quick fix Google limited the size of comments to prevent spammers exploiting the flaw.

Anyhow, 4,096 characters is at least 500 words, or a couple of double spaced pages. I did not intend people making such long comments for the assignments 200 to 400 words should be enough. But be aware that there is this limit so, again, I recommend you compose your assignment comment in a program like MS Word and then paste it in.

Saturday, October 9, 2010

Unlucky in love

Is it possible for a population to suffer from both inbreeding depression and outbreeding depression at the same time?

Well, unfortunately, the answer is yes, and there's an example - the Arabian Oryx.

Simultaneous inbreeding and outbreeding depression in reintroduced Arabian oryx by T. C. Marshall and J. A. Spalton in Animal Conservation (2000) 3, 241–248

(W)e found simultaneous inbreeding depression and outbreeding depression acting on juvenile survival. Outbreeding depression may be more common in vertebrates than previously supposed, and conservation strategies that seek to maximize the genetic diversity of managed populations may risk mixing lineages that are sufficiently differentiated to cause outbreeding depression among descendants.

The Arabian Oryx was driven to extinction in the wild in 1972, primarily due to overhunting. However there were a number of captive populations and reintrodtions to the wild started in 1982. The 34 Oryx reintroduced to the Arabian Oryx Sanctuary in central Oman came from 5 different populations from individuals originally captured in Saudi Arabia, Oman, and Yemen (hence the outbreeding problem). Inbreeding simply compounds this problem as the relatively 'unfit' offspring of parents adapted to different environments have to mate with one another and so problems that might remain hidden in heterozygous individuals become expressed.

Friday, October 8, 2010

Good news for ferret lovers

There's not always a lot of good news in this class so I'm happy to report that when I checked up on the latest status of the black-footed ferret it's been another great year for them with 310 kits born in captivity as of August 2nd and the population in the wild looking like it's doing well. I mean if we can't save a species this photogenic then that would not bode well.

Although most ferret births are a product of natural ferret love the Smithsonian's National Zoo had some success in 2007 and 2008 with artificial insemination using sperm frozen from males who died died in 1999 and 2000.

For more than 10 years, the semen was stored in the Zoo's Black-Footed Ferret Genome Resource Bank, a repository of frozen semen from the most valuable males. In species that have short life spans like the black-footed ferret, the use of cryopreserved, or frozen, sperm extends an individual's reproductive life. The bank's contents help maintain and even enhance genetic diversity by infusing new genes into the population. A genetically healthy and diverse population has a greater chance of survival in the wild. The bank also serves as insurance against catastrophes in the wild populations, such as a disease outbreak.

Okay, one more ferret picture. Here's the happy mother (left) and two month old offspring (right) in 2008. No picture of the sperm vial.

Thursday, October 7, 2010


Who is this?

If you answered 'Edward Norton, star of many fine films' you would be correct.

If you answered 'Why that's the UN goodwill ambassador for biodiversity' you would also be correct.

Strange but true. I only discovered this when I saw this article he wrote for the Guardian, a British Newspaper:

The US must show leadership on biodiversity.

Next month's UN summit will set out bold plans to protect life on Earth. But unless the US ratifies the convention on biological diversity, the battle to halt species loss will be even tougher

Wednesday, October 6, 2010

Where's the outrage?

Okay, you are all young and hipper than me. (Do you kids even say hipper these days?) In my generation when we had a problem we knew the solution - write a song about it. Just read the Wikipedia entry on protest songs for a rich journey through modern history. Boy, we protested everything from Dylan's Masters of War (works for any war!) to Elvis Costello's masterful Shipbuilding (most people don't know it's about war!). We protested apartheid, racial discrimination, nuclear war, nuclear power, the Vietnam War, the Falklands War (well I did anyway), the Iraq War and more.

But, arguably, one of the biggest issues facing this generation is the loss of biodiversity. How can we hope to prevail without a single decent protest song? I'm really coming up blank here. All I can think of is a bunch of older songs:
Help! It's no wonder we have a problem if this is the best we've got. Post a comment if you can think of anything good I've missed (like anything from the last three decades).

Seminar: Toward Food Sustainability in a Warmer World

David Lobell
Assistant Professor, Earth System Science
Stanford University

Thursday, October 7, 2010
11:30 a.m. - 12:30 p.m.
Bren Hall 1414

There is little disagreement now that the climate is changing, and that such changes could fundamentally affect humanity's collective ability to feed itself. However, there is little systematic knowledge of where climate effects will hit hardest, or how agriculture and the broader society might adapt to a rapidly changing climate. Although adaptation decisions are made at a range of spatial and temporal scales, this talk will focus on identifying global priorities over the next decade for adaptation. Possible approaches to setting priorities include identifying crops and regions that are most at risk of climate-induced yield shocks, identifying crop technologies that are most likely to produce effective adaptation, and identifying sectors of the population that are most vulnerable to food price increases. This talk will examine these approaches highlighting new data and model results.

David Lobell is an assistant professor in environmental earth system science at Stanford University and a Center Fellow in Stanford's Program on Food Security and the Environment. His research focuses on identifying opportunities to raise crop yields in major agricultural regions, with a particular emphasis on adaptation to climate change. His current projects span Africa, South Asia, Mexico, and the United States, and involve a range of tools including remote sensing, GIS, and crop and climate models.

Lobell's work is motivated by questions such as: What investments are most effective at raising global crop yields, in order to increase food production without expansion of agricultural lands? Will yield gains be able to keep pace with global demand for crop products, given current levels of investment? And what direct or indirect effects will efforts to raise crop productivity have on other components of the Earth system, such as climate? Answering these requires an understanding of the complex factors that limit crop yields throughout the world, and the links between agriculture and the broader Earth system.

Tuesday, October 5, 2010

Evidence for an Ecological Trap

The Indigo Bunting paper I mentioned today:
The effects of patch shape on Indigo Buntings: evidence for an ecological trap.
by Weldon & Haddad,  Ecology 86:1422–1431.

Habitat loss and fragmentation have led to a widespread increase in the proportion of edge habitat in the landscape. Disturbance-dependent bird species are widely assumed to benefit from these edges. However, anthropogenic edges may concentrate nest predators while retaining habitat cues that birds use to select breeding habitat. This may lead birds to mistakenly select dangerous habitat—a phenomenon known as an “ecological trap.” We experimentally demonstrated how habitat shape, and thus amount of edge, can adversely affect nest site selection and reproductive success of a disturbance-dependent bird species, the Indigo Bunting (Passerina cyanea). We did so within a landscape-scale experiment composed of equal-area habitat patches that differed in their amount of edge. Indigo Buntings preferentially selected edgy patches, which contained 50% more edge than more compact rectangular patches. Further, buntings fledged significantly fewer young per pair in edgy patches than in rectangular patches. These results provide the first experimental evidence that edges can function as ecological traps.

Aerial photos show the two, patch shapes used:

Monday, October 4, 2010

Census on Marine Life

Glass squid photo from National Geographic: Scientists found the squid and other species while mapping more than 1,500 square miles (3,900 square kilometers) of an undersea mountain range in the North Atlantic.

More biodiversity in the news today with the publication of the findings of the Census on Marine Life - a 10 year, $650 million program involving 2,700 scientists from 80 nations.

Scientists estimate that there are more than 1 million marine species but only about 250,000 have been formally described in scientific literature over the centuries. Those figures exclude microbes -- of which the census estimate there are up to 1 billion kinds. 

Thanks to Ryan again for this news tip, especially the Wall Street Journal article which contains this illuminating comment (pun intended):
Dr. Snelgrove likened the census to a flashlight used to explore a dark house. While it's a start, "we haven't turned on the lights yet," he said.

Sunday, October 3, 2010

From Silent Spring to Silent Night

If you are interested in Environmental Science you should check out this seminar on Friday. Tyrone is an excellent speaker and his work is really very interesting and accessible.

Tyrone Hayes,  Professor, UC Berkeley

"From Silent Spring to Silent Night: What happens if our canary stops singing?"

Hosted by Bren Professor Patricia Holden as part of the Seminar in Ecotoxicology

Friday, Oct. 8, 2010
11:00 a.m. - 12:00 p.m.
Bren Hall 1414 

The herbicide atrazine is a potent endocrine disrupter that chemically castrates and feminizes exposed male amphibians. Further, when combined with other pesticides, exposure results in a hormonal stress response that leads to retarded growth and development, and immuno-suppression. The immuno-suppression results in increased disease rates and mortality. Though many factors likely contribute to amphibian declines, pesticides likely play an important role even in populations that appear to decline for other reasons, such as disease. Pesticides like atrazine are ubiquitous, persistent contaminants. Effects of exposure have been shown in every vertebrate class examined (fish, amphibians, reptiles, and mammals) via common mechanisms. These observations demonstrate the critical impact that pesticides have on environmental health. Furthermore, reproductive cancers and birth defects associated with exposure to many of these same chemicals (e.g. atrazine) via identical mechanisms demonstrate that the impact on environmental health is an indicator of a negative impact on public health. Many of these mechanisms are being revealed only now in the scientific literature and agencies (such as the Environmental Protection Agency) are ill-equipped to deal with this emergent science and translate it efficiently into health-protective policies. Given the importance of this science and relevance to public health, there is a strong need to translate this information and provide public access to this knowledge. In particular, minority populations, more likely to be exposed to these chemicals, more likely to suffer health effects associated with exposure, less likely to have access to adequate health care and less likely to have access to this information, need to be informed. It is especially incumbent upon research scientists to make accurate accounts of these data available when industry and agency representatives (e.g. the EPA) provide inaccurate information to the public.

Saturday, October 2, 2010

Five Trillion dollars a year

I think we will see an increasing number of articles like this in the run up to the latest Convention on Biodiversity meeting in Japan later this month. This article is from a Sunday Newspaper in England.

"British scientific experts have made a major breakthrough in the fight to save the natural world from destruction, leading to an international effort to safeguard a global system worth at least $5 trillion a year to mankind.
Groundbreaking new research by a former banker, Pavan Sukhdev, to place a price tag on the worldwide network of environmental assets has triggered an international race to halt the destruction of rainforests, wetlands and coral reefs.
With experts warning that the battle to stem the loss of biodiversity is two decades behind the climate change agenda, the United Nations, the World Bank and ministers from almost every government insist no country can afford to believe it will be unaffected by the alarming rate at which species are disappearing. The Convention on Biological Diversity in Nagoya, Japan, later this month will shift from solely ecological concerns to a hard-headed assessment of the impact on global economic security."
"Biodiversity is where climate change was 20 years ago – people are still trying to understand what it means and its significance. Things that we thought nature provides for free, actually if you lose them, cost money."

Friday, October 1, 2010

Where's my plaque?

Ryan alerted me to the press reports on this paper that was published yesterday:
 Correlates of rediscovery and the detectability of extinction in mammals. by Diana Fisher and Simon Blomberg in proceedings of the Royal Society B,.
(You'll need to be on campus or use the libraries proxy server to read the article). A typical press report:

Conservationists are overestimating the number of species that have been driven to extinction, scientists have said. A study has found that a third of all mammal species declared extinct in the past few centuries have turned up alive and well.
Some of the more reclusive creatures managed to hide from sight for 80 years only to reappear within four years of being officially named extinct in the wild.

Perhaps more interesting are the comments in those online papers that have open comments sections (read at your own risk). It looks like this study is being used by some people to confirm their prejudices - scientists are exaggerating the scale of the problem for their own benefit. Whereas in reality, with the great difficulty in monitoring the population sizes of very rare species it is really not surprising at all that this happens
If you read the actual paper you'll find it is rather more interesting. From their actual aim:
to test whether extinction from different causes is equally detectable
to their results:
We find that species affected by habitat loss were much more likely to be misclassified as extinct or to remain missing than those affected by introduced predators and diseases, or overkill
and conclusion:
Conservation resources are wasted searching for species that have no chance of rediscovery, while most missing species receive no attention. Rather than searching ever more for charismatic missing species, such as thylacines in Australia, it would be a better use of resources to look for species that are most likely to be alive, find out where they are, and protect their habitats.
Or, for an alternative view maybe Robb in Lancaster, PA is onto something.
WOW, what happened to the days when scientists were worried about answers and truth in those answers? I guess all they care about now is the plaque on the wall and federally funded monies in their bank accounts!! govts around the world need to stop financing so called research!
The report in Wired magazine is one of the best I saw and they have some good quotes from the author:
“If you think that a missing species is extinct and the main cause of decline was introduced predators such as feral foxes, cats or rats, then you are very likely to be right,” Fisher said. But, she added, “If the main cause of decline was habitat loss, you are quite likely to be wrong if you say that it’s extinct, unless it was restricted to a very small area.”

“We should be trying to protect the habitat of recently extinct species,” Fisher said. “But this is not easy, because we don’t know where they might be rediscovered. It is not necessarily near where the species was last seen.”