It's not just the genes...

Increasingly we are realizing that it isn't just the genes that are important but how those genes are expressed.

This was nicely illustrated in a Science paper this week where they looked at the role of the Agouti gene in pattern development: The Developmental Role of Agouti in Color Pattern Evolution.

Agouti, ... governs color patterns in deer mice, the most widespread mammal in North America. This gene, found in all vertebrates, may establish color pattern in a wide variety of species, a process that has been poorly understood at both the molecular and the evolutionary level.

Agouti had previously been known to affect the type of pigment found in vertebrate fur, feathers, and scales: Little expression of the gene in adults results in the production of dark pigments, while robust Agouti activity generally yields light pigment production. But Manceau and Hoekstra found that subtle changes in the gene's embryonic activity can also make a profound difference in the distribution of pigments across the entire body.

"During embryogenesis, Agouti is expressed in the belly, where it delays maturation of the cells that will eventually produce pigments," says Hoekstra, John L. Loeb Associate Professor of the Natural Sciences at Harvard. "This leads to a lighter colored belly in adults, which is the most common color pattern across a wide variety of vertebrates, from fish to antelope."

Even small changes in Agouti gene expression can establish a completely new color pattern. In deer mice, natural selection drives changes in the amount and place of Agouti expression, which in turn results in new color patterns that can camouflage animals from visual predators in habitats including dark forests and light sandy beaches.

"It is hard not to speculate that Agouti plays a role in generating more complex patterns -- from stripes to spots -- in a diversity of vertebrates," Hoekstra says.
 

 Looking for a picture of a leopard to add I found this cool picture of a black panther (panthers are just black leopards). Notice how you can see the pattern of spots in the fur even though the fur is all black.

Angel's trumpet poisoning

I looked up some information on the toxic compounds in Brugmansia. The plant contains an unhealthy brew of the alkaloids atropine, scopolamine and hyoscyamine.

Because these can cause hallucinogenic effects they are often ingested by those seeking just such an effect. When combined with alcohol the effects can be rapid. Although the plant can be eaten or smoked the most popular method of ingestion is to prepare a tea from the flowers and seeds.

Unfortunately because the levels of the alkaloids vary widely from season to season it is very easy to overdose and it is estimated that 'teas prepared from as few as 10 flowers could be extremely toxic if not fatal'. Angel's trumpet ingestion produces the classic symptoms of anticholinergic poisoning, so classic that they have their own mnemonic: 'hot as a hare, dry as a bone, blind as a bat, red as a beet and mad as a hatter.'

This paper, Ingestion of Angel's Trumpet: An increasingly Common Source of Toxicity, reports a ten fold increase in Brugmanisa poisoning in Florida in 1994. They failed to locate a particular reason for this (ie reference to Brugmania use in a movie) and suggest the idea was simply spread by word of mouth. And then the internet came along...

Seed Plant Phylogeny

You may be surprised to find out that the relationship between the angiosperms and the gymnosperm groups is still subject to much debate. One of the perennial questions is the position of the gnetophytes.

 One of the reasons for this debate is that the Gnetophytes (one of the gymnosperm taxa we discussed) show several features that are typically associated with the angiosperms, including double fertilisation and vessel elements in their vascular tissue. Do these indicate a close relationship and that the gnetophytes are a sister taxa to the angiosperms or are they the results of parallel evolution?

Wikipedia actually has a nice clear discussion of the alternative hypotheses or for a meatier discussion there's this paper from 2009 in the American Journal of Botany:
Phylogenetic relationships among seed plants: Persistent questions and the limits of molecular data

The Birds and the Bees and the Flowers and the Trees

Given that about 5% of angiosperms are dioecious but only a few cases of sex chromosomes have been discovered this raises the question of how sex is determined in the rest of these species. I found this nice review in the journal Genetics last year:
The Birds and the Bees and the Flowers and the Trees: Lessons from Genetic Mapping of Sex Determination in Plants and Animals

Sex determination is an important area of study in developmental and evolutionary biology, as well as ecology. Its importance for organisms might suggest that sex determination is highly conserved. However, genetic studies have shown that sex determination mechanisms, and the genes involved, are surprisingly labile.

The Evolution of Sex Chromosomes

Sex chromosomes have arisen independently in many taxonomic groups. It is an interesting question whether the same mechanisms were involved each time.

Sex chromosomes are an oddity in flowering plants. They are limited to dioecious species and only a few examples are known. The genus Silene, which includes the White Campion, includes both dioecious and hermaphrodite species and three of the dioecious species, Silene dioica, S. latifolia, and S. diclinis,  have an X-Y sex-determination system where Y specifies maleness.
Although the X-Y system evolved quite recently in Silene (less than 10 million years ago) compared to mammals (about 320 million years ago), our results suggest that similar processes have been at work in the evolution of sex chromosomes in plants and mammals, and shed some light on the molecular mechanisms suppressing recombination between X and Y chromosomes.

Ref:  Nicolas M, Marais G, Hykelova V, Janousek B, Laporte V, et al. (2005) A Gradual Process of Recombination Restriction in the Evolutionary History of the Sex Chromosomes in Dioecious Plants. PLoS Biol 3(1).

There's a synopsis of the article in the same issue: Evolution of Sex Chromosomes: The Case of the White Campion.

The plant in you (and vice versa)

 From: Double-fertilization, from myths to reality, a review from 2007 -

It is becoming gradually clear that although plant and animal kingdoms diverged more than 1 billion years ago, similar mechanisms govern sexual reproduction in both kingdoms. The review by Márton and Dresselhaus (2008) outlines some of these parallels. The current idiosyncratic nomenclature used to designate plant reproduction has obscured the parallels that now become apparent between plants and animals. It is likely to be the time to rethink the designation of each actor of the reproductive process such that the literature in the field becomes relevant to a broader readership working in the field of reproductive biology.
The  Márton and Dresselhauspaper referred to is A comparison of early molecular fertilization mechanisms in animals and flowering plants.

Dating tips

Not only is it adorably left wing but the Guardian newspaper in England actually sometimes has some decent science reporting. I enjoyed their Valentine's Day dating tips from lovestruck scientists. It even includes a list of references at the end - a very welcome trend. Here's an example, 

Tip #4: Cross a scary bridge

Here's another very simple tip for the ladies: frighten him. No, seriously. In 1974, University of British Columbia psychologists were studying human attraction using two bridges that crossed a local river. One bridge was solid, allowed firm footing, and was made of heavy cedar. It was only ten feet above the river, and had steady handrails. The other bridge was a five-foot-wide, 450-foot-long suspension bridge made of wire cables threaded through the ends of wooden boards. It would tilt, sway, and wobble as people tried to cross, 230 feet above the river.
Men who had just crossed one of the bridges were approached by an attractive female experimenter who asked them to complete several questionnaires. The men who had crossed the anxiety-inducing suspension bridge were more likely to attempt further contact with the experimenter than were the men who had crossed the stable bridge. The researchers suggest that it's as if the men misunderstood their anxiety-induced physiological arousal – elevated heart rate, sweaty palms, and so on – interpreting it as sexual attraction and desire.
Moral of the story: scare the crap out of him and he might just make a move.

Oh and don't forget - CCBER tomorrow.

Hidden Leg of an Ancient Snake

No, not an unreleased Jim Morrison poem, but a headline on ScienceDaily today reporting on the latest imaging of a 95 million year old snake fossil published in the Feb. 8, 2011 issue of the Journal of Vertebrate Paleontology.

A novel X-ray imaging technology is helping scientists better understand how in the course of evolution snakes have lost their legs. The researchers hope the new data will help resolve a heated debate about the origin of snakes: whether they evolved from a terrestrial lizard or from one that lived in the oceans. New, detailed 3-D images reveal that the internal architecture of an ancient snake's leg bones strongly resembles that of modern terrestrial lizard legs.

All your fly base are belong to us

Just to clarify, there are over 1,000 species of endemic Drosophila (fruit flies) on the Hawaiian Islands. These are all thought to have descended from a single introduction 26 million years ago.

Over one hundred of these Drosophila species are members of the 'picture wing group'. The figure I showed in class just depicts the hypothesized dispersal events necessary to create the 112 members of the picture wing group. Although the picture wing species are quite distinct from each other in morphology, pigmentation, and behavior it is now known that this explosive adaptive radiation occurred with relatively little change in DNA sequence. These factors make the Hawaiian Drosophila an important model system for analysis of evolutionary processes at the species level.

Learn more at FlyBase - A Database of Wing Diversity in the Hawaiian Drosophila

Speciation in action

The National center for Science Education currently has an excerpt from The Origin Then and Now: An Interpretive Guide to the Origin of Species available as a free preview:

Evolution Today: The mosquitoes of the London underground

This excerpt describes a wonderful example of speciation in action that I'm sure Darwin would have loved.

Public use of the London Underground began on January 10, 1863. That date, or perhaps some earlier date when the tunnels were being readied for traffic, marks the beginning of the path toward the formation of a new species of mosquito. We often wonder how long it takes to form a new species; Darwin speculated timescales on the order of tens of thousand to hundreds of thousands of generations. The mosquitoes of the London Underground show that if conditions are right, the process can be much faster.

Well worth a quick read. The original research paper on which this chapter is based is Culex pipiens in London Underground tunnels: differentiation between surface and subterranean populations.

Heterozygote advantage

At this point it's fairly clear that heterozygote advantage is not going to be a major force in the maintenance of genetic diversity simply because we've found so few examples. Perhaps not surprisingly with our rapidly expanding knowledge of genetics and gene function someone has now found some examples of heterozygote advantage that don't involve partial resistance to a disease. I missed this paper in PLoS ONE a few years ago:

Heterozygote Advantage for Fecundity
Heterozygote advantage, or overdominance, remains a popular and persuasive explanation for the maintenance of genetic variation in natural populations in the face of selection. However, despite being first proposed more than 80 years ago, there remain few examples that fit the criteria for heterozygote advantage, all of which are associated with disease resistance and are maintained only in the presence of disease or other gene-by-environment interaction. Here we report five new examples of heterozygote advantage, based around polymorphisms in the BMP15 and GDF9 genes that affect female fecundity in domesticated sheep and are not reliant on disease for their maintenance.

Rappemonads

Fluorescence micrographs of rappemonads in the North Pacific. The nucleus (blue) was often slightly elongated with a tapering end. Two to four plastids (green) appeared to be present per cell.

Like I said, the use of modern molecular methodology is allowing us to look at microbes within the oceans in ways never before possible and this is leading to some amazing discoveries - not just new twigs on the tree of life but major new branches we did not even know existed. This paper, in PNAS, last week has a fairly self-descriptive title:
Newly identified and diverse plastid-bearing branch on the eukaryotic tree of life

Here, we report a newly discovered uncultured plastid-bearing eukaryotic lineage named the rappemonads. 


Environmental DNA sequencing revealed extensive diversity at North Atlantic, North Pacific, and European freshwater sites, suggesting a broad ecophysiology and wide habitat distribution. 

The rappemonads are unique, widespread, putatively photosynthetic algae that are absent from present-day ecosystem models and current versions of the tree of life. 

Putting the dead to work

There's an interesting article in TREE (Trends in Ecology and Evolution) this month about the emerging science of conservation paleobiology.

There's a report at ScienceDaily: Putting the Dead to Work: Conservation Paleobiologists Dig Deep to Solve Today's Ecological, Evolutionary Questions, and the actual paper: Conservation paleobiology: putting the dead to work.

A new review of the research in this emerging field provides examples of how the fossil record can help assess environmental impacts, predict which species will be most vulnerable to environmental changes, and provide guidelines for restoration.

ScienceDaily is a good source for science news although it is almost always worth tracking down the original papers. They have got a lot better lately at including the full references at the end of their articles.

Overlooking the obvious

Weekend wildcard again.


Until now, the wing colors of many flies and wasps were dismissed as random iridescence. But they may be as distinctive and marvelous as the much-studied, much-celebrated wings of butterflies and beetles.

“Given favorable light conditions, they display a world of brightly patterned wings that are apparently unnoticed by contemporary biologists,” wrote researchers led by University of Lund entomologists Ekaterina Shevtsova and Christer Hansson in a December 3 Proceedings of the National Academy of Sciences paper: Stable structural color patterns displayed on transparent insect wings

Generations of biologists seem to have missed this partly because they didn’t look for it, and partly because the colors are most evident against a dark background. Against a white background, they’re invisible — which is exactly how most entomologists study transparent wings.

Weekend Wildcard

I try to make posts here roughly correspond to what we are covering in class (you don't have to feel quite as restricted) but because I have a life and because it gets hard posting every day I've decided to embrace a concept I dabbled with before - the weekend wildcard. Weekends are open to any posting on any topic of some relevance to the course.

Today is a great example because it pertains to science, the scientific method, how science is done and cards (wild or otherwise). All good fodder for an intro bio class. As some of you may have heard a leading psychology journal is about to publish an article providing evidence for ESP. Even the New York Times is writing about it:
Journal’s Paper on ESP Expected to Prompt Outrage
Some of the experiments are a little odd to say the least:
In another experiment, Dr. Bem had subjects choose which of two curtains on a computer screen hid a photograph; the other curtain hid nothing but a blank screen.
A software program randomly posted a picture behind one curtain or the other — but only after the participant made a choice. Still, the participants beat chance, by 53 percent to 50 percent, at least when the photos being posted were erotic ones. They did not do better than chance on negative or neutral photos.

You can read the actual paper here and a critique here.

The paper was reviewed by 4 referees before being accepted for publication. Should the extraordinary claims have required extraordinary evidence before publication? Should different papers have to meet different standards depending how well they fit our current paradigms? Is the publication of this paper helping or hindering the public perception of science? Is that even an issue scientists should be concerned with?

(I actually lied about having a life, posting here at 11:30 on a Saturday night kind of gives that away, but it does get tricky thinking of something to post every day, especially at the start of the class when we haven't covered very much.)

Chytrid fungi

Available online today through PNAS early edition:

Dynamics of an emerging disease drive large-scale amphibian population extinctions
and
Enzootic and Epizootic Dynamics of the Chytrid Fungal Pathogen of Amphibians

UCSB has the Cliff notes press release: Studies Offer New Insights Into How Deadly Amphibian Disease Spreads and Kills

Scientists have unraveled the dynamics of a deadly disease that is wiping out amphibian populations across the globe. Chytridiomycosis is caused by a microscopic aquatic fungus called Batrachochytrium dendrobatidis (Bd) that attacks the skin of amphibians. The new findings, from two separate studies published in today's online edition of the Proceedings of the National Academy of Sciences (PNAS), suggest that infection intensity –– the severity of the disease among individuals –– determines whether frog populations will survive or succumb to chytridiomycosis. The research identifies a critical tipping point in infection intensity, beyond which chytridiomycosis causes mass mortalities and extinctions. UC Santa Barbara's Cheryl J. Briggs, professor of Ecology, Evolution and Marine Biology and the Duncan and Suzanne Mellichamp Chair in Systems Biology, is lead author of the second study and a co-author of the first study. Other collaborators from UCSB were Roland A. Knapp, a research biologist with the Marine Science Institute, and graduate student Tate S. Tunstall.

Cherie currently has ten undergraduates including at least 4 and possibly 5 CCS students working in her lab on a variety of projects from modeling and database work to PCR and genetic analysis to foodweb and mesocosm studies. So if any aspect of this work sounds interesting then you should contact either Cherie or Mary Toothman, her lab manager, directly.

Not forgetting of course how many ways this work ties into our lectures this quarter - Chytrid fungus (check); vertebrates (check); community interactions (check).

More Museum

Claudia pointed me in the direction of some very topical links from the museum.

First, Paul Collins has a paper in the early edition of PNAS (available May 3 so this is hot off the press). This is a great example of how museums can be used for research and how the original collectors could have had no idea about the uses their collections would be put to.

The paper concerns a story Caludia told you during the ecology section - the changes in the food web on the California Channel Islands: Pleistocene to historic shifts in bald eagle diets on the Channel Islands, California

There have also been a couple of articles in the local Independent newspaper about the museum:

• Museum of Natural History Expands Into 21st Century
• Bye-Bye Blue Whale

Asphalt volcanoes

And on the topic of geology, check out some of the press on the newest members of the CCS Bio team, Professor Dave Valentine of Earth Sciences , has been getting.

Listen to a report on KCLU: A team of researchers has found a group of what are known as "asphalt volcanoes"...some up to 65 feet high...on the ocean floor off the Santa Barbara County coastline.

Or read about it on the National Geographic website or the NSF website.

This is relevant to biology for several reasons. First, in terms of methane production and the creation of 'dead zones':

Eruptions of the California mounds might have once spewed enough methane to dramatically boost populations of methane-eating marine bacteria.

These bacteria depleted the water's oxygen, creating a giant "dead zone" in the Santa Barbara basin that was lethal to most marine life.

and secondly in terms of creating hard substrates for colonization by living organisms:

Asphalt mounds in general help create environments for marine life that might not otherwise exist.

"Processes that produce hard substrates in the deep ocean are rare. ... Generally speaking, the deep ocean is a muddy place," MacDonald said.

"I think it's really cool that there's this other process that we didn't really know about before that, at least in some places, is making pretty extensive hard bottoms for animals to colonize."

Complexity and Diversity

In Science this week: Complexity and Diversity
The mechanisms for the origin and maintenance of biological diversity are not fully understood. It is known that frequency-dependent selection, generating advantages for rare types, can maintain genetic variation and lead to speciation, but in models with simple phenotypes (that is, low-dimensional phenotype spaces), frequency dependence needs to be strong to generate diversity. However, we show that if the ecological properties of an organism are determined by multiple traits with complex interactions, the conditions needed for frequency-dependent selection to generate diversity are relaxed to the point where they are easily satisfied in high-dimensional phenotype spaces.

"When you model one trait at a time--in isolation--you often find that ecological interactions aren't strong enough to drive divergence. But with many traits acting in concert, even very weak interactions can generate diversity. Our approach mirrors the complexity of reality more closely--if you think about it, all living organisms have at least dozens, if not hundreds, of ecologically relevant traits," says Doebeli.

Competition Drives Big Beaks Out of Business

The Darwin's Finch story I briefly mentioned is a fascinating part of a long term study by husband and wife team Peter and Rosemary Grant. They now have an amazing 37 year data set on these small birds on the Galapagos.

One of the latest parts of the story to be revealed was published in Science in 2006 as Evolution of Character Displacement in Darwin's Finches. It's also included in their news summary as Competition Drives Big Beaks Out of Business.

I think the fascinating part of this story is that it is the interaction of environment and competitors that drives evolution. Whilst resources are plentiful competition is weak but during the drought the effects of competition became severe.

Here we report that a Darwin's finch species (Geospiza fortis) on an undisturbed Galápagos island diverged in beak size from a competitor species (G. magnirostris) 22 years after the competitor's arrival, when they jointly and severely depleted the food supply. The observed evolutionary response to natural selection was the strongest recorded in 33 years of study, and close to the value predicted from the high heritability of beak size. These findings support the role of competition in models of community assembly, speciation, and adaptive radiations.