Monday, August 29, 2011

Resetting the Molecular Clock

Figure 1a
 Ya know, I haven't done a new creature feature in a while, and while I was flipping (and by that I mean scrolling) through the table of contents of the newest issue of Nature I came across a rather interesting new eutherian.

The therian mammals include placental mammals and marsupials. All of these animals can be distinguished by the number, morphology, and replacement pattern of their teeth. Eutherians are the true placental mammals. That means they bear live young that developed in and been nourished by a placenta within the mother's uterus, and unlike marsupials (or metatherians, which have a short-lived placenta) the eutherians' placenta contributes significantly to fetal nourishment. This group became common in central Asia during the Upper Cretaceous, and with exception of Australia (where marsupials rule), they have been the largest and most common land vertebrates following the end of the Mesozoic.

This new paper in describes a new species of eutherian the authors are naming Juramaia sinensis, a shrew-like animal alive during the Jurassic period. The fossil was discovered in the Liaoning Province in northeast China and is comprised of an incomplete skull including teeth, part of the skeleton including forepaw bones, and impressions of residual soft tissues such as hair. Juramaia is among the earliest known eutherians, and is a group that evolved to include all other placental mammals. It has adaptive features such as scansorial forelimbs that are good for climbing. When a majority of your mammalian cousins scuttle around on the ground, the ability to climb works to your advantage in evading predators and finding food. The fossil also provides the ancestral condition for dental and other anatomical features of eutherians.

This fossil find is so important because it "establishes a much older geological time for the split of the metatherian-marsupial and the eutherian-placental lineages than previously shown by the fossil record." J. sinensis is dated at 160 million years. Previously the earliest eutherian record is Eomaia and the metatherian record is Sinodelphys, both of which are 125 million years old. Parsimony analysis show Juramaia to be more closely related to extant placental mammals than to all other metatherians. This placement of Juramaia on the placental side of the marsupial-placental divergence means that the divergence itself must have occurred before Juramaia evolved. Add together the older age of the fossil and the parsimony analysis and you get a marsupial-placental divergence date that was at least 35 million years older than anyone previously thought. As it turns out, getting the timing of this divergence right is critical for calibrating the rates of evolution for all therian mammals. It is particularly useful for scientists doing molecular evolutionary studies and comparative genomics and their work in determining a "molecular clock." So far, there has been a discrepancy between the previous fossil record and the molecular age for the marsupial-placental divergence. Molecular studies have provided estimates of fossil ages between 143-178 million years which did not match up with the fossil evidence at the time. This new fossil now corroborates the molecular findings and sets the minimal divergence time to coincide with the molecular time estimates.

Love when things match up.

Here's the paper:
Luo, Zhe-Xi, et al. (2011) A Jurassic eutherian mammal and divergence of marsupials and placentals. Nature: 476, 442-445. (DOI: 10.1038/nature10291)

and...
http://www.sciencedaily.com/releases/2011/08/110824131535.htm

Evolution Made Simple

This is a unique and oh-so-simple way of explaining evolution. All with a line.

Friday, August 19, 2011

Free Market Fungi


For today's post we are going to go below ground and get a little dirty. I read a great paper this week about symbiotic fungi that I really liked because it was a simple, elegant experiment that yielded neat results.

Let's start with defining mycorrhizae (mahy-kuh-rahy-zuh). These are specialized fungi that colonize plant roots, forming a symbiotic relationship, with over 90% of terrestrial plants having these fungi. The plant supplies the fungus with energy substrates, carbon (or sugars), for growth and development. The fungus supplies the plant with water and nutrients from the soil. It grows on the root but also extends an intricate network of hyphae through the soil, greatly increasing the surface absorbing area for the plant, sort of like having extended roots. They can also access hard-to-capture nutrients, such as organic nitrogen and phosphorus, and make them available for the plants to use. The benefits of having mycorrhizae are many. They allow for increased absorption efficiency, increased drought resistance, and increased pathogen resistance. It has also been shown that plants with mycorrhizae are overall healthier and less stressed, grow better as seedlings, and can be transplanted easier. And most plants have several different species of mycorrhizae on them at any one time.

There are three general types of mycorrhizae: (1) ectomycorrhizae, (2) endomycorrhizae, (3) orchid mycorrhizae. The distinction between the types is based on the morphology of the structure formed by the fungi and the plants, if there is penetration of the root cells or not. I'm going to leave out defining the orchid mycorrhizae because they are a pretty specialized group and just stick to the other two main ones. Ectomycorrhizas are mostly Ascomycetes and Basidiomycetes and are often found on woody plants. They are able to penetrate between, but not into, the cortical cells of the plants' root. Because of this, they form a thick hyphal mat that surrounds the root and a network of strands within the cortex called a "Hartig net." This type of fungus also forms a mantle which completely encloses the root tip, this is also where the hyphae extend into the soil. Endomycorrhizae or arbuscular mycorrhizas (alternately or formerly the vesicular-arbuscular mycorrhizas) are far more abundant and classified in the Order Glomales. Arbuscular mycorrhizas (AM) penetrate inside the walls of the cortical cells producing vesicles and highly branched structures called arbuscules.

A new paper in the journal Science takes a closer look at the symbiosis between plants and AM fungi. It is known that plants supply this fungi with carbohydrates and in exchange the AM fungi provide the plants with mineral nutrients (e.g., phosphorus) and the protections I listed above. However, the selective forces that maintain this mutualism are unknown. What keeps the plant from taking nutrients from the fungi and giving nothing back in return? After all, the plant is giving away nutrients that it would otherwise be using, incurring a cost. Or the fungi takes the carbon but gives nothing back to the plant? But if the symbiont interest are tightly aligned then the fungal symbionts should increase their own fitness by helping the plants, and vise versa. Makes sense, right? Now, add multiple fungal species, with each species simultaneously interacting with multiple plants. This is a great opportunity for "cheaters," fungi that exploit the benefits of getting food while avoiding the costs of supplying resources. This paper looks at the question of how these symbiotic partners maintain a fair, two-way transfer of resources. How they keep each other honest.

The researchers used the model plant Medicago truncatula (a small plant that looks kinda like clover) and three arbuscular mycorrhizal (AM) fungal species within the cosmopolitan subgenus Glomus Ab (Glomus intraradices, G. custos, and G. aggregatum). They chose these particular AM fungi because they are closely related and exhibited either high or low levels of cooperation (giving lots or little phosphorus). This cooperation was measured in plant growth responses, costs of carbon per unit phosphorus transferred, and resource hoarding strategies (fungal resource storage). They grew M. truncatula hosts with one, two (G. intraradices versus G. aggregatum), or all three AM fungal species. Then they followed the carbon flux from the plant to the fungi and the incorporation of host carbon into the RNA of the fungal assemblage (because it reflects C allocation patterns).

They found that more carbon was supplied to the more-cooperative fungal species. In both the two-species and three-species experiments the RNA of the cooperative fungus (G. intraradices) was significantly more carbon enriched than the less-cooperative fungus. In fact, the plants showed a host preference in communities where a more cooperative fungus species was available. The extent to which the mutualism can be enforced depends on the scale at which the plants can discriminate in this way. But because we are talking small little fungi, and lots of different kinds, the discrimination scale would need to be fine. This idea lead the researchers to the next part of their experiment, looking at whether fine-scale host discrimination occurs.

To test this they used an in vitro triple split-plate system. It sounds all complex but is actually rather simple. They took a petri dish and divided it into 3 equal sections or compartments.One compartment had mycorrhizal roots and two have fungi composed of the same fungal species but varying in phosphorus supply. Its a good system because it allows the root to "choose" which fungus it wants to partner with based on the amount of nutrients (carbon) transferred from the fungus. They also tested the reverse - if the fungi enforced cooperation by the plant. They used the same split-plate system but used one fungal compartment and two root compartments, making the fungi choose which root it wanted to partner with.

The researchers found that the plant rewarded the fungus that supplied the most phosphorus, more carbon was transferred to the fungus with access to more phosphorus. In the reverse test they found that the cooperative fungus (G. intraradices) transferred more phosphorus to the roots with greater access to carbon resources. So both the plant and the fungi are discriminating. In the less-cooperative species (G. aggregatum) no carbon allocation differences were found, and it transferred more phosphorus to the roots with more carbon access but stored the phosphorus in a host-inaccessible form. It was a little phosphorus hoarder, tsk tsk.

And finally, the researchers wanted to determine whether the fungi are stimulated to provide more phosphorus in direct response to a greater host carbon supply. So they created an experiment to track the simultaneous resource exchange between the plant and fungi by using a two compartment plate and exposing the roots to labeled carbon (U-14C sucrose) in either high or low concentrations and adding labeled phosphorus (32P) to the fungal compartment. They found that increasing the carbon supply stimulated the phosphorus transfer by the cooperative fungus but not the less cooperative fungus.

Overall, this paper shows that the mutualism in this system is different than that you find other systems. It isn't controlled by only one partner but, instead, both sides interact with each other to keep the other honest. Each of the partners cooperates with the other, preferentially rewarding them for good service. And this is where the title for this post comes from. The authors equate this system to a market economy, "where there are competitive partners on both sides of the interaction and higher quality services are remunerated in both directions."

Kumbaya.

Read the entire paper here:
Kiers, E. Toby, et al. (2011) Reciprocal rewards stabilize cooperation in the mycorrhizal symbiosis. Science: 333(6044), 880-882. (DOI: 10.1126/science.1208473)

Learn more about mycorrhizae here:
The Davies Lab at Texas A&M University
Botany at the University of Hawaii
Foresty 442 Notes from Oregon State University

(image from dirtdoctor.com)

Blame It On Reviewer #3

If you have ever submitted a paper for peer review then you will find this video especially wonderful.

(Embedding disabled on this vid so click the picture to take you to it)

Wednesday, August 10, 2011

Friday, August 5, 2011

And So the Lion Fell in Love with the Muggle


When you see an academic, peer reviewed, published paper with the title "Becoming a Vampire Without Being Bitten" you stop, you read, you blog.

To say that most people like being parts of groups would, in my opinion, be stating the obvious. Think about your own life for a minute. You probably belong to all kinds of groups. Maybe it's sports, a hobby, a social group. We are driven by a need for social connection. We can even assimilate into a group where we do not belong by adopting its behaviors, attitudes, and traits. This type of assimilation is the topic of today's post, except this paper tests it in a unique and entertaining way.

Let's combine the idea of reading a good book, getting caught up in the story and the idea of assimilation. The idea that experiencing a story, a narrative, leads to psychological assimilation with the group described in the story is what the authors of the paper are calling the narrative collective-assimilation hypothesis. Now, studies have shown that people experience a sense of belonging when they read a story, or that familiar narratives can alleviate loneliness. Some people may identify with certain characters which may lead to a merging of self with those characters. If you took a look at the brains of readers you would notice that the regions that are activated when they read are very similar to the regions activated when they imagine and actually engage in the activities.

The study tested this hypothesis by having people read a passage from Harry Potter and the Sorcerer's Stone to see if it would lead them to "become" wizards or a passage from Twilight to see if they would "become" vampires. The researchers recruited 140 volunteers and had them go through a series of steps.

Step 1: The participants completed the Collective and Rational Self-Construal Scale to gauge their "tendency to fulfill the need to belong through collective and relational bonds." Basically, the more a person needs to fulfill a social need through identifying with a group the more they will exhibit this narrative collective assimilation.

Step 2: They read. If you are like me then you want to know which sections of the books were picked. From Harry Potter and the Sorcerer's Stone the participants read chapters 7 ("The Sorting Hat") and chapter 8 ("The Potions Master") in which Harry and his wizard friends are sorted into their school houses and Harry first encounters Professor Snape. From Twilight the participants read chapter 13 ("Confessions") where Edward describes to Bella what it is like to be a vampire.

Step 3: The participants answered the Implicit Association Test that asked them questions about their implicit identification with vampires relative to wizards. For example, they were asked to categorize "me" words (myself, mine) and "wizard" words (wand, broomstick, spells, potions) or "not me" words (they, theirs) and "vampire" words (blood, undead, fangs, bitten).

Step 4: The participants completed the Twilight/Harry Potter Narrative Collective-Assimilation Scale. As names for tests go this one is right up there with the best. The questions were designed to measure collective assimilation of Twilight vampires ("Compared to the average person, how high do you think you could jump?" "How long could you go without sleep?" and "How sharp are your teeth?") and of Harry Potter wizards ("How British do you feel?" "Do you think, if you tried really hard, you might be able to make an object move just using the power of your mind?" and "Do you think you might ever be able to make yourself disappear and reappear somewhere else?"). The British one is my favorite.

Step 5: The participants completed the Transportation Scale, that measured their level of absorption into the story, the Positive and Negative Affect Schedule, that measured mood, a life satisfaction measure, and questions about their reading habits.

That's a whole lot of surveys!

After scoring all the answers to all those surveys the researchers found support for their narrative collective-assimilation hypothesis. People who read Harry Potter associated themselves with wizards. People who read Twilight associated themselves with vampires. This association was moderated by the degree to which these people fulfilled their belongingness needs with stories. People also reported positive affect and increased life satisfaction. You can't, and the authors didn't, ignore the fact that people like to affiliate with symbolic groups (like celebrities). They suggest that the mechanism demonstrated in their paper also may help to explain the affiliation people like with these groups.

So next time you pick up your favorite Harry Potter book (mine is Azkaban) or read your Twilight books for the million-and-oneth time think to yourself, "How British am I?" or "Am I sparkling?" Or you could just enjoy your favorite read. Right now I'm reading A Game of Thrones and think I might like to get a direwolf.

Here's the paper:
Gabriel, Shira and Ariana F. Young (2011) Becoming a vampire without being bitten: The narrative collection-assimilation hypothesis. Psychological Science: published online 12 July. (DOI:
10.1177/0956797611415541)

(image via geekcrafts.com)

Wednesday, August 3, 2011

Sweet Home Apparatus

If you love the Golgi Apparatus you will love this.

Gaydar: A Scientific Approach


I've been hearing about some studies recently on various podcasts and news outlets and decided to look them up and see what they were all about. Studies about how people perceive other people are, in my opinion, interesting if often difficult to quantify. Perception, in an evolutionary and/or social context, can be very useful in informing an individual about potential enemies, friends, or mates. The topic of today's post focuses on the latter.

There has been some recent evidence that people are capable of extracting information from nonverbal behaviors and the appearance of other people. The most important social cues are those from the face. Think about it. We recognize faces more accurately than we do most other parts of the body. We can also classify individuals into groups just by looking at their faces. With just a glimpse we can tell identity, emotional states, sex, age, race, etc.

Today's post looks at an article recently published in Psychological Science concerning the perceptions of women to the sexual orientation of men. Studies have shown that gay men tend to make more accurate judgements of sexual orientation than do straight men. This may be due to in-group effects of perception and memory. Similar studies have shown that women tend to be better judges of nonverbal behavior than men are, and that extroverts are better judges of peoples' traits than are introverts. How can we boil this down to a biological, mechanistic explanation? How about fertility? Women can categorize male faces faster than female faces at higher periods of fertility. Also, when they are nearer ovulation, they rate masculinized faces and body gaits as more attractive. Conversely, lesbian women categorize female faces faster than male faces at periods of higher fertility. Today's paper takes a look at women's accuracy in judging male sexual orientation during various points in their fertility cycle as it potentially has sexual relevance. To test this the researchers broke their study down into three parts:

Study 1:
This first study hypothesized that women nearer to peak ovulation would be more accurate in judging male faces. Participants included heterosexual women who were not using any contraceptive medications and who reported regular cycles. They presented these participants with photographs of gay and straight men and asked them to judge sexual orientation. The women were then asked questions to judge where in their cycle they were currently at. The results showed that the women's accuracy was significantly greater the closer they were to peak ovulation. Perhaps this is because a woman's success in conceiving is greater the nearer she is to peak ovulation, and therefore she needs to have greater accuracy in identifying a suitable mate for reproductive success.

Study 2:
The procedures for this study were identical to those in Study 1 with the exception that the participants viewed the faces of 100 lesbian and 100 straight women and asked to judge sexual orientation. The hypothesis here being that ovulation would not affect the categorization of sexually irrelevant women's faces. The results showed that the women's accuracy was not related to their fertility when they judged these other women. Based on this it appears that the link between fertility and accuracy only applies to men. This is consistent with the reproductive success hypothesis suggested in Study 1.

Study 3:
This study used experimental manipulation to examine women's accuracy in judging sexual orientation. To do this they compared the judgements of "women primed with a mating goal" with the judgements of "nonprimed control" women presented with male faces and female faces. What is the first thing you think of when yu read that sentence? Me? It's how do you prime a woman with a mating goal? First, get your mind out of the gutter please. The researchers had the women read a story which "described a romantic encounter." Ok, so I didn't actually look up the story they used but I'm picturing that typical bodice-ripping poolside paperback that so many women are apt to read. Anyway, after reading the story the women were asked to judge faces. The results showed that these primed women were significantly more accurate in judging men's sexual orientations than women who had not been primed. However, this priming had no effect on the accuracy of the judgments of women's sexual orientations.

Overall, these studies suggest that "a disposition toward mating increases heterosexual women's accuracy in detecting the sexual orientation of members of the opposite sex." Basically, hitting on a gay man gets a straight woman nowhere so her gaydar needs to be accurate for her to find an appropriate mate.

Here's the paper:
Rule, Nicholas O. et al. (2011) Mating interest improves women's accuracy in judging male sexual orientation. Psychological Science: 22(7), 881-886. (DOI: 10.1177/0956797611412394)

For additional information on perceptions take a look at the research and publication list of the first author of this paper:
http://www.psych.utoronto.ca/users/rule/

(image from codeproject.com)
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