Yearly Archives: 2007

There are 29 new papers on PLoS ONE this week, and it is difficult to narrow down to just a few of my own ‘choices’:
An Inhibitory Sex Pheromone Tastes Bitter for Drosophila Males:

For animals to breed successfully they must avoid trying to mate with individuals of the same sex. Lacaille and colleagues show that an organic compound, Z-7-tricosene, is carried on the cuticular surface of the fruit fly Drosophila. This compound tastes bitter to flies and acts as a pheromone that prevents male-male courtship.

Protistan Diversity in the Arctic: A Case of Paleoclimate Shaping Modern Biodiversity?:

It is likely that extreme changes in world climate over geological time have shaped the diversity of life on earth. Stoeck and colleagues compared the diversity of single-celled organisms from a very hot refuge (hydrothermal vent communities) with those from a very cold refuge (a tidal flat in the Arctic). Their data suggests that the Arctic community is more diverse, leading to the idea that cold refuges have persisted throughout eukaryote evolution.

The Intersexual Genetic Correlation for Lifetime Fitness in the Wild and Its Implications for Sexual Selection:

The genetic benefits of mate choice are limited by the degree to which male and female fitness are genetically correlated. If the intersexual correlation for fitness is small or negative, choosing a highly fit mate does not necessarily result in high fitness offspring.
Using an animal-model approach on data from a pedigreed population of over 7,000 collared flycatchers (Ficedula albicollis), we estimate the intersexual genetic correlation in Lifetime Reproductive Success (LRS) in a natural population to be negative in sign (−0.85±0.6). Simulations show this estimate to be robust in sign to the effects of extra-pair parentage. The genetic benefits in this population are further limited by a low level of genetic variation for fitness in males.
The potential for indirect sexual selection is nullified by sexual antagonistic fitness effects in this natural population. Our findings and the scarce evidence from other studies suggest that the intersexual genetic correlation for lifetime fitness may be very low in nature. We argue that this form of conflict can, in general, both constrain and maintain sexual selection, depending on the sex-specific additive genetic variances in lifetime fitness.

Biphasic Hoxd Gene Expression in Shark Paired Fins Reveals an Ancient Origin of the Distal Limb Domain:

The evolutionary transition of fins to limbs involved development of a new suite of distal skeletal structures, the digits. During tetrapod limb development, genes at the 5′ end of the HoxD cluster are expressed in two spatiotemporally distinct phases. In the first phase, Hoxd9-13 are activated sequentially and form nested domains along the anteroposterior axis of the limb. This initial phase patterns the limb from its proximal limit to the middle of the forearm. Later in development, a second wave of transcription results in 5′ HoxD gene expression along the distal end of the limb bud, which regulates formation of digits. Studies of zebrafish fins showed that the second phase of Hox expression does not occur, leading to the idea that the origin of digits was driven by addition of the distal Hox expression domain in the earliest tetrapods. Here we test this hypothesis by investigating Hoxd gene expression during paired fin development in the shark Scyliorhinus canicula, a member of the most basal lineage of jawed vertebrates. We report that at early stages, 5′Hoxd genes are expressed in anteroposteriorly nested patterns, consistent with the initial wave of Hoxd transcription in teleost and tetrapod paired appendages. Unexpectedly, a second phase of expression occurs at later stages of shark fin development, in which Hoxd12 and Hoxd13 are re-expressed along the distal margin of the fin buds. This second phase is similar to that observed in tetrapod limbs. The results indicate that a second, distal phase of Hoxd gene expression is not uniquely associated with tetrapod digit development, but is more likely a plesiomorphic condition present the common ancestor of chondrichthyans and osteichthyans. We propose that a temporal extension, rather than de novo activation, of Hoxd expression in the distal part of the fin may have led to the evolution of digits.

More…
Optimal Conservation of Migratory Species:

Migratory animals comprise a significant portion of biodiversity worldwide with annual investment for their conservation exceeding several billion dollars. Designing effective conservation plans presents enormous challenges. Migratory species are influenced by multiple events across land and sea-regions that are often separated by thousands of kilometres and span international borders. To date, conservation strategies for migratory species fail to take into account how migratory animals are spatially connected between different periods of the annual cycle (i.e. migratory connectivity) bringing into question the utility and efficiency of current conservation efforts.
Here, we report the first framework for determining an optimal conservation strategy for a migratory species. Employing a decision theoretic approach using dynamic optimization, we address the problem of how to allocate resources for habitat conservation for a Neotropical-Nearctic migratory bird, the American redstart Setophaga ruticilla, whose winter habitat is under threat. Our first conservation strategy used the acquisition of winter habitat based on land cost, relative bird density, and the rate of habitat loss to maximize the abundance of birds on the wintering grounds. Our second strategy maximized bird abundance across the entire range of the species by adding the constraint of maintaining a minimum percentage of birds within each breeding region in North America using information on migratory connectivity as estimated from stable-hydrogen isotopes in feathers. We show that failure to take into account migratory connectivity may doom some regional populations to extinction, whereas including information on migratory connectivity results in the protection of the species across its entire range.
We demonstrate that conservation strategies for migratory animals depend critically upon two factors: knowledge of migratory connectivity and the correct statement of the conservation problem. Our framework can be used to identify efficient conservation strategies for migratory taxa worldwide, including insects, birds, mammals, and marine organisms.

Is Bacterial Persistence a Social Trait?:

The ability of bacteria to evolve resistance to antibiotics has been much reported in recent years. It is less well-known that within populations of bacteria there are cells which are resistant due to a non-inherited phenotypic switch to a slow-growing state. Although such ‘persister’ cells are receiving increasing attention, the evolutionary forces involved have been relatively ignored. Persistence has a direct benefit to cells because it allows survival during catastrophes-a form of bet-hedging. However, persistence can also provide an indirect benefit to other individuals, because the reduced growth rate can reduce competition for limiting resources. This raises the possibility that persistence is a social trait, which can be influenced by kin selection. We develop a theoretical model to investigate the social consequences of persistence. We predict that selection for persistence is increased when: (a) cells are related (e.g. a single, clonal lineage); and (b) resources are scarce. Our model allows us to predict how the level of persistence should vary with time, across populations, in response to intervention strategies and the level of competition. More generally, our results clarify the links between persistence and other bet-hedging or social behaviours.

Wrinkly-Spreader Fitness in the Two-Dimensional Agar Plate Microcosm: Maladaptation, Compensation and Ecological Success:

Bacterial adaptation to new environments often leads to the establishment of new genotypes with significantly altered phenotypes. In the Wrinkly Spreader (WS), ecological success in static liquid microcosms was through the rapid colonisation of the air-liquid interface by the production of a cellulose-based biofilm. Rapid surface spreading was also seen on agar plates, but in this two-dimensional environment the WS appears maladapted and rapidly reverts to the ancestral smooth (SM)-like colony genotype. In this work, the fitness of WS relative to SM in mixed colonies was found to be low, confirming the WS instability on agar plates. By examining defined WS mutants, the maladaptive characteristic was found to be the expression of cellulose. SM-like revertants had a higher growth rate than WS and no longer expressed significant amounts of cellulose, further confirming that the expression of this high-cost polymer was the basis of maladaptation and the target of compensatory mutation in developing colonies. However, examination of the fate of WS-founded populations in either multiple-colony or single mega-colony agar plate microcosms demonstrated that the loss of WS lineages could be reduced under conditions in which the rapid spreading colony phenotype could dominate nutrient and oxygen access more effectively than competing SM/SM-like genotypes. WS-like isolates recovered from such populations showed increased WS phenotype stability as well as changes in the degree of colony spreading, confirming that the WS was adapting to the two-dimensional agar plate microcosm.

Predicting Prokaryotic Ecological Niches Using Genome Sequence Analysis:

Automated DNA sequencing technology is so rapid that analysis has become the rate-limiting step. Hundreds of prokaryotic genome sequences are publicly available, with new genomes uploaded at the rate of approximately 20 per month. As a result, this growing body of genome sequences will include microorganisms not previously identified, isolated, or observed. We hypothesize that evolutionary pressure exerted by an ecological niche selects for a similar genetic repertoire in those prokaryotes that occupy the same niche, and that this is due to both vertical and horizontal transmission. To test this, we have developed a novel method to classify prokaryotes, by calculating their Pfam protein domain distributions and clustering them with all other sequenced prokaryotic species. Clusters of organisms are visualized in two dimensions as ‘mountains’ on a topological map. When compared to a phylogenetic map constructed using 16S rRNA, this map more accurately clusters prokaryotes according to functional and environmental attributes. We demonstrate the ability of this map, which we term a “niche map”, to cluster according to ecological niche both quantitatively and qualitatively, and propose that this method be used to associate uncharacterized prokaryotes with their ecological niche as a means of predicting their functional role directly from their genome sequence.

Now, you know what to do: read the papers, rate them, add comments/questions….

Interaction Of Just Two Genes Governs Coloration Patterns In Mice:

Biologists at Harvard University and the University of California, San Diego, have found that a simple interaction between just two genes determines the patterns of fur coloration that camouflage mice against their background, protecting them from many predators. The work, published recently in the journal PLoS Biology, marks one of the few instances in which specific genetic changes have been linked to an organism’s ability to survive in the wild.

More…
Birds Learn To Fly With A Little Help From Their Ancestors:

A researcher at the University of Sheffield has discovered that the reason birds learn to fly so easily is because latent memories may have been left behind by their ancestors. It is widely known that birds learn to fly through practice, gradually refining their innate ability into a finely tuned skill. However, according to Dr Jim Stone from the University of Sheffield´s Department of Psychology, these skills may be easy to refine because of a genetically specified latent memory for flying.

More…
Conquest Of Land Began In Shark Genome:

Scientists at the University of Florida have identified genetic activity in sharks required for the development of hands, feet, fingers and toes in limbed animals. The finding shows what was thought to be a relatively recent evolutionary innovation existed eons earlier than previously believed, potentially providing insight for scientists seeking ways to cure human birth defects.

Largest Butterfly In Western Hemisphere Needs Help To Avoid Extinction:

The Homerus swallowtail is the Western Hemisphere’s largest butterfly, but University of Florida researchers say its numbers are so small that conservation and captive breeding efforts are needed to save the insect, found only in two parts of Jamaica.

Tropical Insects ‘Go The Distance’ To Inform Rainforest Conservation:

The long-held belief that plant-eating insects in tropical forests are picky eaters that stay “close to home” — dining only on locale-specific vegetation — is being challenged by new research findings that suggest these insects feast on a broader menu of foliage and can be consistently found across hundreds of miles of tropical forestland.

Simulated Relationships Offer Insight Into Real Ones:

Is it me, or are you a less than ideal partner? For psychologists studying how people manage romantic relationships, that’s not an easy question to answer. What if one of the partners is deeply afraid of intimacy? Could she be acting in ways that undermine the relationship? Or is her partner contributing to the problem? In a new study appearing in Personality and Social Psychology Bulletin, researchers at the University of Illinois explore these issues by looking at the choices people make in simulated online dating relationships. By standardizing the behavior of the romantic “partner,” the study clarifies how each participant’s outlook influences his or her choices and satisfaction with the romance.

A nice integration over several levels of analysis:
Adaptive Variation in Beach Mice Produced by Two Interacting Pigmentation Genes by Cynthia C. Steiner, Jesse N. Weber, and Hopi E. Hoekstra:

The tremendous amount of variation in color patterns among organisms helps individuals survive and reproduce in the wild, yet we know surprisingly little about the genes that produce these adaptive patterns. Here we used a genomic analysis to uncover the molecular basis of a pale color pattern that camouflages beach mice inhabiting the sandy dunes of Florida’s coast from predators. We identified two pigmentation genes, the melanocortin-1 receptor (Mc1r) and its ligand, the agouti signaling protein (Agouti), which together produce a light color pattern. We show that this light pigmentation results partly from a single amino acid mutation in Mc1r, which reduces the activity of the receptor but does not affect the gene’s expression level, and partly from the derived Agouti allele, which shows no change in protein sequence but does exhibit an increase in mRNA expression. We also show that these two genes do not act additively to produce pale color; rather, the derived Agouti allele must be present to see any effect of Mc1r on pigmentation. Thus, the light color pattern of beach mice largely results from the physical interaction between a structural change in a receptor (reducing Mc1r activity) and a regulatory change in the receptor’s antagonist (increasing Agouti expression).

Navigation: Using Geometry To Navigate Is Innate, At Least For Fish:

Many animals, including humans, frequently face the task of getting from one place to another. Although many navigational strategies exist, all vertebrate species readily use geometric cues; things such as walls and corners to determine direction within an enclosed space. Moreover, some species such as rats and human children are so influenced by these geometric cues that they often ignore more reliable features such as a distinctive object or colored wall.
This surprising reliance on geometry has led researchers to suggest the existence of a geometric module in the brain. However, since both humans and laboratory animals typically grow up in environments not entirely made up of right angles and straight lines, the prevalent use of geometry could reflect nurture rather than nature. A new study published in the July issue of Psychological Science, a journal of the Association for Psychological Science, is the first attempt to examine whether early exposure to strong geometric cues influences navigational strategy.

Unravelling New Complexity In The Genome:

A major surprise emerging from genome sequencing projects is that humans have a comparable number of protein-coding genes as significantly less complex organisms such as the minute nematode worm Caenorhabditis elegans. Clearly something other than gene count is behind the genetic differences between simpler and more complex life forms.

Rainforest Biodiversity Shows Differing Patterns:

Rainforests are the world’s treasure houses of biodiversity, but all rainforests are not the same. Biodiversity may be more evenly distributed in some forests than in others and, therefore, may require different management and preservation strategies. That is one of the conclusions of a large-scale Smithsonian study of a lowland rainforest in New Guinea, published in the Aug. 9 issue of the journal Nature.

Evolution Is Driven By Gene Regulation:

It is not just what’s in your genes, it’s how you turn them on that accounts for the difference between species — at least in yeast — according to a report by Yale researchers in this week’s issue of Science.

Gene Regulation, Not Just Genes, Is What Sets Humans Apart:

The striking differences between humans and chimps aren’t so much in the genes we have, which are 99 percent the same, but in the way those genes are used, according to new research from a Duke University team. It’s rather like the same set of notes being played in very different ways.

Which Came First, The Moth Or The Cactus?:

It’s not a good idea to put all your eggs in one basket… unless you’re a senita moth. Found in the parched Sonoran desert of southern Arizona and northern Mexico, the senita moth depends on a single plant species — the senita cactus — both for its food and for a place to lay eggs. The senita cactus is equally dependent upon the moth, the only species that pollinates its flowers. Senita cacti and senita moths have a rare, mutually dependent relationship, one of only three known dependencies in which an insect actively pollinates flowers for the purpose of assuring a food resource for its offspring.