peer-reviewed paper

What do Great Tits Reveal about the Genetics of Personality?

grrlscientist — Thu, 08 Apr 2010 09:59:56 +0000

What do Great Tits Reveal about the Genetics of Personality?

tags: evolutionary biology, behavioral ecology, molecular ecology, personality, novelty seeking, exploratory behavior, dopamine receptor, dopamine receptor D4 gene, DRD4 gene polymorphism, ornithology, birds, Great Tit, Parus major, researchblogging.org,peer-reviewed research, peer-reviewed paper

Bold or cautious? Individuals with a particular gene variant are very curious --
but only in some populations.

Image: Henk Dikkers.

Research suggests that personality variations are heritable in humans and other animal species, and there are many hypotheses as to why differences in personality exist and are maintained. One approach for investigating the heritability of personality lies in identifying which genes underlie specific personality traits so scientists can then determine how the frequencies of specific variants of personality-related genes change in both space and time as well as in relation to changing environmental influences.

For example, in humans, the best-studied "personality gene" is the dopamine receptor D4 (DRD4) gene, which is involved in motivation, pleasure, cognition, memory, and learning. The DRD4 gene encodes a receptor protein that binds to the neurotransmitter, dopamine. When DRD4 binds dopamine, this interaction influences novelty seeking and exploratory behavior in a range of species, including humans and birds.

As is true for most genes, there are variants -- known as polymorphisms -- of DRD4. These polymorphisms alter the binding dynamics of DRD4 for its ligand, dopamine: different variants bind dopamine more or less tightly, and this difference in binding affinity alters behavior. For example, previous research has suggested that variations in the DRD4 gene in the Great Tit, Parus major, are the underlying reason that some of these birds are more curious than others [DOI: 10.1016/j.biopsych.2007.04.006]. This association was originally noted and tested in 2007 in only one population of Great Tits that were hand-raised captives [DOI: 10.1098/rspb.2007.0337].

But association studies such as these rarely show consistent correlations between genes and behavior across populations and environments. Thus, it was decided to repeat this work with large numbers of wild Great Tits from four distantly located populations.

"It was important to confirm the association between the DRD4 variants and exploratory behavior in the original population," explained Bart Kempenaers, director at the Max Planck Institute for Ornithology in Germany.

To repeat this work, Dr Kempenaers and an international team of scientists captured young adult birds captured in the field (Figure 1) from four different populations -- including wild relatives of the original group of captive Great Tits studied; Westerheide.

Fig. 1 Locations of four wild great tit populations investigated for associations between exploratory behaviour and DRD4 SNP830 and ID15 polymorphisms. Populations are Westerheide (WH), Lauwersmeer (LM), Boshoek (BH) and Wytham Woods (WW).
DOI: 10.1111/j.1365-294X.2009.04518.x

To do this work, the team captured only wild birds that had been individually marked with color-coded leg bands when nestlings, so they knew the precise age and family relationships for each bird. After capture, the birds were kept overnight in individual cages adjacent to the test chamber. The following morning, each bird was separately released into the test chamber, a novel environment containing five artificial "trees," and the bird's behavior was documented. The frequency of hops and flights between the perches on the artificial trees were counted and scored as a proxy for exploratory behavior (pictured below).

Test chamber containing five artificial "trees" where the birds' exploratory behaviors in a novel environment were assessed.
DOI: 10.1111/j.1365-294X.2009.04518.x

Image: Anne Rutten.

Prior to releasing the birds in their respective homes, a feather or a small blood sample was collected and then the two DRD4 gene variants (SNP830 and ID15) were identified for each of the 491 individual birds. When the team analyzed the genetic data, they were surprised to learn that the frequency of the SNP830 and ID15 polymorphisms of DRD4 were the same in all of the populations (Figure 2):

Fig. 2 Proportions of DRD4 SNP830 (A) and ID15 (B) genotypes in four wild great tit populations: Westerheide (WH), Lauwersmeer (LM), Boshoek (BH) and Wytham Woods (WW).
DOI: 10.1111/j.1365-294X.2009.04518.x

Interestingly, although the team found that DRD4 polymorphisms were statistically the same, the average exploratory scores differed significantly between the four populations studied (Figure 3):

Fig. 3 Box plots of exploration scores (corrected for seasonal trend) of four wild great tit populations: Westerheide (WH), Wytham Woods (WW), Boshoek (BH), and Lauwersmeer (LM). Box plots indicate medians and the 10th, 25th, 75th and 90th percentiles; 5th and 95th percentiles are indicated by the filled circles; the open circles indicate the population means.
DOI: 10.1111/j.1365-294X.2009.04518.x

To their surprise, the team found that exploratory behavior demonstrated by the Westerheide population was significantly associated with SNP830 genotype, while birds from the other three populations showed either a weak or nonexistent correlation (Figure 4):

Fig. 4 Exploration scores (corrected for seasonal trend; means with standard errors) of wild great tits of four populations in relation to the DRD4 SNP830 genotype. Exploration scores were significantly associated with SNP830 genotype in Westerheide.
DOI: 10.1111/j.1365-294X.2009.04518.x

Additional analyses showed that the strength of this association was not different between the original 2007 group of hand-raised birds and the free-living birds from the population tested in this follow-up study.

"But," Dr Kempenaers cautioned, "we do not yet understand the differences between populations."

They also found that the relationship between the SNP830 genotype and exploratory behavior was independent of the sex of individuals.

"To our knowledge, this is the most extensive study of gene variants underlying personality-related behavioral variation in a free-living animal to date, and the first to compare different wild populations", said Peter Korsten, first author on the paper and a former member of Bart Kempenaers' lab.

These differences between avian populations are a reiteration of the age-old "nature versus nurture" controversy. Basically, an individual gene's influence on behavior is usually subtle and very likely occurs in concert with many other still unidentified genes. Additionally, a gene's located on a chromosome is important: close neighbors on the DNA strand tend to travel together during genetic reassortment, even when their functions are quite different, so these findings could be a "location artifact." Further, genetic effects probably play a small role in personality when compared to the strong influence of the environment, especially in species such as birds where learning is so vitally important to their socialization.

"Perhaps further investigation of Great Tit populations could shed some light on the differences in outcome in the human populations," suggested Dr Korsten optimistically.

For example, several polymorphisms in the DRD4 gene sequence have been identified in humans that are associated with certain mental health and cognitive disorders such as attention-deficit hyperactivity disorder.

Call me a skeptic, but I do not share Dr Korsten's optimism.

Source:

Korsten, P., Mueller, J., HermannstÃ¤dter, C., Bouwman, K., Dingemanse, N., Drent, P., Liedvogel, M., Matthysen, E., van Oers, K., van Overveld, T., Patrick, S., Quinn, J., Sheldon, B., Tinbergen, J., & Kempenaers, B. (2010). Association between DRD4 gene polymorphism and personality variation in great tits: a test across four wild populations. Molecular Ecology, 19 (4), 832-843 DOI: 10.1111/j.1365-294X.2009.04518.x

grrlscientist Thu, 04/08/2010 - 05:59

Most. Misleading. Title. Ever.

Not that misleading. If you were thinking of a great rack, aka human female mammaries, you could easily make a not so great jump to the conclusion that 'Within a population/culture/region individuals with similar phenotypes tend to express similar personalities, but that same phenotype in a different place will most certainly have different personalities from your previous population.'
Right?

not even nearly, Chris. there used to be a webpage around titled "watch these great tits", leading to a webcam of the inside of a birdhouse --- the ornithologist's version of rickrolling.

(the hatchlings were pretty cute, though.)

tits are among the world's cutest birds.

How cute are boobies, though?

They are about as cute as hooters.

At the risk of stoking the fires of innuendo further, Titmouse (the original name of these birds) derives from the Middle English "tit" meaning small and the old German "mees" also meaning small so the bird is really "smallsmall". Anagram says "Timeouts"

Publish or Perish: A Brief Review of Unsuccessful Attempts to Treat Writer's Block

grrlscientist — Thu, 01 Apr 2010 06:59:41 +0000

Publish or Perish: A Brief Review of Unsuccessful Attempts to Treat Writer's Block

tags: writer's block, psychology, abnormal psychology, cognitive psychology, writing, publishing, career, publish or perish, researchblogging.org,peer-reviewed research, peer-reviewed paper, journal club

Sources:

Didden, R., Sigafoos, J., O'Reilly, M., Lancioni, G., & Sturmey, P. (2007). A Multisite Cross-Cultural Replication of Upper's (1974) Unsuccessful Self-Treatment of Writer's Block. Journal of Applied Behavior Analysis, 40 (4), 773-773 DOI: 10.1901/jaba.2007.773

Upper, D. (1974). The unsuccessful self-treatment of a case of "writer's block". Journal of Applied Behavior Analysis, 7 (3), 497-497 DOI: 10.1901/jaba.1974.7-497a

grrlscientist Thu, 04/01/2010 - 02:59

UV, You See? Black Light Reveals Secrets in Fossils

grrlscientist — Tue, 30 Mar 2010 12:29:13 +0000

UV, You See? Black Light Reveals Secrets in Fossils

tags: evolution, evolutionary biology, UV light, flight, dinosaur, dromaeosaur, theropods, Microraptor gui, paleontology, fossils, birds, researchblogging.org,peer-reviewed research, peer-reviewed paper, journal club

Figure 1. The holotype of Microraptor gui, IVPP V 13352 under normal light. This shows the preserved feathers (white arrow) and the 'halo' around the specimen where they appear to be absent (black arrows). Scale bar at 5 cm. [larger view]
DOI: 10.1371/journal.pone.0009223

It has long been known that when exposed to ultraviolent light, fossilized bones and shells -- and even tissues -- will fluoresce, thus rendering undetectable details visible. But this technique has been used mostly to visualize fossilized invertebrates, and inexplicably, has rarely been used to investigate hidden structures in most vertebrate fossils. But a team of paleontologists recently studied the Microraptor gui holotype using UV light.

"UV light work has been going on for decades but few people do much of it, and with the cost of color photos often only a few minor images are published, or the results are simply used to help improve a description," remarked paleontologist David Hone, a postdoctoral fellow at the Chinese Academy of Sciences, Beijing, China and first author of the newly published paper. "As such even within scientific circles this work is not too well known, something I hope will change."

Under visible light, the holotype of the non-avian dinosaur, Microraptor gui, unearthed in China, is associated with many fossilized feathers distributed around its body. In addition to numerous small contour feathers, Microraptor gui fossils also are associated with long asymmetrically shaped "flight" feathers on the arms and tail but also, surprisingly, on the legs, leading some to refer to this species as the "four-winged bird." But these flight feathers don't actually reach the limb bones in any of the dozen or so specimens of Microraptor gui examined. Instead there is a curious 'halo' of space between where the bones end and the feathers start (Figure 1, above).

''[T]here's insufficient evidence of the attachment of these feathers to the hind limbs," said paleontologist Kevin Padian at the University of California-Berkeley [DOI: 10.1641/0006-3568(2003)053[0451:FDBPON]2.0.CO;2].

"There seems to be a gap between the vaned area of feathers that are near the hind limbs and the bones of the hind limbs themselves," Dr Padian explained.

In contrast, flight feathers do reach the tail and limb bones in the basal avialan, Archaeopteryx, and in other feathered non-avian Liaoning fossils, so why is this not seen in any specimens of Microraptor gui? The obvious answer is that the fossil feathers moved from their original locations prior to preservation and thus do not appear as they did in life. They could have come free and drifted away from the bones, for instance, or the portions of the feathers that were close to the body might not have not been preserved, or they might have been destroyed during fossil preparation itself.

But regardless of the underlying reason for Microraptor gui's peculiar 'halo' effect, these specimens have meaningful implications for our understanding of the origin of flight in birds, particularly for the possibility that there might have been a four-winged gliding phase, so it is important to determine whether the fossil flight feathers were actually attached to the animal's body.

Dr Hone, together with his colleagues, Helmut Tischlinger, a retired teacher who was awarded an honorary PhD for his work with Solnhofen fossils, Xing Xu, a research fellow at the Institute of Vertebrate Paleontology and Paleoanthropology of the Chinese Academy of Sciences (CAS) in Beijing, and Fucheng Zhang, a senior research fellow at CAS, wanted to determine if the 'halo' of non-preservation observed between the skeletons and the feathery plumage is real or a preservation artifact.

To carry out this study, they spent several weeks photographing the Microraptor gui holotype while illuminating it with powerful UV-A lamps that produced light with a wavelength between 365 and 366 nanometers. They also used a variety of color correction filters (yellows, blues and reds of different types and densities and in different combinations) made from special colored glass or polyester that were affixed either to the camera or to the microscope lens (Figure 2):

Figure 2. The holotype of Microraptor gui, IVPP V 13352 under UV light. Different filters were employed for parts A [larger view] and B [larger view], hence the difference in colour and appearance. A also is labeled to indicate the preserved feathers (grey arrows) and the 'halo' around the specimen where they appear to be absent (black arrows) as well as phosphatised tissues (white arrows). Scale bars are 5 cm in both A and B.
DOI: 10.1371/journal.pone.0009223

"The mechanics are fairly simple in that we basically just shine some very powerful UV lights at the fossil and take photos," explained Dr Hone. "It can take dozens of shots to get a good one and some of the exposures take an hour or more. It therefore takes a lot of time, skill, patience and especially experience to get these results."

Using this method, the team focused on the hind limbs and found that shafts of the UV-illuminated feathers are visible in the 'halo' region (Figure 3):

Figure 3. Close up of lower hindlimb of the holotype under UV light. This shows that the feathers do indeed penetrate the halo (grey arrows) when seen in UV and approach or reach the bones. These are not seen in natural light due to the overlying soft tissues seen in figure 2. Scale bar at 5 cm. [larger view]
DOI: 10.1371/journal.pone.0009223

"[T]he fact that the leg feathers do have bone-deep attachments could be used as an argument that they are used in flight," continued Dr Hone. "However, the asymmetry of these feathers is a far more important character and we can't really add anything to the previous work in that respect."

Further, the feather filaments around the throat and chest were also quite clear under UV illumination when in fact, they are invisible under natural light (Figure 4):

Figure 4. Close up of the chest of the holotype, close to the sternal plates under UV light. As with figure 3, this shows that the feathers do indeed penetrate the halo (grey arrows) when seen in UV and approach or reach the bones. These are not seen in natural light due to the overlying phosphatised tissues, but the striations of the feathers are clearly visible despite this covering. Scale bar of 1 cm. [larger view]
DOI: 10.1371/journal.pone.0009223

Based on their findings, Dr Hone and his team concluded that Microraptor gui's feathers are probably preserved in their original and natural positions. The feather were not decayed, nor were they moved or otherwise disturbed prior to fossilization. Second, they also found that Microraptor gui's feathers do actually reach the bones of the animal, even though their bases were obscured. Of course, it also means that previously published measurements of the feathers are in error: the feathers are longer than assumed.

Figure 5. Close up of the lower part of the holotype under UV light. Variation in the phosphatised tissues can be seen (white arrows) as well as the bright reflectance of various glues and preservatives that have been applied to the specimen at various times (black arrows). Scale bar of 2 cm. [larger view]
DOI: 10.1371/journal.pone.0009223

Even though the findings reported in this paper provide a nice opportunity to show you lots of detailed photographs of Microraptor gui, the take-home message is about what UV illumination means in regards to fossil preservation and preparation. There is a lot of hidden information waiting to be uncovered in many fossils, even long after they've come to light, and this information can be accessed by using a variety of techniques, such as UV light illumination.

Unfortunately, scientists miss all kinds of rare and valuable soft-tissue information by not using all of the techniques available to them, often because they are unaware of them. If paleontologists and fossil preparators are unaware of the variety of hidden information that a fossil might contain, they risk destroying it during preparation. Already, at least one museum now regularly prepares fossil material with UV light (as already has happened with one famous fossil, Juravenator, for example).

"This lack of awareness is certainly starting to change with UV work slowly gaining attention and prominence but I hope that this paper will accelerate that process," Dr Hone writes on his blog, Archosaur Musings.

Dr Hone and his team hope that publishing their study in PLoS ONE will raise paleontologists' awareness of the utility of this powerful technique.

"PLoS1 is, after all, an open access journal and UV stuff is not especially hard to do. Now that there is extensive documentation of the methods in a very well distributed format, that can only be a good thing bearing in mind the results that UV can bring."

Dr Hone and his colleagues also think that taking another, closer look at well-studied fossils using UV illumination could yield more discoveries that have remained hidden under the light of day.

"Long may [UV illumination] continue, and more importantly, the faster it spreads the more chance we have of being able to write papers like this in the future where we can get new information out of otherwise 'exhausted' specimens."

Source:

Hone, D., Tischlinger, H., Xu, X., & Zhang, F. (2010). The Extent of the Preserved Feathers on the Four-Winged Dinosaur Microraptor gui under Ultraviolet Light. PLoS ONE, 5 (2) DOI: 10.1371/journal.pone.0009223

grrlscientist Tue, 03/30/2010 - 08:29

Categories

Life Sciences

There's an interesting series on the Beeb at the moment about the Natural History Museum in London, and all the stuff they do besides the public galleries. Part of that was about the massive collection of specimens that people don't normally see, kept for reference and for further study with new techniques.

I find it fascinating that people can learn so much from such complicated and obscure things as fossils and microscopy, just by looking at them. I had enough trouble doing cell drawings at school when I knew what I was looking at. (Total absence of artistic talent didn't help.)

Made for Each Other: Evolution of Monogamy in Poison Frogs

grrlscientist — Mon, 29 Mar 2010 06:59:23 +0000

Made for Each Other: Evolution of Monogamy in Poison Frogs

tags: evolution, evolutionary biology, behavioral ecology, animal behavior, molecular ecology, parental care, mating systems, monogamy, sexual selection, frogs, poison dart frogs, Dendrobatidae, Ranitomeya, researchblogging.org,peer-reviewed research, peer-reviewed paper, journal club

Peruvian mimic poison frog, Ranitomeya imitator.

Image: Jason Brown [larger view]

To know the breeding system is to know the genetic architecture of a species.
To know the evolution of a breeding system is to know how evolution works ..

~ Lewis & Crowe, Evolution (1955)

Genetic tests have revealed the secret sex life of a tiny poison dart frog species that lives in the Peruvian rain forests: remarkably, it turns out that these frogs are monogamous. But the reason this species is monogamous is surprising: it's all about the size of the pools that their tadpoles mature in. This is the best evidence yet that just a single cause can affect evolution of a major life history trait, such as a species' mating system.

The forces that underlie the evolution of biparental care have been the subject of lively debate within the scientific community, and in turn, how different forms of parental care affect the evolution of each species' mating system is also not well understood.

According to one long-standing hypothesis proposed by mammologist Devra Kleiman, monogamy may arise as a life history strategy when biparental care becomes critical to offspring survival. In this situation, both parents may experience higher reproductive success by investing in their mutual offspring instead of seeking extrapair reproductive opportunities [DOI: 10.1086/409721]. Life history studies of a variety of avian and mammalian taxa support this hypothesis.

But which ecological factors drive the evolution of biparental care and monogamy? Is just one ecological factor enough, or is more than one necessary? One way of answering these questions is to compare the life histories and ecologies of closely related species where one species is monogamous and provides biparental care while the other is promiscuous and does not provide biparental care. But which species fulfill these criteria?

Jason L. Brown, now a postdoctoral researcher at Duke University, spent six years studying Peruvian poison frogs while a graduate student at East Carolina University. In those studies, he evaluated key ecological and behavioral differences between Peruvian poison frogs and framed those key differences in the context of differing parental care strategies. Building upon his dissertation work, Dr Brown and his colleagues, Victor Morales, at the Ricardo Palma University's Natural History Museum in Lima, Peru, and his dissertation advisor, Kyle Summers, Associate Professor in the Department of Biology at East Carolina University, took a closer look at two closely-related poison frog species: the mimic poison frog, R. imitator, which exhibits biparental care (where both parents care for their tadpoles for a period of months) and the variable poison frog, R. variabilis, which exhibits male parental care (where only the males transport tadpoles to a pool of water and leaves them to fend for themselves).

Like all amphibians, poison frogs are intimately bound to water because that is where they lay their eggs and where their tadpoles mature. But bodies of water are filled with numerous hungry mouths, so the pressures of predation pushed the tiny poison frogs out of the larger ponds and into the considerably smaller (but safer) pools contained in the cup-shaped leaf axils of a variety of plant species that grow in trees. These tree-top plants are not often visited by hungry predators, but their small pools of rainwater, known as phytotelms, lack sufficient nutrients to successfully grow a tadpole (unlike larger ponds of water).

To ensure that their tiny offspring grew up into mature frogs, the mimic poison frogs adopted a new tactic. Merely transporting their tadpoles to individual phytotelms and abandoning them to grow up on their own was no longer enough: the males needed help. Female mimic poison frogs evolved a behavioral strategy known as trophic egg feeding, where they lay unfertilized nutrient-rich eggs into each tadpole's phytotelm for it to eat.

But this strategy requires teamwork: while the female spends her days eating voraciously so her body can manufacture these special trophic eggs, the male visits each tadpole every day or two, for only he knows where they are hidden. Whenever a tadpole nibbles on its father, the male calls to his mate. The female responds to the male's calls by following him to their offspring's phytotelm, jumps into the tiny pool and produces a trophic egg, which the tadpole consumes. The female produces at least one trophic egg for each tadpole every week for a period of months (Figure 1):

Figure 1: Biparental care in Ranitomeya imitator. The male leads a female to a deposition site within their territory. The female will then oviposit one to four eggs on the surface of a leaf, away from water. A, A week after oviposition, the male returns and retrieves its tadpoles, breaking the tadpole free from the egg sack and allowing the tadpole to wriggle onto its back. B, The male then deposits the tadpole in an unoccupied pool of water within the pair's territory. The male will then survey the pool every couple of days and determine when the tadpole is fed trophic egg(s). C, To initiate egg feeding, the male begins to call from the surface of the pool, and after a short period, the tadpole's mother arrives. D, After an extended bout of calling, eventually the female will dive into the pool and deposit a trophic food egg (depicted in white within the center of the plant; female is within the pool). This behavior is repeated on average every 7.3 days throughout the duration of development of the tadpole. [larger view]
DOI: 10.1086/650727.

Dr Brown's dissertation work revealed that the closely related variable poison frogs did not engage in biparental care, despite sharing the same habitat and habits as the mimic poison frog (The mimic poison frog imitates the brilliant color patterns of this poisonous species, so they even look very similar). In variable poison frogs, only the males relocated newly hatched tadpoles to a phytotelm and left them there to mature. But what was different between these two species?

To investigate this question, Dr Brown and his colleagues compiled a variety of natural history data from 404 frog species distributed across the entire amphibian taxonomic order Anura and reconstructed the evolution of these characters. They then analyzed these data to find any correlations between the evolutionary transitions to phytotelm breeding and parental care (Figure 2):

Figure 2: Different scales of this study. Comparative analyses were carried out on a much larger scale than our experimental and genetic analyses both in terms of phylogenetic scope (A; looking at the order Anura vs. two closely related species in the genus Ranitomeya, family Dendrobatidae) and in the context of type of reproductive resources (B; comparing all sizes of reproductive resources being used vs. two small phytotelmata). In general, species that utilize larger bodies of water exhibit lower levels of parental care.
DOI: 10.1086/650727.

The only difference that Dr Brown found between the variable and mimic poison frogs was the size of the phytotelms themselves: male variable poison frogs deposited their tadpoles into pools that averaged 112 mL in volume, compared with just 24 mL in those pools used by mimic poison frogs -- a five-fold size difference. Based on these data, Dr Brown and his colleagues proposed that pool size was the driving force in the evolution of biparental care. The team then tested their hypothesis by moving tadpoles from both species into differently sized pools and monitoring their growth (Figure 5):

Figure 5: Reciprocal transplant experiments. We used five treatments in which the tadpoles of each species were placed in natural phytotelmata and allowed to consume the resources within the pools. The tadpoles were weighed and measured at the start and end of the experiment. Error bars = 2 SEs.
DOI: 10.1086/650727.

The team found that tadpoles in larger pools thrived while tadpoles in smaller pools did not grow. This led them to conclude that tadpoles maturing in larger, more nutrient-rich pools didn't need both parents, unlike their smaller-pond counterparts. Thus, species that raised their tadpoles in smaller ponds required attention from both parents. In turn, this favored parents who remained devoted only to the offspring that they produced together -- but did it also drive the evolution of monogamy?

To answer this question, the researchers first had to determine whether mimic poison frogs are truly monogamous. They sampled DNA from 12 mimic poison frog families and their tadpoles and were surprised to find that in 11 of those frog families, the parents were faithful to one another, while in only one family did the male frog have two mates. This is even more surprising because genetic testing has shown that many animals thought to be monogamous are less faithful than previously believed.

Monogamy "turns out to be relatively rare, even in birds and mammals -- particularly in mammals -- and reptiles," reported Dr Summers. "Finding a frog that has a monogamous mating system was pretty novel for us."

In contrast, genetic studies of 12 pairs of the closely related variable poison frog indicates that this species is promiscuous.

"Others have found evidence of social monogamy in amphibians where parents remain paired, however they didn't look at the genetics of these couples and their offspring to confirm this," explained Dr Brown. "Or they have looked at the genetics and observed that they are actually promiscuous."

But which came first; parental care or small pond size? The team explored this question by estimating the rates of evolutionary change for all four possible combinations of these two character traits, each with two possible states: terrestrial water body breeding versus phytotelm breeding and no parental care versus parental care. Their analysis indicated that the most likely evolutionary pathway from ancestral pond-breeding species without parental care to phytotelm-breeding species with parental care progressed from pond breeding to phytotelm breeding, followed by the evolution of parental care (Figure 3):

Figure 3: Evolutionary pathways from the ancestral condition of terrestrial water body (lentic/lotic) breeding without parental care to phytotelm breeding with parental care. Each value of q represents the rate estimated (via maximum likelihood) for that particular transition from our phylogenetic tree (Supertree [Nexus], available in the zip file in the online edition of the American Naturalist). Simultaneous changes in both characters are not allowed under the maximum likelihood model employed in the method. Log-likelihood ratio tests reveal that the most likely evolutionary pathway involves the evolution of phytotelm breeding followed by the evolution of parental care.
DOI: 10.1086/650727.

The team also investigated the interaction between trophic egg feeding and biparental care to determine which of these characters evolved first. To do this, they mapped those characters onto a "mirror tree." A mirror tree is a graphically elegant analytic method where particular character states are mapped onto a phylogenetic tree to test the evolutionary interaction between those particular characters. The underlying assumption of mirror trees is that these interacting characters co-evolved (Figure 4):

Figure 4: Mirror tree including only those species with egg feeding and one closely related taxon, illustrating the concentrated changes test of an association between egg feeding and biparental care (see Dryad data; Breeding Site Refs, Supertree [Nexus], PhytoEvol, and PCEvol are available in a zip file in the online edition of the American Naturalist).
DOI: 10.1086/650727.

This analytic method reveals that trophic egg feeding evolved before biparental care.

Overall, the researchers think they have found convincing evidence of an evolutionary chain of causation: first, by dramatically reducing the size of their breeding pools, mimic poison frog couples were forced to work together, providing biparental care for their offspring so the tadpoles would survive and mature. That change then culminated in both social and genetic monogamy.

"This is the first discovery of a truly monogamous amphibian," said Dr Brown. "These frogs are truly devoted to their offspring, and to each other."

Is it possible to draw any parallels between mimic poison frogs and human behaviors?

"People are interested in whether there are parallels between mating systems of other species and our own. Of course, the human situation is so different from other species. It's somewhat perilous to over interpret the similarities," Dr Brown wisely cautioned. "You can't just translate it."

Dr Brown's fascinating research into the reproductive habits of mimic poison frogs was filmed by the BBC and included in their natural history documentary series Life in Cold Blood, narrated by David Attenborough:

Source:

Brown JL, Morales V, & Summers K (2010). A key ecological trait drove the evolution of biparental care and monogamy in an amphibian. The American Naturalist, 175 (4), 436-46 DOI: 10.1086/650727; PMID: 20180700

Read more about Jason Brown's fascinating work in Poison Dart frogs (index of PDF links to most of his published work).

grrlscientist Mon, 03/29/2010 - 02:59

Categories

Life Sciences

Thanks -- this is great and I will use it in my animal behavior class!

oh, wow! i am surprised and pleased that you dropped in to read this essay! i actually have pitched an idea to write an essay (or maybe a series of essays) in a story-like format (similar to this essay) about the evolution of the red queen hypothesis. i imagine that you, in particular, will have some interesting things to contribute to that .. !

Gender-Bending Chickens: Mixed, Not Scrambled

grrlscientist — Fri, 12 Mar 2010 11:59:43 +0000

Gender-Bending Chickens: Mixed, Not Scrambled

tags: evolution, evolutionary biology, gynandromorph, bilateral gynandromorph bird, half-sider, mixed-sex chimaera, sex determination, molecular biology, genetics, developmental biology, endocrinology, birds, chicken, Gallus gallus, ornithology, researchblogging.org,peer-reviewed research, peer-reviewed paper, journal club

Half-sider.

Almost exactly one year ago, hundreds of American birders
were thrilled by sightings and photographs of this remarkable
Northern Cardinal, or Redbird, Cardinalis cardinalis,
photographed in Warrenton, VA.
Image: DW Maiden, 2 March 2009.

I'll never forget the first time I saw a bilateral gynandromorph. I was a bird-crazy teenager reading my way through a stack of avicultural publications when I spied the strangest bird I'd ever seen on the cover of one magazine: an eclectus parrot that was very precisely divided down the middle: one side was rich scarlet and the other was brilliant emerald. Because eclectus parrots are sexually dimorphic -- females are red and males are green -- this remarkable bird was easily identifiable as being composed of both sexes, one on each side.

Even though this was the first time I'd ever seen a gynandromorph, these mysterious birds do pop up from time to time. For example, bird watchers occasionally run across them in the wild (see above photograph) and poultry farmers sometimes find them in their flocks: it is estimated that roughly one in 10,000 domestic chickens -- another sexually dimorphic species -- is a gynandromorph.

Bilateral gynandromorphs are mysterious because nothing like them has been seen in mammals, so they generate a lot of speculation whenever they turn up.

It was widely assumed that sexual development in birds and mammals follows basically the same trajectory. In almost all mammals, including humans, embryonic cells start off being "unisex"; indistinguishable regardless of which sex chromosomes they contain. Early in development, the sex-determining region of the Y chromosome (Sry) controls whether a testis or ovary forms: if Sry is present, testes grow, while ovaries develop in the absence of Sry. By the seventh week of embryonic life, the developing gonads begin secreting chemical messengers -- hormones -- that direct other cells to develop as either male or female.

Given this paradigm, scientists studying gynandromorphs were surprised to discover that sexual development in birds is dramatically different from most mammals: unlike mammals, individual chicken cells apparently "know" which sex they are at the time of fertilization and they maintain their own male or female identities throughout life.

"We assumed that sex determination in birds would follow the mammal pattern," reports Michael Clinton, a developmental biologist at the University of Edinburgh in Scotland. Because Dr Clinton has spent much of his scientific life scratching his head over why it was so difficult to find the avian Sry in chicken chromosomes, he was intrigued by these peculiar chickens and quickly assembled a team of scientists to study the birds.

Dr Clinton and his colleagues originally hypothesized that one side of bilaterally gynandromorphic birds would be a genetically normal female (or male) while the other side suffered some kind of chromosomal anomaly or mutation. In their journey to understand the molecular and cellular mechanisms that lead to a gynandromorph, these researchers made a fundamental and bizarre discovery about sexual development.

This story begins serendipitously enough. A few years ago, an employee in the poultry industry described to Dr Clinton some peculiar chickens on nearby farms. These rare chickens were bilateral gynandromorphs; half male and half female. Like my eclectus, these birds were neatly divided down the middle between their male and female sides, almost as if two individuals of opposite sexes had been stitched together.

These "half-siders," as poultry farmers and aviculturists often refer to bilateral gynandromorphs, are rare, but have been seen in a number of avian families, ranging from finches to pigeons to parrots. Most recently, a wild gynandromorphic Northern Cardinal, Cardinalis cardinalis, was photographed on the East Coast of the United States almost exactly one year ago, re-igniting interest and speculation among online birders throughout the world (see featured image at top).

Like northern cardinals, domestic chickens are sexually dimorphic. So when Dr Clinton first saw these oddly lopsided chickens, he was immediately impressed by the birds' striking appearance: the larger male side had white feathers, spurs, large wattles and breast muscles, whereas the smaller female side showed the characteristic dark coloring, small wattles, and the lack of spurs (Figure 1):

Figure 1 | Image of gynandromorph bird (G1). ISA brown bird where the right side has female characteristics and left side has male characteristics (white colour and larger wattle, breast musculature and spur).
DOI: 10.1038/nature08852

Dr Clinton's team eventually obtained three of the unusual birds, which are referred to in their newly published paper as G1, G2 and G3. All three were ISA brown birds, a commercial breed with sex-linked plumage color. ISA brown males are heterozygous for the dominant silver and recessive gold genes (Ss) so they have white plumage; females possess only the gold gene (s-) and thus have brown plumage.

Careful observations of the behaviors displayed by one of the team's gynandromorphs, G1, which came to them already named "Sam" -- Samantha for the right side and Samuel for the left -- showed that it not only looked strange, but it was also a bit confused.

Although gynandromorphs are nearly always sterile, "Sam seemed to think it was male," reports Dr Clinton. "But when we put it in with a couple of females I don't think they were too sure."

This confusion was also apparent when the birds' gonads were examined: G1 contained a testis-like gonad on the left side, G2 contained an ovary-like gonad on the left side, and G3 contained a swollen testis-like structure on the left side (in contrast to G1 and G2, G3 appeared female on the left side and male on the right).

G1's testis-like gonad was composed primarily of sperm containing seminiferous tubules, whereas the G2 ovary-like gonad was composed predominantly of large and small follicles. The gonad from G3 comprised a mixture of empty tubules and small follicularlike structures (ovo-testis).

While the researchers were observing their three odd chickens, they were also collecting tissue samples and examining the chromosomes to decipher the molecular mechanisms underlying bilateral gynandromorphs.

The team tested whether the chickens suffered from a genetic anomaly by examining the chromosomes found in tiny samples of blood as well as skin, breast muscle and wattles collected from both sides of each gynandromorph. They color-coded the chromosomes in these cells with fluorescent dyes that stick to either the Z or W sex chromosomes and examined them with confocal microscopy.

Contrary to their prediction, they found that fluorescently-labeled cells collected from opposite sides of the same bird were either predominantly normal male or female cells, while the blood was a mixture of normal male and female cells. The gynandromorphs were in fact nearly perfect male:female chimæras comprised of normal female cells with ZW sex chromosomes on one side, whereas the cockerel side contained mostly normal male cells with male sex chromosomes, ZZ (Figure 2):

Figure 2 | Male and female cells in gynandromorph birds. a, FISH analysis of sex chromosomes in gynandromorph blood cells. Shown are interphase nuclei prepared from cultured blood cells from gynandromorph G1 hybridized according to standard FISH procedures with probes specific to both the W and Z chromosome (XhoI repeat on W chromosome, and Z chromosome bacterial artificial chromosome (BAC) containing the VLDL receptor gene identified by screening the HGMP chicken BAC library). Erythrocytes were hybridized with probes for Z chromosome (green) and W chromosome (red). Cells contain either two Z chromosomes or one Z and one W chromosome. b, Mean relative proportions of ZZ and ZW cells in tissues from male and female sides of gynandromorph birds. The average percentage of ZW and ZZ cells (Supplementary Table 2 [GrrlScientist comment: data not shown here]) in three tissues from the phenotypically female side and from the phenotypically male side of three gynandromorph birds is shown. Tissues from the sides that appear female contain more ZW (female) than ZZ (male) cells, whereas tissues from the sides that appear male are composed predominantly of ZZ cells. BM, breast muscle; Sk., skin; Wa., wattle. [larger view]
DOI: 10.1038/nature08852

Because mammalian cells are strongly influenced by sex hormones after embryonic gonads begin to develop, the team wondered if this was also true for birds. They investigated whether sex differences between male and female cells exist independently of gonadal hormone influences or if individual cells assume the same sexual identity as their neighbors. To test this, they compared gene expression in male and female embryos during the developmental stages before the gonads form, and discovered that even at these early stages, male and female cells already "know" their sexual identity by showing sex-specific gene expression profiles (Figure 3):

Figure 3 | Sexually dimorphic expression in early chick embryos. a, Expression of FAF in male and female embryos before development of genital ridge/gonads. Whole-mount ISH showing expression of FAF (purple) in embryos at 18 h, 48 h and 72 h of development (H&H stages 4 (original magnification, 340), 14 (320) and 20 (310), respectively). FAF is clearly expressed throughout the female embryos at all developmental stages and is not expressed in male embryos. FAF is not expressed in extraembryonic tissues of the female. The FAF transcript is encoded by the genomic DNA complementary to the intergenic regions between copies of the W-chromosome repeat gene Wpkci (also called HINTW) and transcribed in the opposite orientation. f, female; m, male. b, Expression of novel chicken miRNA (Gallus gallus mir-2954). Expression in whole embryos at 48 h (H&H 14) and 72 h (H&H 20) of development is shown. This miRNA is clearly expressed in a sexually dimorphic fashion at stages before the sexual differentiation of the gonads. This miRNA matches sequence present in chicken Z-chromosome BAC clones AC192757 and AC187119. U6 RNA was used as a loading control. [larger view]
DOI: 10.1038/nature08852

Intrigued, the team then tested whether individual cells respond to the overwhelmingly male or female environment seen on each side of bilateral gynandromorphs -- do male cells "conform" to a mostly female environment by assuming a female role, and vice versa? To examine this possibility, they created embryos containing chimæric gonads by embedding female cells in male host tissue and vice versa. They found that male donor cells embedded in female host cells didn't take on female roles. Similarly, female donor cells embedded in male host cells didn't assume male functions, either (Figure 4):

Figure 4 | Expression of male and female markers in chimæric gonads. a, Generation of chimæras. Left: schematic illustrating transplantation of presumptive mesoderm from GFP-expressing embryo to non-GFP embryo at day 2. Right: image of mesonephros and gonads from chimæric embryo at day 9 showing donor contribution to left gonad (g), mesonephros (m) and Müllerian duct (md). Original magnification, 320. b, Expression of female and male markers in embryonic gonads. Expression of aromatase (AROM) in ovary and anti-Müllerian hormone (AMH) in testis at day 9 is shown by IHC. Original magnification, 3400. c, Integration of GFP-expressing donor cells into host gonads. Panels in the first column show a low-magnification view of sections through host gonads and illustrate the extent of donor cell contribution. Panels to the right show higher-magnification views of highlighted areas. Using IHC, donor cells are marked by GFP (green) whereas expression of AMH and aromatase are shown in red. The fourth column is a merged image of the images from the second and third columns. In same-sex chimæras, GFP-expressing donor cells co-localize with AMH expressing and aromatase-expressing cells in host testis and ovary, respectively (yellow/orange in the fourth column). In mixed-sex chimæras, GFP-expressing donor cells do not co-localize with AMH or aromatase. m, mesonephros; o, ovary; t, testis. d, Retention of female donor phenotype in mixed-sex chimæras. IHC showing expression of AMH(red in top row) and aromatase (red in bottom row) in neighbouring sections from the gonad of a female:male (donor:host) chimæra. Donor contribution is illustrated by GFP (green) expression. The right column shows a merged image of the images in left and middle columns. Regions containing a significant host contribution (defined by the bottom bracket) formed sex-cord-like structures and expressed AMH. Female donor cells were not incorporated into AMH-expressing sex cords, as shown by the lack of GFP and AMH colocalization. Regions composed primarily of female donor cells (defined by top bracket) behaved as ovarian-like tissue and expressed aromatase, as shown by co-localization of GFP and aromatase (yellow/orange). Scale bars in c and d indicate 100 μm. IHC was performed following standard procedures. Primary antibodies were (1:100) goat anti-human AMH (Santa Cruz Biotechnology), (1:200) mouse anti-human cytochrome P450 aromatase (AbD Serotec) and (1:250) rabbit anti-GFP conjugated to Alexa Fluor 488 (Invitrogen). Secondary antibodies were conjugated to Alexa Fluor 594 (Invitrogen). [larger view]
DOI: 10.1038/nature08852

Based on these data, the team concluded that individual avian cells maintain their own sexual identity and were not able to switch sexual roles despite developmental signals from nearby cells: their gender orientation was fixed from their inception.

Since these data clearly establish the presence of both ZZ- and ZW-containing cells, the team realized that it is highly unlikely that gynandromorphs arise as a consequence of either a mutation or a loss of a sex chromosome at the two-cell stage of development, as they originally predicted. Thus the team proposed that bilateral gynandromorphs start at the very beginning: they result from the failure of the developing ovum to extrude a polar body during meiosis (refer to figure at right). When this abnormal ovum containing two pronuclei is fertilized (by two sperm, a situation known as polyspermy), it contains both a Z- and W-containing nucleus, which then give rise to each half of the whole bird -- a bilateral gynandromorph. (Avian sperm only contain the Z sex chromosome, whilst a mature egg cell has either a Z or W sex chromosome.)

Further, because both sides of the bird are exposed to exactly the same hormones, individual cells respond to these chemical signals according to their own inherent chromosomal complement rather than simply following orders sent out by the gonads.

Based on their studies, the team proposed two different models of sexual development; one for birds and a second, contrasting model to account for most mammals (Figure 5):

Figure 5 | A novel mechanism of sex determination in the chicken. A sexual identity is genetically imposed on the male and female chicken soma at fertilization and is the major factor in determining the adult sexual phenotype. At the appropriate stage in development, the sexually-dimorphic transcripts underlying the male/female identity trigger expression in the genital ridge of the gene cascade responsible for testis/ovary development. The gonads have limited effects on the sexual phenotype. In contrast, in mammals, gonadal fate is dependent on transient expression of the testis-determining Sry gene in the indifferent early gonad. The mammalian gonads have a major influence on the sexual phenotype. [larger view]
DOI: 10.1038/nature08852

Interestingly, birds aren't the only exceptions to the mammalian model of sexual development. The mammal model also fails for some marsupials. Previous studies have shown that formation of mammary glands and scrotum in the wallaby, a marsupial, is independent of gonadal hormones [DOI: 10.1038/331716a0]. Additionally, the platypus (a monotreme) has a complex sex chromosome system that is unique among mammals [DOI: 10.1038/nature06936] documented so far, although like birds, they also lack the mammalian sex determining region (Sry). It would be interesting to identify whether there are platypus gynandromorphs and if so, to find out if each cell in the platypus has its own sex identity, as in birds.

Interestingly, sex determination in reptiles appears closer to the mammalian system but again, it's complicated, and there are species where sex is dependent upon ambient temperature experienced during specific stages of embryonic development.

Of course, this makes me wonder if any bilateral gynandormorphic Maniraptoran fossils have ever been identified?

"The problem is, once people develop a hard and fast rule, it becomes the only game in town," explained Dr Clinton. Certainly, Sam's "tubes and plumbing" would suggest there is no universal rule for all vertebrates.

Source:

Zhao, D., McBride, D., Nandi, S., McQueen, H., McGrew, M., Hocking, P., Lewis, P., Sang, H., & Clinton, M. (2010). Somatic sex identity is cell autonomous in the chicken. Nature, 464 (7286), 237-242 DOI: 10.1038/nature08852

grrlscientist Fri, 03/12/2010 - 06:59

Ancient DNA from Fossil Eggshells May Provide Clues to Eggstinction of Giant Birds

grrlscientist — Wed, 10 Mar 2010 14:50:47 +0000

Ancient DNA from Fossil Eggshells May Provide Clues to Eggstinction of Giant Birds

tags: evolution, evolutionary biology, ancient DNA, aDNA, molecular biology, molecular ecology, archaeology, paleontology, fossil eggshell, extinct birds, giant moa, Dinornis robustus, elephant birds, Aepyornis maximus, Mullerornis, Thunderbirds, Genyornis, researchblogging.org,peer-reviewed research, peer-reviewed paper, journal club

Elephant bird, Aepyornis maximus, egg
compared to a human hand with a hummingbird egg balanced on a fingertip.

To conduct my avian research, I've isolated and sequenced DNA from a variety of specimens, such as blood, muscle, skin and a variety of internal organs, dry toepads from long-dead birds in museum collections, feathers, the delicate membranes that line the inside of eggs, and even occasionally from bone. But I was surprised to learn that avian DNA can also be extracted directly from fossilized eggshells -- eggshells that completely lack eggshell membranes.

An international team of scientists just published a paper demonstrating for the first time that fossil eggshells are a rich source of DNA.

"Researchers have tried unsuccessfully to isolate DNA from a fossil eggshell for years," reports first author Charlotte Oskam, a doctoral student in biology at Murdoch University in Perth, Western Australia.

"It just turned out that they were using a method designed for bone that was not suitable for a fossil eggshell."

According to Michael Bunce, a professor of biology at Murdoch University, extracting DNA from bone involves removing all the calcium from the bone. This calcium extract is then discarded -- a mistake when dealing with eggshells.

"Turns out that the DNA is trapped within the calcium carbonate matrix," said Dr Bunce.

Using their newly developed method, the team isolated ancient DNA (aDNA) from a variety of fossil eggshells, including a 19,000-year-old emu eggshell as well as eggshells from an extinct species of giant moa, Dinornis robustus, and the enigmatic elephant bird, Aepyornis maximus, from Madagascar. Eggshells from two other extinct species, the little bush moa, Anomalopteryx didiformis, and the heavy-footed moa, Pachyornis elephantopus, both from New Zealand's north island, were estimated to be more than 3,000 years old. Attempts to isolate DNA from a 50,000-year-old flightless Australian Thunderbird, Genyornis, failed because the DNA was too fragmented.

In the eyes of the casual observer, avian eggshells are deceptively simple in appearance. However, a closer examination reveals that eggshells do not have a uniform structure (Figure 1):

Figure 1. Avian eggshells. (a) Stylized radial cross-section (upper) with corresponding pictorial view (lower) of a moa eggshell (Dinornis robustus). (b) Outer surface of a moa eggshell (D. robustus). Pores are visible and are aligned towards the poles of the egg. (c) Elephant bird (Aepyornis maximus). (d) Duck (Anas sp.). (e) Emu (Dromaius novaehollandiae). Scale bar, 2 mm. [larger view]
DOI: 10.1098/rspb.2009.2019

Using their new method, most eggshell samples from both ratites and from other Holocene birds yielded aDNA, indicating that avian eggshells can potentially preserve DNA for very long periods of time, even in hostile environments that have not traditionally been conducive to long-term DNA survival.

To further optimize their new method, the team stained fragments of fossil eggshells from a New Zealand giant moa and a Madagascar elephant bird with a fluorescent dye that binds only to double-stranded DNA to determine where aDNA is physically located and to determine its source. Using confocal microscopy, the team found that aDNA is distributed fairly uniformly throughout the eggshell matrix as well as on its inner surface (Figure 2):

Figure 2. Confocal images of ratite eggshells stained for DNA. (a) Confocal radial cross section of an Aepyornis eggshell, stained with SYBR Green, displaying the DNA distributed throughout the matrix: 5Ã objective lens, scale bar, 400 Âµm. Inset, orientation of confocal image. (b) Confocal inner surface of a D. robustus eggshell, stained with Hoechst dye, displaying mammillary cones (outlined) with peripherally located DNA: 40Ã objective lens, scale bar, 50 Âµm. Inset, orientation of confocal image. Red arrows, fluorescently labelled DNA. [larger view]
DOI: 10.1098/rspb.2009.2019

These data shows that the aDNA almost certainly comes from the mother rather than the developing embryo. As the developing egg moves through the hen's oviduct, some the mother's cells are mixed in the calcium carbonate shell as it thickens.

Eggshell is already used for a variety of scientific tests, such as radiocarbon dating and isotope analysis, which provides important information about diets, environments, past biodiversity and evolutionary processes. But obtaining genetic information from both mitochondrial and nuclear DNA isolated from the same samples promises even richer reconstructions of evolutionary history than is currently possible.

The aDNA has not yet been sequenced, but researchers are working on expanding their catalogue of aDNA samples from extinct birds: currently they are extracting genetic material from eggshells held in museums and excavated at archaeological and fossil sites throughout the world.

Combining this newly-devised aDNA extraction method with older, more established techniques will provide more clues into the lives of these ancient birds, and may shed some light on why they mysteriously died out.

The extinction of Aepyornis is especially mysterious. This giant bird lived on Madagascar for nearly 2 million years, but went extinct by the middle of the 17th century. Related to other ratites like the ostrich and emu, the herbivorous Aepyornis was approximately 10 feet tall and weighed roughly 1,000 pounds, making it the heaviest bird to ever live (at 11 feet tall, the now-extinct giant moa is the tallest bird to ever live). It is thought that Europeans saw (and were impressed by) this giant bird before it went extinct.

"This mysterious bird was probably the inspiration behind stories in the Thousand And One Nights as told by Marco Polo," said study co-author Mike Parker-Pearson, an archaeologist at the University of Sheffield in the UK.

Even though it's known that Aepyornis went extinct after the arrival of humans on Madagascar, there's actually no convincing evidence that the bird was hunted by humans.

"There's not even evidence that they ate the eggs -- even though each one could make omelettes for 30 people," remarked Dr Parker-Pearson.

It is possible that humans might have destroyed the birds' habitat or perhaps their domestic animals, such as dogs and pigs, hunted and ate Aepyornis eggs and chicks, which then drove the species to extinction.

"It's amazing that we now know so much about its genetic make-up, its diet and its habits," said Dr Parker-Pearson. "Sadly, it seems to have been yet another casualty of human population growth."

Will it be possible to use aDNA to resurrect these long-extinct birds? Unfortunately, this is unlikely: although aDNA can be sequenced, scientists must know how to correctly repackage the DNA into chromosomes, those giant molecules that contain millions of genes. This is the same challenge facing scientists who wish to bring woolly mammoths back to life, even though mammoth DNA was sequenced from well-preserved specimens recovered from the Siberian permafrost.

"As with all ancient DNA, the DNA we isolated from eggshell is very fragmented," Ms Oskam pointed out. "It will be possible to sequence extinct genomes from fossil eggshell but it is a huge leap to imagine we can clone an extinct species."

Source:

Oskam, C., Haile, J., McLay, E., Rigby, P., Allentoft, M., Olsen, M., Bengtsson, C., Miller, G., Schwenninger, J., Jacomb, C., Walter, R., Baynes, A., Dortch, J., Parker-Pearson, M., Gilbert, M., Holdaway, R., Willerslev, E., & Bunce, M. (2010). Fossil avian eggshell preserves ancient DNA. Proceedings of the Royal Society B: Biological Sciences DOI: 10.1098/rspb.2009.2019

grrlscientist Wed, 03/10/2010 - 09:50

Categories

Life Sciences

That's really cool.

Sorry, all the "convincing evidence" needed, to assign this to human predation is- the utterly uniform behavior of hunter-gatherer peoples, and specifically the proto-polynesian peoples that wound up in Madagascar. Wherever they landed, they ate everything. Always. All the flightless birds wound up in the pot, and extinct (ok, except kiwis and kakapos, but don't forget the many moas).

This is a symptom of the distressingly common fallacy that "if I can't find a peer-reviewed paper on it - then, it isn't true, or demonstrated, and we don't know it". Such malarky- I'm quite sure the creators of "science" did not intend to just wipe out all human experience, and start from scratch- but somehow we're training scientists who do not understand that.

Most of these "fossils" incidentally, are only called that out of courtesy- they are not fossilized in the usual sense, of having minerals substituted for bone. Which doesn't mean you can't get DNA from true fossils.

greenpa: well, as they say; making assumptions can make an "ass out of you and me."

good point about the use of the word "fossil" in this paper. it appears that the use of this word is different for archaeologists than for paleontologists (dictionary implies it is a rather general word; specific definitions come from context). i think these eggshells might be more correctly known as "subfossils" by the paleontologists amongst us.

@Greenpa: Actually it would be silly to say that people must have eaten the bird and thus driven it to extinction. There are any number of other reasons the bird may have been hunted and any number of other reasons it could have been driven to extinction. So scientists suspend judgement as Bertrand Russel puts it, rather than make statements which they cannot demonstrate to be true because they want to imagine that they know something. Even if bird pieces were found in ancient garbage pits and indicated that humans ate the birds, scientists can still only say that hunting may have been a contributing factor. We know for example that the dodo did not become extinct because humans hunted it for food - so there goes your theory that they are always hunted to extinction for food. The Carrier Pigeon is another animal which was not driven to extinction due to its value as food. Otters were driven to extinction in many places due to their pelts, and the North American Buffalo was almost extinguished for its pelts; there are accounts of the animals being shot and skinned and the carcass left to rot, with only the occasional carcass taken for food.

The Carrier Pigeon is another animal which was not driven to extinction due to its value as food.

Indeed, because it isn't extinct! No doubt you meant the Passenger Pigeon...

And the Passenger Pigeon was hunted for food, and quite aggressively.

Mad Scientist- you caught me writing too fast. :-) You're absolutely correct, of course. I posted some very similar comments over on the post re ancient musk ox DNA.

And, I did that terribly human thing- repeating something I'd heard repeatedly. Among many people studying the Pacific, the bit about "they ate everything!" is in vogue, though not intended as absolute truth.

Good catch. :-)

llewelly - yes, indeed, but the picky ones will point out that it was not hunting, per se, that caused the extinction, but the interference with reproduction. Most ornithologists I think now accept the idea that Passenger Pigeons had a very large minimum flock size required for initiation of a nesting colony - like a half-million birds or so. Smaller flocks refused to nest. Our host may have the most recent information?

Which points out of course the frustrating difficulties of scientists from different disciplines attempting to communicate. The ethologist might focus on the nesting disruption, and the anthropologist on the practice of feeding pigs on the knocked down nestlings.

My own preference is to suggest that the introduction of any novel top predator into a naive population will render virtually the entire ecosystem metastable. Extinctions can easily result- and historically- its clear they do. One stellar example being the broad extinctions of the South American marsupial mega fauna - where Homo was not even involved.

And, actually, Mad scientist- Carrier Pigeon!!?? lol. We all do it. :-)

And, re: American bison- the anthropologists and historians will claim that the near extinction was the direct result of a US Federal policy, established and pushed by General WT Sherman, of eradicating them to starve out the Native Americans. From Wikipedia (sorry):

"In July 1865, only three months after Robert E. Leeâs surrender at Appomattox, General W. T. Sherman was put in charge of the Military Division of the Missouri, which included every territory west of the Mississippi. Sherman's main concern as commanding general was to protect the construction and operation of the railroads from attack by hostile Indians. In his campaigns against the Indian tribes, Sherman repeated his Civil War strategy by seeking not only to defeat the enemy's soldiers, but also to destroy the resources that allowed the enemy to sustain its warfare. The policies he implemented included the extensive killing of large numbers of buffalo, which were the primary source of food for the Plains Indians.[104]"

Sherman, and his successors, I believe, greatly encouraged and facilitated the kind of slaughters you describe-where only the robe and tongue were taken; salted; and shipped east on the railroads the Army was protecting...

but the picky ones will point out that it was not hunting, per se, that caused the extinction, but the interference with reproduction.

Err, yes. And how did their population sizes get that low? Hunting, perhaps?

maybe not hunting, per se. didn't the pigeon pope come to america and impose regulations on avian sexual behavior?

The pigeon pope !!?? lol!

And Bob- yes, we're talking about the "picky" ones; people who like to cherry pick which direction information leads. And hunting? Are you familiar with the primary harvest methods? Hard to call them hunting- if one is picky.

Standard method- several hundred people would wait outside one of the miles-long nesting sites until well after dark. Then, with torches, they would move in, and club- everything. Some would be assigned to pick up unmangled adults and squabs big enough for eating. Afterward, they'd turn the pigs in, to clean up the ones missed or stepped on, or just superfluous.

Appalling and shameful beyond words- and a far cry, many would say, from "hunting".

Now- where I live in SE Minnesota, unlimited market hunting DID eradicate whitetail deer and wild turkey, when they were hunted to feed the riverboats and loggers in the 1800s. The deer are pests now, and it's hard to remember that until around 1950, seeing a deer around here would get your name in the paper; rare as Great Auks.

@John Hawks: Oops ... silly me. Yes, the Passenger Pigeon.

@llewelly: The shooting of Passenger Pigeons was actually promoted, and not for food either. I don't know if it's that "shoot 'em for fun" or shooting for food which eventually reduced their numbers too much; I've always heard it was shooting for fun. It's easy to imagine shooting them for food though; pigeons are tasty and just large enough to be worthwhile hunting or trapping for food.

@Greenpa: It's easy to make those mistakes. Sometimes we see so much of one case that we forget about other cases. There are a number of migratory birds in Asia which will probably be driven to extinction due to (1) hunting for food and (2) extermination due to being (incorrectly) perceived as pests. The Asian Mynah is being driven towards extinction as well but I'm not aware of anyone using the bird as food (which doesn't mean the bird isn't used as food - but certainly not eaten in places I've been to).

@llewelly: Hmm ... OK - according to the Wikipedia they were hunted for a variety of reasons including food. So hunting for food probably was a big part. The stories I remember (or think I remember) must be largely hearsay then.

Mad- I'm sure there was plenty of "fun" shooting, but Passenger Pigeons were also an abundant commodity at the time, and without refrigeration, the waste must have been phenomenal. They were typically just packed, un-plucked, ungutted, into wooden barrels, and tossed on the train. Here is a first-remove narrative; the story on pigeons is 3/4 of the way down the page-

http://genealogytrails.com/ill/jefferson/articles/vol2hist4.html

I'd never heard of this particular method- injuring a bird and then shooting the responding mobs- a rather un-pigeonlike behavior I think. A fascinating fragment about the behavior of the vanished.

Faith-Based Birding 201: Fraudulent Photos and Federal Funding

grrlscientist — Fri, 12 Feb 2010 13:30:38 +0000

Faith-Based Birding 201: Fraudulent Photos and Federal Funding

tags: faith-based birding, mass hysteria, endangered species, extinct species, conservation, politics, Ivory-billed Woodpecker, Campephilus principalis, IBWO, ornithology, birds, researchblogging.org,peer-reviewed research, peer-reviewed paper

The Cornell Lab of Ornithology has posted a reward of $50,000
to be given to anyone who can provide "video, photographic, or
other compelling information and lead a project scientist to a
living wild Ivory-billed Woodpecker."

Mass hysteria is that strange psychological phenomenon where a group of people experience the same hallucination at the same time. Such hallucinations include observing statues or paintings of the Virgin Mary either bleeding or crying at certain times of the year. But mass hysteria is not limited to religious fanatics. During the past five years, there has been a marked increase in what I refer to as "faith-based birding," where groups of people believe they've seen the Ivory-billed Woodpecker, Campephilus principalis, a large bird that has been extinct in the US for more than 50 years.

Ever since a small group of birders and ornithologists from Cornell University published their very controversial claim in Science in 2004 that they captured this extinct species on video, the number of other people who have likewise "seen" the Ivory-billed Woodpecker have increased. Unfortunately, many of these so-called sightings are based on manufactured photographic evidence.

Apparently unable to distinguish reality from hysteria, Cornell's Lab of Ornithology has only added fuel to this fire by advertising a $50,000 reward to anyone who can provide "video, photographic, or other compelling information and lead a project scientist to a living wild Ivory-billed Woodpecker." Why would the "Lab of O" even get involved in this when they should be devoting their precious time and resources to avian research? Why not admit that their original video ID was mistaken and move on already? (my hypothesis: testosterone poisoning)

Further, if they are really serious about finding this species, why wouldn't they refocus their energies from their sensationalist "wanted dead or alive" advertising campaign (above) to one where they educate the public by showing them how to distinguish this bird from other, similar species (below)?

Image: David Sibley (designed for internet use).

Worse, some so-called birders, such as landscaper and gambler Daniel Rainsong, who claims to have photographed the bird, resort to harassment to assert their claims to this $50,000 prize. According to the current kerfuffle on the intert00bz, Rainsong apparently refuses to allow anyone to see his December 2009 photographs of the Ivory-billed Woodpecker until his "right of claim" (huh?) for this discovery is established (huh??). But despite the self-imposed veil of secrecy surrounding his supposed photographs, Rainsong is allegedly harassing professional ornithologists by filing "formal complaints" against them because (he claims) they refuse to accompany him on an extended search in the Sabine River basin in east Texas to "prove" the validity of his photograph(s). Which he won't permit them to examine.

But the furor has reached far beyond the machinations of a few self-important fortune-seekers: it has even infected the US government. During the past five years, hysterical public officials redirected $14 million of precious conservation funds into developing the Ivory-billed Woodpecker recovery plan -- never mind the fact that this species has not been seen in more than 50 years and is extinct in the USA. But this raises the question; why not spend that $14 million on implementing recovery plans for endangered species that actually exist and that we have a chance of recovering?

Further, after five years of fruitless searching, even some ornithologists at the Lab of O have given up all hope by deciding the bird is either extinct or hopelessly irrecoverable.

"We don't believe a recoverable population of ivory-billed woodpeckers exists," said Ron Rohrbaugh, a conservation biologist at Cornell University in Ithaca, New York, who headed the original search team.

Ivory-billed Woodpeckers in a museum bird collections drawer.

Image: Orphaned.

Source:

Dalton, R. (2010). Still looking for that woodpecker. Nature, 463 (7282), 718-719 DOI: 10.1038/463718a

Free Press Release

Addendum: an opposing point of view.

grrlscientist Fri, 02/12/2010 - 08:30

a couple of things:

The photos have been seen by appropriate people and will be addressed (why it's taking this long I have no idea; it's a pretty open-and-shut case, and the longer it drags out the more of a fiasco it becomes). I'll have a wrap-up at my blog as well, once officials have their say (I reluctantly broke this story back on Jan. 19th.)

The reward is actually offered by an "anonymous" source, and the impetus for it was to encourage anyone who might know the whereabouts of IBWOs, but not wish to tell (for example, if they are on private lands), an incentive to speak up. The criteria for the reward are actually so stringent it should be a DISincentive to most hoaxers to try (and put themselves through such a grill), but unfortunately Rainsong didn't realize that.

It's hardly news that most birders' life-lists are filled with fleeting glimpses and wishful thinking. But spending $14 million on a recovery plan, on the strength of a dubious videotape, is the sort of thing that gives conservation biology a bad name.

'Faith-based' birding is about right. Maybe we need a Society for Skeptical Birders?

Can someone photoshop that poster so it says "Wanted: Dead or Alive" on it? Please?

But how does it taste?

i think it must taste like crow, but lab of o might have first-hand information (and recipes) they'd like to share?

When you say "extinct in the US" do you think that there is a chance of it still existing in Cuba?

why not spend that $14 million on implementing recovery plans for endangered species that actually exist and that we have a chance of recovering?

Because political appointees under the Bush administration got wind of it, swooped in, declared it a "success story", and dictated a ridiculous PR media blitz, much to the consternation of the field staff. Such heavy-handed political management was very commonplace from 2000-2008.

How do I know? I'm a USFWS recovery biologist.

i think it must taste like crow, but lab of o might have first-hand information (and recipes) they'd like to share?

Nah. It tastes exactly like pileated, but there are people who, despite all the evidence, claim they can tell the difference. :-)

I'd say $14 million is a bargain, if there's any chance at all that the bird exists. I don't buy that video, but I at least initially put "faith" in the sightings by experienced Cornell researchers, and the Auburn group.

Given how much time has now elapsed, and given the lack of conclusive evidence, my "faith" is a lot less now. But...I have a hard time getting worked up over $14 million to potentially save a species, when that $14 million quite literally will only buy a couple of hours for the U.S. war effort in Iraq.

terry: that $14mil was NOT redirected from bombing innocent iraqi civilians into the next ice age. it was redirected from other endangered species budgets supporting species that are still alive. the fact that other endangered species might be un(der)funded in the process was actually another win for the bushies, who have never been especially keen to protect anything except their own bank accounts.

I'm the last one to support any win for the Bushies, but I have a hard time getting worked up over this one.

Of that $14 million, $8 million as spent on habitat conservation, including an expansion of the Cache River National Wildlife Refuge.

That's a good thing. As for the rest of that money...again, if there's ANY chance such a magnificent bird exists, I say go for it. You had some well-respected Cornell researchers ID the bird by sight. Could they have been mistaken? Too enthusiastic? Sure. But should doubt be a reason to ignore a chance to save a species?

So throw $14 million dollars at an extinct species rather than spending that money to save species we know for a fact are not extinct, because someone claims to have seen it? we're going to let other programs die from lack of funding for that?

Because political appointees under the Bush administration got wind of it, swooped in, declared it a "success story", and dictated a ridiculous PR media blitz

Well, as recovery plans go, it's done better than some - there's been no further decline of the species, after all! :)

(count me in the "it's extinct" camp)

"We don't believe a recoverable population of ivory-billed woodpeckers exists,"

It depends what your definition of "recoverable" is. Clone those museum specimens. OK, so it's not easy... the ibex was not extinct for only seven minutes so far. How much cloning effort can $14 million buy?

Sure, some of the money spent on the 'search' team could have been redirected, but they tried and it didn't work out....time to move on. I'm playing devil's advocate here but some might argue we've been wasting tons of conservation money on habitat specialist species of serious decline whose populations can't survive without our assistance...say Kirtland's warbler? Least Bell's Vireo? I still think we should try.

Personally, I think whether the Ivory-billed still exists is a moot point. Bringing attention to the degradation and loss of bottomland hardwood habitat in Arkansas, Florida Pan, etc. is the real success in the woodpecker story. What those areas really needed was more public awareness and conservation and I think the ivory-billed search helped alot in that respect. Maybe these efforts might help stop the decline of another bottomland hardwood species before it's too late....say the rusty blackbird? (Big Woods had great flocks when I visited last).

What's 14Million? NObama spent that on the Photo Opt of Air Force 1's over New York City. Scared the entire city again. Not o mention the billions he has wasted on his the recovery act which has yet to produce a single job.

> recovery plan

Restore it and they will come back?

Well, what's the worst thing that could result from doing this?
There's a reason they call'em 'charismatic megafauna' -- they need the same kind of environment restored that many others will find habitable, and usually a bit more of it.

The Ivory Billed Woodpecker is in fact a werebird. For nearly the whole of the month, it sneaks about in the shape of a common Pileated Woodpecker. But on the night of the full moon, it transforms! Then, and only then, can its true form, in all its ivory-billed glory, be seen. Thus it has eluded the cleverest of searchers for all these many years.

Citation for the $14 million price tag, just for preparing a plan? I see it on a lot of websites (also $10m) but no citation. Also if some/most of the money's spent on land acquisition, that isn't money spent on a plan, and I wouldn't call it wasted even if the bird's not there.

Never attribute to testosterone poisoning what can be adequately explained by caffeine intoxication.

Your blog post is, to say the least, misinformed.

1. Actually there is a precedent from 1930s, when a naturalist reported seeing IBWO to the museum curator and received the answer that it is already extinct. He then asked if he will be believed if he shot one. The answer was yea, and the naturalist returned and threw the skin on the table. It was one of the last IBWO skins collected.

So, a faith-based non-birding.

2. For 50 years, not a single serious conservation body (I'm not talking about popular books etc) dared to claim IBWO is extinct. The reason is simple - low observer coverage in swamp forests plus regular reports without the photo evidence - some coming from respected public figures or experienced birders.

3. Cornell lab kept secret about the original observation and film for a year and spent considerable money on buying land near the secret sighting during that time.

So it is plainly wrong that it sought publicity or government money.

If president Bush had not made a misguided speech about developing the area, the observation and film would probably be secret to this day.

4. Habitat protection, on which most of money is spend, is protecting also black bears and other species. The protection of bottomland forest is worthy goal in its own right.

If the $14 million was spent on habitat restoration or land conservation I have no problem with that. As far as the IBWO goes, I will believe it when I see positive proof. If people want to look for it using their own funds or those of a philanthropist I think that's great.

The fact is that there are 192 critically endangered species on this planet that can use our help. Maybe we should direct our attention to those species.

No naturalist who has seen Peterson's painting picture of this bird in the legendary Field Guide has not dreamed of seeing it... perhaps even scientists from Cornell can get carried away by their emotions. But why is it that no one who claims to have seen it has ever been able to produce a convincing photograph -- even, as with Kulivan, when they supposedly had a camera? Perhaps this bird really only survives in our collective subconscious, because we know we have lost something truly great and yearn to see it. So unless the miraculous happens and a real encounter occurs, the only hope may be if science, at some future date , figures out a way to produce them by cloning them from genetic material... even if so, however, could these creatins be re-integrated into their natural environment? One has to wonder...

Here is a fun scenario -- what if there really were a couple of these birds blithely fluttering about, careening about the treetops, in the general vicinity of where Sparling, Harrison et al think they saw them... so let's say a small group of them was hanging around the area, literally in plain view of any kayaker paddling through, gazing at them curiously with their big yellow eyes...
but then, after the big announcement was made, with the cat out of the bag so to speak, could a secret, strategic decision have been made by USFWS to covertly take them down and relocate them to an outdoor aviary-type facility for observation and/or captive breeding? (These then would be survival insurance for the species while allowing that others could still possibly exist in the wild)

Remember, there are precedents for this with california condors, black-footed ferrets, red wolves... maybe these too???

Then again, our government can't even cover up something like the Monica Lewinsky scandal, so I'm not sure... :-)

Few people realize that the origins of the ivorybill's popular nickname of "Lord-God bird" are more prosaic than one might think -- locals simply thought of it as a "logcock" -- quite similar to the pileated woodpecker, which also was so called... back in Tanner's day, the Singer Tract population remained in place, raising their broods, easily located time and again for photos, until this, their last refuge, was tragically cut down. But could it be that a small band of their descendants found refuge at the Cache River, where they were being spotted by all those people? But then, justly unnerved by the possibility of this news falling on the wrong ears, USFWS simply had to relocate them, quietly? (They were like a few Hope Diamonds or original Picassos, but innocently just fluttering about, unable to be guarded constantly.)

Conspiracy theories are fun! We've had ones relating to the JFK assassination, Roswell... what about an secret ivorybill operation?

Another possibility could be that some are hanging out on some private land someplace. But for obvious reasons, it's being kept a secret...

Racehorse Research Identifies Speed Gene

grrlscientist — Mon, 08 Feb 2010 14:10:42 +0000

Racehorse Research Identifies Speed Gene

tags: evolutionary biology, molecular biology, Thoroughbred race horses, horses, aerobic capacity, muscle development, myostatin, MSTN, myostatin-suppressing C variant, myostatin-suppressing T variant, Horse Genome Project, Equinome, researchblogging.org, peer-reviewed research, peer-reviewed paper

Emerging from the mist is Rachel Alexandra, a champion American Thoroughbred who excels at winning both long and short distance races.

Image: Rob Carr, 2009, Associated Press [larger view]

If you've worked at or been around a racetrack very much, as I have, you'll quickly realize that everyone there has their own pet idea for picking winners. Horse breeders rely on pedigree analysis and studying the horse's conformation to predict whether a particular racehorse is better suited for running short or longer distances. But this is an art that requires both practice and experience and it can waste valuable time, money and sometimes, horses. Which makes one wonder whether modern science can be applied to the challenge of identifying specific genes that make a particular horse better suited to running sprints or distances?

"Everybody knows one horse can run faster than another -- most people want to know which one," said Emmeline Hill, a genetics researcher at University College Dublin in Ireland. "I want to understand why."

Dr Hill is no stranger to horseracing: her grandmother, Charmain Hill, was the owner of the famous Irish mare, Dawn Run, the only racehorse to have won both the Cheltenham Champion Hurdle (1984) and Gold Cup (1986). Pursuing this research provided Dr Hill with a rare opportunity to merge her academic interest in genetics with her passion for racing horses.

To gain an understanding of the athletic ability of Thoroughbreds, Dr Hill spearheaded a team of researchers that investigated the genetic factors that contribute to muscle growth. Muscle growth in animals is influenced in part by the myostatin gene (MSTN). MSTN produces a protein that contributes to muscle size development in a range of mammalian species: the animal can either have a compact, muscular body that is suited to short sprints or a longer, leaner body that is better for endurance. Horses, especially thoroughbreds, have a very high muscle mass to body weight ratio (55%) compared to other mammalian species (30-40%).

"The main focus is to understand the genes that contribute to athletic ability in the thoroughbred," Dr Hill explained. "We're selecting candidate genes that we know have an association with health-and-fitness-related traits in humans" and other animals.

Earlier work showed that whippets, a common breed of racing dogs, that have two different MSTN gene variants have significantly greater racing ability than those that are homozygous for either the wild-type gene or the MSTN variant that contributes to enlarged muscles. This research made Dr Hill wonder if thoroughbreds might also have MSTN gene variants that affect their athletic abilities.

Thoroughbred race horses compete in two types of races: steeplechases (also known as "national hunts") where they jump a variety of obstacles and generally run long distances, and flat races. Flat races lack jumps and are run over a variety of surfaces at distances ranging from five furlongs (5/8 mile or 1,006 m) to 20 furlongs (4,024 m) [1 furlong = 1/8 mile = 201.2 meters]. The International Federation of Horseracing Authorities recognizes five race distance categories: Sprint (5-6.5 f, â¤1,300 m), Mile (6.51-9.49 f, 1,301-1,900 m), Intermediate (9.5-10.5 f, 1,901-2,112 m), Long (10.51-13.5 f, 2,114-2,716 m) and Extended (>13.51 f, >2,717 m) races. The horses that compete in these races are generally known as 'sprinters' (8 f).

To carry out this study, the team identified specific MSTN sequence variants by re-sequencing the entire equine MSTN gene from 24 unrelated Thoroughbred horses. The team identified a total of six MSTN variants, but four were quite rare, so they analyzed only the two most common alleles, which they dubbed as either "C" or "T", by comparing race distances to allele types for 79 winning horses (Figure 1).

Figure 1. MSTN genotype distributions among Thoroughbred horses. Distribution of a. C/C, b. C/T and c. T/T genotypes among (n = 79) Group race winning Thoroughbreds. The non-uniformity of the distributions (b. and c.) may be explained by the absence of 9 f races among the 84 Group 1 races held in Great Britain. d. To avoid the bias introduced by racing distances for two-year-olds limited to â¤8 f (in Great Britain and Ireland), the distribution of genotypes was plotted for individuals with best race distance >8 f and for those two-year-olds that won their best race â¤8 f mean three-year-old race distances were used. e. Genotype distributions among National Hunt racing Thoroughbreds (aqua) f. Genotype distributions among Flat racing Thoroughbred (orange) and Egyptian (purple) horse populations. a.-e. C/C - blue, C/T - red, T/T - green, vertical axes indicate frequency, horizontal axes indicate best race distance (furlongs). The International Federation of Horseracing Authorities recognizes five race distance categories: Sprint (5-6.5 f, â¤1,300 m), Mile (6.51-9.49 f, 1,301-1,900 m), Intermediate (9.5-10.5 f, 1,901-2,112 m), Long (10.51-13.5 f, 2,114-2,716 m) and Extended (>13.51 f, >2,717 m); S-M-I-L-E [Note: 1 furlong = 1/8 mile = 201.2 meters].
DOI: 10.1371/journal.pone.0008645

The researchers' data revealed that horses homozygous for the MSTN-C variant (C/C) were more likely to win short races up to 6.5 furlongs (1.3 kilometers), whereas horses with two copies of the MSTN-T (T/T) variant did better in longer races of up to 13.5 furlongs while the heterozygotic horses (C/T) generally did best at intermediate distances. Predictably, mass-to-height ratio was significantly related to allele type, especially for 2-year-old colts, which are typically larger and more muscular than fillies of the same age: C/C males had a 6.7% greater mass per cm than T/T colts. Further, the team found that C/C and C/T horses matured earlier and typically began their racing careers as 2-year-olds.

The researchers also found a correlation between MSTN alleles and overall lifetime earnings: C/C horses earned 1.6-fold more than did T/T horses. But this finding should not surprise those who are familiar with horse racing since I think it is an unfortunate reflection of the relative scarcity of long distance races and their generally smaller prizes.

Based on a summary of their data (Figure 2), the researchers predicted that a strategy of training and racing only C/C and C/T individuals as two-year-olds may the most financially desirable strategy.

Figure 2. Optimal MSTN genotype for racing distance. Distribution of C/C (blue), C/T (red) and T/T (green) genotypes among n = 179 Group and Listed race winning Thoroughbreds.
DOI: 10.1371/journal.pone.0008645

These data provide an interesting application for molecular technology to provide genetic profiles to those who work with racehorses so they can make better management decisions. Indeed, the lead author of this paper is so convinced of the usefulness of this test that she is patenting this work and recently formed the company, Equinome, with Irish racehorse trainer and breeder, Jim Bolger, to market a genetic profiling test that identifies these alleles in horses for a mere â¬1000 ($1400).

"When ... spending millions in a sales ring for a thoroughbred ... you might want to take a look at its engine as well," said Dr Hill. "Genetic profiling will give you an extra level of information that wasn't there before."

As these data become more available to the racing industry, many more important questions will be examined: for example, which horses (C/C vs T/T) are more likely to retire sound? Which have a longer racing career? Which are less expensive to train, feed and run?

Although this study is interesting, but I can't help but think that it provides genetic information that will likely be over-interpreted, especially when the racing industry itself admits that overall racing ability of an individual horse is attributable to "no more than 35% genetics." But Dr Hill disagreed.

"Using the Equinome Speed Gene test [.. will make it] possible to definitively know a horse's genetic type within weeks of a sample being taken," Dr Hill pointed out, "thus reducing much of the uncertainty that has been typically involved in selection, training and breeding decisions."

Based on my own experience at the racetrack and working with horses, it appears to me that those people whose livelihoods depend upon horses should be able to accurately assess their physical attributes and make sound decisions as to which distances are most suitable to each horse without having to purchase an expensive genetic test whose results aren't available until nearly one month later.

More important, the Equinome Speed Gene test cannot predict an individual horse's personality; its trainability, tenacity, or its desire to run and -- most importantly -- to win. This test can only provide an additional (and very small) piece of information to that information-rich soup that is gambling.

That said, I can't help but recall the early life of American racehorse, Rachel Alexandra (pictured at top). Despite having a very good sire (Medaglia d'Oro), Rachel Alexandra was less-than-impressive as a foal. By the time she was a weanling, she was described as "raw-boned and rather scruffy," and was almost sold. She was held back from public auction at the last minute only because an unusual X-ray finding shortly before sale might jeopardize the $125,000 price that her owner thought she should fetch. So her owner sent the "scruffy" filly to his trainer and after a few adjustments to the personnel working with her, the rest is history: Rachel Alexandra developed into a racing phenomenon and was sold for more than $10 million less than two years later.

Would the results of this test have made any difference in her brilliant career? I certainly doubt it.

"This is a test for what your horse will be good at, not how good he will be," agreed Dr Hill.

Source:

Hill, E., Gu, J., Eivers, S., Fonseca, R., McGivney, B., Govindarajan, P., Orr, N., Katz, L., & MacHugh, D. (2010). A Sequence Polymorphism in MSTN Predicts Sprinting Ability and Racing Stamina in Thoroughbred Horses. PLoS ONE, 5 (1) DOI: 10.1371/journal.pone.0008645

grrlscientist Mon, 02/08/2010 - 09:10

Categories

Life Sciences

So, a biologist, an engineer, and a mathematician were hired to advise a wealthy investor on how to select the fastest racehorses ...

The joke may have to be revised.

Great post!

My best friend and roommate during my PhD was a physiologist specialising in horses. She payed her way through her high school, undergrad, and PhD days by working in various vet school and racing stables in the UK and Ireland, and she's the one who first took me to the races and taught me to read the form and pedigrees on the card. She always said that pedigree matters much more for flat races; for any kind of jumping, you "go by eye". We only ever went to jump meets, and she taught me well: I lost money on my first visit, but after that I always at least broke even, and she says I have the best eye for a good horse of any non-"horsey person" she knows.

My Canadian friends aren't into the racing (and who can blame them - flat races on sand are so much less interesting than jumps over grass and mud), but we did all go to the races once. While my friends picked their horses based on sheer size, or the jockey's colours, or a cool name, I sat out the first race, noted the name of the winner (by several lengths), and only bet on its half-siblings for the rest of the day. Everyone else lost money; I left with a $140 profit in my pocket! That'll teach them to mock me for being a typical scientist and betting according to genes...

Fossil Feather Colors Really ARE Written In Stone

grrlscientist — Fri, 05 Feb 2010 09:10:58 +0000

Fossil Feather Colors Really ARE Written In Stone

tags: evolutionary biology, paleontology, taphonomy, plumage color, feathers, color, melanin, eumelanin, phaeomelanin, dinosaurs, theropod, paravian, avialae, fossils, Anchiornis huxleyi, ornithology, birds, researchblogging.org,peer-reviewed research, peer-reviewed paper

New research reveals that recently-described 155-million-year-old Anchiornis huxleyi,
a woodpecker-like dinosaur the size of a modern-day domesticated chicken,
had black-and-white spangled wings and a rusty red crown.

Image: Michael DiGiorgio, Yale University [larger view]

Fig. 4. Reconstruction of the plumage color of the Jurassic troodontid Anchiornis huxleyi. The tail is unknown specimen BMNHC PH828, and reconstructed based on the complete specimen previously described. Color plate by Michael A. Digiorgio.

Ever since dinosaurs were discovered, scientists, artists and children everywhere have speculated about what they really looked like. Fossilized bones, skin impressions and recently, feathers, provide a general mental image of these animals' appearances, but these materials also leave important questions unanswered, basic questions such as what color were dinosaurs?

Originally, it was thought that we would never know the true colors of dinosaurs, but new technologies show that assumption is in error. Scanning electron microscopy now reveals that the 155-million-year-old paravian theropod, Anchiornis huxleyi, which resembles a large woodpecker, actually sported flashy black-white-and-red coloration.

But the new field of fossil feather color had an unlikely beginning: while squinting at electron photographs of ink sacs in ancient squid, Yale University graduate student, Jakob Vinther, suddenly realized that the microscopic grains he was seeing were not bacteria, as many scientists thought. Instead, these tiny structures appeared to be melanosomes -- organelles found inside cells that contain melanin, a light-absorbing pigment that gives color to fur and feathers alike.

Because melanins are also present in modern bird feathers, it just might be possible to use them to figure out the colors and color patterns of ancient birds and feathered dinosaurs, Mr Vinther proposed.

Mr Vinther tested his hypothesis by looking at a 112 million year old fossil feather from Brazil and then used those methods to infer the colors of an extinct 47 million-year-old bird, providing an intriguing glimpse into the colors and color patterns that might have existed in dinosaurs (DOI: 10.1098/rsbl.2008.0302).

That dramatic discovery inspired another team of British and Chinese scientists to examine bird-like dinosaur fossils that are covered with feather-like projections. They found that the bristles growing out of the skin of the 125-million-year-old species, Sinosauropteryx, also contained melanosomes. Based on their examinations, they concluded that the dinosaur had reddish-and-white rings along its tail as reported last week (DOI: 10.1038/nature08740).

Meanwhile, Mr Vinther continued his own work in collaboration with an international team of scientists. Together, they studied fossil feathers on the bird-like dinosaur, Anchiornis huxleyi, which was recently unearthed in Liaoning Province, China. This fossil is important in its own right because it is part of the growing body of fossil evidence confirming the once-controversial hypothesis that modern birds are descendants of theropod dinosaurs.

But it also has beautifully preserved feathers that contain melanosomes. The team deciphered the microscopic clues hidden within its feathers, bringing to light this creature's vibrant plumage colors for the first time in 155 million years.

"This was no crow or sparrow, but a creature with a very notable plumage," stated co-author Richard O. Prum, chair and the William Robertson Coe Professor of Ornithology, Ecology and Evolutionary Biology at Yale University, and thesis advisor to Mr Vinther.

To do this work, the team used scanning electron microscopy to examine 29 fossil feathers from all body regions of one spectacularly-preserved specimen of Anchiornis huxleyi (BMNHC PH828; Figures 1 & 2).

Fig. 1. Anchiornis huxleyi (BMNHC PH828) with scanning electron micrographs (SEMs) of samples from the feathers. (A) Part with inset of isolated right hindlimb. The left forelimb is seen in ventral view, the right in dorsal. (B) Explanatory drawing: numbered dots indicate samples from the part (red) and counterpart (blue). (CH) SEMs of melanosomes and melanosome impressions taken from samples 7 (C), 6 (D), 5 (E), 18 (F), 24 (G) and 21 (H). Abbreviations: (Ga) gastralia, (Fu) furcula, (Lh) left humerus, (Lm) left manus, (Lp) left pes, (Lr) left radius, (Ls) left scapula, (Lu) left ulna, (Mu) manual ungual, (Rh) right humerus, (Rm) right manus, (Rr) right radius, (Ru) right ulna, (Rs) right scapula. Scale bars: (A, B) 5 cm except insert, 2 cm; (C-H) 1 Î¼m. [larger view]
DOI: 10.1126/science.1186290

Fig. 2. Anchiornis huxleyi (BMNHC PH828), isolated skull with SEMs of samples from the feathers. (C) Skull. (D) Explanatory drawing: numbered dots indicate samples. Abbreviations: (J) jugal, (L) lacrimal, (Ld) left dentary, (M) maxillare, (N) nasale, (Pm) premaxillare, (Rd) right dentary. (A, B, EE, FF) SEMs of samples 26 (A), 25 (B) and 27 (E, F). Scalebars: (A, B, E, F) 1 Î¼m; (C, D) 1 cm. [larger view]
DOI: 10.1126/science.1186290

They identified the fossilized feather inclusions as melanosomes based upon morphology and size: elongated eumelanosomes contain grey or black pigments while round phaeomelanosomes contained rufous (reddish or chestnut) coloring.

In collaboration with Matthew Shawkey, a biologist from the University of Akron who is an expert in plumage coloration, the team compared the types of melanosomes known to create particular colors in living birds. Using Dr Shawkey's statistical methods, the team was able to describe with 90 percent certainty the colors of individual feathers and, by extrapolation, the color patterns of this ancient bird-like dinosaur (Figure 3).

Fig. 3. Quadratic discriminant analysis of color (black, brown or grey) in extant birds (dots) and in samples from BMNHC PH828 (numbers). The analysis identified properties of melanosome morphology and distribution that predicted color in extant birds and then used these data to predict colors in the fossil sample. Canonical axis 1 is strongly positively associated with melanosome aspect ratio, and axis 2 is strongly positively associated with melanosome density skew. When present, arrows point to the locations of the samples in canonical space: This was done to avoid overlap of sample names. [larger view]
DOI: 10.1126/science.1186290

This data analysis formed the basis of the artist's representation of the color patterns of Anchiornis huxleyi (Figure 4, top). [Note: other molecular pigments such as carotenoids and porphyrins also produce plumage colors, but are not preserved morphologically; structural plumage colors were also not addressed in this study]

"This would be a very striking animal if it was alive today," remarked an excited Dr Prum.

The proposed color pattern of Anchiornis resembles that of living birds. A breed of domestic chickens called Silver Spangled Hamburgs, for example, has white wings with black-tipped feathers.

But this was no barnyard chicken: Anchiornis's color patterns were so extravagant that the scientists are confident it served some visual function.

"It was definitely for showing off," agreed Mr Vinther.

The chestnut-colored crest might have allowed the animal to attract mates.

These findings support the idea that dinosaurs first evolved feathers not for flight but for some other purposes.

"This means a color-patterning function -- for example, camouflage or display -- must have had a key role in the early evolution of feathers in dinosaurs, and was just as important as evolving flight or improved aerodynamic function," explained co-author Julia Clarke, an associate professor of paleontology at the University of Texas at Austin's Jackson School of Geosciences.

In addition to providing more evidence that dinosaur feathers may have evolved due to sexual selection and for communication, these new discoveries also add insight into the history of feather evolution in dinosaurs prior to the origin of modern birds. This study also went on to document that color patterning within feathers and among feathers evolved earlier than previously believed (Figure 5).

Fig. 5. The distribution of integumentary types in coelurosaurian theropod dinosaurs and inferred distribution of plumage patterning. Protofeather-like appendages appeared at the base of Coelurosauria, if not earlier. Color patterns reported in the tail of the compsognathid Sinosauropteryx indicate that among-feather color patterns may have also appeared at this stage. Pinnate feathers and within-feather color patterns first appear in Maniraptora, observed in the striped pinnate tail feathers of the oviraptorosaur Caudipteryx and the troodontid Anchiornis huxleyi. [larger view]
DOI: 10.1126/science.1186290

"There is a big chapter of dinosaur biology that we can open up now," Mr Vinther concluded.

"Writing the first scientifically-based 'field guide' description of the appearance of an extinct dinosaur was a exciting and unforgettable experience -- the ultimate dream of every kid who was ever obsessed with dinosaurs," exclaimed Dr Prum. "Now that dream is really possible."

Source:

Li, Q., Gao, K., Vinther, J., Shawkey, M., Clarke, J., D'Alba, L., Meng, Q., Briggs, D., Miao, L., & Prum, R. (2010). Plumage Color Patterns of an Extinct Dinosaur. Science DOI: 10.1126/science.1186290

Backstory:

Fossil Feathers Reveal Their Secret Colors.

Orange Stripey Dinosaurs? Fossil Feathers Reveal Their Secret Colors

Read more about plumage colors;

Carotenoid-based plumage colors indicate male quality.

Schemochromes: The Physics of Structural Plumage Colors.

Vinther, J., Briggs, D., Clarke, J., Mayr, G., & Prum, R. (2009). Structural coloration in a fossil feather. Biology Letters, 6 (1), 128-131 DOI: 10.1098/rsbl.2009.0524

grrlscientist Fri, 02/05/2010 - 04:10

Categories

Physical Sciences

A great post Grrl, I now have further reading to do on my favourite group of animals.... thanks very much ( I think) so much reading so little time...ah well.

Brian wrote something about this on Dino Tracking, too.
http://blogs.smithsonianmag.com/dinosaur/2010/02/05/dinosaurs-now-in-li…

adrian: i worship you.

Grrl may not be entirely sober...

You should see what she's just done to the cat (and my laptop).

Bob,

or are you just concerned about "deferred idolatry": you worship Grrl, Grrl worships Adrian ergo you worship Adrian?

Nice.
When I was a kid, all the dinosaurs were grey or olive green. Then people started making them coloured, just because that seemed likely. Now we can actually figure out what at least some of those colours were.

It's wonderful that so much information can be obtained from a bunch of rocks.

well, SimonG, not sure what you're on about, but MY dinosaurs were always delightful shades of purple, neon green and scarlet red. it's nice to see that scientists are finally catching up.

Lovely bird 'innit? Beau'iful plumage! (Even if it isn't a Norwegian Blue.)

Good post. Learned something new.

Unfortunately that means I will forget something tonight. I hope it isn't anything important.

@MadScientist,

Yeah but... 'E's not pinin'! 'E's passed on! This parrot is no more! He has ceased to be! 'E's expired and gone to meet 'is maker! 'E's a stiff! Bereft of life, 'e rests in peace! If you hadn't nailed 'im to the perch 'e'd be pushing up the daisies! 'Is metabolic processes are now 'istory! 'E's off the twig! 'E's kicked the bucket, 'e's shuffled off 'is mortal coil, run down the curtain and joined the bleedin' choir invisibile!! THIS IS AN EX-PARROT!!

Just re-visited the comments and blushing madly!!

my son just asked me two weeks ago.

"mommy how do people know the color of dinosaurs?"

Now I have an answer,

Thanks for this post.

That's funny - It could be a Norwegian Blue, if what I heard elsewhere is correct and blue pigment isn't shown by this technique! Ha!

well, SimonG, not sure what you're on about, but MY dinosaurs were always delightful shades of purple, neon green and scarlet red.

Noo!!! Not purple!!

If you want to see a 360-degree view of Anchiornis huxleyi in all his stripey glory, check out this spinning graphic on the National Geographic News site: http://news.nationalgeographic.com/news/2010/01/100127-dinosaurs-color-…

Amazing. I can't quite wrap my brain around the possibility that feathers evolved first not for flight but some other purpose. A mind-bender, somehow. Thanks for the post. Love the dino version of Woody Woodpecker.

Fetid Fish Revise Understanding of Fossil Formation

grrlscientist — Mon, 01 Feb 2010 12:19:58 +0000

Fetid Fish Revise Understanding of Fossil Formation

tags: evolutionary biology, paleontology, fossils, fossilization, fossil forensics, Taphonomy, taxonomy, zoology, deep time, paleoceanography, amphioxus, Branchiostoma lanceolatum, lamprey, Lampetra fluviatilis, chordates, researchblogging.org,peer-reviewed research, peer-reviewed paper

Three rotting Amphioxus heads.
A sequence of images showing how the characteristic features of the body of amphioxus, a close living relative of vertebrates, change during decay. Colours are caused by interference between the experimental equipment and the light illuminating the specimens.

Image: Mark Purnell, Rob Sansom, Sarah Gabbott, University of Leicester.
[larger view]
DOI: 10.1038/nature08745

How do you know what something looks like when you've never seen it before? This is the question that paleontologists deal with every day: describing the appearance of ancient animals based on incomplete information gathered from small fossilized fragments of those animals. As if that is not difficult enough, they also use this incomplete information about physical appearances to build family trees that describe the evolution of these animals.

A team of paleontologists from the University of Leicester devised a new method for extracting information from 500 million year old fossils: they studied the rate and sequence of decomposition for individual physical features to better understand how our ancient fish-like ancestors might have originally looked. The team's findings indicate that some of the earliest vertebrate fossils may have been more evolutionarily advanced than previously thought.

"It seems contradictory, but decomposition is an important part of the process by which animals become preserved and fossilized," explained paleontologist Robert Sansom from the University of Leicester in the UK, who led the research. "By knowing how these important anatomical features change as they rot, we are better able to correctly interpret the most ancient fossils representing the lowest branches of our part of the evolutionary tree."

Fish-like fossils from 500 million years ago form the early, basal, portion of our evolutionary heritage because they possess characteristic physical features, such as two eyes, a tail, and the precursor to a spine, known as a notochord (Figure 1).

Figure 1 | Phylogeny and anatomy of chordates. a, Deuterostome phylogeny based on data from extant forms. Asterisks mark the extant proxies used in the experiments. Each fossil taxon (coloured) has been proposed to have a wide range of affinities, with little consensus existing. b, Cephalochordate anatomy (top) and ammocoete anatomy (bottom). C, chordate synapomorphy; V, vertebrate synapomorphy. [larger view]
DOI: 10.1038/nature08745

"The idea that characters are lost -- especially in soft-tissue creatures -- to decomposition is not a novel idea," remarked Leicester team member Mark Purnell, a paleobiologist in the Geology Department at the University of Leicester, UK.

Up until now, paleontologists relied upon the assumption that decaying bodies lose their identifying characteristics in a random order. The Leicester team decided to test this hypothesis by carefully documenting how modern boneless fish -- similar to the early ancestors of humans -- decay. Their findings show that this assumption is in error.

To conduct this simple yet elegant study, the team collected adult amphioxus, Branchiostoma lanceolatum and juvenile lamprey, Lampetra fluviatilis, from the wild and killed them. The researchers placed the bodies into clear plastic boxes filled with saltwater, sealed the lids, and incubated them at 25 degrees Celsius for up to 200 days, recording the changes that the decaying bodies experienced (video).

Adult lamprey decomposition: 200 days in 36 seconds.

Three specimens of each species were destructively sampled at different time intervals to document rapid early decay as well as the later, slower stages of decomposition. The Leicester team recorded the decay process for each anatomical feature both visually and via dissection, and scored observed changes according to a simple rating system: pristine (same condition as at death), decaying (morphology altered from its original state) or lost (no longer present, or present but unrecognizable). These data were then analyzed (Figure 2).

Figure 2 | Results of experimental decay. a, Anatomical characters of larval Lampetra ranked according to last occurrences in decay sequence (horizontal scale shows time in days). Observations are scored as pristine (yellow), decaying (orange), onset of loss (red) or complete loss (terminal point). Plesiomorphic characters are labelled for Chordata (C), Vertebrata (V) and Bilateria (B). Decay stages are indicated in blue. b, Character decay for adult Branchiostoma (as in a). 'Storage organ' has been historically termed 'fin rays'. c, Quantitative morphological decay through time for Lampetra (green) and Branchiostoma (red). d, pH changes through time for Lampetra (green) and Branchiostoma (red); initial pH differences reflect salinity. Lines connect means in c and d; d, days. [larger view]
DOI: 10.1038/nature08745

These data revealed a surprisingly consistent pattern of decomposition throughout time. This pattern shows that as these modern fish decayed, the most recently evolved features -- those characters that are most informative because they distinguish closely related animals within the same lineage -- rotted first. The last features to disappear were more ancient; those that are shared by all vertebrates, such the notochord.

These findings raise important questions regarding just how "primitive" the early ancestors of vertebrates were 500 million years ago.

"The issue is: is a character not present because it was never there or is it that the character was there and had rotted away," explained Dr Purnell. "In cases where all we have are [fossils of] decay resistant structures, we have to be very careful."

The Leicester team documented this pattern of character loss so other scientists could better interpret the most ancient marine fossils.

Based on their data, the team proposed that misinterpretation of decayed fossils led to "stem-ward slippage" where organisms are classified as more basal than they really were (Figure 3).

Figure 3 | Morphological decay stages of Branchiostoma (left) and larval Lampetra (right) and the phylogenetic position of each stage if interpreted as a fossil. Rectangles on branches of the phylogeny are morphological characters, their shade indicating order of loss (white, early; dark, late). As each organism decays, its phylogenetic position moves down the tree; thus, taphonomic bias exists in identification of fossil chordates. Characters are colour coded according to the hierarchical level for which they are informative (green, chordate; yellow, cephalochordate; blue, vertebrate; purple, cyclostome and vertebrate (sensu DOI: 10.1666/06-130.1); red, petromyzontid). [larger view]
DOI: 10.1038/nature08745

This misinterpretation of some fossil materials might contribute to "a widespread but currently unrecognized bias in our understanding of the early evolution of a number of phyla" because failure to recognize that some important features might have disappeared before fossilization. This can be interpreted to suggest that many ancient animals belonged to very primitive and bizarre groups when they might actually have shared more features with modern animals than previously thought.

"In some organisms that have been interpreted there has been way too much speculation and the data have been extended beyond what is scientifically acceptable," Dr Purnell stated. He also pointed out earlier in a review paper that it is important to recognize that some fossil organisms are simply too just incompletely preserved for their evolutionary significance to be realized (DOI: 10.1002/bies.200800128).

Further, this study lends support to the hypothesis that many early vertebrate groups experienced short, rapid bursts of evolutionary change followed by long periods of basic tinkering of forms.

I think this study is interesting because, as a molecular biologist, I had no idea that the decay sequence followed by dead animal bodies had not already been worked out. For that reason alone, this study is long overdue. Additionally, I find it fascinating to learn that the sequence in which an animal's distinguishing features are lost to decay is not random, and appears to follow a reverse-phylogenetic pattern.

"We need to understand how they decayed if we're going to put them in the right place in the tree of life," agrees Dr Purnell. "The work doesn't appeal to everyone, but it's worth the effort."

NATURE video report.

Source:

Sansom, R., Gabbott, S., & Purnell, M. (2010). Non-random decay of chordate characters causes bias in fossil interpretation. Nature DOI: 10.1038/nature08745 [many thanks to Henry Gee, senior editor at Nature, for responding to my request to make this PDF open access. It will be freely available to the public for the next two weeks].

Also see:

Donoghue, P., & Purnell, M. (2009). Distinguishing heat from light in debate over controversial fossils. BioEssays, 31 (2), 178-189 DOI: 10.1002/bies.200800128

grrlscientist Mon, 02/01/2010 - 07:19

Categories

Life Sciences

Cool! Hooray for open access!

So decomposition recapitulates phylogeny -- fascinating!

(One question: since when are Branchiostoma termed "fish"?)

There are parts of a fish that are more distorted by decomposition than others. The abdominal region, for instance, can be severely distorted by decomposition gasses formed in the gut. Parts of the skull, thoracic & caudal spine, pelvic girdle, on the other hand, undergo relatively little distortion. Morphometric analysis of fossil fish is typically based on markers in these less distorted regions.

Question for Mike Keesey: Which bit of 'ancient fish-like ancestor' did you not understand?

palaeobill - in fairness Grrl does use "Fish" in her title. Fetid fish-like ancestors" doesn't have the same ring, alas.

darwinsdog - what you say may well be true, but we are not talking morphometrics or distortion of bodies here. The results of our decay work concern the sequence of loss of phylogenetically informative anatomical characters.

seriously, i see these titles and i think Yong!

Cool. It's the Body Farm for fish.

great post! Nasty taphonomy at it's best. It reminds of a paleontology class where the teacher presented a study by a colleague that decided to check how coprolites were formed by making a parrot crap on trays full of various sediments. The parrot was someone's mother's pet...

the title is the work of my own twisted mind. but if you must know, each piece i write has somewhere between 10-20 titles before i finally settle on one that i like (either that or i finish the story and the title it has at that point is the one it's stuck with).

this is a question another reader asked (i hope you're still out there, mark purnell);

Okay, this may be a dumb question, but I thought creatures were fossilized because they became encased in mud before there was much decomposition.

If that's the case, couldn't studying decomposition in water where the bits of flesh could fall off the body be a bit misleading? In mud, it would rot where it sat, but it seems like water would allow for some buoyancy and scattering.

…the most recently evolved features -- those characters that are most informative because they distinguish closely related animals within the same lineage -- rotted first. The last features to disappear were more ancient;…

Is this to be understood that more recent features rot more easily, or that those features are thought to be more recent becuase they rot more easily?

On the issue of being entombed in mud (post 11 â a good point), our animals were rotted in relatively small containers, so they couldn't float away; they pretty much trotted where they sat (take a look at the lovely lamprey video). But there is a more important point here regarding experiments: the process by which an organism becomes a fossil is a complex interaction between a number of variables, including decay, burial, the nature of the sediment in which it is buried, the chemistry of the water flowing through that sediment, etc. etc. If we try to study all these variables at once, we don't have a hope of understanding what's going on because we won't know which variables are causing the patterns of decay/preservation we observe. The way to build up an understanding of the whole process is to start simple: we need to understand decay in a simple experimental system, without sediment, before we can understand what the effects of sediment and other variables might be.

each piece i write has somewhere between 10-20 titles before i finally settle on one that i like

Did you consider "A fish rots from the head down"? ;)

Dr. Parnell, I'm the one who asked about the entombment. Would encasing the corpse in an inert, clear gel like ballistics gel simulate the conditions of burial without causing extraneous variables?

Thanks for taking the time to answer my original question. This study has me very curious.

Will they try this experiment with various amounts of sedimentary mud or sands covering the dead material. That could also change the rates of decomposition. My only fear is this simple re-adjusted thinking in researched paleontological finds would be used to say there has never been any evolved animals, all animal fossils found had fully formed modern appendages that just rotted fast......during the FLOOD in 6000yrs.