Sixty years ago this month Nature published the famous paper by Watson and Crick solving the structure of DNA. At the time many researchers pursued this goal, made difficult by the complexity of the DNA itself. A key contribution to the solution of the puzzle was the x-ray diffraction data provided by Rosalind Franklin. Indeed, without [...]... Read more »
WATSON, J., & CRICK, F. (1953) Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid. Nature, 171(4356), 737-738. DOI: 10.1038/171737a0
Inokuma, Y., Yoshioka, S., Ariyoshi, J., Arai, T., Hitora, Y., Takada, K., Matsunaga, S., Rissanen, K., & Fujita, M. (2013) X-ray analysis on the nanogram to microgram scale using porous complexes. Nature, 495(7442), 461-466. DOI: 10.1038/nature11990
A fish swims along a sandy lake bottom, carrying one of its babies in its mouth. It approaches the nesting cave of another family of fish. With a furtive "ptooey," it leaves the baby behind for adoption. For certain fish, this seems to be a common scene: giving up your young and taking on others' may be the best way to ensure your offspring grow past snack size.
The fish in question is Neolamprologus caudopunctatus, a type of cichlid (pronounced like a compliment for someone's hat).* Just a couple of inches long, the diminutive fish lives only in East Africa's Lake Tanganyika. Males and females form monogamous pairs. They raise their young in burrows under rocks; carrying sand in their mouths, they pile it up around the rocks to build narrow entrances.
For the first 40 days or so in the lives of the young fish (called fry), both parents work to protect them from predators. They guard the nest and attack any other fish that come by looking for a meal. Cichlids can also protect their young by carrying them inside their mouths.
As the fry grow older and start swimming on their own, they may wander away from their parents' nests and into nearby ones. However, cichlids have also been spotted carrying young in their mouths and leaving them at other nests. Scientists at the Konrad Lorenz Institute of Ethology in Vienna set out to see how much of the baby swapping among N. caudopunctatus is intentional.
Researchers scuba dived down to the home of the cichlids, mapped the locations of their nests, and collected DNA samples. Back on land, like the crew of a daytime talk show for African lake bottoms, they analyzed the DNA to find out just how these fish were related.
Out of 32 nests, more than half held adopted fry, the authors report in Behavioral Ecology. Within nests that housed adopted fish, those outsiders made up anywhere from 10% to 77% of the nest.
The researchers took their DNA analysis a step further for a dozen adopted fry, hunting down their biological parents. They found that while some fry had been adopted from nearby nests, others were a very long way from home—as far as 40 meters or more. "It is virtually inconceivable that they swam there alone," says senior author Richard Wagner. The lake is packed with hungry predators. It would be, he says, "like a toddler walking across a busy city without mishap." It's more likely that parents deliberately carried these young fish in their mouths from one nest to the other.
There was another piece of evidence that adoptions happened on purpose. Adopted fish were on average larger (which is to say older) than non-adopted fish across the whole sample. But within each nest, the size difference wasn't significant. This suggests that when cichlid parents give up their young, they select nests with fry that are close in size to their own. Such a strategy might make the adopted fish less conspicuous to predators.
Parents who leave their fry at other nests may be hedging their bets, making sure that at least some of their offspring survive if their own nest is wiped out by a predator. As for adoptive parents, they could just kick out the freeloading fry. But keeping adopted fish around means that when predators attack, there's a smaller chance of your own offspring ending up in another fish's mouth.
"Our paper adds evidence that adoption is an adaptive strategy," Wagner says, rather than simply the result of wandering babies. We humans aren't the only animals that regularly choose to raise others' young. One hopes, though, that human foster parents aren't in it for the reduced predation.
Schaedelin, F., van Dongen, W., & Wagner, R. (2012). Nonrandom brood mixing suggests adoption in a colonial cichlid Behavioral Ecology, 24 (2), 540-546 DOI: 10.1093/beheco/ars195
Image: N. caudopunctatus by Varmer (via Flickr)
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Schaedelin, F., van Dongen, W., & Wagner, R. (2012) Nonrandom brood mixing suggests adoption in a colonial cichlid. Behavioral Ecology, 24(2), 540-546. DOI: 10.1093/beheco/ars195
One of the earlier advocates of using evolutionary biology in economics was Jack Hirshleifer, a professor of economics at the University of California, Los Angeles. Hirshleifer was author of The Dark Side of the Force: Economic Foundations of Conflict Theory, which includes evolutionary analysis of cooperation and conflict, and some discussion of the unification of law, [...]The post Economics from a biological viewpoint appeared first on Evolving Economics.... Read more »
Eyes are good things to have in the light. But if you lived in the dark... all the time... would those eyes become so much a nuisance that you might lose them?
Animals that live in caves are often blind. People sometimes mistake this as evidence that features can be lost just by a “Use it or lose it” rule. That would be an example of inheriting an acquired character, which doesn’t happen in evolution. Instead, the typical explanation is that because there is no advantage to maintaining eyes if you’re a cave dwelling population, any mutation that messes up making eyes is on an equal footing with the genes for making eyes.
It’s not that there’s an advantage for blindess... it’s just that there’s no disadavantage to it. And eyes are complex things to make, so lots of mutations could interfere with making eyes.
A recent paper by Klaus and colleagues suggests that sometimes, blindness in a cave-dweller is an advantage, not just neutral. They examined a group of crabs (genus Sundathelphusa; pictured, showing most cave adapted at bottom) in the Philippines. These are freshwater crabs, and some live in lakes and rivers and such above ground, and some live in caves. In fact, these crabs invaded caves over half a dozen times in the genus. The repeated examples make for nice natural experiments.
Using a combination of genetics plus the shape of the animal, they found that the eyes of the cave crabs had evolved just as fast as other features. Klaus and company argue that if the loss of eyes was genuinely neutral, you would expect it to be happening more slowly than other features, which are presumably under selection. Instead, the eyes were evolving just as quickly as the other featured, which suggests there is some sort of advantage to being blind.
What the advantage might be... the authors don’t say, surprising. In the introduction, Klaus and colleagues mention the idea that losing eyes “frees up” compuational power for other sensory organs. But they don’t follow that up in the discussion. They don’t even speculate a tiny little bit in the discussion. Other papers have also suggested some sort of advantage to blindness, but as far as I know, nobody has yet come up with a testable hypothesis. That it seems to be the case with both vertebrates and invertebrates suggests that whatever that selective factor is, it is very general.
Klaus S, Mendoza JCE, Liew JH, Plath M, Meier R, Yeo DCJ. 2013. Rapid evolution of troglomorphic characters suggests selection rather than neutral mutation as a driver of eye reduction in cave crabs, Biology Letters 9(2) 20121098. DOI: 10.1098/rsbl.2012.1098
Turning light and going blind: A tale of caves and genes
Once more into the cave
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Klaus S, Mendoza JCE, Liew JH, Plath M, Meier R, & Yeo DCJ. (2013) Rapid evolution of troglomorphic characters suggests selection rather than neutral mutation as a driver of eye reduction in cave crabs. Biology Letters, 9(2), 20121098-20121098. DOI: 10.1098/rsbl.2012.1098
How do you catch a dragon? Do you go looking for a brave knight to send forth on a difficult quest? Or a legendary hunter without fear?
No. You use cameras to capture their image.
To be clear, the dragons we’re talking about here are Komodo dragons (Varanus komodoensis), the largest living lizards, which can be found on some Indonesian islands and can reach a length of 3 meters. Their size, along with the absence of large mammalian carnivores on the islands, makes them apex predators in their habitat.... Read more »
Ariefiandy, A., Purwandana, D., Seno, A., Ciofi, C., & Jessop, T. (2013) Can Camera Traps Monitor Komodo Dragons a Large Ectothermic Predator?. PLoS ONE, 8(3). DOI: 10.1371/journal.pone.0058800
One of the largest cancer genetics studies ever conducted adds a wealth of information about the disease, but also highlights continuing difficulties with predicting cancer risk.
Researchers say that the work, conducted through the Collaborative Oncological Gene-Environment Study (COGS), will advance understanding of the biological causes of cancer. However, they caution that they still do not know enough about the cancers included in the study — breast, prostate and ovarian — to predict who will develop the diseases on the basis of genetics alone.... Read more »
Check Hayden, E. (2013) Huge cancer study uncovers 74 genetic risk factors. Nature. DOI: 10.1038/nature.2013.12675
SR1 bacteria are not exactly a household name, even among microbiologists. They were first discovered in contaminated aquifers, and since then they were found to be also in animal and insect guts, as well as in human mouths. They are even suspected of being a cause of periodontal disease. I should probably say here that SR1 is a whole phylum of bacteria, and not a single genus or species. The reason that they are not that well known is that their discovery was fairly recent.
Also, no one has ever actually seen or grown SR1.... Read more »
Campbell, J., O'Donoghue, P., Campbell, A., Schwientek, P., Sczyrba, A., Woyke, T., Soll, D., & Podar, M. (2013) UGA is an additional glycine codon in uncultured SR1 bacteria from the human microbiota. Proceedings of the National Academy of Sciences. DOI: 10.1073/pnas.1303090110
This week, I found a paper that I’m calling the best of both worlds. Well, for me at least. This paper combines my past (and lingering) interest in island biogeography with a current interest in climate change and carbon storage.If you have been reading my blog long enough then you already know my love of islands. They are just so darn useful. In the past, I have focused on oceanic islands, but lake islands are also really neat. These types of islands typically form when lower lying land areas fill with water, effectively cutting off higher areas from the mainland and making them into islands. As such, these islands usually already contain forest as opposed to an oceanic island that emerges from the ocean and must be colonized. A new study, published in journal Science, looks at a fire-driven boreal forest chronosequence on forested lake islands in northern Sweden. Such a chronosequence allows the study of soil carbon sequestration over time scales of centuries to millennia.This new study looks at roots and their associated fungi (mycorrhizae) as sources of this stored carbon. I’m not going to spend the space to describe mycorrhize, but will, instead, send you over to my Free Market Fungi post for more information, if you need it. It is known that 16 percent of the global carbon stock is sequestered in soils. To date, most carbon studies of this type focus on aboveground leaf litter as the fundamental determinants of this carbon accumulation. But a large portion of photosynthetically fixed carbon is actually directed belowground to the roots and, subsequently, the mycorrhizae. Now, let’s add fire. It has been shown that when a forest doesn't burn, the soil and ecosystem carbon accumulate unabated, and in a linear fashion. Add this information together and it becomes a big deal when it comes to correctly allocating carbon, calculating the long term sequestration rates, and predicting how forests will respond to climate change and other environmental shifts.The study sites were in two adjacent lakes, Lake Hornavan and Lake Uddjaure, in northern Sweden. The islands in these lakes were formed after the most recent glaciation and come in a variety of sizes. In terms of fire, larger islands burn more frequently because they are larger targets for lightning strikes. As a result, several of the large islands in these lakes have burned in the last century, whereas some of the small islands haven’t burned in at least 5000 years. This lack of fire leads to very thick humus layers (or organic layers towards the top of the soil column) on smaller islands, up to 1 meter thick!The researchers divided islands into three size classes of 10 islands each: large (over 1 ha), medium (0.1-1.0 ha), and small (less than 0.1 ha). They took soil samples from these islands to look at the organic soil profiles and found that large islands accumulated 6.2 kg of C per square meter belowground with a mean time since fire of 585 years, medium islands accumulated 11.2 kg of C per square meter with a mean time since fire of 2180 years, and small islands 22.5 kg of C per square meter with a mean time since fire of 3250 years. Then they looked at the carbon dynamics across this chronosequence by analyzing bomb 14C. This allowed them to determine the age since fixation of soil carbon. Then they fitted a mathematical model to measurements of carbon mass and age distribution across the soil profiles for six of the islands (3 large, 3 small). This model revealed that the distribution of carbon mass and age could only be predicted when they included carbon from roots. This root-derived carbon accumulation was found to be larger on small islands (70 percent, that's a LOT!) than large islands (47 percent). They were able to explain the entire carbon sequestration difference on small islands from these root-derived inputs. The model also showed that small islands store a major proportion of their soil carbon in the deeper soil layers, those over 100 years old. However, below 20 cm depth, the root-derived carbon inputs were shown to be low and to decompose slowly. So the root-derived carbon input into the upper layers probably contributes to the long-term buildup of humus that is seen on these islands. But, as usual, that's not the end of the story.We know that fungi play very important roles in forest ecosystems, both as decomposers and in root-assoicated carbon transport and respiration. So the researchers also profiled the relative abundance of major groups of fungi by depth in the soil profiles. They found that the upper soil layers are dominated by free-living saprotrophs (fungi that obtain their nutrition heterotrophically from non-living organic materials), and greater depths were dominated by mycorrhizal and other root-associated fungi. Their model suggests that these mycorrhizae live at the spots where the largest difference in carbon sequestration between the island size classes exists, which also tends to be the areas of highest root mass. When they ran tests for fungal biomass throughout each soil profile they found greater mycelial (the vegetative part of a fungus, consisting of a mass of branching, threadlike hyphae) production on large islands, but less mycelial necromass (dead stuff) on small islands. This suggests that the large production is counterbalanced by faster decomposition of mycelial remains. “Correspondingly, the 14C model indicated faster decomposition of root-derived [carbon] on large islands, despite inputs being conservatively constrained to be equal across all islands.” I found these conclusions to be interesting because of the amount of soil carbon from roots and mycorrhizal fungi, especially on small islands. And although they saw less carbon accumulation on large islands, these islands have a greater root density and so should have more carbon allocation to roots and the associated fungi. Did you catch the contradiction? Well, in response to increased carbon dioxide, there will be an increase of carbon inputs to the roots which will accelerate the turnover of soil organic matter. This counteracts carbon accumulation and enhances nitrogen cycling through the microbial pools, an effect these researchers observed when they tested the C:N-ratios in the humus of large islands. This is much lower on small islands, possibly because of impared mycorrhizal nitrogen mobilization and the accumulation of nitrogen in fungal remains. This leads to progressive nutrient limitations, then leads to changes plant productivity, leading to changes in community composition, which leads to changes in total belowground carbon allocation, that leads to changes in fungi. Definately starting to grasp the importance of the belowground dirty stuff. There’s a whole lot of carbon down there that we need to start looking at, accounting for, and seeing where it goes. We know that changes in the environment such as climate change, soil fertilization, fire suppression, and forest management make big differences to the aboveground stuff. It only makes sense that the belowground stuff is impacted as well.Clemmensen, K., Bahr, A., Ovaskainen, O., Dahlberg, A., Ekblad, A., Wallander, H., Stenlid, J., Finlay, R., Wardle, D., & Lindahl, B. (2013). Roots and Associated Fungi Drive Long-Term Carbon Sequestration in Boreal Forest Science, 339 (6127), 1615-1618 DOI: 10.1126/science.1231923If you would like some follow-up reading I suggest:Treseder, K. K. (2013-03-29) Fungal Carbon Sequestration. Science, 339(6127), 1528-1529. (DOI: 10.1126/science.1236338) Also check out the write-up in Nature "Fungi and roots store a surprisingly large share of the world's carbon"... Read more »
Clemmensen, K., Bahr, A., Ovaskainen, O., Dahlberg, A., Ekblad, A., Wallander, H., Stenlid, J., Finlay, R., Wardle, D., & Lindahl, B. (2013) Roots and Associated Fungi Drive Long-Term Carbon Sequestration in Boreal Forest. Science, 339(6127), 1615-1618. DOI: 10.1126/science.1231923
What do comedian Lucille Ball, impressionist painter Pierre-Auguste Renoir, actress Kathleen Turner, chemist Dorothy Hodgkin and physician Christiaan Barnard share in common? Apart from being famous, they all had rheumatoid arthritis.... Read more »
John M. Eisenberg Center for Clinical Decisions and Communications Science. (2012) Drug Therapy for Rheumatoid Arthritis: Comparative Effectiveness. Agency for Heathcare Research and Quality. PMID: 23285486
Bartelds GM, Krieckaert CL, Nurmohamed MT, van Schouwenburg PA, Lems WF, Twisk JW, Dijkmans BA, Aarden L, & Wolbink GJ. (2011) Development of antidrug antibodies against adalimumab and association with disease activity and treatment failure during long-term follow-up. JAMA : the journal of the American Medical Association, 305(14), 1460-8. PMID: 21486979
I'm hopefully not setting myself up for a fall by discussing the study published by Frank DeStefano and colleagues* (open-access) suggesting no link between the 'too many too soon' argument of vaccination and risk of autism. As probably would be expected with such study results, there has been a flurry of interest on this paper (see here and here for example) and so once again I'm not going to add too much to the details which have already been reported.The basics:Based on a final comparison of 256 children diagnosed with an autism spectrum disorder (ASD) with an asymptomatic control group of 752 children (all born between 1994 -1999), vaccination histories were examined and exposure to "total antibody-stimulating proteins and polysaccharides from vaccines was determined by summing the antigen content of each vaccine received". For those like me, who are not too well-versed in the immunological principles of vaccination, the antibody-stimulating proteins and polysaccharides bit basically refers to the constituents of vaccines designed to invoke an immune response and the production of antibodies to recognise and fight the bacteria/virus being vaccinated against. Quite by coincidence, the BBC recently carried an interesting article about new vaccines potentially coming from some analysis on the UK synchrotron, the Diamond Light Source (see here - click on the interactive video) which quite neatly sums up the hows and whys of vaccination. The study produced odds ratios (ORs) for ASD 'outcomes' during the first 2-years and found no evidence for any increased risk of autism based on antigen exposure. Bearing in mind quite a few other potentially interfering variables were also collected (maternal exposures, child birth conditions, etc.), the results similarly suggested "no associations when exposures were evaluated as cumulative exposure from birth to 3 months, from birth to 7 months, or from birth to 2 years, or as maximum exposure on a single day during those 3 time period". In short, no statistical association between too many vaccines too soon and autism.There's little more to say about the findings that hasn't already been said. I've talked before about immunisation uptake in siblings of children with autism (see here) and how the general topic of vaccination has been a real source of discussion/debate/argument in some quarters of the autism landscape; more often than not as a result of the disparity between personal experiences vs. the scientific literature.Appreciating that quite a few people want to draw a line under the whole vaccination-autism affair in light of this and other data quite explicitly detailing no population-wide link between the two, I'm always open to further scientific inquiry on any aspect of autism. Take for example the work by Harumi Jyonouchi and colleagues on SPAD - specific polysaccharide antibody deficiency - in relation to cases of autism (see here) which may or may not be relevant and which is crying out for further independent replication. Or even the suggestion that post-vaccination paracetamol (acetaminophen) use might be tied into risk of autism as per the paper by Schultz and colleagues** (thanks Jen).And then there are the various reports on cases being conceded on vaccination and 'autism-like symptoms' developing as per Hannah Polling. Indeed, with the n=1 very firmly in place, I note from the linked Time article "she received an unusually large number of vaccines in 2000 (when thimerosal was still in use). Because of a series of ear infections, Hannah had fallen behind in the vaccine schedule, so in a single day she was given five inoculations covering a total of nine diseases: measles, mumps, rubella, polio, varicella, diphtheria, pertussis, tetanus, and Haemophilus influenzae." According to the DeStefano results, the total antigen load was not an issue? So what might have been the issue/s? Did a mitochondrial problem show some involvement or not? (see the CDC FAQs on this topic).I'm going to finish this post by highlighting just how important vaccination is (see here, again from the CDC), save any charges of irresponsible blogging being levelled against me. At the same time though, realising that no medicine is infallible and that continued vigilance and monitoring is required as per the article by Roberta Kwok*** and the recent flu vaccination - narcolepsy example.----------* DeStefano F. et al. Increasing Exposure to Antibody-Stimulating Proteins and Polysaccharides in Vaccines Is Not Associated with Risk of Autism. J Pediatrics. March 2013.** Schultz ST. et al. Acetaminophen (paracetamol) use, measles-mumps-rubella vaccination, and autistic disorder: the results of a parent survey. Autism. 2008; 12: 293-307.*** Kwok R. Vaccines: The real issues in vaccine safety. Nature. 2011; 473: 436-438.----------Frank DeStefano, Cristofer S. Price, & Eric S. Weintraub (2013). Increasing Exposure to Antibody-Stimulating Proteins and Polysaccharides in Vaccines Is Not Associated with Risk of Autism The Journal of Pediatrics... Read more »
Frank DeStefano, Cristofer S. Price, & Eric S. Weintraub. (2013) Increasing Exposure to Antibody-Stimulating Proteins and Polysaccharides in Vaccines Is Not Associated with Risk of Autism. The Journal of Pediatrics. info:/
If you’ve never heard of Tetrahymena thermophila, your world is about to get much stranger. This little beauty, a single-celled …Continue reading »... Read more »
Cervantes, M., Hamilton, E., Xiong, J., Lawson, M., Yuan, D., Hadjithomas, M., Miao, W., & Orias, E. (2013) Selecting One of Several Mating Types through Gene Segment Joining and Deletion in Tetrahymena thermophila. PLoS Biology, 11(3). DOI: 10.1371/journal.pbio.1001518
RNA FISH is a powerfull tool to measure not only the amount of mature mRNAs in the cytoplasm (or other compartments) but also to asses the amount of nascent transcripts that are still at the transcription site. These nascent transcripts are RNAs … Continue reading →... Read more »
Mueller, F., Senecal, A., Tantale, K., Marie-Nelly, H., Ly, N., Collin, O., Basyuk, E., Bertrand, E., Darzacq, X., & Zimmer, C. (2013) FISH-quant: automatic counting of transcripts in 3D FISH images. Nature Methods, 10(4), 277-278. DOI: 10.1038/nmeth.2406
As the reader will discover, the wolves—given just a fragment of chance and space—wove a story while we, with our supposedly vast powers of imagination, did well to just sit back and watch and learn. –Rick Bass, Preface to the Mariner Books edition of The Ninemile Wolves (2003) This post is a final analysis of [...]... Read more »
Axelsson, E., Ratnakumar, A., Arendt, M., Maqbool, K., Webster, M., Perloski, M., Liberg, O., Arnemo, J., Hedhammar, �., & Lindblad-Toh, K. (2013) The genomic signature of dog domestication reveals adaptation to a starch-rich diet. Nature, 495(7441), 360-364. DOI: 10.1038/nature11837
I bet a lot of you have that ex-girlfriend or ex-boyfriend who just hangs on….and hangs on tighter even though you’ve driven off to college and totally matured past the desire to want someone who can crush a beer can on his/her forehead. He/she was totally pulling an endoplasmic reticulum, and the paper that brought us today’s image shows us why.Endosomes form at the plasma membrane, where they take in material from outside the cell. They mature, with some cargo recycled back to the plasma membrane and some cargo trafficked to lysosomes for degradation. The cytoskeletal tracks (microtubules) that endosomes depend on for movement around the cell are also used as tracks for the endoplasmic reticulum (ER), where proteins are synthesized, folded, and sorted. Recent work has shown interactions between endosomes and the ER, and a more recent paper characterizes these interactions. Friedman and colleagues used high-resolution three-dimensional electron microscopy and found that ER tubules wrap around maturing endosomes, while both organelles maintain contact with microtubules. As the endosomes mature, they become more tightly connected to the ER. Similarly, as an endosome traffics, the interacting ER rearranges its structure in order to maintain endosome contact. In the images above, early endosomes (Rab5, red) are tightly associated with ER membranes (green). Higher magnification images (bottom) of the boxed region show three early endosomes (numbers 1,2, and 4) that are and remain in contact with the ER over the course of two minutes, and one endosome (number 3) that becomes associated.Friedman, J., DiBenedetto, J., West, M., Rowland, A., & Voeltz, G. (2013). Endoplasmic reticulum-endosome contact increases as endosomes traffic and mature Molecular Biology of the Cell, 24 (7), 1030-1040 DOI: 10.1091/mbc.E12-10-0733... Read more »
Friedman, J., DiBenedetto, J., West, M., Rowland, A., & Voeltz, G. (2013) Endoplasmic reticulum-endosome contact increases as endosomes traffic and mature. Molecular Biology of the Cell, 24(7), 1030-1040. DOI: 10.1091/mbc.E12-10-0733
In August 2011, a blog post highlighted a study by Starink et al. (2011), which described a condition known as familial multiple discoid fibromas (FMDF). This rare skin disorder is characterised by the early onset of multiple firm papules on the … Continue reading →... Read more »
Wee, J., Chong, H., Natkunarajah, J., Mortimer, P., & Moosa, Y. (2013) Familial multiple discoid fibromas: unique histological features and therapeutic response to topical rapamycin. British Journal of Dermatology. DOI: 10.1111/bjd.12315
Hello Julie,My, oh my! What an exciting time it was last week, witnessing Dog Spies' migration to the Scientific American Blog Network. Such a great day for dogs, for science and for YOU! Yah! for this recognition of your fabulous writing achievements, communicating the field of canine science to a broader audience. WELL DONE!As for your question about writing and how I do it, I have to admit I'm 'between systems' currently. By this, I mean that I sometimes map out ideas and plan my writing on paper before hitting the laptop; other times I just let rip straight onto the keyboard. I don't know if I'll ever migrate to a completely paperless system, but I feel that I'm moving in that direction. I still take most of my notes in meetings on paper, which is ridiculous as my handwriting is barely legible, even to me!Thanks also for the link to that piece by Clive Wynne about academic writing - I really enjoyed reading it.META-ANALYSIS You said it. I'm neck-deep in meta-analysis goodness right now and I'd love to tell you more about it. The meta-analysis data set I'm currently involved in compiling is about canine salivary cortisol (that just means cortisol found in dog spit). Cortisol is a hormone (more detail here) regularly used in research concerning animal stress and welfare. I've been interested in canine salivary cortisol for a while now. That's partly because I collected a lot of it (dog spit, that is) from dogs living in home environments and working dog kennels as part of my PhD research; and partly because its really interesting! But my data alone is just one piece of a bigger puzzle. While it's really valuable information (of course it's valuable, it's part of my PhD!), it only offers insight into around 75 dogs from one population of purpose-bred dogs in one geographic area during one two-year period. How do the results of these dogs in my study compare to 'normal' dogs?Well, you see - that's the thing. What is the normal range for salivary cortisol in dogs? We don't really know. What is it?Meta-analysis is a way of evaluating and interpreting the results from research about a particular topic. It adds together the data from different studies, then looks at the compiled data pool to see what patterns and relationships might emerge in the larger body of available information created by the many research projects.Throw another dog in the (data) pool! (source)Why use it?The patterns and groups we might look at within a meta-analysis of salivary cortisol (often used as an indicator of stress/welfare in dog research) are things like: Effects of different environments (do all the results from dogs housed in 'unfamiliar kennel environments' or 'familiar home environments' clump together at different or similar points within the range of values as a whole?); Effects of breed/age (is the range for labradors the same as that for german shepherds? Are all the young dogs in the same place as the old dogs?); Methodological aspects (such as what collection media was used: cotton swabs / synthetic rope / swabs with a saliva stimulant, etc. - does this effect where the cortisol results lie within the whole range?) All this information (and much more!) can be investigated and the information will help to provide further context for the existing studies, while also informing the design and interpretation of future studies. ... Read more »
Liberati Alessandro, Altman Douglas G., Tetzlaff Jennifer, Mulrow Cynthia, Gøtzsche Peter C., Ioannidis John P.A., Clarke Mike, Devereaux P.J., Kleijnen Jos, & Moher David. (2009) The PRISMA statement for reporting systematic reviews and meta-analyses of studies that evaluate health care interventions: explanation and elaboration. Journal of Clinical Epidemiology, 62(10). DOI: 10.1016/j.jclinepi.2009.06.006
Dorey Nicole R., Udell Monique A.R., & Wynne Clive D.L. (2009) Breed differences in dogs sensitivity to human points: A meta-analysis. Behavioural Processes, 81(3), 409-415. DOI: 10.1016/j.beproc.2009.03.011
What will climate change mean for the forests of southcentral Alaska? A podcast interview with NPS ecologist Carl Roland.... Read more »
Roland, C., Schmidt, J., & Nicklen, E. (2013) Landscape-scale patterns in tree occupancy and abundance in subarctic Alaska. Ecological Monographs, 83(01), 19-48. DOI: 10.1890/11-2136.1
As I’ve mentioned before, scientists are so conservative that when you see an adjective like “extraordinary” in the title, you should at least open up the paper if you can and have a peek.
I came across a paper titled, “An extraordinary tail – integrative review of the agamid genus Xenagama” in Google Reader *. I was a bit curious (and miffed) because I had no idea from the title what kind of organism this paper would be about. All kinds of animals have tails.
I love me spikes and spines and armor on critters, so I flipped out a bit when I learned this belonged to the Xenagama:
That is indeed an cool looking lizard (Xenagama taylori) with a cool looking tail. The genus Xenagama originally contained two species that was defined by this short, club-like, spiky tail. But there’s a problem when you use a single extraordinary feature to classify animals: you might overlook all the other features that tie it to other relatives.
A new paper Wagner and colleagues uses a lot of different tricks to tease apart the evolutionary relationships of the lizards in this genus: morphology, genetics, climate, and so on.
By looking at all the morphology, and not just the tails, they found that a long-tailed lizard previously put in another genus (Acanthocercus zonurus; below) sorts out with Xenagama and not Acanthocercus. Genetic analysis on this species also put it in with the rest of the Xenagama group, although it’s an early offshoot from the tree of these related lizards.
The authors also discovered a new species in the genus, that, like Acanthocercus zonurus, has a reasonably long tail; sort of intermediate between the short known species and the misidentified one. This new species is dubbed Xenagama wilmsi.
It turns out that the short tail of most of the lizards in this genus was something that was obscuring some of the relationships. There were similar problems with data on breeding colours. Some of the males in this group show different colours, which was used in creating their classifications, but the males don’t show those breeding colours all year round.
All of which doesn’t answer the obvious question: why do some of these lizards have these short tails? The tails do seem to have an adaptive function. The two species with long tails seem to be tree dwellers, while the two short-tailed species are rock-dwelling burrowers. Xenagama taylori will use its short spiked tail to close its burrow, which you can see in action below:
How this tail has been molded through development and genetic to get so short would be a great doctorate for someone. While native to northern Africa, some of these lizards seem to be fairly available in the pet trade. Don’t know how easily these lizards would be to breed in captivity, though.
* You know, that allegedly useless service that absolutely nobody needs because all of the people on Twitter and social media are so good at finding stuff that I want to read, yet who somehow let me down on discovering this.
Wagner P, Mazuch T, Bauer AM. 2013. An extraordinary tail - integrative review of the agamid genus Xenagama. Journal of Zoological Systematics and Evolutionary Research: in press. DOI: 10.1111/jzs.12016
Top photo from here; Acanthocercus zonurus from here.... Read more »
Wagner Philipp, Mazuch Tomas, & Bauer Aaron M. (2013) An extraordinary tail - integrative review of the agamid genus Xenagama . Journal of Zoological Systematics and Evolutionary Research. DOI: 10.1111/jzs.12016
We started trying to manage fisheries using science-based principles more than 150 years ago. Today, despite great improvements, we are still struggling to manage fisheries well. Perhaps the greatest missing piece in our understanding is an ability to accurately link the number of spawning adult fish with the number of their offspring that survive to replenish the population. Recognition that individual differences play a role in the dynamics of natural populations promises to greatly improve fisheries management.A classic example of our inability to effectively manage harvested fish populations is the collapse of the northwest Atlantic cod fishery. Despite being managed using best practices, in 1992 the number of cod had collapsed to less than 1% of the number present in 1977. A moratorium was declared to allow the fishery to recover. It was predicted to rebound within a decade, but twenty years on and cod stocks are still at less than 5% of their previous levels and some authorities suggest the fishery may never fully recover.An Atlantic cod, Gadus morhua (photo Wikipedia).Most fishes are highly fecund, releasing tens to hundreds of thousands or even millions of eggs. Mortality during the early life of fish is incredibly high, often with fewer than one in a thousand surviving the first few days. But, because of the shear number of offspring, small changes in the mortality rate can lead to enormous differences in the number of fish that survive to replenish the population. The great difficulty has been to determine which factors contribute to changes in mortality rate.Predation and starvation are the two greatest sources of mortality for fish eggs and larvae. Neither of these is random. Bigger, better provisioned eggs are more likely to produce larvae that survive the larval period and replenish the adult population. There are also characteristics of the parents that effect the survival of their offspring, such as when and where they choose to spawn, and how big or old they are.Predators of fish eggs and larvae are numerous. Jellyfish, like Aurelia aurita, are among them (photo Wikipedia).Early hypotheses about what regulated survival in the larval period focused on starvation. Hjort's 'critical period' hypothesis (1914) proposed that food resources must be present when larval fish were switching from using their yolk reserves to feeding. Cushing's 'match-mismatch' hypothesis (1975, 1990) recognised that as larvae grow they need progressively larger prey and timing of prey requirement needs to be a match with the timing of prey availability.Good evidence to support these hypotheses has only emerged recently, with the arrival of technology that can provide long-term measurements over large spatial scales. Platt et al. (2003) combined data from remote-sensing satellites with long-term population surveys of haddock, Melanogrammus aeglefinus. Their data showed that when the peak of spawning occurred after the peak in the spring plankton bloom, survival of larval haddock was much higher.A haddock, Melanogrammus aeglefinus (photo Wikipedia).Beaugrand et al. (2003) used data from continuous plankton sampling devices that are opportunistically attached to merchant ships. The devices gave them not only plankton abundance data, but allowed them to measure the size of prey species. Data on cod, Gadus morhua, were obtained from two largely overlapping population surveys. Like Platt et al., they found that the timing of the plankton bloom was important for larval survival, but they also found that the abundance and average size of prey species were important too.Predation was recognised early on as an important factor influencing the survival of fish larvae. However, research into its effects on fish populations didn't begin in earnest until the 1970's. The research showed that bigger, faster growing larvae were more likely to survive that larval period. Several, subtly different mechanisms were proposed to explain this pattern and are often combined into the 'growth-predation' hypothesis. Testing the growth-predation hypothesis in the wild has proved tricky. But, fish have structures in their ears called otoliths that lay down growth rings a bit like the growth rings in a tree. Because the growth rings in otoliths are laid down daily in many fish species they can be used as proxy measurements of size and growth. Several studies have used otoliths to calculate size and growth rates and have universally supported the growth-predation hypothesis (e.g. Hare & Cowen 1997, Meekan et al. 2006).The otolith of a black rockfish, Sebastes melanops, showing the light and dark bands of yearly growth incre... Read more »
Beaugrand, G., Brander, K., Alistair Lindley, J., Souissi, S., & Reid, P. (2003) Plankton effect on cod recruitment in the North Sea. Nature, 426(6967), 661-664. DOI: 10.1038/nature02164
Beldade, R., Holbrook, S., Schmitt, R., Planes, S., Malone, D., & Bernardi, G. (2012) Larger female fish contribute disproportionately more to self-replenishment. Proceedings of the Royal Society B: Biological Sciences, 279(1736), 2116-2121. DOI: 10.1098/rspb.2011.2433
Cushing, D. (1969) The Regularity of the Spawning Season of Some Fishes. ICES Journal of Marine Science, 33(1), 81-92. DOI: 10.1093/icesjms/33.1.81
Cushing, D. H. (1990) Plankton production and year-class strength in fish populations - an update of the match mismatch hypothesis. Advances in Marine Biology, 249-293. DOI: 10.1016/S0065-2881(08)60202-3
Hare, J., & Cowen, R. (1997) Size, Growth, Development, and Survival of the Planktonic Larvae of Pomatomus saltatrix (Pisces: Pomatomidae). Ecology, 78(8), 2415. DOI: 10.2307/2265903
Hedgecock, D., Launey, S., Pudovkin, A., Naciri, Y., Lapègue, S., & Bonhomme, F. (2006) Small effective number of parents (N b ) inferred for a naturally spawned cohort of juvenile European flat oysters Ostrea edulis. Marine Biology, 150(6), 1173-1182. DOI: 10.1007/s00227-006-0441-y
Hjort, J. (1914) Fluctuations in the great fisheries of northern Europe viewed in the light of biological research. Reun. Cons. Int. Explor. Mer, 1-228. info:/
Marshall, D., Heppell, S., Munch, S., & Warner, R. (2010) The relationship between maternal phenotype and offspring quality: Do older mothers really produce the best offspring?. Ecology, 91(10), 2862-2873. DOI: 10.1890/09-0156.1
Meekan, M., Vigliola, L., Hansen, A., Doherty, P., Halford, A., & Carleton, J. (2006) Bigger is better: size-selective mortality throughout the life history of a fast-growing clupeid, Spratelloides gracilis. Marine Ecology Progress Series, 237-244. DOI: 10.3354/meps317237
This week’s video tip of the week introduces you to Enzyme Portal, an interface to explore data about these important proteins, from the EBI. In the video, Jenny Cham–one of the authors of the paper below–takes you through the main features of their newly designed resource. I learned about the new effort from this blog [...]... Read more »
de Matos, P., Cham, J., Cao, H., Alcántara, R., Rowland, F., Lopez, R., & Steinbeck, C. (2013) The Enzyme Portal: A case study in applying user-centred design methods in bioinformatics. BMC Bioinformatics, 14(1), 103. DOI: 10.1186/1471-2105-14-103
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