One picture is worth a thousand words.
DeFaveri J, T. Shikano, Y. Shimada & J. Merilä. High degree of genetic differentiation in marine three-spined sticklebacks (Gasterosteus aculeatus). Mol Ecol, in press.
Catching sticklebacks can be a lot fun: some of us might even feel excitement in pulling up funnel traps and seeing what is in them. After doing that for a while, one starts to perceive patterns and get ‘the hunch’: some places and traps seem to yield more, some less. Both ‘black’ (nylon coated) and ‘silver’ (galvanized) funnel traps have served many generations of fishermen and scientists, and there is plenty of unpublished knowledge about factors influencing funnel-trap catches. The Great Cheese Debate being one of them.
In the course of trapping sticklebacks for research purposes, the folklore in our lab has become that that the ‘silver traps’ catch more than the ‘black traps’, not to mention the ‘orange abominations’.
Last summer, we decided to put a stop to the speculations and soaked the two trap types in the same pond in a rigorously controlled manner. The results were clear: the ‘silver’ traps outperform the ‘black’ traps – hands down. Fished side-by-side in pairs, the silver ones catch always more fish than the black ones.
Merilä J et al. (2013) Large differenrences in catch per unit effort between two minnow trap types. BMC Research Notes, http://www.biomedcentral.com/1756-0500/6/151
Not long ago, I wrote about six + six herrings (read the post from *here*). Little I knew about them before reading this:
This may not be as delicious as Roach Veronique or fish assholes (check out them here), but possibly of some interest for the fans of our finned friends.
Uncovering and filtering signatures of natural selection from the effects of confounding neutral processes is not often easy. This goes both with molecular and quantitative traits. Few years ago, we described a new method to detect selection on quantitative traits (Ovaskainen et al. 2011), but the applicability of this mathematically rather hairy approach has been limited by access to flexible software application. Situation has now changed: Karhunen et al. (2013) describe a R-package capable of implementing the method. The package, code and manual can be downloaded from EGRU home pages here.
Karhunen M., J. Merilä, T. Leinonen, J.M. Cano Arias & O. Ovaskainen (2013) driftsel: an R package for detecting signals of natural selection in quantitative traits. Molecular Ecology Resources, in press.
Ovaskainen O., M. Karhunen, C. Zheng, J.M. Cano & J. Merilä (2011) A new method to uncover signatures of divergent and stabilizing selection in quantitative traits. Genetics 189: 621-632.
DRIFTSEL sofware site: http://www.helsinki.fi/biosci/egru/software/index.html
Someone has been busy. The results of a heroic road trip around the Baltic Sea followed by months of laborious counting, pipetting and data formatting are now about to start to bear fruits. As a follow up for a recent Evolution paper, Jacquelin has recently pushed out couple other gems from her database.
The map above – borrowed from a soon-to-appear paper from the Journal of Evolutionary Biology – shows the frequency of EDA-gene alleles (inner circle; black = high plate allele; white = low plate allele) and average proportion of lateral plates at phenotypic level (outer circle; expressed as proportion of 25 possibles plates) in different Baltic Sea samples of three-spined sticklebacks. Apart of the visual attraction (at least for those obsessed by maps), the notable discoveries in this paper include strong genetic evidence for (rare) adaptive phenotypic differentiation across a large marine sea area (yes, it is salty), as well the (sticklebackish) fact that the patterns of plate morph differentiation do not quite obey the typical salt/freshwater doctrine. Just check out the Russians.
The other paper cited below provides an empirical testimony and justification underlying the choice of microsatellite markers for the above mentioned Evolution paper: small number of SNPs can contain only limited amount of information about population differentiation in the scale of the map pictured above. If time and resources are limiting, microsatellites can still do pretty good job in answering consequential questions.
DeFaveri J. & J. Merilä (2013) Evidence for adaptive phenotypic differentiation in Baltic Sea sticklebacks. Journal of Evolutionary Biology, in press.
DeFaveri J., H. Viitaniemi, E. Leder & J. Merilä (2013) Characterizing genic and nongenic molecular markers: comparison of microsatellites and SNPs.
Molecular Ecology Resources, in press.
The story is from the Eastern Ghats (different from the Western Ghats!). Geckoella Jeyporensis thought to be extinct 130 years ago, has made a comeback. My friends and colleagues from CES-IISc were involved in the rediscovery. Its good to see efforts being put into herpetology research in these poorly studied regions harboring high endemic diversity. Search is also on for many lost amphibians from these regions!
read further here:
Can it be adaptive to have your head in ass? Possibly, at least if you are butterfly chased by a jumping spider. See the enclosed image and read the paper from the link below.
Sourako A (2013) Two heads are better than one: false head allows Calycopis cecrops (Lycaenidae) to escape predation by a Jumping Spider, Phidippus pulcherrimus (Salticidae). Journal of Natural History, doi:10.1080/00222933.2012.759288
Animals have been fine tuned to do the right thing – right? Then what about the enclosed images? They show to X-rays of Elvis – a fourteen year old dwarf snautser – from two time points. What can be seen is the first image is 287 g small stones in his stomach. The second image shows the post-surgical situation several months later after all the stones from the first feast had been removed. Does not quite look that he had learned much from the first incidence. But on the positive note, stones are moving! Blame the domestication? Or perhaps senescence – the old black boy thinks his a black grouse? Silly beast – I am sure there is a rationale explanation for his obsession, but I have not figured it out yet.
Studying animal behaviour might be boring and tricky to some geneticists (at least, Scott hates it!), considering that, it is too subjective to quantify, too vulnerable to environmental influences, too plastic and may not be repeatable. However, an exciting recent study by Weber et al., (2013) demonstrated that behaviour might not be as plastic as speculated earlier; rather it follows straightforward Mendelian genetics. The study has been published in Nature (493, 402-405; 2013), where the genetic architecture of burrowing behaviour of mice has been revealed by using two sister species called oldfield mice (Peromyscus polionotus) and deer mice (P. maniculatus). The oldfield mice has complex burrowing behaviour with long entrance and escape tunnels (allows to escape if a predator comes to front gate), and that burrow length is consistent across populations. In contrast, the burrow architecture of deer mice is very simple and small, with having no escape tunnel. Biotic ecological factor (e.g. predation from snake), has been reasoned to shape these kinds of burrowing behaviour (Weber and Hoekstra, 2009).
To determine the genetic architecture of the burrowing, at first, the genetic basis of this behaviour was confirmed by inspecting burrow under controlled laboratory condition. The burrowing inclination in the common garden was consistent with the field observation, which confirmed the genetic basis of this behavior (Weber and Hoekstra, 2009). The inheritance patterns of this behavioural variation were determined by observing the burrow of their hybrids. Where, all the F1 offspring built similar length of entrance tunnel with escape tunnel like Oldfield mice, thus, the alleles contributing to this burrowing behaviour appear to segregate in a dominant mode. Recombinant backcross with Oldfield mice revealed that, there are at least two separate behavioural modules for complex burrows of this species, one for tunnel length and one for the occurrence of an escape tunnel. Furthermore, QTL mapping identified four chromosomal locations (three for entrance tunnel length variation and one for the presence of an escape tunnel). These QTLs were unlinked and segregated on separate chromosomes. This is an exclusive landmark study, shows how a small numbers of independent genetic loci can contribute to the evolution of complex burrowing behaviour of mice.
Weber, J.N., Peterson, B.K., and Hoekstra, H.E. Discrete genetic modules are responsible for the evolution of complex burrowing behaviour in deer mice. Nature 493:402-405 (2013).
Weber, J. N. & Hoekstra, H. E. The evolution of burrowing behavior in deer mice. Anim. Behav. 77, 603–609 (2009)
I still remember how torn I was when I first read about the counter-intuitive possibility that natural selection could favor suicide. Apparently, sometimes one can increase one’s inclusive fitness by looking into barrel of a gun. Now, as it turns out, natural selection can favor also functional necrophlia. Read more about it from here, or consult the original publication. And who are these corpse humpers? Our beloved frogs.
Izzo et al (2012) Functional necrophilia: a profitable anuran reproductive strategy. Journal of Natural History 46:2961-2967.
It was back in 2006 or so when the idea of having a bit closer look on the large nine-spined sticklebacks in north-eastern Finland was lifted out of naphthalene. A mental model driving this interest was my earlier back-seat excitement over Anders Forsman’s PhD study of body size evolution of giant adders in outer archipelago of Stockholm. With a bit of sweet-talk and persuasion – and quite a few beers – I managed to convince Gabor to drop his copper-pipes and lizards and move over to fearful territory of working with an insignificant, small brown fish.
Half a decade and couple PhD-thesis later – not to mention all those hours spent in the basement (not me though) – we start to know how little we actually know about these fish. Not to mention the unknown unknowns. In attempt to summarize what we do and do not know, a short review paper is about to come out in Year in Evolutionary Biology. Stay tuned and you will soon be able to read it!
Merilä J. 2013. Nine-spined stickleback (Pungitius pungitius): an emerging model for evolutionary biology research. The Year in Evolutionary Biology (Annals of the New York Academy of Sciences), in press.
Sajid who just returned home to Bangladesh to have a brief break from the mid-winter melancholy of Finland has just recieved a prestigious price from his goverment for his efforts to map the country’s biodiversity. Congratulations Sajid!
More coverage about Sajid’s accomplishments here.
Times, they are a-changing. Picture shows our well-served MegaBace capillary sequencers behind the BioCenter 3. The image might have also symbolic dimensions: something that in one time point is critically important for a scientific community can lose its significance in less than 12 years. And even faster. It will be interesting to see how the research and ideas these machines supported to develop will stand and resist the effect time.
Lot of great evolutionary biology research has been done using the ‘evolutionary biology’s new supermodel’ – the three-spined stickleback – as a model system. The focus in best part of this research has been in evolution and adaptation of the ancestral marine ecotype to freshwater environments, whereas less is known about differentiation and adaptation within the marine environment. By studying genetic differentiation in the scale of entire Baltic Sea (n = 38 populations), Jacquelin has been patching up this gap. In paper to appear soon in a special issue (Genome Evolution and Speciation) of Evolution edited by Jeff Feder and Patrik Nosil, Jacquelin uncovers hidden genetic structuring among the marine stickleback populations. By exploring divergence in relation to environmentally relevant factors, evidence is provided for isolation by adaptation and significant adaptive population structuring is uncovered across the relatively young Baltic Sea in spite of ample opportunities for gene flow.
DeFaveri J., P. Jonsson & J. Merilä (2013) Heterogeneous genomic differentiation in marine threespine sticklebacks: adaptation along an environmental gradient. Evolution, in press.
The adipose fin is a small, fleshy fin found in all salmonid fishes and regarded as vestigial without clear function. It is routinely removed from millions of salmonids each year to mark their hatchery origin.
In this perspective, the paper by Bucland-Nicks et al. published in Proc R Soc B in 2011 (yes, this has escaped my radar) raises concerns: By studying the ultrastructure of the adipose fin the authors find it to contain extensive nervous tissue, as well cells equipped with primary cilia. Most ironically, the fin was not found to contain adipose tissue.
The results support the hypothesis that the adipose fin may act as a precaudal flow sensor, and its removal can be detrimental to swimming efficiency in turbulent water. I would not be the first time in the history of human race when strive to improve things takes us two steps back.
Buckland-Nicks JA, M Gillis and TE Reimchen (2011) Neural network detected in a presumed vestigial trait: ultrastructure of the salmonid adipose fin. Proc. R. Soc. B
Timing of maturation is an important life history trait that is likely to be subjected to strong natural selection. Although population differences in timing of maturation have been frequently reported in studies of wild animal populations, little is known about the genetic basis of this differentiation.
Izza investigated population and sex differences in timing of maturation within and between two nine-spined stickleback (Pungitius pungitius) populations in a laboratory breeding experiment. She found that fish from the high-predation marine population matured earlier than fish from the low-predation pond population, and males matured earlier than females. Timing of maturation in both reciprocal hybrid crosses between the two populations was similar to that in the marine population, suggesting that early timing of maturation is a dominant trait whereas delayed timing of maturation in the pond is a recessive trait. Thus, the observed population divergence is suggestive of strong natural selection against early maturation in the piscine-predator-free pond population.
Why are these cool results? Well, consider this. Fisheries-induced changes in maturation reaction norms are common, but the relative importance of environmental and genetic influences on maturation in this context remain uncertain. Many commercially exploited fish populations appear to have evolved towards earlier maturation – a trend that has been found to be difficult to reverse after closing the fisheries. This inability of the fish stocks to recover and reverse the trend back towards later maturation would be reinforced by the recessive nature of the alleles responsible for delayed maturation. After being driven to low frequency (if not eliminated) by the fisheries, reversal towards delayed maturation would be slow to occur because selection on rare recessives is not very efficient (check your population genetics text book). This is because almost all individuals with the rare allele are expected to be heterozygous, and the heterozygous individuals for the recessive allele would have the same phenotype (maturation time) and fitness as homozygotes for the dominant allele. In other words, the trend towards earlier maturation would be expected to be more swiftly reversed if the delayed maturation was a dominant trait.
Therefore, sticklebacks can have a lesson to tell – cods and governments should listen.
Ab Ghani NI, G Herczeg, T Leinonen & J Merilä (2013) Evidence for genetic differentiation in timing of maturation among nine-spined stickleback populations. Journal of Evolutionary Biology, in press.
Nature News article with the abovesaid headline reports interesting findings on the effects of drug residues in waterways. Fluoxetine – the active ingredient in antidepressant Prozac – was found to have adverse effects on fish mating behaviour.
Rebecca Klaper (University of Wisconsin-Milwaukee’s Great Lakes Water Institute) tested the effects of fluoxetine on a freshwater fish fathead minnow (Pimephales promelas) behaviour. Normally fathead minnows express complex mating behaviour with males building a nest and taking care of the eggs (very much like sticklebacks). When fluoxetine is added to the water, male fathead minnows start to spend more time building their nest, and even “become obsessive, to the point they’re ignoring the females”. With even higher fluoxetine consentrations, males start killing females.
Klaper presented her findings at the 2012 meeting of the North American division of the Society of Environmental Toxicology and Chemistry in Long Beach, California. At the same symposium, Dan Rearick (St Cloud State University, Minnesota) reported that a chemical found in birth-control pills reduced the ability of fathead minnow larvae to elude predators. Thus, chemical residues could affect not only reproductive success, but also survival.
Teleosts were not considered as model for aging research until relatively recently. Despite quit late start and poor crowd support teleosts are now increasing their pace and seem to have a bright future in a very competitive field of senescence research. Presented as a model for aging studies in around 70′s Nothobranchius sp. is quickly gaining popularity and is among the leaders of the teleost “team”. Representative of the genus- N. furzeri usually live up to12 weeks under laboratory conditions and is at the lower end of the lifespan spectrum among the organisms adapted for fast growth (Valdesalici and Cellerino, 2003; Genade et al. 2005). However, different populations and laboratory strains can vary in life span as much as 100% (Hartmann et al. 2009). Thus, it is not surprising that N. furzeri is now poked from different angles, from telomeres (Hartmann et al. 2009) to QTL mapping (Kirschner et al. 2012). Anyway, what is the connection between and Nothobranchius and French Paradox you might ask? Seems there is at least one. Resveratrol-natural phenol found in red wine and hypothetically responsible for a good health of French people eating saturated fat rich diet (French Paradox). Data on yeast and invertebrates demonstrated how resveratrol can modify life span, however first experimental data for vertebrates on the effect of this phenol came from Nothobranchius. Experimental fish were feed gellatinised Chironomus and resveratrol. Such treatment caused a dose-dependent increase of median and maximum lifespan (Valenzano et al. 2006). Though human clinical trials are on their way, Hector et al. (2012) presenting their meta-analysis remind that it is still too early to run into pharmacies and beg for resveratrol. Agreed! Nevertheless, who could argue that one glass of a nice red wine (just for medical purposes and just in case we have similar sensitivity to resveratrol as Nothobranchius) could hurt?
Genade et al. 2005. Aging Cell 4:223-233.
Hartmann et al. 2009. Mechanisms of Aging and Development 130:290-296.
Hector et al. 2012. Biology Letters 8: 790-793.
Kirschner et al. 2012 Aging Cell 11:252-261.
Valdesalici and Cellerino, 2003 Proc. R. Soc. Lond. B 7 . 27: S189-S191.
Valenzano et al. 2006. Current Biology 16:296-300.
Atlantic herring in the Baltic Sea is classical example of a marine fish species showing almost no genetic structuring in neutral marker genes over a vast range studied. It has been thought traditionally that this reflects high levels of gene flow and panmixia across the Baltic. Ever since I got familiar with these results, I have suspected that the idea of panmixia is likely to be just a reflection of the large effective size of local herring populations: QST-FST comparisons from range of taxa subject to strong gene flow (e.g. Scots pine) show extensive genetic divergence in quantitative traits in spite of no structuring in neutral marker genes. Existence of this kind of genomic heterogeneity has been self evident for people with background in quantitative genetics for a good while (few decades), but this realization has penetrated the brains of molecular ecologists only recently in the advent of technologies that have given access to broader range of genomic markers.
Not surprisingly, I am pleased to look the results of a RAD-seq project in which we uncovered quite a bit of cryptic population structuring in the Baltic herring over just a range of 400 km. Although this was ‘just’ a pilot study, it was made even so interesting by the novel numerical methods employed. The latter which underlines and illustrates the demands – and opportunities – that reside in ‘new generation’ of population genetic studies based on massive amounts of data.
Corander J, KK Majander, L Cheng & J Merilä (2013) High degree of cryptic population differentiation in the Baltic Sea herring Clupea harengus. Molecular Ecology, in press.
The facts: nine-spined sticklebacks in many Fennoscadian ponds reach ‘giant’ body sizes. This gigantism has a genetic basis. The speculations: since the occurrence of these giants is confined to ponds, it is unlikely that they have evolved in them by chance. Rather, it seems likely that gigantism is evolved in response to reduced predation mediated mortality which is expected select for early maturation at small size. Actually, a lot evidence (behavioural, neuroanatomical, morphological) supports this interpretation, but the ultimate test would be direct measurement of selection in the wild. Since this is next to impossible, the next best approach is modeling.
We analyzed the conditions leading to gigantism by modelling stickleback growth. The model was parametrized with empirical growth data and analysed for optimal growth strategy at different mortality levels. We found that optimal fish size, fitness and life span decreased with predator-induced mortality. At low mortality, the fitness of pond populations was higher than that of sea populations. In the scenario where all populations mature at the same age, the pond populations performed better at low mortalities and the sea populations at high mortalities. The conclusion became that together with a trade-off between growth constant and asymptotic size, different mortality rates can explain a significant proportion of body size differentiation between populations. In this particular case, it seems to provide a sufficient explanation of gigantism in pond nine-spined sticklebacks.
Aikio S, G. Herczeg, A. Kuparinen & J. Merilä (2013) Optimal growth of nine-spined sticklebacks at different mortalities. Journal of Fish Biology, in press.
Where to get the next good idea for a scientific breakthrough? From a vending machine? Perhaps, at least if you think correlation might imply causation. A recent paper published in New England Journal of Medicine suggest that the positive correlation between number of Nobel prize laureates and per capita rate of chocolate consumption across different nations might owe to cognition enhancing effects of flavanols contained by chocolate. Interesting outlier are the Swedes – more laureates than expected by their chocolate consumption. Of course it is not a footprint of nepotism, but their higher sensitivity and response to flavonoids. I was left to wonder how salty liquorice would explain variance in laureate numbers?
Messerli, FH (2012) Chocolate consumption, cognitive function, and Nobel laureates. New England Journal of Medicine, DOI: 10.1056/NEJMon1211064
While sampling sticklebacks along the Baltic Sea coast, I often wondered which capture method was more stressful to my poor victims: being squished against hundreds of their buddies while dragged up on shore with a giant seine net – if only for a few minutes, or spending several hours being trapped in a shiny basket while watching their buddies freely swim by.
Mandelman et al. (2012) had a similar question in mind, though for a more commercially relevant species: Atlantic cod. They measured the biochemical status of blood sampled from cod that were captured either rapidly by jig or more slowly by longline, in order to assess the physiological impact of capture. They found that longline capture seemed to be significantly more stressful than jigging (possibly due to extended hook times), and that mechanical removal of hooks after longline capture created more physical injury than if the hooks were removed gently by hand. Interestingly, the increase in physical trauma was not reflected in the blood chemical status.
I still dont know what this means for my sticklebacks….
Mandelman et al. 2012. The blood chemical status of Atlantic cod Gadus morhua following capture by jig and demersal longline with differential hook removal methods. Journal of Fish Biology 81: 1406–1414