Why is Jolly Jumper horsing around?

By Juha 12.11.2009 – 8:45 in Journal club
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Likaa_töitä

Performing unconscious stereotypic behaviors – such as repetitive bobbing of head or windsucking – after work hours? Watch out, you might overworked and/or stressed. This is at least what the results of a recent French study of horses are suggesting.

By observing prevalence and types of stereotypic behaviors among horses in relation type of work they were used for, it was found that these depended strongly upon the type of work the horses were performing. The results are interpreted as evidence that stress at work may have variety of negative and durable effects on one’s behavior. As short as one hour spell of work per day may suffice to inflict the symptoms!

Hausberger et al. (2009) Could work be a source of behavioural disorders? A study in horses. PLoS ONE 4(10): e7625. doi:10.1371/journal.pone.0007625

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Open Access in Sweden

By Juha 10.11.2009 – 11:34 in Random picks
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Starting from 2010, all research financed by the Swedish Research Council should be available for public for free. In other words, research results need to be published in Open Access journals or journals allowing also this format. Unfortunately, there will be no extra budget to cover the costs of this requirement – research projects will take the damage (on the benefit of the public?).

Read more about this from Tentakel

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Narrowing scope of knowledge

By Anna 9.11.2009 – 19:41 in Random picks
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The observation that the accumulation of scientific knowledge has forced scientists to focus on narrower and narrower areas is by no means surprising. However, along this development attitudes about the broadness of education have also changed. A couple of centuries back an educated man was expected to know about arts, politics, sciences etc, but nowadays for one being considered educated it is sufficient to be knowledgeable in one’s own field but remain rather ignorant of any other. The same is reflected to school education: the choice of the subjects on which to focus is done earlier and earlier. In the latest issue of “Intelligent Life” (a quarterly lifestyle and culture magazine of “The Economist”) there was an article dealing with the narrowing scope of knowledge and how it is becoming harder and harder for polymaths (those knowledgeable and active on multiple fields) to exist. This development can hardly be halted, given how structures of knowledge are changing, but the article pointed out one drawback: largest scientific innovations tend to come from outside rather than from inside. Thus, narrowing scope of knowledge can also lead to degradation of thinking. This point is undoubtedly arguable but there is still something. Let’s for example think about the communication of science: the better one can place his/her findings into a broader context and the more fluently the story is written, the higher ranked the results usually are. Therefore, in addition to a good knowledge on one’s own field a successful scientist might need broader perspectives to science and society as well as literary skills. Interesting reading anyway: 

The last days of the polymath. Intelligent life: Autumn 2009

See also:

The age of mass intelligence. Intelligent Life: Winter 2008

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Background of blackness remains unresolved in common frogs

By herczeg 1.11.2009 – 0:00 in In press
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Geographic variation in the level of melanism in common frogs (Rana temporaria) has been repeatedly observed. Vences et al. (2002) described a strong altitudinal cline (increasing melanism with altitude) and we observed a similar cline along a latitudinal gradient. A widely accepted intiutive explanation for these clines is thermal adaptation, as it has been shown for different ectotherm species that more melanistic individuals can heat up faster, which supposed to be beneficial in cold environments (e.g. Forsman 1995; Vences et al. 2002). Read More »

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Thick – they die quick?

By Juha 30.10.2009 – 7:00 in Journal club
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Jan

Reading a recent paper about growth rate differences among fish selected for high and low angling vulnerability, I started to think the possible explanations for these differences. And why would the fish with low vulnerability for angling possess higher growth rates than those selected for high vulnerability?

There are many possible explanations, but somehow the most likely explanations seem to boil down to behavioral differences. But since the angling vulnerability is also – at least in fishermen’s head – about cognitive differences, could these differences in vulnerability relate somehow to cognitive differences among individuals? If so, could there also be a common, underlying namer for growth rate and vulnerability differences?

Who knows. Such a possibility has been suggested at least in the case of humans. Increasing childhood IQ – measured at age 11 in a Scottish survey – correlates positively with likelihood to survive to age 76. In a study of 1 million Swedish military recruits tested around age of 19, IQ predicts their likelihood of survival over next two decades. In short, there are numerous studies showing that early-life intelligence and mortality are associated across different populations, in different countries and epochs.

One hypothesis to explain these human results is ‘system integrity idea’. According to this hypothesis, well-wired body is more able to respond to environmental insults – hence the association with cognitive capacity and reduced mortality risk. This hypothesis has gained some support from experimental tests, but the jury might still be out. As are some of the really big fish.

Deary I (2008) Why do intelligent people live longer? Nature 456:175-176.

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Is the three-toed woodpecker a genetically monogamous species?

By Menghua 25.10.2009 – 16:02 in In press

In socially monogamous birds, extra-pair paternity (EPP) is widespread as revealed by genetic analyses. In contrast, extra-pair maternity, also known as quasiparasitism (QP), is rare. A closer examination of previous studies reveals unequivocal evidence for occurrence of QP due to possibility of rapid mate switching and/or insufficient molecular work.

In a recent paper published in PLoS ONE, we found both EPP and QP in a population of three-toed woodpeckers in southern Finland. In this study, we genotyped a total of 80 samples from a field-study conducted during 2004 – 2007 in a close collaboration with researchers from Finnish Museum of Natural History. As compared to previous studies in this species, we used twice as many microsatellites in the molecular genotyping and more advanced stastitical methods and procedures in order to get high confidence in the parentage assignment.

We found co-occurence of low levels of both EPP and QP, which can be due to constrains set by the large paternal effort and intensive parental care. A previous study of the same species in Germany has also documented occurrence of EPP as well as CBP (conspecific brood parasitism, which is as a result of egg-dumping or QP). However, in contrast to our study, the German study could not resolve if the observed CBP was due to egg-dumping or due to QP.

On the basis of our results, it is for sure that the three-toed woodpecker is not a genetically monogamous species. It is also certain that both EPP and QP occur at low levels in this species. Last but not the least, we might have to reassess the occurence of QP in the wild birds – is it really rare or rare just because of the technical (cf. genetic and statistical methods) difficulties detecting it?

Li M.H., K. Välimäki, M. Piha, T.Pakkala  & J. Merilä. Extrapair paternity and maternity in the three-toed woodpecker, Picoides tridactylus: insights from microsatellite-based parentage analysis. PLoS ONE, in press.   

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Fountain of youth in Kilpisjärvi?

By Juha 22.10.2009 – 6:00 in Journal club
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Y chromosomes have a problem: as they cannot (usually) recombine with X chromosomes, they tend to degenerate due to progressive accumulation of deleterious mutations. Yet, in most lower vertebrates, sex chromosomes are undifferentiated (homomorphic). In other words, the expected degeneration of Y is not occurring. Why?

In a nice paper published on the pages of Evolution, Nicola Perrin puts forth a interesting hypothesis: occasional sex reversals known to occur e.g. in common frogs (Rana temporaria) might serve as fountains of youth for Y chromosomes. How?

Sex-specific recombination patterns appear to depend on phenotypic, rather than genotypic sex. Therefore, homomorphic X and Y chromosomes are expected to recombine in sex-reversed females. This could serve as mechanism to counteract Muller’s ratchet and prevent the evolutionary decay of Y chromosomes goes the argument.

And how does Kilpisjärvi fit the picture? Through the fact that sex reversal appear to occur in Kilpisjärvi common frogs (see here). In fact, Nicola uses data on Kilpisjärvi frogs to illustrate his arguments.

Perrin N (2009) Sex reversal: fountain of youth for sex chromosomes. Evolution, in press. 10.1111/j.1558-5646.2009.00837.

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Occam’s professor

By Anna 14.10.2009 – 1:00 in Random picks
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Occam’s razor is a principle frequently referred to in statistic textbooks as a guideline for model selection. In brief, the idea is that simplicity is preferred over complexity, leading to the minimal adequate model being preferred over the more complicated ones. However, the latest PhD comics strip comes up with a new concept: Occam’s professor.

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Lost objectivism?

By Anna 1.10.2009 – 18:28 in Journal club
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Public audience, administrators and policy makers generally trust science and scientific advices because these are considered objective and free from commercial, religious or national interests as well as personal relations and ambitions. Thus, the power of science can be seen in its ultimate attempt to retain objectivism -even in situations where reporting flashy results and findings would be tempting in contrast to being hesitant in conclusions due to uncertainties and unknowns. Science is not a matter of faith, but a matter of arguments, counterarguments, posing new questions and exploring them. This is because in the light of the fact that our knowledge is virtually always incomplete, we can never come up with a water-proof conclusions and firm acceptance/rejection of a hypothesis.

In the light of the ‘philosophical’ introduction above, let’s now shift the focus on the largely debated evolutionary impacts of fishing. In the latest issue of ICES insight, there was an article titled by “The Dawn of Darwinian Fishery Management” . What struck me in this article was the following:

“Although there may be some residual scepticism within the community of fishery scientists, and although the practical implications of fishery-induced evolution have yet to be examined more closely, the evidence supporting the likely and widespread occurrence of fishery-induced evolution has become sufficiently strong that fishery scientists and managers can no longer ignore the evolutionary dimension of fisheries.”

What is here denoted as “residual sceptism” is, in fact, work of several scientists reporting low patterns of selection and evolutionary rates induced by fishing, questioning evolutionary inference being based on phenotypic time series collected on wild, or asking whether demographic issues (i.e. keeping stocks alive) would be in the first priority before worrying about evolution. This “residual sceptism” is a vital element in the process of gaining objective scientific knowledge and coming up with new questions and aspects to investigate.  This is what science is all about -not dividing scientific community into ‘believers’ and ‘sceptics’.

Dieckmann U., Heino M. & Rijnsdorp A. (2009) The Dawn of Darwinian Fishery Management. ICES insight 46: 34-43.

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Climate change and body size – what about Habsburgian horses?

By Juha 28.9.2009 – 7:00 in Journal club
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horse

There has been quite a bit of recent interest to potential evolutionary responses to warming climate in terms of decreasing mean body size of animals (e.g. Millien et al 2006. Ecology Letters 9:853–869). However, as pointed out by EGRU research, much of these declines could actually reflect environmentally induced plastic stress responses, rather than genetic adaptation to warming climate (Gienapp et al 2008. Molecular Ecology 17:167-178; Teplitsky et al 2008. PNAS 105: 13492-13496).

Due to course of scanning literature, I stumbled on an curious paper by Komlos published in Historical Methods in 2004. The point of this paper was to provide an additional test to disentangle in between disease and general nutritional conditions as explanations for the well-documented decline in mean body size of humans in Europe in the late part of 1700 century.

Kolmos reasoning was that if the cause of this decline was diseases – which impair effective conversion of nutrients to growth – the declining trend in body size should be confined to humans, and not show up in the size domestic animals, such as horses, which do not share their diseases with humans. However, if the cause was general shortage of nutritional resources, both horses and humans should show parallel decline in body size.

Using a database of horses purchased by Fourth Austrian Dragoons Regiment between 1774 and 1820, Kolmos was able to establish that the mean size of the horses declined as a function time in the similar way as the human stature (e.g Hungarian soldiers: 3.1% decline in mean stature). Hence, the conclusion was that declining resource availability, rather than diseases, was the likely cause of human body decline in late 1700 century.

What I found interesting in these results was that the decline in mean body size of humans and horses coincide with period known as “Little Ice Age”. I guess this might strengthen someone’s hunch that much of the trends in mean body size in response to climatic variations reflect plasticity rather than adaptation.

Komlos J. (2004) The size of horses during the industrial revolution. Historical Methods 37:47-53.

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Toxins and intersex fish

By JL 21.9.2009 – 9:37 in Random picks

Next time you are stumped when trying to figure out the  sex of a  fish, keep in mind that (through the wonders of pollution) the answer  can be…  both!

Hinck et al. recently reported on their findings (link) from fish species in the United States, which revealed that intersex fish (at least for a few species) are quite a bit more common  than they thought.

In polluted areas egg cells were commonly found in male gonads in largemouth (18% of all males) and smallmouth (33%) bass. However, intersex fish were only rarely found in catfish and carp, and never found in 10 other fish species (sticklebacks weren’t assessed).

It is likely that the numerous toxins found in the fish habitat are to blame, but this study wasn’t able to narrow it down to which are the most likely culprits.

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Sharing

By Juha 21.9.2009 – 7:18 in Journal club
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Many journals nowadays have a policy in respect to data sharing typically requesting authors to share the data used for a given publication with those requesting the data. For instance, the guidelines for Journal of Evolutionary Biology state as follows:

The editors and publisher of this journal expect authors to make the data underlying published articles available. An investigator who feels that reasonable requests have not been met by the authors should correspond with the Editor-in-Chief. Authors must use the appropriate database to deposit detailed information supplementing submitted papers, and quote the accession number in their manuscripts.

I recall that this sort of policy – and even more stringent – would also apply to grant applications in some countries’ national funding agencies: one has to promise to share the data inorder to get a grant. But how does the sharing work?

In recent paper Savage et al (2009) found that sharing does not come easy. 1 out 10 requests lead to success. That is, 90% of the authors refuse to share their data despite they have promised so to get their work published.

Savage Sj et al (2009) Empirical study of data sharing by authors publishing in PLoS journals. PLoS One4(9): e7078

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Fishing and phenotypic variance: part 2

By Anna 18.9.2009 – 23:21 in Journal club
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Harvesting and its impacts on phenotypes in the targeted populations have been of interest particularly in fisheries context, but most of the studies in this field have explored shifts in mean traits values. Earlier, I have blogged about a study by Olsen et al. (2009) challenging this view by demonstrating how fishing might have decreased phenotypic variance in cod without impacts on mean, but now opposite results in this respect have been found. The recent study on Windermere (UK) pike population illustrates how intensive fishing mortality at intermediate sizes might actually have increased phenotypic variability in the populations. In the light of the theory of life-history evolution this may not be surprising, but viewed from practical fisheries management’s perspective the outcome is interesting. Is selection increasing phenotypic variability actually favorable? In theory, phenotypic variability helps a population to survive in a changing environment, but if variance increases because of population being more clearly split into two alternative life-history strategies, how might that affect population’s current and future viability? I guess that “warrants for future research”…

Edeline et al. (2009) Harvesting-induced disruptive selection increases variance in fitness related traits. Proc R Soc B (in press)

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In the News

By Bob O'Hara 18.9.2009 – 15:02 in Random picks

Here are a couple of items from the scientific blogosphere for a Friday.
Read More »

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Sticklebacks spotted

By Juha 11.9.2009 – 8:58 in In press
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SB

The threespine stickleback is one of the first first wild animal species for which any significant genomic resources were developed (see Ensembl inofrmation here). First Centre of Excellency in Evolutionary Genetics and Physiology contribution to genomic resources for sticklebacks is now out. The paper published in pages of BMC Genomics describes a ca 44000 probe (ca 20 000 gene) Aligent microarray to be utilized in studies of gene expression in this species. Follow this space – more is on the way.

Leder EH et al. (2009) A flexible whole-genome microarray for transcriptomics in three-spine stickleback (Gasterosteus aculeatus). BMC Genomics 10:426.

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Gräddfil gone

By Juha 10.9.2009 – 17:28 in Journal club
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Times they are changing – PNAS will eliminate communicated submissions in July 2010. Read more about this from the recent editorial here.

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The great killer tits of Hungary

By herczeg 10.9.2009 – 10:37 in Journal club, Random picks
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Condsidering how many fanatic birders can be found in EGRU,  I guess you will be interested in some (for me) surprising observations on bloodthirsty great tits (Parus major). Read More »

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Gigantism – what makes the good example

By herczeg 8.9.2009 – 0:35 in Random picks
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Check out the cool video(s) of the giant rat!

http://news.bbc.co.uk/earth/hi/earth_news/newsid_8210000/8210394.stm

Huge, extremely bold creature in a typical island environment (crater of a volcano in New Guinea).  Shouldn’t we make the same film on Rytilampi ninespines? Pity is that there is permanent light in summer, so we cannot get the night scenery. Combined with ice-fishing, probably.

“Huh, I had a goldfish at home, and it was the same size as this ninespine.”

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Bombastic creatures

By Juha 3.9.2009 – 12:42 in Journal club
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Having a big brain or synthetic armor are not the only means to reduce risk of being predated. Marine biologist have recently discovered seven species of deep-sea annelid worms that are capable of producing green bioluminescent ‘bombs’, apparently as a way of distracting predators. In other words, the bombs which can glow intensively for seconds can draw predators attention away from the bomber and help it to propel to safety. Leaving the silly fish to stare the darkness.

Osborn KJ et al. (2009) Deep-sea, swimming worms with luminescent “bombs”. Science 325: 964 DOI: 10.1126/science.1172488

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Successful science – pt. 2

By Juha 2.9.2009 – 8:34 in Random picks
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The biannual meeting of the Centre of Excellence in Evolutionary Genetics and Physiology (www.coe.fi) – this time held at the premises of University of Turku (Aug 31- Sep 1) – was again a success of many dimensions. Judging from the presentations, a noticeable shift in the CoE activities has taken place towards work focused on genomics and fish models. Albeit diversity has its benefits, the increased coherence in terms of model systems is likely to yield towards even more frequent interactions and collaborations among people at different nodes. Apart of the exciting scientific program and stimulating discussions with the Scientific Advisory Board (‘the three wise men’), the CoE sailed one of the least famous salmon rivers of Europe and enjoyed delicious salmon soup out in the archipelago of Turku.

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Fisheries induced evolution – on the dark side of the moon?

By Juha 26.8.2009 – 7:00 in Journal club
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Jarvari

I remember vividly a meeting from early 1990’s on the premises of the Royal Swedish Academy of Sciences where prominent populations geneticists had gathered to ponder the loss of genetic diversity in the wild. One of the keynote speakers made the point that lets not worry about the genetics yet, but focus first on demographics. The motivation was that there will be time to deal with the genetic issues later on. He did not warm up for the idea of establishing a bio-bank on the dark side of the moon, but suggested that perhaps the people with the bio-bank idea should be send to the dark side of the moon to be retrieved if or once their services are needed.

Something along the same lines might be read in between the lines of a recent article by Andersen and Brander published in PNAS. They estimated expected rates of fisheries induced evolution using simulations parametrisized with reasonable numbers. The outcome of these exercises was that rates of fisheries induced evolution are expected to be very slow, typically less than 0.5% per year. These estimates are much lower than those implicated by experimental data and (shaky) data collected from the wild. The reason for the discrepancy can be found from the truncated (unnaturally strong) selection used in experimental studies, and problems with the data from the wild. The famous data on Atlantic cod (Olsen et al 2004, Nature) is binned to latter category – the rates of evolution in the (phenotypic) cod data are likely to have been overestimated.

The conclusion? Dealing with evolutionary effects of fishing may be less urgent than anticipated by some: we might do best by reducing the direct detrimental effects of (over)fishing and destruction of marine ecosystems. Evolutionary effects can wait – authors say.

Andersen KH & K Brander (2009) Expected rate of fisheries-induced evolution is slow. PNAS 106: 11657-11660.

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e-thing

By Juha 24.8.2009 – 7:26 in Journal club
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Hirch index is here to stay, but not anymore as the only game in town. In a recent paper published in PLoS One Zhang (2009) introduces e-index to complement the h-index.

The basic idea with this new index is to make use of the ‘excess’ citations in ‘h-core’ papers, that is, in papers on which given h-index is based on. This can help to differentiate in between individuals having similar h-index.

Useful? You decide.

Zhang C-T (2009) The e-Index, complementing the h-Index for excess citations. PLoS ONE 4(5): e5429. doi:10.1371/journal.pone.0005429

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Breed classification = genetic classification? – A case study of cattle in Eurasia

By Menghua 22.8.2009 – 14:01 in In press
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The book ‘Cattle Breeds – An Encyclopedia‘ is  a very great work in the field of agriculture, particularly in animal genetics. It includes detailed information of almost all cattle breeds in the world, which provide us our daily consumption of meat and milk,  leather for coats and shoes, as well as the labour power for the farmers in some regions. It is a interdisciplinary study in agriculture, humanity, art, archaeology and history and has costed several years to accomplish. It has been extensively cited by other scientists for maybe tens of thousands of times.

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The book gives the most comprehensive breed classification of cattle breeds, which is mostly based on geographical, morphological, and historical data, as well as on production records. However, so far no study has investigated if and how the breed classfication is consistent with their genetic origins. In addition, of the three or four factors used for the classfication, which of them plays the most important role?

In a study by Menghua Li and Juha Kantanen in a collaboration with the members of the North European Cattle Genetic Diversity Consortium (more than 10 researchers from different countries), we studied this for the first time using as many as 48 Eurasian Bos taurus cattle breeds using microsaellites recommended by FAO.

Our study revealed that the genetic classification is basically consistent with the subgroups defined in the book, with a few exceptions stemming from intercrossing in their breeding history. In addition, for the five breeds which have not yet classfied into any subgroups in any literature, we provide a preliminary classification according to the genetic clustering results. However, in the further analysis, we found that despite some correspondence between geographical proximity and genetic similarity, the breed classification appears to be a good indicator of genetic structure in the Eurasian cattle breeds. 

Li M.-H.  and J. Kantanen (2009) Genetic structure of Eurasian cattle (Bos taurus) based on microsatellites: clarification for their breed classification. Animal Genetics (In Press)

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Celebrating the Burgess Shale

By JL 20.8.2009 – 10:04 in Random picks
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One hundred years ago this month Charles Doolittle Walcott (secretary of the Smithsonian Institution in Washington DC)  stumbled upon what would become the most significant find of Cambrian fossils ever uncovered, and one of the greatest discoveries in the study of evolution. The first discovery of the Burgess Shale’s  fascinating creatures was made after Walcott cracked open a rock that he was worried his wife’s horse might trip on.  The crustaceans he found inside were just the beginning of what would be uncovered from the deposits in British Columbia, Canada.

Dinocaridia Read More »

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Waves of Lake Onega

By Juha 17.8.2009 – 19:54 in Random picks
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Continuing in the fishing theme, the stories about salmon catches at the Lake Onega, Russia, started to bug my mind to the point that I had to see them with my own eyes. With several healthy spawning stocks of landlocked salmon (Salmo salar) together with stocked salmon, the lake is literally packed with salmon. In six days, ca 200 salmon visited our boat, majority of which were released back without even lifting them into the boat. Hell or heaven – I cannot really decide. But one thing is for sure – there is no other place in the face of the earth where getting into contact with Atlantic salmon is as easy as it is on the beautiful Lake Onega.

Landlocked salmon, 6.2 kg
Salmons
To be released
Small salmon
Another grower
Hooked
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