Page Not Found
Page not found. Your pixels are in another canvas.
Sitemap
A list of all the posts and pages found on the site. For you robots out there is an XML version available for digesting as well.
Pages
Gene flow - page about admixture
About me
Page not in menu
This is a page not in th emain menu
Posts
PCI made Google doc temlpates
Published:
Have you heard about PeerCommunityIn, or PCI for short? It’s an organisation, that runs a peer reviewing platform and a diamond-open access journal. The way it works is, you submit a preprit to any of the preprint servers (such as bioRxiv) and then pass the details to appropriate PCI (there are 15 are moment for all sorts of disciplines). There will be a recommender (moreless like an editor), who will manage your preprint, evaluate if it is a credible piece and then send invitations to reviewers. Once you get through the review process, your priperint will get recommended. Once that happens, it’s up to you what you do next, you can either submit the already reviewed preprint to one of the classical journals, or you can right away publish it in the PCI Journal. The initiative is great for reducing work load for reviewers, bringing transparency to the review process and finally brings a sustainable solution to scientific publishing - you should totally check it out.
Testing FastK on a difficult genome
Published:
Once per while there is a new way how to do things and speed up computations in the world of kmer genomics. Sometimes the tricks are simply more efficient algorithms, but sometimes the tricks are shortcuts that don’t do excatly the same thing. Here I would like to dig a bit in the relatively new k-mer counter FastK and compare it with my personal favourite KMC. If you are wondering if it is worth learning new tool, this blogpost might be able to help you make your mind.
How exciting is parthenogenesis in condors?
Published:
Few days ago, the world learned about two California condor chicks that were products of parthenogenesis, a reproduction where unfertilised eggs hatch and develop in an adult from maternal genome only. This IS exciting for multiple reasons, but perhaps not as exiting for conservation of condors and I will try to explain why… It will take a bit of background on parthenogenesis and sex determination, but bear with me.
Morality of academic publishing
Published:
When I was young naive aspiring scientist I did not comprehend all the aspects of publishing. To be honest, I did not think about it much, but for me it’s the same as the climate change, it’s harder and harder to turn a blind eye. The last drop for me was the announcement of Nature’s Open Access option, it’s shocking €9,500, (or $11,390 / £8,290)! How did we come to this? Are we really going to let a private company to drain the already poor scholarly funds by these obscure amounts? And the problem is not just Nature…
Flawed justification of journal impact factor
Published:
About a year and half ago an article by John Tregoning was published in Nature News. The short piece was openly defending the prevalent usage of journal impact factor for evaluation of junior scientists for their sake. As a junior scientist I felt bitter. The publishing system is a huge academic problem we should do something about it! And as far as I know, young scientists are the loudest in pointing out new ways for less morally corrupted sharing of knowledge and therefore I find unfair a senior academic takes us, as an argument for keeping the status quo.
How common is polyploidy among eukaryotes?
Published:
This easter I have spent on thinking / writing / editing of an introduction to the paper about smudgeplot - a tool for predicting ploidy and visualization of genome structure. I collaborated on this tool for my own data, I have not really thought through how far it goes, so I started to wonder how many polyploid species are out there. So I asked on Twitter and guess what, so many people have responded to the tweet that I have decided to compile the answers in a blogpost.
Speculations about Genomic Features of Asexual Animals
Published:
About a month ago we have posted a preprint to bioRxiv about genomic features of asexual animals. We found plenty of cool things I will try to summarize here the main points and mostly do the speculations that were too bold for the manuscript.
The expected genetic diversity of Iceland
Published:
I was on my way back from Arthropod Genomics Symposium (which was a great conference by the way). The plan was to change planes in Iceland and get home in one go, but my flight to Iceland got delayed and I missed my connection. Fortunately, Iceland is amazing country and even around Reykjavik there is plenty to see. I decided to go to Perlan, a museum of Iceland natural history. I was shocked to hear that the island did not exist more than couple of millions years ago. I did not manage to remember the numbers, so I will take them from this web, where they say that the oldest rock is ~15 ml. Alright, 15 millions is not that little from the perspective of population genetics, enough time to generate some variability. However, we should also consider that the land was fully covered by ice during 30 rounds of glacial periods and the last time whole Iceland was under ice is 13,000 to 10,000 years ago. That means that all (or at least the most of) the macro life have started back then either as:
- tiny population that survived glaciation period (bottleneck).
- or colonization (founder effect).
Data on request
Published:
At the beginning of December 2017 we have decided to do a meta-study/review of several published genomes. I optimistically started to collect data for some supplementary analyses. But then I found that about one fifth of genomes were were available “on request” and about one third of genomes were missing sequencing reads. It was a shock for me, I thought that every paper needs to deposit data to DDBJ / EMBL-EBI / NCBI. This was also the case for genomes published in journals that actually claim that data need to be accessible as PloS Biology.
Loss of heterozygosity during inbreeding
Published:
This beauty is Bacillus rossius a proud mum of the tiny green stick insect crawling over her. You are maybe asking, who is father? Well, it’s her brother.
Reference-free inference of repetitions using long reads
Published:
The ultimate goal of my PhD project is to analyze genomic consequences of asexuality. The species we are working with (Californian stick insects) are real hardcore asexuals - they just clone, they do not recombine (or at least if they do they do very very rarely). This kind of “pure” asexuality should lead to independent evolution of both haplotypes. There are a lot of very very cool consequences (think of how a coalescence of haplotypes of couple of individuals should look like), one of them is the activity of transposons (TEs). All the transposons that were active in asexual genome will leave trace only in one haplotype only, and it sounds to be a great fun to track them.
Initial point of secondary contact
Published:
One of the most basic questions of evolutionary biology remains unanswered - how do species evolve? And what makes species separated species? What is causing sexual reproduction barrier between sister taxa? One of very popular systems for study of speciation are hybrid zones.
publications
SigHunt: horizontal gene transfer finder optimized for eukaryotic genomes
Published in Bioinformatics, 2013
A scalable method for prediction of candidates for horizontally transferred genes.
Recommended citation: Jaron, K.S., Moravec, J.C. and Martínková, N., 2013. "SigHunt: horizontal gene transfer finder optimized for eukaryotic genomes." Bioinformatics, 30(8), pp.1081-1086. http://doi.org/10.1093/bioinformatics/btt727
White-Nose Syndrome Fungus: A Generalist Pathogen of Hibernating Bats
Published in PLoS ONE, 2014
We have reported European bat species infected by White-nose syndrome, a disease devastating American population. We have also showed that the fungus is a generalist pathogen attacking bat species of very diverse ecological traits.
Recommended citation: Zukal, J., Bandouchova, H., Bartonicka, T., Berkova, H., Brack, V., Brichta, J., Dolinay, M., Jaron, K.S., Kovacova, V., Kovarik, M. and Martínková, N., 2014. "White-nose syndrome fungus: a generalist pathogen of hibernating bats." PLoS One, 9(5), p.e97224. http://doi.org/10.1371/journal.pone.0097224
White-nose syndrome without borders: Pseudogymnoascus destructans infection tolerated in Europe and Palearctic Asia but not in North America
Published in Scientific Reports, 2016
We have reported White-nose syndrome in Asia and quantified fungal loads of bat wings using qPCR. Surprisingly loads we observed were higher than loads detected in American bats that have way way worse response to the infection.
Recommended citation: Zukal, J., Bandouchova, H., Brichta, J., Cmokova, A., Jaron, K.S., Kolarik, M., Kovacova, V., Kubátová, A., Nováková, A., Orlov, O. and Pikula, J., 2016. "White-nose syndrome without borders: Pseudogymnoascus destructans infection tolerated in Europe and Palearctic Asia but not in North America." Scientific reports, 6. http://doi.org/10.1038/srep19829
Sequence-dependent separation of trinucleotides by ion-interaction reversed-phase liquid chromatography—A structure-retention study assisted by soft-modelling and molecular dynamics
Published in Journal of Chromatography A, 2016
We showed nearly-deterministic relation of retention times of trinucleotides with their nucleotide composition. We modeled properties of trinucleotide molecules that actually explained most of the variability of the original model. I was invited to this study to construct models.
Recommended citation: Mikulášek, K., Jaroň, K. S., Kulhánek, P., Bittová, M., & Havliš, J., 2016. "Sequence-dependent separation of trinucleotides by ion-interaction reversed-phase liquid chromatography—A structure-retention study assisted by soft-modelling and molecular dynamics." Journal of Chromatography A, (1469), 88-95. http://doi.org/10.1016/j.chroma.2016.09.060
Consequences of asexuality in natural populations: insights from stick insects
Published in Molecular biology and evolution, 2018
Taken from the abstract: We find strong evidence for higher rates of deleterious mutation accumulation, lower levels of segregating polymorphisms and arrested GC-biased gene conversion in asexuals as compared with sexuals. Taken together, our study conclusively shows that predicted consequences of genome evolution under asexuality can indeed be found in natural populations.
Recommended citation: Bast, J., Parker, D.J., Dumas, Z., Jalvingh, K.M., Tran Van, P., Jaron, K.S., Figuet, E., Brandt, A., Galtier, N. and Schwander, T., 2018. "Consequences of asexuality in natural populations: insights from stick insects." Molecular biology and evolution, 35(7), pp.1668-1677. https://doi.org/10.1093/molbev/msy058
Genomic features of asexual animals
Published in bioRxiv, 2019
Are there any universal consequences of asexuality in animals? We have collected genomes of 26 asexual animals and found that indeed there is not any really universal.
Recommended citation: Jaron, K. S., Bast, J., Nowell R. W., Ranallo-Benavidez, T. R., Robinson-Rechavi, M., & Schwander, T., 2018. "Genomic features of asexual animals." bioRxiv, 497495. https://doi.org/10.1101/497495
GenomeScope 2.0 and Smudgeplots: Reference-free profiling of polyploid genomes
Published in Nature Communication, 2020
Genome sequencing can be messy and genome assembly is complicated and non-transparent process. Here we provide tools that allow some elementary characterisation of genomes using directly short read data. Now also aiming to provide help for polyploid genomes.
Recommended citation: Ranallo-Benavidez, T. R., Jaron, K. S., Schatz, M. C., 2020. "GenomeScope 2.0 and Smudgeplot for reference-free profiling of polyploid genomes" Nature Communication, In press. https://doi.org/10.1101/s41467-020-14998-3