Posts by Tags

Conjunction

Initial point of secondary contact

3 minute read

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.

asexuality

Speculations about Genomic Features of Asexual Animals

7 minute read

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.

Reference-free inference of repetitions using long reads

4 minute read

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.

early career researchers

Flawed justification of journal impact factor

2 minute read

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.

ethics

Morality of academic publishing

10 minute read

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

2 minute read

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.

evolution

How common is polyploidy among eukaryotes?

4 minute read

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

7 minute read

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

2 minute read

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).

Loss of heterozygosity during inbreeding

7 minute read

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

4 minute read

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

3 minute read

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.

genomics

How common is polyploidy among eukaryotes?

4 minute read

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

7 minute read

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

2 minute read

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

2 minute read

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.

Reference-free inference of repetitions using long reads

4 minute read

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.

heterozygosity

Speculations about Genomic Features of Asexual Animals

7 minute read

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.

Loss of heterozygosity during inbreeding

7 minute read

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.

htc

Data on request

2 minute read

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.

hybrid zones

Initial point of secondary contact

3 minute read

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.

inbreeding

Loss of heterozygosity during inbreeding

7 minute read

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.

inference

Reference-free inference of repetitions using long reads

4 minute read

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.

journal impact factor

Flawed justification of journal impact factor

2 minute read

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.

long-reads

Reference-free inference of repetitions using long reads

4 minute read

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.

open data

Data on request

2 minute read

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.

polyploidy

How common is polyploidy among eukaryotes?

4 minute read

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.

publishing

Morality of academic publishing

10 minute read

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

2 minute read

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.

repetitions

Reference-free inference of repetitions using long reads

4 minute read

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.

secondary contact

Initial point of secondary contact

3 minute read

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.

sex

Loss of heterozygosity during inbreeding

7 minute read

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.

simulation

Initial point of secondary contact

3 minute read

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.

speciation

Initial point of secondary contact

3 minute read

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.

transposons

Speculations about Genomic Features of Asexual Animals

7 minute read

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.

Reference-free inference of repetitions using long reads

4 minute read

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.