Nav: Home

Story of silver birch from genomic big data

May 10, 2017

Big data is a buzzword that is often used in customer behavior analyses or social network modeling. However, big data is also being created in biology, where modern high-throughput DNA sequencing can easily produce loads of data. Exponential decrease in the cost of sequencing during this decade has made it possible to analyze whole populations of organisms instead of a small set or only one selected individual. Population-level data opens up completely new ways of studying the organisms. For example, history of the species can be inferred from patterns imprinted in the genomes by long-term evolution and more recent natural selection. These types of analyses have earlier been carried out for humans where there already exists plenty of data, but the low cost of DNA sequencing makes it now possible to look at altogether different species, such as ones of importance to forestry and Finnish culture.

Here, researchers collected birch samples from twelve sites spanning a range from Ireland to the heart of Siberia and from Loppi, southern Finland, up to Kittilä, northern Finland.

"The project produced altogether over 700 Gigabases of genome sequence, resulting in over 20 Terabytes of data from various analyses," reports Research Director Petri Auvinen from DNA sequencing and genomics lab.

Computational analyses showed population bottlenecks, periods of extremely low number of individuals, at times with known climatic upheaval. The first bottleneck occurred around 66 million years ago (Mya), at the time when dinosaurs became extinct, followed by bottlenecks 34 Mya, 14.5 Mya, and 1 million years ago.

"This may be connected with speciation events in birches, since fossil evidence shows that the alders and birches split already around 60 Mya, and the white-barked birches had appeared around 10 million years ago," says Professor Victor Albert.

After the last bottleneck the birch population has been steadily increasing. The last ice age split the birches into two populations, a European and a Siberian one, which have been mixing in Finland since the melting of the continental ice sheet.

In addition to silver birch, the genomes of six other birch species were also sequenced, as well as two closely related alders, grey and black alder. Making a distinction between diploid silver birches and tetraploid downy birches (which have doubled their genomes compared to diploids) proved to be more difficult than expected, since some of the sampled silver birches themselves turned out to have four sets of chromosomes.

"This illustrates that there has been and most likely still is some gene flow between the two species," says researcher Jarkko Salojärvi from the Department of Biosciences.

Natural selection has helped birch survive in harsh environmental conditions

In addition to population genomic analyses, the project assembled a reference genome for silver birch and predicted its genes.

"This hybrid assembly combined data from four different next generation sequencing platforms," says researcher Olli-Pekka Smolander.

Population genomic analyses identified 900 genes under natural selection, which have evolved birch into its current state as a cold-tolerant and fast-growing pioneer species. Genes under selection are in key positions in the development of birch phenotypes, which is why breeding could focus on these key genes when developing new birch lines for biotechnology purposes.

"When the candidate genes have been identified, further breeding is rather rapid since birch is the only tree species that in special growth conditions can be made to flower within less than one year. This makes it possible to grow one breeding population in one year," says Professor Jaakko Kangasjärvi.

"A unique trait in a single birch line can result from a mutation in a single gene, for example, the weeping birch cultivar known from gardens, Betula pendula "Youngii", had a truncated LAZY gene," says Professor Yrjö Helariutta.

A mutation in this gene is known to produce a relaxed phenotype also in maize and thale cress.
The research was carried out by D.Sc Jarkko Salojärvi and Professor Jaakko Kangasjärvi (Dept. Biosciences, University of Helsinki, Finland), D.Sc Olli-Pekka Smolander and Petri Auvinen (Institute of Biotechnology, University of Helsinki , Finland), Professor Yrjö Helariutta (Dept. Biosciences and Institute of Biotechnology, University of Helsinki and Sainsbury laboratories, Cambridge, UK), and Professor Victor Albert (University at Buffalo, USA). The gene models were curated by researchers from University of Helsinki, University of Turku, University of Eastern Finland, Estonian University of Life Sciences, Umeå University, and the Natural Resources Institute of Finland.

University of Helsinki

Related Natural Selection Articles:

The argument for sexual selection in bacteria
The evolutionary pressure to pass on DNA can produce behavior that otherwise makes no sense in a struggle to survive.
Sexual selection influences the evolution of lamprey pheromones
In 'Intra- and Interspecific Variation in Production of Bile Acids that Act As Sex Pheromones in Lampreys,' published in Physiological and Biochemical Zoology, Tyler J.
Hydrogen-natural gas hydrates harvested by natural gas
A recent study has suggested a new strategy for stably storing hydrogen, using natural gas as a stabilizer.
Infection biology: Signs of selection in the stomach
Helicobacter pylori, a globally distributed gastric bacterium, is genetically highly adaptable.
Study finds natural selection favors cheaters
Natural selection predicts that mutualisms -- interactions between members of different species that benefit both parties -- should fall apart.
Natural selection and spatial memory link shown in mountain chickadee research
Chickadees with better learning and memory skills, needed to find numerous food caches, are more likely to survive their first winter, a long-term study of mountain chickadees has found.
Birds-of-paradise genomes target sexual selection
Researchers provide genome sequences for 5 birds-of-paradise species: 3 without previous genome data and 2 with improved data.
How much are we learning? Natural selection is science's best critic
Even as they've struggled to highlight parts of the human genome worth investigating, scientists have wondered how much they're actually learning through the methods they use.
Natural selection in the womb can explain health problems in adulthood
Conditions encountered in the womb can have life-long impact on health.
Leafcutter ants' success due to more than crop selection
A complex genetic analysis has biologists re-evaluating some long-held beliefs about the way societies evolved following the invention of agriculture -- by six-legged farmers.
More Natural Selection News and Natural Selection Current Events

Best Science Podcasts 2019

We have hand picked the best science podcasts for 2019. Sit back and enjoy new science podcasts updated daily from your favorite science news services and scientists.
Now Playing: TED Radio Hour

Rethinking Anger
Anger is universal and complex: it can be quiet, festering, justified, vengeful, and destructive. This hour, TED speakers explore the many sides of anger, why we need it, and who's allowed to feel it. Guests include psychologists Ryan Martin and Russell Kolts, writer Soraya Chemaly, former talk radio host Lisa Fritsch, and business professor Dan Moshavi.
Now Playing: Science for the People

#538 Nobels and Astrophysics
This week we start with this year's physics Nobel Prize awarded to Jim Peebles, Michel Mayor, and Didier Queloz and finish with a discussion of the Nobel Prizes as a way to award and highlight important science. Are they still relevant? When science breakthroughs are built on the backs of hundreds -- and sometimes thousands -- of people's hard work, how do you pick just three to highlight? Join host Rachelle Saunders and astrophysicist, author, and science communicator Ethan Siegel for their chat about astrophysics and Nobel Prizes.