Author Archives: Sam Perrin

Donald Hobern: Cataloguing the Planet’s DNA

I spoke with GBIF’s executive secretary and amateur lepidopterist Donald Hobern about how DNA barcoding fits into modern conservation and ecology (Image Credit: Donald Hobern, CC BY-2.0, Image Cropped)

DNA barcoding has revolutionised science. Ask anyone working in evolution or taxonomy these days what the biggest changes are the they’ve seen in their discipline, chances are it’ll be to do with gene sequencing and DNA processing. So when the International Barcode of Life (iBOL) Conference came to Trondheim last week, I jumped at the opportunity to learn more about the behind the scenes work that goes into cataloguing the DNA barcodes of life on earth.

I sat down with Donald Hobern, Executive Secretary of iBOL and former Executive Secretary of the Global Biodiversity Information Facility (GBIF) and Director of the Atlas of Living Australia (ALA). Donald joined iBOL just as they launched BIOSCAN, a $180 million dollar program which aims to accelerate the cataloguing of the world’s biodiversity in DNA form. We spoke about BIOSCAN, the technology behind bringing occurrence and genetic data together, and how the work iBOL and GBIF do ties into the bigger picture of global conservation and sustainability.

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Using eDNA to Monitor Fish Dispersal

Environmental DNA is a hot topic in biomonitoring. But what is it exactly, and how can it be used to monitor the dispersal of a reintroduced fish species? (Image credit: Gunnar Jacobs, CC BY-SA 2.0, Image Cropped).

Guest post by Christopher Hempel

Using environmental DNA to monitor the reintroduction success of the Rhine sculpin (Cottus rhenanus) in a restored stream (2019) Hempel et al., PeerJ,

The Crux

The term “environmental DNA (eDNA)” is currently booming in molecular ecology. But what exactly is this technological marvel? Essentially, eDNA comprises all DNA released by organisms into their environment, and originates from mucus, scales, faeces, epidermal cells, saliva, urine, hair, feathers – basically anything an organism might get rid of during its life. The eDNA can be collected from the environment, extracted, and analyzed to detect species using molecular approaches. As this is a very sensitive and non-invasive approach, it is a very hot topic for biomonitoring.

eDNA can be collected from any animal (in theory), but aquatic organisms in particular have been shown to be good target individuals (as eDNA is easiest to handle in water samples). Consequently, there are many studies using eDNA to monitor the activity of fish, reaching from the presence of invasive species to the effects of aquaculture. Here, we applied eDNA analysis to monitor a reintroduced fish species, the Rhine sculpin. The sculpin’s poor swimming ability make it useful as a bioindicator of the passability of streams and rivers. We wanted to investigate the potential of using eDNA to monitor the dispersal of the species in a remediated stream on a fine spatial and temporal scale.

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Pinning it on the Polar Bear

Image Credit: Christopher Michel, CC BY 2.0, Image Cropped

It’s an image that is ubiquitous in the media when the words ‘climate change’ pop up. The lone polar bear, drifting through the sea on a single ice floe. It is an effective image, evoking emotions like pity, loneliness and general despair for the plight of what has become the flagship species of what seems like the entire Arctic. But is associating the health of an entire ecosystem with one species useful, or dangerous?

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Parrots in Norway

The Norwegian landscape is a beautiful thing. Spruce and pine groves piled on the side of mountains and fjords, moose and deer popping up in backyards, woodbirds flitting about on pristine hiking trails. Parrots screeching bloody murder into your ears as you re-enter the city.

No you did not read that wrong. It’s not happening yet, it in a couple of decades parrots, a type of bird not really associated with the sub-Arctic, could be a regular presence around Norwegian cities. So how could this happen, and why is it really quite concerning?

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Tim Robertson: The World of Ecological Data

When I was a child, I’d often study books of Australian birds and mammals, rifling through the pages to see which species lived nearby. My source of information were the maps printed next to photos of the species, distribution maps showing the extent of the species range. These days, many of these species ranges are declining. Or at least, many ecologists believe they are. One of the problems with knowing exactly where species exist or how they are faring is a lack of data. The more data we have, the more precise an idea we get of the future of the species. Some data is difficult to collect, but yet more data has been collected, and is simply inaccessible.

At the Living Norway seminar earlier this month I sat down with Tim Robertson, Head of Informatics and the Global Biodiversity Information Facility. GBIF is an international network that works to solve this data problem worldwide, both by making collected data accessible and by helping everyday people to collect scientific data. I spoke with Tim about the journey from a species observation to a species distribution map, the role of GBIF, and the future of data collection.

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Monitoring Freshwater Populations in the Chernobyl Exclusion Zone

Radiation can have extremely negative effects on an individual. But is it as easy to measure its effects on an entire population? (Image Credit: Hnapel, CC BY-SA 4.0, Image Cropped)

Variation in chronic radiation exposure does not drive life history divergence among Daphnia populations across the Chernobyl Exclusion Zone (2019) Goodman et al., Ecology and Evolution, DOI: 10.1002/ece3.4931

The Crux

As anyone who has recently watched HBO’s Chernobyl can tell you, large doses of radiation are capable of doing some pretty serious damage to an organism. But whilst examining the effect of radiation on an individual might be simple, monitoring those effects on a population can be difficult. Whilst radiation negatively effects fitness, it can also help individuals with higher radiation tolerance to reproduce and dominate within the population of a single species, making it difficult to monitor the exact effects of radiation on that population. If a population is filled with only those who were strong enough to survive, you don’t get an idea of the variation in the radiation’s effects.

This week’s researchers tried to break through that problem by looking at different populations of a water flea in Chernobyl’s Exclusion Zone (CEZ) – the area still barred from entry in eastern Europe.

What They Did

The researchers sampled populations of the water flea Daphnia pulex (see below) from 8 lakes within the CEZ, all of which had experienced different doses of radiation since the Chernobyl disaster. Information on how much radiation those lakes were subject to was taken from Ukraine’s radiation databases and water samples collected at the site. The 38 types of Daphnia from the 8 lakes were then transported back to a laboratory and bred for three generations. The survival and reproductive success of this third generation was then modelled against radiation dose.

Did You Know: Daphnia as Study Organisms

Some species are frequently used across different ecological disciplines as model organisms. One example is the genus Daphnia, a genus of water fleas. They have a short life cycle, and can reproduce asexually. This means that scientists have the opportunity to disentangle environmental effects on populations of genetically similar individuals, as well as between populations of different genetic backgrounds.

What They Found

Whilst reproductive success and survival varied between the populations of Daphnia at different lakes, this did not seem to occur as a result of radiation dose. Radiation did not have a pronounced effect on any fitness variable.



The water flea Daphnia, here used to test the effects of radiation on populations (Image Credit: Paul Hebert, CC BY 2.5)

Sample size is of course an issue here. Only having 8 lakes to compare the effects of radiation on populations was always going to make an effect of radiation dose hard to find. It was made more difficult by the fact that the effects of one lake were significantly different to the others, skewing results considerably. This is of course no fault of the authors, and hopefully technology in the future will allow us to expand the data used in these projects.

So What?

It’s important to note here that these results do not necessarily mean that radiation has no effect on Daphnia populations. Radiation is known to have negative effects on individual fitness, so what this study could tell us is that we need to view radiation as an environmental process which acts in concert with a variety of other biotic factors. Perhaps a study which takes into account further environmental variables and more lake populations would be able to further advance the work done in this paper.

The Roles of Aquatic Predators

Image Credit: Neil Hammerschlag, Oregon State University, Image Cropped, CC BY-SA 2.0

Ecosystem Function and Services of Aquatic Predators in the Anthropocene (2019) Hammerschalg et al., Trends in Ecology and Evolution,

The Crux

Aquatic predators play an important role in many ecosystems, and are often among the more charismatic species in the ecosystem. Because of this, they are often the target of conservation for ocean management bodies worldwide. This paper aims to provide a synthesis of the ecosystem services that aquatic predators provide in marine and freshwater ecosystems worldwide. Below, we’ve chosen 4 of the more interesting and important roles to go into.

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