Tag Archives: genomics

The Changing Face of Ecology: Part Six

Image Credit: Lahiru Prabudda Fernando, CC BY-SA 4.0, Image Cropped

In a year like 2020, when everything short-term seems disastrous, it’s hard to focus on long-term change. How everything from ecology’s relationship with the public, to the health of freshwater ecosystems, to just our general sanity seems to be in flux at the moment.

But we’ve been reading about that ad nauseam recently, and I’m sure there will be plenty more to come. So instead, let’s return to an ongoing segment, and have a look at some of the ways that ecology has changed over the last few decades, according to some of the intriguing and prominent researchers we’ve had the chance to speak to over the last few months.

As usual, full interviews with each ecologist can be found by clicking on their names.

Dan Baldassarre, Associate Professsor at the State University of New York, Oswego

Behavioural Ecology

I think for me probably the biggest thing has been the “-omics” explosion. Genomics, transcriptomics, microbiomics, the incorporation of genetic data into anything that anybody does. It has gotten cheaper and the software has gotten better, so it has just sort of exploded. When I started my dissertation I was really a behavioural ecologist, I didn’t know anything about genetics or wetlab work at all. I started dabbling a little bit with genetic techniques that when I started were pretty rudimentary compared to what people do now. What we can do now was completely unheard of back then. So I would say those types of technologies, and the expectations to have those types of data in a lot of ecology projects, that’s the biggest change for me.

Vigdis Vandvik, Centre Director for bioCEED, University of Bergen

Community & Global Change Ecology

The availability of big data, which has made global biogeography scale down and local experiments scale up. It’s meant that these two aspects of ecology on very different scales have started to meet.

But also, especially in the last few years, a big change has been the talk of ecology and sustainability as a global threat to the world economy in reports by organisations like IPBES and the World Economic Forum. In 2011 when climate change appeared on the WEF’s list of global economic threats I remember I felt the hairs rise on my neck. And even then, if someone had told me then that in 2020 almost all of the top ten threats to the world economy would just be biology-related, I would have bet half my house against that. If organisations like the WEF are recognising the severity of the climate crisis, it gives me hope.

David Lusseau, Professor at the Technical University of Denmark

Marine Sustainability

I think the biggest change has been that we now take the human element in ecology more seriously. Simply because it’s a more pressing need. During my undergraduate as an ecologist, I was working in population ecology, we were concerned about population growth rates, understanding the role of vital rates in population ecology. And we would process the data, create some models, and as far as conservation went, we would give the results to the managers and let them deal with it. And now we’re realising how important it is for ecologists to understand the human element in ecology. And not just from a conservation perspective, but as an interesting ecological topic in its own right. From the natural research perspective it’s an interesting subject to ask questions about. So I think that’s been the biggest change.

Screenshot from 2020-08-10 17-13-20

Pictured from left: Cecilia Medupin, Dan Baldassarre & Vigdis Vandvik (All images licenced to relevant ecologists, CC BY 2.0)

Cecilia Medupin, University of Manchester

Freshwater Ecology

Although my academic and work experience has been in industry, environmental regulation and academia, I have an overview of the social, technological, core biological and regulatory application of environmental management including river monitoring and assessment. In order to have a holistic understanding of environmental challenges, it is important to have a broader mind-set to informing solutions/decisions. For example, when I started my PhD, I wanted to understand the cause of pollution on an urban river. To do this effectively, I needed to relate with the regulators to acquire long term data for that location, connect with the water companies who manage the water infrastructure for that location, relate with members of the public and then relate with the researchers who were my supervisors. Ecology provides you with that type of opportunity. I have seen an increase in awareness of the need for this sort of integration, and funders are keen. We’re heading towards a future where environmental challenges to our rivers, our lakes can only be resolved through broader and effective interactions of disciplines and people. This way, we would make informed decisions and provide solutions that are stronger and more sustainable for all.

Jane Reid, International Chair Professor, Norwegian university of Science and Technology

Evolutionary Ecology

The increase in quantitative skills has been enormous because. When I did my PhD, I hadn’t really gotten any training in statistics, and certainly not in any form of statistical programming. An equivalent to R did not even exist yet. The level of my experience with statistical analysis coming out of my undergraduate were along the lines of doing a t-test or possibly a linear regression. That was all we had. And then even during my PhD, people were trying to run a mixed model, like a really simple Gaussian mixed model, and there was one person in the department that had some kind of software package that could just about do it, but only he knew how to do it. So anyone who wanted to use that approach had to talk to him and he had to battle with a programming language that could barely be said to have a user interface. So just the transformation in how we can now all implement really complicated statistical analyses has revolutionized things I think.

Sam Perrin is a freshwater ecologist currently completing his PhD at the Norwegian University of Science and Technology who is just hoping that ecology doesn’t change too much more before he finishes his PhD. You can read more about his research and the rest of the Ecology for the Masses writers here, see more of his work at Ecology for the Masses here, or follow him on Twitter here.

The Changing Face of Ecology – Part One

The Changing Face of Ecology – Part Two

The Changing Face of Ecology – Part Three

The Changing Face of Ecology – Part Four

The Changing Face of Ecology – Part Five

Surprises From the Past: The Revelations of Ancient DNA

Forest Tundra on the Taymyr Peninsula between Dudinka and Norilsk near Kayerkan, Russia, taken in 2016. Was it always look like this? Should it look like this?
Image Credit: Ninaras, CC BY 4.0, Image Cropped

Although obtaining ancient DNA can be quite a headache, it is a very rewarding headache. After all the work that goes into obtaining DNA from a bone, fur, hair, or Viking’s leftover meal, researchers have to make sense of the apparent random sequence of nucleotide bases. But once that’s taken care of, there are a series of really interesting questions we can start to answer. Were DNA strands that are present in the modern times inherited from the past? How similar are today’s species to their forebears? Where is my pet velociraptor?

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Preserving Biological Heritage: The Importance of Type Specimens

Museum collections may seem like they’re just for display, but they often house important biological information (Image Credit: Andrew Moore, CC BY-SA 2.0, Image Cropped)

Last September, the devastating news of a fire in Brazil’s National Museum in Rio de Janeiro hit the world. The fire destroyed most of the collection, including about 5 million insect specimens. Many of the samples were holotypes, a subset of type specimens which are particularly valuable to the scientific world. If you want an indication of just how valuable, some researchers even charged back into the building while it was on fire to rescue these specimens, saving about 80 % of the mollusc holotypes.

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Does Invading Change You?

The red lionfish, an aggressive, fecund, and competitive species invasive to the Atlantic Ocean (Image Credit: Alexander Vasenin, CC BY-SA 3.0, Image Cropped).

The genomics of invasion: characterization of red lionfish (Pterois volitans) populations from the native and introduced ranges (2019) Burford Reiskind et al., Biological Invasions, https://doi.org/10.1007/s10530-019-01992-0(0123456789

The Crux

Invasive species are one of the most destructive forces and largest threats to native ecosystems, second only to habitat loss. The “how” and “when” of a species invading new habitats is obviously important, and as such many studies focus on if invasive species are present and if they are spreading. Yet these studies often disregard the mechanisms behind why a species is spreading or succeeding in these new environments. The mechanisms are important here, because by and large most invasive organisms will have very small populations sizes, leaving them vulnerable to stochastic events like environmental flux, disease, and inbreeding depression.

Two key paradoxes of invasive species are that these small groups of invasive organisms tend to not only have more genetic diversity than the native species (making them more adaptable to environmental change), but they are also able to outcompete the native organisms, despite having evolved in and adapted to what may be a completely different environment. The authors of this study used genomic approaches to address and try to understand these paradoxes.  Read more

Changing with the Climate

An immature female blue-tailed damselfly (Ischnura elegans)

An immature female blue-tailed damselfly (Ischnura elegans) (Image Credit: Charles J Sharp, CC BY-SA 4.0, Image Cropped)

Signatures of local adaptation along environmental gradients in a range-expanding damselfly (Ischnura elegans) (2018) Dudaniec et al., Molecular Ecology http://doi:10.1111/mec.14709

The Crux

Terrestrial organisms aren’t always stationary entities, they often move around the landscape searching for food, potential mates, or more ideal environments. Over time, these movements may introduce the species into new environments, as some change allows the species to expand their historical range.

An interesting aspect of this shifting of the species range is how the organisms at the edge of the distribution are maladapted to the novel environments, as most of the species will be adapted to conditions at the core of the species range. To overcome this, they must adapt to the new conditions. Successful adaptation is dependent on changes in gene frequencies away from the historical genotypes, with an increase in genes that promote survival in the new habitats. The authors in this study used molecular techniques to identify genes that new environments might select for.

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