World Migratory Bird Day 11-12 May

Guest blog by David Paton. Associate Professor Paton specialises in ecology, evolution and landscape science at the University of Adelaide.birds midflight

Migration usually refers to the regular annual movements of animals from one location (usually a breeding area) to another location (a non-breeding area).  Migrations are much more prominent in the northern hemisphere than the southern hemisphere, primarily because the northern continents extend to higher latitudes than southern continents. Many birds take advantage of the high productivity and long summer days to breed at these high latitudes, but must move away during autumn to avoid harsh winters, returning in spring. Many of these northern birds make intercontinental movements, and some cross the equator shifting to Africa, South America and even Australia, arriving at southern destinations from August to November and departing back to the northern hemisphere from February to May.

Much of man’s initial interests in migrations centred on understanding how the birds navigated, and the morphological and physiological mechanisms that were used to migrate. To make long-distance flights birds need to generate fuel stores, a combination of fat and protein. These stores are combusted during long distance flights to provide energy and are particularly important when crossing inhospitable areas such as oceans and deserts. Although satellite tracking has shown that some birds can fly continuously for days at a time, most species migrate by stopping frequently along the migratory route. During these stops the birds recover from the exertion of an extended period of flight and refuel before making the next part of the journey. This makes migratory birds particularly vulnerable to changes to the destination locations or to key stopovers along the route.

The most conspicuous northern hemisphere birds to visit Australia are a suite of migratory shorebirds including sandpipers, plovers, godwits and curlews. These birds breed in the Palaearctic region and move along the East Asian Flyway to Australia. A series of international migratory bird agreements between Australia and other Asian countries (e.g. China, Japan, Republic of Korea) have been established to help protect key habitats. Within Australia these agreements sit under the Environment Protection and Biodiversity Conservation Act, and signatory countries are obliged to protect the important habitats used by the birds in their respective countries. These agreements, in theory, should protect the habitats used by these birds but in practice this is not the case.

Growing human populations, coastal areas utilised by birds being developed, key wetland areas being reclaimed and area and quality of remaining habitats diminishing, almost all species of migratory shorebirds that visit Australia are in decline. Australian bird populations are also declining. South Australia’s Coorong is a key destination for migratory shorebirds and was listed as a Wetland of International Importance in 1985. However, since 1985 the Coorong has changed and migratory shorebirds are now far less abundant, some experiencing more than 10-fold declines. Changes to the Coorong have been brought about by increasing extraction of water from the Murray Darling Basin, resulting in decreasing flow quantity and timing, and endemic shorebirds such as Pied Oystercatchers and Red-capped Plovers and other waterbirds such as the Fairy Tern using the Coorong have also declined.

Other migratory birds’ movements within Australia are less conspicuous. Short-tailed Shearwaters that breed on offshore islands around the southern coasts of Australia arrive in the tens of thousands at breeding grounds, often on the same day each year, and in many cases occupy the same burrow or one nearby as used in previous years. Other migratory birds are bush birds that move within the Australian continent. The more notable movements involve birds departing southern latitudes, such as Tasmania in autumn and moving northwards. Amongst the species that move are threatened species such as the Orange-bellied Parrot and Swift Parrot. Other smaller birds like the Silvereye, Tree Martin, Fairy Martin, Grey Fantail, Dusky Woodswallow, Flame Robin, Rufous Whistler, White-naped Honeyeater, and Yellow-faced Honeyeater also move during autumn, but not all individuals depart from all locations each year. Although aggregations of some of these species are detected during autumn migration, the movements are more diffuse and many may move as individuals or in small flocks consisting of a handful of individuals. These birds have the potential to forage along the routes that they take and so the need for specific stopovers is not at a premium. The return journeys in spring are even less conspicuous. For these birds with diffuse movements that feed along the way, protecting habitats to allow the movements to continue may be even more challenging than well defined routes with key stopovers. The movements of our bush birds remain poorly documented, yet understanding and documenting the movements will be critical to managing these species into the future.  Modern technologies (such as miniature satellite trackers) may eventually allow these movements to be documented.

There are two other types of movements of birds within Australia. Altitudinal movements are prominent in autumn as flycatchers such as robins, whistlers and fantails move to lower altitudes where slightly warmer conditions may provide more favourable conditions for foraging and survival during winter. Even the relatively small elevation gradient provided by the Mt Lofty Ranges is sufficient to stimulate these birds to move down slope as winter approaches, and one of the delights for bird watchers is seeing some of these species in suburban gardens of Adelaide in autumn and winter.

The other movements often attributed to Australian birds, particularly those of the interior, are described as nomadic. These often consist of large numbers of birds such as Budgerigars, Crimson Chats and Pied Honeyeaters appearing in more temperate southern latitudes after a boom period. The boom periods follow a period when significant rainfall has stimulated plant growth in the arid interior. The boom times, however, give way to periods with little rain, forcing the birds to move. These potentially nomadic movements are usually not considered migrations because they lack a regular annual cycle and are not, as yet, predictable.

Guest post by Associate Professor David Paton.
If you would like to contribute as a guest blogger on the Environment Institute blog, email environment@adelaide.edu.au.

New paper: Evaluating options for sustainable energy mixes in South Korea using scenario analysis

A new paper involving Environment Institute members Corey Bradshaw and Barry W. Brook has recently been published in the journal Energy.

The paper, titled Evaluating options for sustainable energy mixes in South Korea using scenario analysis, examines the possibilities for sustainable energy generation in South Korea.

ABSTRACT

To mitigate greenhouse gas emissions, coal-fired electricity infrastructure needs to be replaced by low-carbon electricity generation options. Here we examine a range of possible alternative scenarios for sustainable electricity generation in South Korea, considering both physical and economic limits of current technologies. The results show that South Korea cannot achieve a 100% renewable energy mix and requires at least 55 GW of backup capacity. Given that constraint, we modelled seven scenarios: (i) the present condition, (ii) the First National Electricity Plan configuration, (iii) renewable energy (including 5 GW photovoltaic) with fuel cells or (iv) natural gas backup, (v) maximum renewable energy (including 75 GW photovoltaic) with natural gas, (vi) maximum nuclear power, and (vii) nuclear power with natural gas. We then quantify levelised cost of electricity, energy security, greenhouse gas emissions, fresh water consumption, heated water discharge, land transformation, air pollutant emissions, radioactive waste disposal, solid waste disposal and safety issues for each modelled mix. Our analysis shows that the maximum nuclear power scenario yields the fewest overall negative impacts, and the maximum renewable energy scenario with fuel cells would have the highest negative impacts.

Visit ScienceDirect to find out more.

Jen’s amazing lotus flower (research)

Lotus open 1

The beautiful and amazing sacred lotus flower is of great cultural and religious significance throughout Asia. Nearly all parts of the plant are used in various Asian cuisines, the self-cleaning leaves have inspired modern engineering innovations, and it’s seeds have incredible longevity, some have even germinated when over1000 years old. One more trait makes the sacred lotus exceptional: it’s flowers can generate heat, and even maintain a constant temperature, just like warm-blooded animals. Ancient Hindu writings make many references to the sacred lotus and many Asian deities are depicted seated on a lotus flower.

Associate Professor Jennifer Watling, Head of the School of Earth and Environmental Sciences at the University of Adelaide, which houses the Environment Institute, has been studying the physiology of the sacred lotus and other plants. If you get the opportunity to speak with Jen about her work for any length of time you will come away inspired by her passion for exploring a deep understanding of some of the amazing life-support systems in the plant world. I have had the privilege of working on a small film project with Jen and ‘her amazing lotus flower’ stories. I have become totally enchanted by her tales about ‘thermogenesis’ – the way the lotus flower can generate heat and regulate it’s own temperature, in an almost human way.

Lotus pond 1            Lotus pond 2
Wading-Mike & Jen Watling2

Research by Jen and her collaborators into the pathways which drive thermogenesis in plants has resulted in many papers, some of which have graced the covers of significant journals. This research shows that the ‘alternative pathway of respiration’ is used for thermogenesis by these plants and is absolutely foundational to our understanding of these types of mechanisms in all living things (including us!). Even more interesting are some of the stories which emerged when I asked ‘why might plants regulate their temperature’?

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Many of the theories as to why a plant might benefit from an ability to regulate temperature (up to 40 deg C above ambient) involve pollinators in a ‘birds and bees’ kind of way. The notion of a ‘thermal reward’ to the small bugs that crawl into the flower is rather interesting. The reward might be the cozy feeling of a warm hug or a warm place to spend the night in return for sexual favours. You could think of this as a bit like a ‘beetle nightclub’ in which the beetles crawl inside a warm, scented flower, and are treated to an all night party as the flower closes and temperatures rise. This is an area of research that deserves much more attention and support in my opinion. Heat is also likely to assist in the transmission of the scents which attract pollinators. Of course, heat is also useful in surviving the harsh effects of low temperatures on plants. Another area where more research is required is in understanding exactly how these plants sense the temperature they have become so good at regulating.

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Fundamental scientific research on the physiology of plants by Jen, her collaborators and others who work in this area, is an important foundation for understanding not just how individual plants work, but also how plants influence our lives. From these foundations we can begin to understand similar mechanisms in all living things – including humans. There are implications for improved healthcare and innovations in seemingly un-related fields. The amazing properties of plants have long inspired religious writings of cultural significance and can now be examined and mimicked to create all sorts of products from medicines to self cleaning windows. Now do you see why I say “Jen’s amazing lotus flower?”.

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Papers:
Made the comver of Plant Physiology April 2006 vol. 140 no. 4 1367-1373
“Contribution of the Alternative Pathway to Respiration during Thermogenesis in Flowers of the Sacred Lotus” Link: http://www.plantphysiol.org/content/140/4/1367
Made cover of Journal of Experimental botany, Vol 59, No 3, 2008 doi: 10.1093/jxb/erm333 “Synchronicity of thermogenic activity, alternative pathway respiratory flux, AOX protein content, and carbohydrates in receptacle tissues of sacred lotus during floral development” Link: http://jxb.oxfordjournals.org/content/59/3/705.short
New Phytologist: In the heat of the night – alternative pathway respiration drives thermogenesis in Philodendron bipinnatifidum – Miller – 2011 – New Phytologist – Wiley Online Library New Phytologist, 189: 1013–1026

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More Images:
Guest Post by Mike Seyfang, if you would like to contribute as a guest blogger on The Environment Institute Blog email environment@adelaide.edu.au.

Biodiversity ‘Arks’ – anatomy of a Nature paper

Guest post by Mike Seyfang. Mike is a media coordinator with the University of Adelaide.

This special edition ‘Talking Paper’ takes a look behind the scenes at the PROCESS of crafting a Nature paper (with 216 Authors). So, what is the big deal about getting your science published in Nature? For many researchers it is a career highlight. For some it can be the launch of a stellar career. For an already distinguished scientist like lead author Prof. William F. Laurance, it can re-enforce a position of world leadership in a significant area of research. With some clever wording (e.g. ‘Biodiversity Arks’) and a little promotion, it may be possible to track the influence of your work as it reverberates through the global media, is talked about online and maybe even influences the tone of twitter for a short while! Follow this up with some discussion and engagement in online platforms like ‘the conversation’ to further broaden the reach and impact of your life’s work.

Thanks to the Environment Institute at the University of Adelaide, I was able to spend an hour or so chatting with Professors Corey Bradshaw and Bill Laurance about the process underlying the publication, the motivation behind the years of work leading up to it and some of the key analaysis and findings. Even though my screen recording software failed, I am able to bring you the following fifteen minute video from that conversation.

Bill and Corey begin by introducing the basic idea of the paper “to look at the effectiveness of protected areas – the cornerstone of our preservation efforts”. A key motivation was to find out what is really going on at ground level, something that is not able to be determined from the vast amounts of satellite data that is currently available.

PROCESS:

This work is based on two hundred and sixty two expert interviews which seek to extract and objectify years of knowledge from experts around the world. Corey and Bill discuss the joy and pain of getting the interviews done, fights over words, working with interview data the idea of BAD “Best Available Data”. Bill explains that getting all these people together and leading the endeavour was like herding cats. Scientists are trained to disagree, examine, pull-apart and ask questions. Work began when Bill was at the Smithsonian institute in Panama. There he had a well resourced team to get things started. “Substantial person power” is required for an endeavour like this one.

Corey played a significant role by performing quantitative analysis on interview data.  A whole bunch of information and over three thousand five hundred comparisons had to be distilled down into a nature paper “because those are just a couple of thousand words”. One of the key findings of the research is the importance of threats around protected areas. It was surprising “just how much of what happens outside of the park affects the inside of the park, regardless of the size of the park”.

CONCLUSION:

Bill says “I Don’t know how else one could have tackled this kind of analysis”, where decades of work by (each of) hundreds of experts was gathered and analysed. He explains that it was hard work, and he is relived to see it accepted by Nature and will be pleased to have it see the light of day.

So, if you are considering a career in Science or Communicating Science, go back and look at the video again and ask yourself some questions like:

  • How did a scientist from the University of Adelaide get involved with research like this?
  • How did Prof Laurance get so many people to contribute to his research?
  • What did it take to persuade one of the world’s top journals to publish this work?
  • How many years of detailed learning is summarised in this paper?
  • Can I see myself leading an effort like this?

Hopefully some of you will be inspired to think about a career in science, or at least catch some of the infectious enthusiasm that I certainly felt as I spoke with Bill and Corey in preparing this article for you.

Guest Post by Mike Seyfang, if you would like to contribute as a guest blogger on The Environment Institute Blog email environment@adelaide.edu.au.

Talking Papers: Bison Epigenetics – a new tool to study rapid adaption to environmental change

Guest post by Mike Seyfang. Mike is a media coordinator with the University of Adelaide.

Recent work from the Australian Centre for Ancient DNA (ACAD) has attracted a lot of media attention with headlines such as “Ancient bison bones hold climate clues”, “How stressed bison got around the dictates of DNA” and “Bisons adapted to climate change”. I caught up* with Alan Cooper (Director ACAD) to find out what all the fuss was about and learned a lot more than I had expected in the process. It turns out that this area of research examines certain modified DNA bases that can control whether genes are turned on or off, and provide a means for adaptive traits to be stably inherited from one generation to the next. In effect, this provides a means for species to rapidly adapt to environmental change and ACAD researchers set out to see whether these  ‘epigenetic markers’ are also preserved after death and can be measured in extinct species. The work described in the paper “High-Resolution Analysis of Cytosine Methylation in Ancient DNA” gives scientists a new tool for probing mechanisms which have allowed populations to adapt rapidly to changed environments in ancient history. If you need a quick introduction to terms like ‘epigenetics’, ‘methylation’ take a peek at the definitions section at the bottom of this article.

The study of Ancient DNA brings with it many challenges. I asked Alan – “exactly how does one get one’s hands on a thirty thousand year old specimen of bison DNA?”. As he explains in this short (2:33) video:

Fieldwork in the Yukon region (Klondike goldfields) is amazing. In a harsh environment surrounded by ice, brown bears and dynamite the trick is to convince gold miners to let you crawl around picking up bits and pieces lying among freshly unearthed gold“. Judging by the smile on Alan’s face as he re-counts these adventures it is obvious he really enjoys the field work of collecting specimens of ancient DNA.

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The next set of challenges will sound familiar to people who spend a lot of time working in labs. “it took us 6 bison to find one that contained good enough quality DNA” … then “the technique we use is to destroy everything except what you are looking for in tiny samples where you hardly have anything to begin with“. Currently, the standard technique maps cytosine bases that have been epigenetically modified with a methyl CH3 group by using a chemical that destroys all normal cytosines and leaves only the modified bases.  Alan describes this process as like looking for a needle in a haystack with a few clues to start with and the added challenge of being limited to a small number of attempts. Some of the clues were obtained by using a cow as a proxy for the bison. Studying methylation patterns in DNA from ‘fresh bovine tissue’ provided important clues about what to look for and where in the genetic sequence. Even with these clues the task was difficult because researchers didn’t know that the methyl group would still be there from 30-40 thousand years ago. There was some good fortune in this project, the team could see methylated bases and that they were often associated with 50/50 (half methylated, half not) signaling. This is encouraging because it is what you expect for a trait inherited from two parents, one epigenetically modified, one not. Soon, with the aid of new next generation sequencers, it will be possible to make equivalent measurements in real time, without destroying the sample.

A further challenge for this work was getting the paper published -“The medical people measure epigenetics but evolutionists aren’t really that interested“. It took about a year of getting bounced around from publisher to publisher to find a journal where anyone could be convinced that the study of epigenetics in (ancient) DNA was important.

In conclusion, Cooper and team have given researchers a new tool to examine how epigenetic markers (methylation patterns) change through time in response to climate and other environmental changes.  The next steps will be to refine the tools available through incorporation of next generation sequencing technology. Then it will be possible to take the method forward and study whole populations, measuring them as they go through extreme events such as the ‘last Galacial Maximum’ and asking questions such as ‘how do animals and populations adapt?’. We now have a way to measure a means of rapid adaption, we need to go out and get the funding to examine how this works in large numbers of Bison across space and time. As Cooper says, funding applications are the next step in the long line of science. Science that can give us answers to some of the really big questions we will face as our own environment changes with ever increasing speed.

Audio recording of full interview.

Some definitions:

Epigenetics: (video) the study of heritable changes in gene expression or cellular phenotype caused by mechanisms other than changes in the underlying DNA sequence. In the words of the researchers: “Interposed between genes and environment, epigenetic modifications can be influenced by environmental factors to affect phenotype for multiple generations.”

Methylation: (video)

A methyl group (CH3) attached to something. When many cytosine bases are methylated genes can be turned off, a form of epigenetics.

Bison: (video) large ‘cow’ like creature , modern species include the American Plains and Woods Bison.

Bases: a group of nitrogen-based molecules that are required to form nucleotides, the basic building blocks of DNA and RNA. Nucleobases provide the molecular structure necessary for the hydrogen bonding of complementary DNA and RNA strands, and are key components in the formation of stable DNA and RNA molecules.

C’s: Carbon atoms.

Lamark (Lamarkian evolution):  see also “science in seconds” and this article.

Last Galacial Maximum: a period in the Earth‘s climate history when ice sheets were at their maximum extension, roughly between 23,000 and 18,000 years ago.

BisonEpigeneticsImages

Links:

Environment Institute blog post

Some of the press:

http://www.cosmosmagazine.com/news/5268/ancient-bison-bones-hold-climate-clues

http://yukon-news.com/opinions/columns/27402/

http://www.huffingtonpost.com/2012/02/03/yukon-bison-bone-discovery-permafrost_n_1250520.html

http://www.thehindu.com/sci-tech/science/article2851155.ece

http://epigenie.com/epigenetics-at-the-intersection-of-environment-and-selection/

http://digitaljournal.com/article/318900#ixzz1vZZi9SpQ

Media: archive.org collectionimages more images

The paper

Guest Post by Mike Seyfang, if you would like to contribute as a guest blogger on The Environment Institute Blog email environment@adelaide.edu.au.