Reading group: Environmental DNA sampling — hope or hype?

In our latest QAEco reading group, Emily McColl-Gausden and Reid Tingley led a discussion on ‘Environmental DNA for wildlife biology and biodiversity monitoring’ by Kristine Bohmann, Alice Evans and colleagues.

Bohmann et al. examined eDNA from a monitoring/ecology perspective, and therefore didn’t delve too deeply into the genetic details (which some of our less genetically-inclined members appreciated!). The paper did, however, highlight some very interesting, and perhaps less well-known eDNA applications from both aquatic and terrestrial environments. Surveying for endangered deer using leech blood and collecting eDNA from Arctic fox paw prints were two intriguing examples. Bohmann et al. also highlighted some important limitations of eDNA sampling, such as the occurrence of false positive detections both in the field and in the lab. The paper looked to the future in its longer term aspirations for eDNA, in addition to more realistic shorter-term goals.

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Former QAECO student, Adam Smart, takes a water sample for eDNA analysis from a roadside drain (Image: Reid Tingley)

We all agreed that there were many potential applications of eDNA sampling, and that researchers were only beginning to tap into its potential. There are also certainly benefits from an animal ethics point of view. However, one issue that caused much discussion was the ability to estimate abundance from eDNA. Some members of the group were rather dubious about the strength of this correlation, and how it might change in different environments. We came to the conclusion that eDNA-based abundance data could potentially be used as an index to rank the abundance of species, rather than an absolute number (e.g., for differentiating rare vs. common species).

For some in the group, the paper was too optimistic in its predictions of global networks of eDNA monitoring stations. Others, however, thought that technological advances could enable widespread data collection in the not-too-distant future. Handheld devices for sampling and analysing eDNA data were mentioned as an example of such an advance.

More broadly, this paper catalysed an interesting discussion regarding how intensely we scrutinise new technologies in ecology. The point was raised that we don’t seem to question the more established sampling techniques as much as we probably should. For example, electrofishing is not 100% effective for detecting fish, yet imperfect detection is rarely discussed or considered. And, of course, as a group of quantitative ecologists who are interested in conservation decision-making, we wondered about the value of resolving many of the uncertainties regarding eDNA sampling. Given a fixed budget, should we invest in resolving such uncertainties, or are we better off taking additional environmental samples? Following on from that point, we agreed that we would like to see more papers on the cost-effectiveness of eDNA sampling, as well as more focus on imperfect detection. Did we mention that we’re quantitative ecologists?

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Reading group: towards unification

This is the second instalment of our fortnightly reading group blog series. This time, our group was led by Skip Woolley and we discussed the paper Towards a unification of unified theories of biodiversity by McGill 2010.

This is an interesting paper that identifies different community ecology theories that are generated by inherently different mechanisms, but in turn, generate very similar community ecology patterns. These patterns are: species-area relationships, a hollow shaped abundance curve (RAD) and distance-decay relationships (Fig. 1).

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Figure 1. Intrinsic patterns in community ecology. a) Species-area relationship; b) Rank abundance distributions; and c) Distance-decay relationships.

A case is put forward by McGill (and others) that this generality can be used to unify these theories and establish a set of rules that are applicable to all these approaches and thus, can be taken as generality.

McGill settles on the rules:

  1. Individuals within a species are clumped together
  2. Abundance between species follows a hollow shaped curve
  3. Species are treated as independent and are placed without regard to other species.

As a group, we liked the summation of these approaches and the respective patterns they produce. Lending us to accept certain mathematical forms, the rules are shared in common across these approaches and thus can be taken as generality. Similar concepts have been applied to other fields of science and the concept has previously been discussed amongst our reading group (The common patterns of nature by Frank 2009).

We did feel that the unification of these theories was a slight stretch, and that a way forward would be to test under which conditions these rules stand up? For example, a number of our reading group participants are involved in modelling joint species distributions, so we felt that the assumption of species independence was not a requirement to generate the patterns. Given this, what would be the bare number of rules required to generate these patterns? One way to do this would be to start with a set of necessary starting conditions (for example, species interactions from a food web) and assess which patterns arise from these interactions.

We also felt a more interesting question was: what drives these patterns? Along these lines of reasoning, we discussed the idea that these patterns could be viewed as null models and further investigation via theoretical or empirical studies could help highlight deviations from these expected patterns. As a whole, we felt that understanding the cases where these rules breakdown would help us understand their underlying mechanisms. In this vein, McGill touches on a need to understand processes that drive richness and abundance patterns at the end of the paper. A better understanding on the processes that shape these patterns will help theoretical ecologists more accurately investigate the relationships between these theories, and have the added benefit of assisting applied ecologists in their efforts to manage biodiversity.

Until next time.

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Introducing BECR: the BioSciences Early Career Researchers Network

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BECR is a recently-formed group of early career researchers (ECRs) who work in the School of BioSciences at The University of Melbourne.

BECR aims to:

  • provide opportunities for networking and career development;
  • represent ECR interests within the School and the Faculty of Science; and
  • make life in BioSciences more sociable and enjoyable!

BECR will be holding regular networking events, so make sure you check out the new website for updates. Of particular interest is the BECR Research Summit – the group’s premier event. The BECR Research Summit will be held on the 9th of December 2016, so save the date!

BECR will also host a lunch at Naughtons on Royal Pde every month. These lunches will be on alternate days each month, to ensure that all BECRs have the opportunity to come along. The inaugural BECR lunch was attended by almost 20 ECRs, and hopefully the network will continue to grow in the coming months!

BECR lunch

The inaugural BECR lunch

If you have any suggestions for events, or information you think may be useful to other BioSciences ECRs, please drop them a line. Examples include conferences with an ECR focus, or funding opportunities for ECRs. There’s already an excellent list of funding opportunities on the website, so make sure you check that out too!

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Reading group: Toxic Trojans

At QAECO we have a fortnightly reading group where we get together and discuss a paper, blog or piece of research – anything from seminal papers in ecology, new research, ideas from related fields, or just something we find interesting.

This is the first in a series of blog posts where we will be describing the papers we cover and the main points that come from our discussions.

This week’s paper was Toxic Trojans: can feral cat predation be mitigated by making their prey poisonous? which was recently published in Wildlife Research by John Read and colleagues.

This paper was chosen because it presents a novel idea for controlling feral predators. Predation by feral cats is a huge concern for conservation of Australian wildlife, as even low numbers of cats can drive population declines of native fauna and thwart reintroductions. However cat control is notoriously difficult as cats will rarely consume baits or enter baited traps when live prey are available.  There are also potential ethical concerns, such as the negative impacts of baiting on non-target species.

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Feral cat, Otway Ranges (image: C. Mildwaters)

 

John Read and colleagues (2015) present a novel strategy to add to the current arsenal of control methods: the use of Toxic Trojans — live prey that that appeal to the hunting instincts of cats but are lethal when consumed. They describe how Trojans have the potential to bolster reintroduction programs where predation by feral cats is the main impediment to population viability, and could be deployed as part of monitoring or management programs.

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Merlion conservation? #ConsAsia2016

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Suddenly there’s a flurry of regional conservation meetings! While many will escape the cold and head up to Brisbane next week for the Society for Conservation Biology Oceania meeting; this week it’s the joint meeting of SCB Asia and Association for Tropical Biology and Conservation Asia-Pacific chapter in steamy Singapore: Conservation Asia 2016. Here’s what Qaecologists are up to in the City in a Garden this week:

Thursday, the  30th of June

Honorary Qaecologist Catharina Karlsson (she’s at conference host NUS, but spent a few months with us in Melbourne working on detectability with Mick McCarthy and Gurutzeta Guillera-Arroita) is talking Automatic acoustic monitoring: Current use and challenges, in the symposium Amphibian Conservation in Asia: Approaching Standard Methods.

11.00 – 11.15, LT51

Saturday, the 2nd of June

Qaeco alumnus Paing Soe has a poster and speed talk on Circuit theory based corridor modelling for wildlife crossing infrastructure placement along a planned major highway in southern Myanmar  from his current work with WWF -Myanmar.

9.45-11.45, LT53, Speed talk session 3, and poster P51.

And Qaecologist Gerry Ryan is foolish keen enough to be giving two talks on the same day:

Getting mixed up about vultures: new methods for estimating abundance from count
data, in the Averting Species Extinctions in Southeast Asia symposium.

 13.00-13.15, LT52

Dolphins behaving badly: Investigating the role of infanticide and
boat traffic as threats to the Mekong River Irrawaddy dolphin.

17.30-17.45, LT50 (Last session of the conference!)

 

Have a great time if you’re going to the Lion City, and if not, keep a retina pointed at #ConsAsia2016 for updates from passionate practitioners and awesome academics later this week.

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Homage to Hanski

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A tribute from QAECO

Ecology lost a giant last week. It was with great sadness that we at QAECO heard of Professor Ilkka Hanski’s passing after a long illness. Ilkka’s career profoundly affected us. From metapopulation theory, through expansive empirical research, to conservation planning, Ilkka’s research stood as an exemplar that focused our minds and spurred us on. He delivered not just a framework for understanding the complex world of spatial population dynamics, but set a bench mark of rigour that lifted our own aspirations.

Looking back at Ilkka’s career takes one on a fascinating journey. It begins in the fields of Finland, where Ilkka spent long hours of his youth collecting butterflies, bees and beetles. In his own words, it left a lasting impression (Hanski 1999), searing two key elements of population dynamics onto his mind: the importance of habitat patchiness to species distributions, and the changeability of species distributions through time. Ilkka’s PhD at Oxford (1976-1979) provided just the opportunity to tackle these subjects. In an early example of lateral thinking, Ilkka found a study system that was ideally suited to these topics, but which many of us might turn up our nose at: dung beetles dotted among cow manure and carrion flies inhabiting that most patchy of resources, rotting wildlife. Not the most glamorous of systems, but it proved rich ecological pickings. Ilkka finished his doctorate in three years, and published 19 papers on the subject of insect spatial dynamics by 1981.

Returning to Finland, Ilkka continued his work on insects, but also dabbled in the island population dynamics of shrews, spurred on by island biogeography and the equilibrium theories of the preceding decades. It was an important stepping stone in his career, cementing his lifelong fascination with metapopulation theory (Levins 1969, 1970). Ilkka’s key papers from this period tell the story (Hanski 1985; 1986; 1989, 1991, 1992, 1993). Each takes simple equilibrium models of extinction and colonization dynamics as inspiration, and builds in more complex ecological phenomena. His paper in 1992 was pivotal, bringing conceptual advances from island biogeography to bear on metapopulation theory. Ilkka’s idea was to parameterize a model of a species’ extinction and colonization rates from ‘incidence functions’ (Gilpin & Diamond 1981) – the relationships between the rate of occurrence of species among patches and the properties of those patches, particularly their area and isolation. His famous paper in 1994 formalised the approach (Hanski 1994), and the ‘incidence function model’ of metapopulation dynamics was born. It spread like wildfire, with 1300 citations as of today (Google Scholar).

In the 22 years since that foundational work, Ilkka, along with his burgeoning Metapopulaton Research Centre (MRC), transformed spatial ecology and evolution, and blazed a trail in conservation biology. With generations of students and postdocs, Ilkka fostered a unique integration of ecological theory, empirical research and computation. The MRC have published ecological theory in the most prestigious journals (e.g., Hanski 1998; Hanski & Ovaskainen 2000; Hanski 2011; Hanski et al. 2013), completed some of the grandest and most complex empirical studies ecology and evolution has seen (e.g., Saccheri et al. 1998; Ojanen et al. 2013; Jousimo et al. 2014), and developed conservation software that is world beating in its reach and impact (Moilanen et al. 2014). It is a legacy of which Ilkka must have been immensely proud.

But of course, his legacy reaches much further, into research institutions across the globe via MRC alumni, and through his shaping of ecological research, teaching and conservation policy over many decades. Our group is one of many to sport a professional descendant of Ilkka’s; his first academic great grand-daughter, Heini Kujala (Heini completed her PhD with Mar Cabeza, a PhD student of Atte Moilanen’s, who in turn completed a PhD with Ilkka in 1998). Likewise, our group is one of many whose research owes much to Ilkka’s influence. The citation statistics are revealing. Looking back at our own publications, 65 have cited one or more papers authored by Ilkka (data from Scopus). Little wonder Ilkka’s Google Scholar page is something to behold. Since his first paper in 1971, Ilkka’s work has been cited a whopping 44,481 times as of today, giving an h-index of 99. All told, we calculate that Ilkka wrote or co-wrote 291 articles, 71 book chapters and 6 books, and edited or co-edited another 6 books. A remarkable contribution.

We extend our sincere condolences to Ilkka’s family, and to his friends and colleagues at the MRC. We are thinking of you at this difficult time. We will miss him and his unique contributions to the field of ecology, evolution and conservation.

Kiitos kaikesta

A personal tribute from Heini Kujala

Many times during my years in QAECO I have been asked what it was like to work with the famous Professor Ilkka Hanski at the Metapopulation Research Centre (MRC). In truth, Illka and I worked directly on only one project. But being a close working community, everyone in MRC knew Ilkka well, and he made the extra effort of getting to know everyone himself. Which is not always easy in a group of 70+ members. And whereas Ilkka’s scientific achievements are unquestionable, to me his most amazing merits lay in the type of scientist he was: humble, fair and forever driven by the passion to learn more about the world around us.

After winning several prestigious international prizes and being nominated as one of the 12 Finnish Academicians of Science (the highest academic title in Finland, that one holds the rest of their life), Ilkka was often asked what it means to a researcher to be acknowledged at such high level. Being the type of person he was, Ilkka replied that whereas winning prices and achieving titles is always nice, the feeling often soon passes, as the true reward for many scientists, him included, was the joy of doing research itself. Ilkka was a passionate scientist. Even when leading the large Metapopulation Research Centre, supervising students and postdocs and coordinating various other side projects, he never gave up doing hands-on research himself. This included field work, often on the mountainous parts of Madagascar and Borneo. For example, about 10 years ago, when Ilkka was in his early 50s (and me in my early 20s) I was helping him to collect beetles on the steep slopes of Marojejy National Park in northern Madagascar. Already on day one I had to admit he was far more fit running up and down the steep tracks than I was.

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Breakfast before a big day on the slopes. Marojejy National Park, Madagascar. Photo: Tiina Avomaa

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The end result – Malagasy beetles collected with Ilkka. Photo: Heini Kujala

In addition to being a passionate scientist, Ilkka was a passionate environmentalist and science communicator. He wrote several popularized articles and books about science and nature (including the book Messages from Islands), and gave numerous talks to non-academic audiences. He was firmly of the opinion that one of a researcher’s key responsibilities was to bring the scientific evidence to public discussion. Everyone who knew him knows that he never shied away from saying his opinion, but he always based them on facts and knowledge, and he was quite willing to change his mind if, eventually, he was proven wrong. I am sure his ability to explain complex scientific problems and causalities in simplified and understandable terms greatly aided his career as a successful scientist.

Looking back, I realize that Ilkka left several permanent marks in my life as a researcher, some of which I’ve always known and some of which I’ve come to understand only after leaving MRC. I remember well how Ilkka always told us to be humble with science. To learn from failures and let the data, not the scientist, tell the story. He never put himself on a podium – not even after receiving all possible acknowledgements and prizes an ecologist could ever achieve. He liked to point out that his work was the result from collaborating with so many great minds, building on the findings of those before him. The door to his office was always open, he was always interested in everyone’s work, always happy to meet new people. One of Ilkka’s wonderful characteristics as a group leader was that he never stopped looking for improvements to the way the group worked. And by this I do not mean just finding the most competitive and best suited candidates for open positions. No, Ilkka put significant effort in making the MRC a great working community. He regularly brought foreign researchers into Helsinki for visits, for student seminars, and to act as PhD examiners or as collaborators, and encouraged students, post docs and colleagues to network, travel and garner experience from outside MRC (mostly leaning on the lab’s own funding). But he also considered the less obvious things. Like insisting (in his kind persistent way) that everyone in the lab participated in the daily coffee breaks. Or organizing annual lab retreats where much of the discussion was about how to make the lab a better working environment for everyone, and how the make MRC succeed together. That is where I see he made one of his most amazing breakthroughs – by being the strong leader everyone could trust and count on, but at the same time, making everyone in the group feel that decisions, and achievements, were made together. I hope to learn some day how exactly he did this.

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The MRC in Stockholm. Ilkka took the entire team with him to attend his Crafoord Prize Gala. Photo: Evgeniy Meyke.

As stated by many, Ilkka left behind a huge scientific legacy. But for an early-career scientist such as me, he left something far more precious – an idea of a great, humble and persistent researcher who was always looking for ways to improve both his work and the broader research community while trying to solve the mysteries of life. I am sure I speak for many when I say that it is not just his scientific merits that make his passing so overwhelmingly sad, but the fact that he was such a wonderful and inspiring colleague, mentor and a friend to so many people around the world.

Kiitos kaikesta Ilkka. Thank you for all your time and everything you taught us. You will be greatly missed.

– Heini

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Literature cited

Gilpin M.E. & Diamond J.M. (1981). Immigration and extinction probabilities for individual species: relation to incidence functions and species colonization curves. Proccedings of the National Academy of Sciences, 78, 392-396.

Hanski I. (1985). Single-species spatial dynamics may contribute to long-term rarity and commonness. Ecology, 66, 335-343.

Hanski I. (1986). Population dynamics of shrews on small islands accord with the equilibrium model. Biological Journal of the Linnean Society, 28, 23-36.

Hanski I. (1989). Metapopulation dynamics: does it help to have more of the same? Trends in Ecology and Evolution, 4, 113-114.

Hanski I. (1991). Single-species metapopulation dynamics: concepts, models and observations. Biological Journal of the Linnean Society, 42, 17-38.

Hanski I. (1992). Inferences from ecological incidence functions. The American Naturalist, 139, 657-662.

Hanski I. (1993). Dynamics of small mammals on islands. Ecography, 16, 372-375.

Hanski I. (1994). A practical model of metapopulation dynamics. Journal of Animal Ecology, 63, 151-162.

Hanski I. (1998). Metapopulation dynamics. Nature, 396, 41-49.

Hanski I. (1999). Metapopulation Ecology. Oxford University Press, Oxford.

Hanski I. & Ovaskainen O. (2000). The metapopulation capacity of a fragmented landscape. Nature, 404, 755-758.

Hanski I., Zurita G.A., Bellocq M.I. & Rybicki J. (2013). Species–fragmented area relationship. Proceedings of the National Academy of Sciences, 110, 12715-12720.

Hanski I.A. (2011). Eco-evolutionary spatial dynamics in the Glanville fritillary butterfly. Proceedings of the National Academy of Sciences, 108, 14397–14404.

Jousimo J., Tack A.J.M., Ovaskainen O., Mononen T., Susi H., Tollenaere C. & Laine A.-L. (2014). Ecological and evolutionary effects of fragmentation on infectious disease dynamics. Science, 344, 1289-1293.

Levins R. (1969). Some demographic and genetic consequences of environmental heterogeneity for biological control. Bulletin of the Entomological Society of America, 15, 237-240.

Levins R. (1970). Extinction. In: Some Mathematical Questions in Biology (ed. Gerstenhaber M). The American Mathematical Society, Providence. pp. 75-108.

Moilanen A., Pouzols F.M., Meller L., Veach V., Arponen A., Leppanen A. & Kujala H. (2014). Zonation: Version 4, User Manual. Conservation Biology Informatics Group, Department of Biosciences, University of Helsinki, Finland.

Ojanen S.P., Nieminen M., Meyke E., Pöyry J. & Hanski I. (2013). Long-term metapopulation study of the Glanville fritillary butterfly (Melitaea cinxia): survey methods, data management, and long-term population trends. Ecology and Evolution, 3, 3713-3737.

Saccheri I., Kuussaari M., Kankare M., Vikman P., Fortelius W. & Hanski I. (1998). Inbreeding and extinction in a butterfly metapopulation. Nature, 392, 491-494.

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Exposing the creatures of the deep

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For the first time, a light has been shone on the diversity of creatures that exists in the world’s dark, deep seas.An international team of scientists have created the first map of seafloor diversity across the world’s oceans. The map reveals how patterns of biodiversity in deep oceans fundamentally differ from those in shallow waters or on land, and will be critical for conservation efforts.Focusing on brittle and basket stars (related to starfish), the ground-breaking results, that have taken almost 20 years to compile, have been published in Nature.

Brittle star, Ophiothrix spongicola. Picture: Julian Finn

Brittle star, Ophiothrix spongicola. Picture: Julian Finn

“The deep seafloor remains the least explored ecosystem on Earth,” said lead author Skipton Woolley, from the School of BioSciences, University of Melbourne and Museum Victoria.

This area exists from 2k to as far as 6.5k deep, and covers 70% of the ocean’s seafloor.

“We have an innate understanding of the important regions of biodiversity on land, but are much less aware of what is going in the deep-sea,” says Mr Woolley.

“It is immense, remote and expensive to survey – so gaining accurate knowledge about the variety of life in the deep sea is difficult.”

Over the past two decades, the team has visited museums around the world and combined their collection databases with information from scientific literature to create one ‘mega database’, which charts where marine invertebrate species have been found.

There are over 2000 species of brittle and basket stars, and they are found in all oceans, from coastal areas, to polar regions.

Distribution of all survey sites that collected biodiversity data. Picture: Dr Tim O’Hara, Museum Victoria

Distribution of all survey sites that collected biodiversity data. Picture: Dr Tim O’Hara, Museum Victoria
“We lack information about where seafloor animals are distributed and why some areas support more species than others,” said co-author Dr Tim O’Hara, Senior Curator of Marine Invertebrates at Museum Victoria, and an Honorary Research Fellow in the School of BioSciences, University of Melbourne.“This is a problem for deep-sea conservation. It is very difficult to protect deep-sea animals and sustainably manage human activities such as deep-sea fishing and mining if we don’t know where animals live.”New technology is making activities such as deep-sea mining for minerals including gold and cobalt increasingly viable.
Tim O’Hara with Deep Ocean Biodiversity Map and Brittle Star specimens. Picture: Rod Start

Tim O’Hara with Deep Ocean Biodiversity Map and Brittle Star specimens. Picture: Rod Start

Using sophisticated computer software, the team of researchers from Australia, Canada and the United Kingdom analysed the global distribution of thousands of species of brittle and basket stars to predict and measure patterns of where species occur across the seafloor. They were then able to use this data to compare biodiversity patterns across three different ocean depths: the continental shelf (20-200m), upper continental slope (200-2,000m) and deep-sea (2,000-6,500m).

The ARC Centre of Excellence for Environmental Decisions (CEED) and BioSciences researchers Associate Professor Brendan Wintle, Dr Gurutzeta Guillera-Arroita, and Dr José Lahoz-Monfort have particular expertise in the statistical methods used in the study.

Tiny brittle star, Amphipholis linopneusti. Picture: Caroline Harding

Tiny brittle star, Amphipholis linopneusti. Picture: Caroline Harding

“Our major finding is that patterns of biodiversity in the deep-sea differ from those on land or shallow water,” says Mr Woolley, who is currently completing his PhD with CEED.

“The number of species peaks in tropical regions on land and in the sea down to 2000 metres. There are more species per square kilometre near the equator than there are in polar regions. In the deep-sea however, the number of species peaks at temperate latitudes, (between 30 and 50 degrees south and north).

“Deep waters off southern Australia, New Zealand and the North Atlantic are diversity hotspots.

“This surprising difference in diversity patterns can be explained by the amount of energy available to support life.

“Ecosystems on land and in shallow water receive energy from the sun – this energy is highest in tropical areas, which therefore support a higher number of species,” said Mr Woolley.

“In the deep sea however, very little light or heat from the sun penetrates. Energy comes instead from microscopic animals and plants (plankton) that grow in the warm surface waters and ultimately sink to the seafloor to be consumed by hungry creatures living in the dark. There are more plankton in the southern and northern oceans than near the equator.”

Brittle star, Sigsbeia oloughlini. Picture: Caroline Harding

Brittle star, Sigsbeia oloughlini. Picture: Caroline Harding

The team hopes that as data from around the world is collected, global maps of seafloor diversity will continue to become more detailed, increasing our knowledge about the distribution of marine biodiversity. Such maps are crucial for managing the conservation and sustainable use of the deep oceans.

The United Nations is currently negotiating a new international agreement for the management of the high seas through the UN Convention on the Law of the Sea. This research will help inform this process by identifying marine biodiversity in areas beyond national jurisdiction.

 

This article was first published on Pursuit. Read the original article.

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