Tag Archives: Taxonomy

The road to degradation: is “naming all the species” achievable or even desirable?

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In 2013 Mark Costello, Robert May and Nigel Stork published a review paper in the journal Science called “Can We Name Earth’s Species Before They Go Extinct?”  It’s a paper that I discuss with my students in their final year Biodiversity and Conservation module, and it always generates a lot of interest, and it’s has been well cited since it first appeared (143 citations* to date according to Web of Science).  There was an interesting response by Mora et al., with a riposte by Costello et al., but overall the original paper has been rather influential in framing some discussions about taxonomic effort and description of species, and the idea that we can “name everything” with additional resources.  At the end of the review Costello and colleagues answered their own question by stating: “We believe that with modestly increased effort in taxonomy and conservation, most species could be discovered and protected from extinction” [my emphasis].

Is their optimism justified?  Can “most species be discovered”?  And what are the implications for how we go about “discovering” these species that are unknown to science?

In my professional life I’ve been fortunate enough to carry out field work with some great colleagues in some wonderful parts of the world, including tropical rainforest and savannah in Guyana and Gabon, mountain scrub in the High Andes of Peru, seasonal dry forest in Australia, montane grasslands in South Africa, Namibian desert, and Brazilian cerrado and Atlantic rainforest.  All of these were sites where non-biologists would rarely venture: off the beaten track and (usually**) away from the typical tourist haunts.  It would be tempting to describe these places as “remote” but really they were not, because they all shared something in common: accessibility.  We were able to reach these sites by traveling along roads, of variable quality, usually in four-wheel drive vehicles.  The roads were often not in good condition, and frequently not metaled, but they were roads nonetheless.

It’s sometimes said that if one were to map the geographical coordinates of plant specimens stored in herbariums such as the one at Kew, you would end up with a road map of the world.  That’s because collecting biological specimens, or carrying out field work, requires us to be able to gain access to an area.  And accessibility usually means roads, unless one is working on the coast or along a river or lake, or have lots and lots of funding to allow teams to be helicoptered into an area (which is rare, but makes for exciting television).  Therefore most collecting of biological specimens is done in areas not far from roads.

So, any initiative that intends to “name all the species” in a particular group is going to require access to the remotest parts of the planet, areas that currently have no roads running through them.

There are still areas of the world that we can consider “remote” and “wilderness”, areas that are more than 100km from the nearest road – as a study published at the end of 2016 demonstrated.  But these are often found in the most biologically rich parts of the planet, for example tropical rainforest and mountainous areas, where we wouldn’t necessarily want to put roads to make them accessible to taxonomists (or even ecologists).  That’s because where roads go, people go, and accessibility to an area is usually followed by exploitation and degradation: illegal hunting, logging, mining, poaching of specimens for sale, etc. etc.

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Now, don’t get me wrong, taxonomy is absolutely vital to the conservation of the earth’s biodiversity.  It also underpins much ecological, bio-molecular and agricultural research and technology.  But the trade off for taxonomists is that they must gather their specimens and data from accessible areas, and that often means roads, and roads mean degradation.

The impetus for this post came from Twitter where a taxonomist highlighted the very good work done by the Virtual Institute of Spider Taxonomy Research (VINT) and described it as an “initiative to discover all spider species of the world in 30 years”.  Interestingly I can’t find that aspiration on the VINT website, but if it exists I’m not sure it’s achievable for spiders or any other diverse group of species, without being able to access parts of the world that are best left un-degraded.  Again, this is particularly true of the tropics where species can have very limited distributions.  A number of years ago an Australian botanist told me about how he was only able to collect some epiphytic Hoya specimens in Papua New Guinea by going into areas of rainforest that had been illegally logged, removing the plants from crowns of the felled trees, with no little risk to his own safety if the loggers had spotted him.  Some of those species might have remained undescribed if the area had not been opened up by a road prior to deforestation.  That would have been a loss for Hoya taxonomy, but surely positive for conservation.

Can “most species be discovered”?  Is this even a desirable thing?  I used to think so, because of the oft-stated view that we can’t conserve what we don’t know.  Now I’m not so sure, for reasons I hope I’ve articulated.  But as always I’d welcome your comments and criticisms.

 

*Including one in the conference: Annual Forum on Grumpy Scientists: the Ecological Conscience of a Nation:Royal Zoological Society, Sydney, Australia.  I’d have liked to have been a fly on the wall at that meeting!

**Usually, but not always: I have a few papers where some or all data collection was done in and around back-packers hostels, hotels, and tourist lodges.  Hey, you take your opportunities where you find them in this game!

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Engaging students with the fundamentals of biodiversity (2) – an assessed plant taxonomy questionnaire

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In my post last week I described “The Taxonomy of Gastronomy“, a first year undergraduate exercise aimed at giving students experience and confidence using scientific names for species, as well as providing an understanding of taxonomic hierarchies and food diversity.  The follow-up to this is an assessed questionnaire that focuses more deeply on plant taxonomy, phylogenetics, and human uses.  Here’s the text of the exercise [with a few annotations in square brackets for clarity]:

 

ENV1012 Biodiversity: an Introduction

Assessed Questionnaire

This exercise is assessed and is worth 25% of your final grade for this module.

The questionnaire is time constrained; you have two hours in which to complete it. Once completed, upload it to NILE using the Submit Your Work folder [NILE is our Blackboard e-learning platform]. Any questions, please ask or email me if I’m not in the room [email provided – the class is so large that I had to split it across two computer suites].

The Task

At the beginning of this session you will be given the name of a plant family.  Your job over the next two hours is to research that family and answer the questions below. Each of you will be researching a different plant family so by all means discuss what you are doing and collaborate, but everyone’s final answers will be different.

For this exercise focus on the following websites:

The Tree of Life Project: http://www.tolweb.org/tree/

Wikispecies: https://species.wikimedia.org/wiki/Main_Page

Wikipedia: https://en.wikipedia.org/wiki/Main_Page

Note that we don’t usually recommend Wikipedia as a source of information, but much of the taxonomic material on this site is quite good because it is produced and maintained by experts.

 

The Questions

Be accurate in your answers: you will lose marks for misspelled scientific names, genus and species names not italicised, appropriate use of capital initials, etc.

Do not copy and paste from websites – this will be spotted with the software that we use and your answers will be rejected.

 

  1. What is the scientific name of the plant family you are researching?
  1. Which botanist named the family? Hint – you will find an abbreviation of the name on the Wikipedia page.
  1. Does this family have a common name? If so, what is it? If not, say so.
  1. What is the distribution of the family, e.g. tropical or temperate, New World or Old World, global?
  1. Fill in this blanks on this taxonomic hierarchy:

Kingdom:  Plantae

Order:

Family:

Subfamilies (if present):

Tribes (if present):

 

  1. What is the estimated number of genera in the family?
  1. Provide the names of up to three of those genera:

a.

b.

c.

  1. What is the estimated number of species in the family?
  1. What mode(s) of pollination do species in this family possess (e.g. wind, animal, water)?
  1. Provide a short description of the human uses of this family (no more than 50 words):

 

Using the Tree of Life site, find and list:

  1. The sister family or families to your family (hint: it’s the family or families closest on the evolutionary tree).
  1. The first “containing group” for your family (may be an unranked, informal taxonomic level).
  1. The next “containing group”.
  1. Keep going until you get to the final “containing group” – where do you end up? [a slightly trick question – everyone ends up at the same place]
  1. State one surprising or unexpected thing that you have learned from doing this exercise (no more than 25 words).

 

My students have now completed this exercise and I was very pleased with the outcome: the average grade was around A-/B+ and no one failed (yet, there are still come non-submissions…).  The answers to question 15 were particularly interesting and included things like: “I had no idea that potatoes and chillies were closely related”, “amazed at the diversity of plants”, “didn’t realise that plants were so fascinating”.

The fact that students were able to do this in small groups, and discuss their findings, yet still produce largely unique answers, added a lot to the enjoyment of this exercise I think.  Certainly there was a buzz in the room while they were researching their answers.  It will be interesting to see what the module feedback is like at the end of term.

The grading criteria for this assessed questionnaire were fairly simple and straightforward:

  1. All questions answered.
  2. Answers are grammatically correct, with appropriate use of scientific conventions, e.g. underlined genus and species names, use of capitals, etc.
  3. Information presented is accurate

 

As always, feel free to comment, make suggestions, and point out errors and improvements.

 

 

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Engaging students with the fundamentals of biodiversity (1) – “The Taxonomy of Gastronomy”

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This term we have started refreshing and reformatting our first year undergraduate modules, partly in preparation for the move to our new Waterside Campus, but also because they were beginning to feel a bit tired and jaded.  We have begun with ENV1012  Biodiversity: an Introduction, a 20 CATS module which mainly services our BSc Environmental Science and BSc Biology programmes.

One of the changes has been to go from a “long-thin” delivery of 2 class hours per week over two terms, to a “short-fat” delivery of 4 hours per week in one term.  The advantages of this, we think, are two-fold: (1) it provides students with a richer, more immersive experience because they are not mind-flitting between different topics; (2) it frees up longer blocks of time for academic staff to focus on programme development, research activities, etc.

For now we have opted to deliver the 4 hours in a single session.  That’s quite a long time for the students (and staff) to be taught (teaching) but it’s punctuated by short breaks and includes a lot of practical work in the field, lab, and computer suite.

One of the aims of ENV1012  Biodiversity: an Introduction is to engage the students with the use of taxonomic names of species and higher groups, familiarise them with the principles of biological classification, why this is important (and why it underpins the rest of biology and much of the environmental sciences), and so forth.  Building confidence in how scientific names are used, and the diversity of species that all of us encounter on a day-to-day basis, are important aspects of this, and I developed a couple of new exercises that we are trialling this term which are focused on these areas.

The first one is called “The Taxonomy of Gastronomy” and was partly inspired by a conversation I had with Steve Heard when he posted about The Plant Gastrodiversity Game.  It works like this. I begin with an interactive lecture that sets out the basic ideas behind taxonomic classification and its importance.  After a short break the students then begin the hands-on part of the exercise.  Working in groups of three they use a work sheet that lists 10 culinary dishes, including:  fried cod, chips, and mushy peas; spotted dick; spaghetti bolognese; Thai green curry with tofu & okra; chocolate brownies, etc. (this can easily be varied and adapted according to needs).

The students’ first task is to find a recipe online for each dish.  For each biological ingredient in that dish, they list its common name and find its taxonomic family, genus, and species (italicising the latter two, as per taxonomic conventions).  I emphasise that it is important to be accurate with names as they will be doing something similar in a later assessed exercise.

This takes a couple of hours and then they feedback their results in a debriefing session, including finding out who had the longest list of species in a meal – the winner was 17 species in a moussaka recipe, with a Jamie Oliver fish and chips recipe coming a credible second with 12!  We also discuss particularly common taxa that turn up frequently, for example plant families such as Solanaceae – the relatedness of tomatoes, chillies, peppers, potatoes, and aubergine, the students found very intriguing.

By the end of this exercise the students will have gained familiarity with researching, understanding, handling, and writing scientific names of species and higher taxonomic groups.  In addition they will have a better understanding of the taxonomic diversity of organisms that we consume, and their relatedness.  It may also have encouraged them to try out some new recipes!

If anyone wishes to comment or add suggestions for improvements, please do.  If you’d like to try this yourself with your own students feel free to adapt it to your own needs, though an acknowledgement somewhere would be polite.

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Filed under Biodiversity, Biodiversity and culture, Personal biodiversity, University of Northampton

Something for the weekend #3

The latest in a regular series of posts to biodiversity-related* items that have caught my attention during the week:

 

  • A new report by WWF documents over 1000 new species discovered in Papua New Guinea between 1998 and 2008, and the risks to their survival from logging and other human activities.

 

  • How does history inform ecological restoration?  Ian Lunt has a great post on this topic.

 

 

  • In the latest in a series of high-profile rewilding initiatives, the conservation charity Lynx UK Trust has launched a survey to elicit public views on their proposal to reintroduce these large cats – make your views known here.

 

 

  • The University of Northampton’s annual Images of Research exhibition is available to view online and you can vote for your favourite three images.  Now I’m not saying that you should vote for “An ecosystem in a cup”.  But you could.  If you wanted to.

 

  • Staying with the University of Northampton, the Press Office has made me the first Staff Blogger of the Month.  Which is nice.  Not sure exactly how many other staff blog, but my impression is that it’s not many so it may be only a matter of time before I’m honoured again.  I thought I’d share what I wrote when asked about why I blog:

“Why do I blog? The main aim is to communicate the science relating to the importance of biodiversity and ecosystem services (and therefore why we need to conserve species and habitats) to as wide an audience as possible, including the general public, students, non-governmental organisations, businesses, and policy makers, as well as other academics.  Some of that communication relates to examples from our own research, and I also draw on the work of others in the field.  A secondary aim is to give my students a flavour of what it is that I actually do in the rest of my job: teaching is only part of the story!”

 

  • All of which links nicely to the recent post by Jeremy Fox, and subsequent discussion, over at Dynamic Ecology about whether science blogging (and specifically “ecology” blogs, whatever they might be) is on the decline.  For what it’s worth, I don’t think it is and I also think that the definition of what “ecology” blogging actually covers is much wider than the discussion suggests.

 

Feel free to recommend links that have caught your eye.

*Disclaimer: may sometimes contain non-biodiversity-related links.

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Filed under Biodiversity, Personal biodiversity, University of Northampton, Urban biodiversity