Last month I attended the Numerical Analysis of Biological and Environmental Data course at University College London (UCL) in order to decipher which techniques of multivariate data analysis would be useful to apply to my data from Lake Bosumtwi (Ghana). The course was led by Dr Gavin Simpson (UCL) and Prof. John Birks (University of Bergen), both of whom are well experienced in quantitative palaeoecology.
The course provided an introduction to the methods, guidance as to when to use the techniques and then outlined the assumptions, limitations and strengths of the various methods. The need to fully understand the techniques applied before attempting to critically evaluate the results was also strongly emphasised.
The course consisted of lectures covering measures of dispersion, cluster analysis, dendrograms, regression analysis, tree models, gradient analysis, transfer functions, time series and hypothesis testing. Afternoon practical computer classes involved using R, C2 and CANOCO to implement the various techniques covered in the lectures.
Overall the course was a great introduction to statistical analysis which I would certainly recommend for anybody working with complex and noisy datasets. In the next few days I will be using my newly learnt R skills to run indirect gradient analysis such as PCA, CA, DCA and NMDSCAL to search for environmental gradients within my data.
Numerical Analysis of Biological and Environmental Data training couse is an annual event and was held at UCL, on 14-25th May 2012. For more information about the course see Gavin’s website or read his blog From the bottom of the heap.
Time seemed to escape me in April so I have a lot of research group action to report in this post! Here are some highlights…
At The Open University (OU) the research students have all been busy (of course): Natalie presented her 3rd year talk at the CEPSAR student conference and attended a meeting in Durham, Lottie spent two weeks at University College London (Environmental Change Research Centre) learning to become a statistics guru studying the “Numerical Analysis of Biological and Environmental Data” course, while Hayley and Frazer have been writing up their first year probation reports ahead of their mini-vivas next month. Over in Florida Bryan submitted his first PhD paper and has headed off on field work in Peru; and most significantly… I am very pleased to report that Nikki successfully defended her PhD thesis! Congratulations Nikki!
Thinking of PhD I was also pleased to have the opportunity to welcome my PhD supervisor, Frank Mayle, to The OU to give a CEPSAR seminar last week. It was great to be able to show off the labs to Frank at last having promised to invite him down when I arrived at The OU in 2005! He gave a very interesting talk on new archaeological findings from beneath the rain-forest in the Amazon Basin.
Away from The OU a couple of weeks ago I was down at Charles Darwin House for the British Ecological Society meetings committee meeting! We were working on the program for the annual meeting in Birmingham during December this year and it is shaping up to be a very exciting event; keep up to date by following the BES on twitter (@BritishEcolSoc).
CHIRONOMIDAE AS A PALAEO-ECOLOGICAL TOOL
Chironomidae is a family of two-winged flies more commonly referred to as non biting midges. This diverse group of insects have been known for a long time to be sensitive environmental indicators. Early research in the field showed that the trophic status of lakes could be classified according to the characteristic chironomid assemblages found within them (Thienemann, 1922). Furthermore the head capsules of the larvae are well preserved within the sedimentary record. As a result palaeolimnological researchers became increasingly interested in the potential for using Chironomids to track the trophic development of a lake through time by examining the changing assemblages within the accumulated sediments. With geographically close lakes displaying significantly different midge faunas the potential for the insects being used as climatic indicators was dismissed and the following hypothesis became established: Chironomid assemblage composition reflects in-lake variables, e.g. lake depth, pH, dissolved oxygen, trophic status and substrate. However work by Walker and Matthews (1989) demonstrated that temperature was by far the most significant variable in controlling the broad scale distribution and abundance of midge fauna.
Walker and Matthews realised the potential for the non biting midge to be used as a palaeoclimatic indicator from two initial observations. Firstly within the fossil records, as climate began warming following the deglaciation of the northern hemisphere, the relative abundance of taxa associated with cold oligotrophic lakes (Heterotrissocladius) abruptly declined. Secondly they noticed the best analogues for late glacial assemblages were found in modern day arctic and alpine settings. Overall Walker and Matthews concluded that the northern limit of temperate taxon was controlled by cold summer air and/or water temperatures. The southern limit of Arctic species was instead driven by cold oxygenated refugia in the profundal zone of deep, temperate lakes. These temperatures were significant with respect to the insect’s life cycles as many species require critical temperature thresholds to complete pupation and emergence stages.
Since the pioneering work of Walker and Matthews (1989) and others the debate linking Chironomids to temperature has raged. Debate has centred upon what controls chironomid distribution and how suitable, if at all, the insects are in the context of palaeoecological studies. Recently Velle et al. (2010) discussed some key factors which must be considered when working on chironomid based temperature resonstructions.
Below I present some of the debate around the midge-environment-temperature debate; focusing on both midge distribution and identification and the potential of this proxy as a indicator of past environmental and climatic change.
HOW DO WE UNDERSTANT PAST VEGETATION CHANGE?
Our understating of vegetation in the past, and how it has changed through time, comes mainly from the examination of macrofossils (e.g. wood and leaves) and microfossils (e.g. pollen and spores) found in the sedimentary record. The potential for microscopic fossils to provide an insight into past vegetation change on a landscape scale was pioneered by von Post (Von Post, 1916, reprinted 1967) and has been subsequently used to understand changes in regional floras (Godwin, 1956), and address conservation issues (Willis et al., 2007). Analysis of fossil pollen and spores (palynology) is now widely used on late Quaternary timescales to answer ecological questions linking vegetation and wider environmental/climatic change; these include:
Palynological analysis relies on obtaining a sub-sample of the pollen contained within the sediment at a specific depth (time) which allows the vegetation at that time to be reconstructed. This sub-sample is known as a pollen count. To build up a picture of vegetation change through time it is necessary to generate a sequence of pollen counts. The size of the sub-sample (pollen count) required from any particular depth (time period) is dependent on the nature of the vegetation association being investigated and the ecological question being addressed . For example, the amount of pollen analysed to determine if the vegetation was predominantly wooded or grassland is different to that required to provide information on the biological diversity within the vegetation assemblage.
Discussed below are some of the conventions related to choosing an appropriate pollen count size within palynology, with particular reference to the challenges of dealing with diverse tropical floras.
In March the Palaeoenvironmental Change Research Group (PCRG) have been involved with data collection in the labs, training, fieldwork planning (and un-planning) and outreach.
Two notable pieces of pollen data collection have made significant progress this month: 1) Hayley has been working at collecting data to establish what is a suitable pollen count size to assess vegetation change within her highly diverse Amazonina samples, and 2) Lottieis on to about the last dozen samples to complete the overview of 500,000 years of pollen from Lake Bosumtwi (Ghana); an amazing pollen record and an excellent research effort which will be the cornerstone of her PhD thesis! More soon on both these pollen stories as they unfold… In addition, I am pleased to report that the list of taxa within our pollen reference collection has finally been fully digitized – Thank you Jason; details of the >3000 taxa collection will soon be available on the lab web pages.
Also in the lab: Alice Kennedy, working on ‘deep time’ palaeoecology, has identified a bloom in the foraminifera Reinholdella macfadyeni and gigantic Prasinophytes associate with marine annoxia in sediments from Yorkshire. Will be interesting to find out what these all mean at the next lab meeting!
At the beginning of March four of us (Frazer, Hayley, Lottie and myself) attended a First Aid for field work training course run by Mediact. The course was excellent with plenty of useful information and the opportunity to practice techniques such as cardiopulmonary resuscitation (on dummies) and bandaging (on each other). Unfortunately we will have to wait to practice any of the techniques in the field as our planned trip to Ecuador looks likely to be postponed due to injury to one of our members! Get well soon Frazer 🙂 On the up side this should allow me to catch up with the piles of papers I should be writing.
The month finished with an exciting outreach event. I was asked to present our research to the Oxford Geology Group. The event was hosted at the Oxford University Museum of Natural History. It was an excellent day of talks and it was fun to discuss our research with interested people.
Laboratory activity has continued through February with progress on pollen counts (Lottie and Hayley) and chironomid (non-biting midges) picking (Frazer). Hayley also managed to escape the microscope lab for a short period: 1) to commence work on selecting samples from tephras for Ar-Ar dating, and 2) to counduct loss-on-ignition analysis of organic samples to identify the constituents of her sediment. I did not make it on to the microscope 😦
I was however very pleased to welcome Macarena Cardenas back into the lab as a visiting Research Fellow. Maca will be working on the pollen reference collection, assisting with PhD student analysis and continuing to write papers during her renewed association.
Frazer, Hayley and I have also begun planning for field work in Ecuador for April-May. We will be working in collaboration with the Instituto Geophisico in Quito and the plan is to visit the Mera site which Hayley is working on, and to collect lake surface samples for Frazer to examine the midges. In preparation for the collection of midges samples expert, and project co-supervisor, Steve Brooks (Natural History Museum) visited for a day to brief us on how best to do this.
Away from research I have been working on writing exam questions and tutor marked assignments for the level 3 module The geological record of environmental change (S369, to those familliar with OU codes!). Hopefully, I have managed to set some interesting and challenging tasks for our students. . .