Conducting and publishing my first systematic literature review – A unique experience

PROTECTS project PhD student Elena Zioga reflects on her experiences publishing her first paper…

To begin with, YAY, excitement all over the place!!!

Frankly, when I started my research quest back in September 2018, I was not thinking that it would end up being a paper for publication. It started as a literature review, in order to set up the basis for my PhD research on characterizing pesticide residues in floral resources for bees. Upon discussions with the rest of the members of the project in which I am involved (PROTECTS), we decided that there was a need for establishing the existing knowledge in terms of the pesticide residues ever found in pollen and nectar collected from plants. We wanted to know which compounds have been evaluated until now, and what their exact concentrations in pollen and nectar were. This knowledge would be very helpful for the risk assessment studies for pollinators. Soon, we discovered that instead of finding an answer to that specific question, we could also identify major knowledge gaps in the area; gaps that had to be highlighted.

There was a need for not only recording what was already known in the field, but also identifying the major gaps by summarizing results from a diverse inter-disciplinary research combining the research areas of bee biology, ecotoxicology, botany and chemistry. Setting up a basis not only for my PhD thesis, but also for future residue studies requested for a Reliable, Quantifiable and Reproducible systematic literature review. Hence, with my supervisor Jane Stout (Trinity College Dublin) and co-supervisor Blanaid White (Dublin City University), we started working towards that. One of the most important steps of this process was the beginning of the literature search and making sure that our question was clear and specific, in a way that our search terms over the various databases were well identified and established. Lesson learnt – During this stage, EVERYTHING need to be recorded, or everything will be forgotten. Try to keep notes of how, when and why you did things, as you will soon need this information regardless using it or not.

Since I had a 50 year period of interest, and given the technological advance during all these years I had come across studies with various methods of chemical analysis. As there were not many studies on the topic, I was trying to include as many as possible, but in the meantime I had to critically evaluate whether the studies contained the information we needed and in a form that could be further processed in our analysis. Lesson learnt – Critical thinking, Strike 1.

Once the studies relevant to our research question were identified, we were ready to proceed with the extraction of the data of interest. This is the stage where Excel was our best friend. As such, it supported us and was there for us, but also did not hesitate to ‘slap’ right in the face when wrong decisions were made. Lesson learnt – Excel is wise, take full advantage of its opportunities, Critical thinking, Strike 2. Make sure you name your columns in a strategical way and then fill the rows with all the essential information provided by the studies of interest. Keep in mind you research question, as this is the best guide during his stage.

When the data are collected in an excel layout they can be easily quantified. This is where I got to explore them and tried to see how and if they could be further analyzed in order to get more information out of them. Given the limited amount, the nature and the knowledge gaps of the residue studies, we could not perform a meta-analysis. However, the data indicated that we could go a bit beyond of just reporting the major gaps and the median values of the compounds found in pollen and nectar. That was when Dr Ruth Kelly, who was a Postdoc in our lab at the time, came to the rescue, joined our paper and offered her valuable information and skills on stats. It turned out that even though we were restricted to few compounds (neonicotinoid insecticides), we could identify a positive relationship between their residues found in pollen and nectar of plants. This is very important as it means that for those compounds, we could use the concentrations found in pollen to predict those in nectar. Taking into account how difficult nectar collection is and that it is slightly easier to collect pollen, this would facilitate future residue studies. Also, this could imply that this relationship may apply to more compounds belonging to other chemical groups (e.g. herbicides, fungicides and other non neonicotinoid insecticides), pointing out new roads for research. Lesson learnt – Listen to your data!

Once we got the results from the data analysis, all I needed to do was to think of the best way to present them to the rest of the scientific community. I tried to create a story that would make sense to other people, keep them interested while reading the article and potentially positively influence the future research of some of them. All was going great until we reached to a point where I was asked to reduce the size of my discussion part as I had written too much… For example, a discussion of 10 pages is a discussion good for a thesis, but can be tiring for a paper – very true. Managing to reduce that to six pages was a great challenge for me. Lesson learnt – Critical thinking, Strike 3.

While writing this paper, there were times I reached what seemed to be a dead end or this crucial spot were decisions had to be made. This is when my supervisors and/or co-authors of the paper came as my saviors and gave the solutions to all my problems. Lesson learnt – It is OKAY to not being able to answer to some questions. Remember we are here to learn. Discuss about your thoughts and worries with people that are more experienced, and are willing to help you.

To me, a paper is always a team effort. The better the teamwork, the better the outcome. From the contribution of the co-authors, to the discussions with the people of your research project, from the discussions with the rest of your lab members to the comments of the reviewers, every single person adds a small or a larger stone to it. A big ‘THANK YOU’ to my co-authors, to all the PROTECTS’ group that is so supportive and especially to Dara Stanley (University College Dublin) who triggered us in starting this paper, to the rest of the plant-insect interactions lab members for the fruitful discussions, and to all those who contributed in making this paper ready to be published!

Lesson learnt – Good things can happen through good collaborations!

In case you are interested in reading the full paper entitled ‘Plant protection product residues in plant pollen and nectar: a review of current knowledge’, here is the link:

Elena graphical abstract
Graphical abstract summarizing the paper

You may follow the general updates on our research through our project’s twitter account @ProtectsProject and my personal account @ZioElena.

For an excellent guide on how to conduct a systematic quantitative literature review visit the following link:




Monitoring habitats? The simplest approach is not always the best

From billabongs to vernal ponds and from wadis to turloughs, seasonal wetlands occur all over the world and are home to vulnerable freshwater species. According to the most recent World Wildlife Fund Living Planet Report, freshwater ecosystems are suffering more severe losses than terrestrial or marine ecosystems, with population abundance declining by 83% between 1970 and 2014. Effective monitoring is a crucial element of biodiversity conservation, and a small change, widening the taxonomic range of indicator species used in habitat assessments, could make a big difference for freshwater biota.

Seasonal wetlands experience frequent disturbance, which can interfere with the effectiveness of indicator species in habitat monitoring. In our paper, we showed that the simplest monitoring approach can yield misleading results.


Biodiversity, the set of organisms living on earth in all their variety, is in crisis.  International organizations such as the IPBES, FAO and leading scientists have repeatedly sounded the alarm, pointing out that the range and abundance of life forms are decreasing rapidly, and that we may lose the multiple benefits derived from nature, including pollination.

To combat biodiversity loss, conservation measures have been put in place around the world, and the European Union Habitats Directive is one such measure. The Habitats Directive aims to conserve over 230 selected natural habitats which occur in 28 countries in Europe through a network of protected areas. As with any good conservation program, a monitoring system is in place to assess its effectiveness, and in 2019, the status of protected European habitats was reported. The scale of the work is enormous, and a detailed inventory of all species and environmental variables affecting each habitat would be prohibitively expensive and time-consuming. Using selected species as proxies or indicators of overall habitat condition offers a more achievable means of assessment and this approach is incorporated into the Habitats Directive.

The use of indicator species exploits a trend for patterns of diversity or species composition across multiple taxa to coincide. We call this cross-congruence, and it enables us to infer the conservation status of a habitat by assessing a small number of key species. However, cross-congruence is weaker in habitats which have experienced human disturbance, and little is known about diversity patterns in habitats which are characterized by regular natural disturbances. A disturbance is likely to reduce cross-congruence if different taxa respond differently to a change or if they exploit different resources in a habitat. If diversity or composition of different taxa using the same habitat does not coincide, then using indicator species could lead to misleading habitat assessments. Indicator species are widely used in conservation assessment, and so this is an issue that could affect protected habitats around the world.

We aimed to test whether diversity patterns across different taxa were consistent in a habitat characterized by frequent natural disturbance, and whether a habitat assessment reliant on plants as indicator species reflected the provision of resources for organisms with contrasting habitat requirements. We focused on dune slacks: isolated freshwater wetlands occurring between the ridges in coastal sand dunes. They were an ideal model habitat because they are protected under the EU Habitats Directive, and so in many cases experience low human disturbance, but they flood in winter and dry out in summer, leading to regular natural disturbance. Because dune slacks can be small, we surveyed two small-bodied invertebrates which have been recommended as indicator species in the past (snails and water beetles) and compared their diversity and composition to that of plants, which are generally used as indicator species for the habitats protected under the EU Habitats Directive.

A water beetle in a slack at Kincasslagh, Co. Donegal, Ireland. Image courtesy Aoife Delaney

Plants, snails, and water beetles have shown cross-congruence in pond systems elsewhere, but they have contrasting environmental requirements, so they may respond differently to flooding and desiccation. We also carried out a habitat assessment based on the methods used in the EU habitat assessments for Irish dune slacks, which incorporates plants as indicator species.

We found no evidence that the species richness or diversity of snails, water beetles and plants were correlated in dune slacks, and nor could the composition of plant species be used to predict the likely suite of beetles or snails at a site. No significant difference could be detected between the diversity or composition of snails or water beetle species at sites that passed and failed the habitat assessment.

In this case, cross-congruence between plants, snails and water beetles was not observed and a habitat assessment based on indicator species from a single taxonomic group, plants, failed to deliver information on the snail and water beetle species in dune slacks.

The contrasting biological requirements of the three species groups has probably led them to respond differently to disturbance. For example, six sites failed to flood during the year of survey, even though it was a wetter year than average, and three of these passed the habitat assessment. The water table may have risen sufficiently close to the surface to support the typical wetland plants, but flooding is vital for aquatic snails and beetles to persist, and the failure of a site to flood will dramatically change the snail and water beetle assemblages present in any year when flooding does not occur. Drying out is a major threat for dune slacks in the EU and it is of concern that the current conservation assessment methods are not adequate to detect sites which are at risk, as the damage may be permanent by the time the plant composition has changed.

The habitat assessment is intended to identify sites which contain habitat of good quality and those which require interventions to improve their habitat quality. We found ten species listed as vulnerable on the Irish Red Lists for snails and water beetles in sites that failed the habitat assessment, and they could be lost if management aimed at restoring the plant community is put in place. Because the diversity of plants, snails and water beetles in dune slacks are not congruent, the current habitat assessment methods put them in danger of misguided conservation interventions that could have a negative effect on biodiversity.

This might seem to be bad news, but there is a potential solution: selecting indicator species from taxa with contrasting biological requirements is likely to make the assessment more robust and reliable.

These findings are described in the article entitled Principles of cross congruence do not apply in naturally disturbed dune slack habitats: Implications for conservation monitoring, published in the journal Ecological Indicators.

A previous version of this article was originally posted on Science Trends

About the author: Dr Aoife Delaney completed a PhD in dune slack ecohydrology, supervised by Drs. Jane Stout and Catherine Coxon at Trinity College Dublin

All-Ireland Pollinator Plan Engagement Survey

We need your input! TCD MSc student, Lizzy Elli, is researching motivations and engagement with the All-Ireland Pollinator Plan…

The All-Ireland Pollinator Plan (AIPP) was launched in 2015 and the support for it has been phenomenal. As the plan reaches the end of its first five-year phase, we’re trying to find out why people have got involved.

The AIPP Engagement Survey will generate data for Lizzy’s research project, which aims to elucidate user motivations to engage with pollinator-friendly activities. The survey is targeted at those who have already participated in activities outlined by the AIPP. Critically, this research will enable us to understand what it is precisely that motivates people to act when it comes to pollinator friendly activities.

This research is not only useful for developing phase II of the AIPP, but it has far reaching applications across various sectors such as businesses, schools, and others by illuminating how and why people interact with certain activities. With the information obtained from this survey, we can create more tailored action programs that are more effective and user-friendly. Specifically, the results of this study will be used to produce an even more engaging and efficient AIPP in phase II, enabling us to help protect Ireland’s threatened pollinator species!

The study is conducted with the National Biodiversity Data Centre. The survey is anonymous and data collected will be used for the sole purpose of this study.

If you have any interest in the AIPP, please click on the link below and take the survey! It only takes 5-10 minutes to complete and the responses will be used to create a more pollinator-friendly Ireland!

Thank you!

All Ireland Pollinator Plan logo


Biodiversity in West African parklands promotes pollination of shea

This blog by Aoife Delaney was first published in The Applied Ecologist.

With demand on shea parklands increasing, We explored the pollination services to shea and how we can better support this resource of both ecological and economic importance. Our new research was recently published in Journal of Applied Ecology.

P1010379Shea parklands occupy over 1 million km2 in the Sudano-Sahelian semi-arid zone of sub-Saharan Africa, from Senegal in the west to Uganda in the east, and are home to up to 112 million people.  In this ancient form of agroforestry, trees of value to humans are scattered throughout cultivated fields and fallows.  The trees are not generally planted, but specimens are retained when fields are cleared after fallow periods that have traditionally lasted up to 15 years.

The dominance of shea trees in parklands of West Africa reflects their value to society.  The fruits ripen at a time when there are few food sources available, and the butter derived from shea nuts is the primary cooking oil for 88% of rural dwellers in Burkina Faso. It has been estimated that about 10kg of shea butter is consumed per person every year in the shea zone. Given that 20kg of fruit may be expected to yield 1.5kg of butter, the collection and processing of shea fruits requires considerable human effort, and this effort is almost exclusively furnished by women. In most households, the women who collect and process shea fruit own any related income, and they are more likely than men to set aside money for educating children in the family.

Today, shea parklands face unprecedented changes: population density in many parts of the shea zone has increased and the expectation of financial return from farming has grown. Fallow periods have become shorter as there is more demand for land in cultivation. With less time for regeneration, fewer saplings remain when fields are cleared. Simultaneously, the international market for shea butter is increasing, prompting attempts to commercialise shea cultivation.  Now more than ever, it is vital that we understand the ecological services that support fruiting of shea.


Shea benefits strongly from pollination by insects, primarily bees, to produce fruit.  This link between shea trees and bees means that shea is connected with conditions in the wider environment because bees need a range of resources to survive.  We investigated the relationship between pollination services to shea and the diversity of trees and shrub species in cultivated fields as well as the amount of uncultivated habitat near the fields. We found honey bees more frequently, and other bees in greater abundance, in sites with a greater diversity of trees and shrubs.  We also found that fruit production of shea was limited by lack of pollination, and that this limitation was greater at sites with less tree and shrub diversity.  These findings show that more pollination occurs in fields with a greater range of trees and shrubs. This might be because a location that has a wide range of different species is likely to contain a variety of plant-based resources used by bees, like nesting sites, pollen, nectar and resin, throughout the year.

Unexpectedly, given the role of local site-level diversity in driving pollination service, natural fruit set was lower at sites close to larger areas of uncultivated land. However, this may be because shea is a food source for fruit-eating wildlife including birds and mammals that might be more prevalent in larger, uncultivated areas. Thus although local biodiversity promotes pollination, and landscape biodiversity may promote natural levels of frugivory.  Since only 42% of shea fruit is estimated to be harvested by people each year, this leaves a share for nature, but intensification of shea exploitation needs to consider both these biotic interactions.

Shea fruit represents an important ecological, societal and economic resource, and if there were more pollinators in the landscape, more fruit would be produced. Conditions beneficial to both honey bees and other bee species should be fostered to maximise pollination. We recommend that pollination services to shea are supported by maintaining a diverse assemblage of woody species in parklands. Our findings corroborate existing research, showing that the ecosystem services provided by tree and shrub diversity support the well-being of millions of people living in the Sudano-Sahelian zone of West Africa.

Read the full, open access article, Local‐scale tree and shrub diversity improves pollination services to shea trees in tropical West African parklands, in Journal of Applied Ecology.

See also EurekAlert and PhysOrg articles.

About the Author: Aoife Delaney was a postdoc based with Jane Stout in the Plant-Animal Insect Interactions Research Group at Trinity College Dublin. She worked with Juliet Vickery in RSPB on Building resilient landscapes and livelihoods in Burkina Faso’s shea parklands, led by BirdLife International, funded by the UK Government’s Darwin Initiative.

Bee orchids: habits and habitats in Ireland

Bee Orchids have some of the most fascinating and wonderful flowers of all plants in Ireland. They are relatively rare, but have been recorded popping up in the most unlikely sites recently – e.g. on roadsides where regular mowing regimes have been changed (e.g. from Co. Cork and Kerry in 2020), and in sites managed according to the All-Ireland Pollinator Plan (e.g. in Waterford). In fact, my motivation to write this blog was a photo sent to me by former postdoc Ruth Kelly, who just found a specimen in a scruffy site next to a railway line in Co. Armagh, and my mum, who has them growing in her 1970s housing estate lawn!

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Bee Orchid (Ophrys apifera) flowering in Donegal coastal grasslands (photo: J. Stout 2014)

The unusual looking flower that gives this plant its name (Ophrys apparently comes from the Greek for “eyebrow” and apifera from the Latin meaning “bee-bearing” or “bee-bringing”) has evolved as as a result of its pollination system, which relies on sexual deception. The flower looks, feels and smells like a female bee (to a male bee) who is attracted, and attempts to copulate with the flower. In doing so, he unwittingly picks up a packet of pollen (orchid pollen is packaged into pollinia), and when he gives up on the current flower, and moves on to be deceived by another, he transfers it. Hence the plant disperses its pollen to other bee orchids. This pollination mechanism is known as “pseudocopulation”.

Although the Ophrys apifera flowers doesn’t look, feel and smell like bee to us, it does give enough “female bee” signals to fool the males – the “furry” texture of the rounded lower petal that looks and feels like a bee’s abdomen whilst she forages from the pink bloom, and the iridescent patterns that catch the light in a similar way to the folded wings of a foraging bee. Each of these signals on their own may not fool a male bee, but the flowers also emit a scent that mimics the female pheromones (see the wonderfully titled paper by Florian Schiestl “Orchid pollination by sexual swindle“). And this is what seals the deal. In fact, research has shown that the scents emitted by a closely related species (Ophrys exaltata) are not a perfect mimic of the female bee pheromones, but are actually more attractive to the male bees than female bees themselves!

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The flower that pretends to be a bee (photo: J. Stout 2014)

The genus Orphys contains a broad range of species across Europe, north Africa and western Asia, each of which has evolved specific signals to attract particular species of insect pollinator. The only other species from this genus present in Ireland is the Fly Orchid Orphys insectifera, which is found in a limited number of calcareous wetland sites (fens, peaty depressions in limestone pavements, and turloughs) in the midlands and west of Ireland (in England it’s found more often in woodlands and scrub) and, despite the name, attracts digger wasps to its flowers.

The Bee Orchid Ophrys apifera is widespread in central and southern Europe, but at their northern limits in Ireland and Britain. And here in Ireland, where flowers appear in June and July, we don’t have the bees that these orchids have evolved to fool (solitary long-horn bees, Eucera longicornis). So instead, this species has evolved the ability to self-pollinate in areas where the pollinators are not present. This occurs as the pollinia (the yellow blobs hanging from the top of the flower entrance) swing freely and either contract or bend as they age, or a gust of wind can blow them onto the stigmatic surface (as in the picture above).

Bee Orchids long been know from botanical hotspots like the Burren in Co. Clare and Bull Island in Dublin, and this perennial species tends to be found in open, semi-dry grasslands on limestone, and calcareous dunes. It’s a protected species in Northern Ireland, but not on the Floral Protection Order in RoI. Bee Orchids colonise sites disturbed by human activity, like roadside verges, old quarries, gravel pits and in urban settings. They prefers open habitats, and are out-competed by shrubs and trees if a site becomes overgrown. Thus to maintain populations of Bee Orchids, mowing or grazing needs to occur at the end of the season, and the cuttings removed.

Like many orchids, Bee Orchids form symbiotic relationships with mycorrhizal fungi, which extract nutrients from the soil and transfer them to the plant via its roots. The use of fungicides could reduce the prevalence of these mutualists, which may limit where the bee orchids can grow. Other pressures on Bee Orchid populations include ploughing of grasslands, and if mowing occurs during flowering or before the tiny, wind-dispersed seeds have formed and been released, populations can decline.

Despite their remarkable flowers, the plants can be easily overlooked unless you are looking for them. But because the flowers are so bizarre, and can’t be confused with anything else, Bee Orchids can excite even the least botanically minded people.

mum's bee orchid
Bee orchids growing (and protected ) in my mum’s lawn! (photo: V. Stout 2020)

For more information see “The Orchids of Ireland” by Tom Curtis and Robert Thompson or “Ireland’s Wild Orchids – a field guideby Brendan Sayers and Susan Sex.

Edit: coincidentally this wonderful video by John Feehan was published on the same day as this blog – part of the Wildflowers of Offaly series.

About the author: Professor in Botany, Jane Stout leads the Plant-Animal Interactions Research Group in Trinity College Dublin, and teaches botany, entomology and plant-animal interactions to undergraduate students.