Old collection scale insect slides and the power of confocal microscopy

Following a tweet I saw today on Plecoptera slide collection, I became nostalgic of scale insect collections.

Scale insect descriptions and identification are done using mounted material of stained insect cuticle. Because both males and females don’t have very sclerotized cuticle, they become transparent and outer structures are very easy to observe with a light compound microscope.

An example here, we have wax scale insects on a leaf (top left). After removing the inside to keep only cuticle for staining and mounting, we can have a better view of micro structures (top right). This helps making descriptions illustrated by diagrams (bottom).


In the past, male samples were not mounted or if they were, the quality of mounts was not as good as female samples. This is mostly because males being ephemeral, they were not used for identification or description. There are however quite a few old slide mounted males in collections and especially for species that are difficult to find, they are in my opinion, quite valuable to study for phylogenetic purposes.

When I was working on a phylogenetic study of scale insects, I spent a lot of time examining male samples in old collections. Knowing that males are so rare compared to females, finding an old slide mounted male of a rare species was like finding a treasure.

For a couple of years, I focused on fossils and male morphology of the ensign scale insects (Ortheziidae).  So I found slide mounts for Ortheziidae males but some of them couldn’t be observed clearly because the cuticle was not cleared properly. Using a traditional light compound microscope, it is just impossible to look at details of setae and secretion pores.

During my master’s degree, I worked in the Natural History Museum in Paris, and my supervisor showed how to unmount samples, and reprocess them for clearing and staining. But these Ortheziidae males were rare so I tried another alternative: confocal scanning laser microscopy.

So here it is:


A lot of surface structure were easily revealed at 633 nm. This is not surprising as normally, staining is made with fuchsin acid, its emission wavelength is 630 nm.

So how much detail can we actually see?

These are abdomens of mounted samples. Setae and secretion pores are easy to see.Screen Shot 2018-04-16 at 19.56.45

When you look more closely, it is actually quite incredible how much detail can be captured! Screen Shot 2018-04-16 at 19.57.23

I think confocal imaging is a great non-invasive option to work on old collection samples, especially ones that are slide mounted, obscured and rare. Although not every place has a confocal microscope (especially museums), the American Museum of Natural History is equipped with a Zeiss LSM710 which was really handy!

Do you know any confocal images of old collection slides? I would love to see them!




News about my research: Evolution2018 conference and E93 manuscript available on BiorXiv

Hello everyone!

Spring is (almost) in Edinburgh, and here are some news on my research activities!

This is an update that I will be presenting a talk at Evolution 2018 in Montpellier this summer in the symposium S-35 Combining fossils and phylogenies in studies of diversification organised by Fabien Condamine and Daniele Silvestro.

Combining fossils and living species to better understanding scale insect evolution was the main work of my Ph.D but even if I have since switched my research activities, I intend to continue on working on this project as there is still more data to acquire! Getting a more stable dated tree of scale insects will help to answer questions on their evolution and adaptation.

Additionally, I just submitted a manuscript on mealybug female neoteny and E93 transcription factor with links to the juvenile hormone. This work was conducted at Nagoya University where I am still collaborating on examining mealybug metamorphosis in the context of the juvenile hormone.  You can find a preprint on BiorXiv.

Insect-fungus symbiosis: a scale insect feeds her own roof!

Scale insects are often associated to fungus. Females secreting honeydew trigger sooty mold growth and harm the host-plant. Induced undesirable sooty mold on plants makes scale insects some of the most damaging phytophagous insects.  For instance, Cryptococcus fagisuga, a felt scale insect living on beech trees is associated to a fungus called Neonectria coccinea that will grow from the holes created by the insect’s puncture hole from which it feeds. Ultimately, the mold growth becomes more lethal to the tree than the insect. This is so true that I remember my Master mentor telling me that beech trees have almost disappeared from Paris because of this species!

Sooty mold are also harmful to scale insects, as the female secreting honeydew are sessile and they would literally die in their own moldy poop. This is when ants comes into play as essential mutualistic animals: by profiting from scale insect honeydew droplets as a food source, ants naturally clean their secretive waste, preventing sooty mold growth.

Images showing the fungus structure in which the mealybug lives in (left) and details of fungus mealybug interaction (right) . Source: modified from Gavrilov (2017)

In an extraordinary situation, a species of scale insects from the mealybug family (Pseudococcidae) has taken advantage of mold and developed a unique symbiosis with a fungus species. Orbuspedum machinator, a newly described species from bamboo twigs of Thailand, has legless females and uses hyphae of a fungus Capnodium species to make herself a roof. In exchange, the mealybug secretes honeydew and feed the fungus.

A win win situation.


Hypothetical scheme of the formation of a fungal domicile by Orbuspedum machinator gen. et sp. nov. (Gavrilov 2017)



Open access: Gavrilov (2017) An amazing symbiosis between an animal and a fungus in a new species of legless mealybug (Insecta: Pseudococcidae)


Manuscript self-archiving #1: many questions!

Hello all!

If you have read the Preprint , you know that I am trying to act and become 100% open access with my manuscripts. I made a list of the publications with links to the PDFs available online without a paywall (if the paper is open access or available in other websites) but there are still a few publications that require a subscription to the journal.

I thought it would be interesting to write about my “becoming open access” process as it seems that it will be tricky (but I am sure feasible) for a few reasons:

1-  Which version of the manuscript is acceptable to make a preprint of when the manuscript has already been published?

  • Should I use the first submission version (but sometimes major changes have been done before the second submission)?
  • Can I make a preprint of the resubmission (without the publisher’s proofreading)?
  • Or can I make a preprint of the last version of the manuscript before they prepared the layout?

2- Are there any publishers that do not allow at all to have a preprint version of my work after I published it?

For instance, what does that mean??

Screen Shot 2018-01-19 at 14.41.19.png

Please don’t judge me for signing things I don’t understand, I was a naive Ph.D. student that wanted to have a publication (Okay you can judge me….)



New research life in Edinburgh: fieldwork in California, blogging about nature crazy sex life and more

2017-04-11 11.54.31
Vine mealybugs in North California vineyard

Hello everyone,

A lot has happened since I moved to Edinburgh. Here are the main updates:

  • I am currently carrying out fieldwork in California until May, and looking for obscure mealybugs with B chromosomes. Follow me on Twitter!
  • In August, you will see me at ESEB2017 in Groningen, where I will present my work on scale insect adult metamorphosis.

Why should biologists use GitHub?

Screen Shot 2016-05-08 at 3.45.28 PM
from GitHub repository here

Today, all biologists use computers on a daily basis, produce and analyse data. A lot of us now have to learn programming (even just some bits of it).

I am not a computer scientist/engineer, and I am far from a bioinformatics person (yet), but I have started to discipline myself to make my published research as reproducible as possible and this is not only by depositing DNA sequence data to NCBI, but also analysis pipelines and command lines made available to the public on GitHub.

GitHub is a great public repository hosting service for publishing programming source code, but it can also be used to detail your analysis pipeline and code, and even create tutorials on softwares or pipelines for others.

For example, the Trinity tutorial from Brian Haas was a life saver for a biologist like me that had never touched any next-generation sequencing data.

As a biologist, to support my recent publication on scale insect phylogenetics, I created a GitHub repository that details all the steps and command lines in MrBayes and R analyses. This provides transparency to the reader and more rapid reproducibility.

Tip: If you are worried about your analysis pipeline or data being online during the manuscript review process, academic researchers can apply for free space for 5 private repositories. For more information, check here.

Nowadays, a lot of biologists will come to work in a multidisciplinary environment, and it implies learning new skills. In bioinformatics in particular, workshops are available but the internet is a great resource to learn skills by ourselves and GitHub can help both learning how a software works, but also making the details of informatics methods available to other biologists that are also learning how to use these softwares (from command lines for de novo assembly using Trinity or making a simple plot with R).