Biodiversity in a bird’s nest: DNA as a tool for bird conservation

Researchers employ eDNA to investigate ‘fascinating microcosms’ inside birds’ nests.

Researchers have found that advanced DNA technologies can get a detailed snapshot of insect diversity within a bird’s nest, showing everything from the bird’s last meal to disease-causing parasites.

A bird’s nest. Photo by Farrini

“Birds’ nests are fascinating microcosms, but until now, studies have only examined the living insects that can be seen crawling and flying around the nests,” says Valerie Levesque-Beaudin, lead author on the study and a leading expert in Diptera taxonomy at the Centre for Biodiversity Genomics (CBG) at the University of Guelph (U of G).

With newer DNA-based methods, researchers can pick up traces of environmental DNA to get a snapshot of all the species in these tiny ecosystems. “The analysis of nest contents and environmental DNA, or ‘eDNA’ as it’s called, via metabarcoding helps us to gain more insight into a bird’s diet, parasites, and other factors that could impact a bird’s health and breeding success,” says Levesque-Beaudin.

For the study, published in Metabarcoding and Metagenomics, researchers collected 20 birds’ nests from the 162-hectare Arboretum at U of G. They examined the nests using DNA barcoding to identify insects to species and DNA metabarcoding to look at the entire nest ecosystem.

Organisms leave traces of DNA behind as they move through the environment, and researchers can use metabarcoding to build a comprehensive picture of life in the nest. Metabarcoding pulls all DNA traces in a bulk sample – in this case, parts of dead insects, debris, and dust from birds’ nests. This method differs from DNA barcoding, where a single specimen – an insect in this case – is DNA sequenced to identify it to species level.

The CBG team used emergence traps for a first sweep of the nest’s contents followed by a second, deeper probe using DNA metabarcoding to identify all the species encountered in the nest. Researchers passed the nests through a sieve, collecting insect remains and the dust for DNA extraction. “We not only found insects making a living in the nest, but traces of prey, parasites, and many other things,” says Levesque-Beaudin. “The most unexpected was the amount of information gained on other birds’ species whose feathers were either used for nest building or whose nests were essentially overbuilt by the nesting species.”

A tent-like emergence trap is used to contain and collect insects living inside the nest debris. PHOTO: VALERIE LEVESQUE-BEAUDIN

“This approach has the potential to revolutionize how we study bird nests as a micro-ecosystem. It unravels connections between different ecological guilds within the nest and connections of the birds with their environment, which would otherwise remain hidden,” says Dr. Bettina Thalinger, senior author of the study.

The CBG’s Associate Director of Analytics, Dr. Dirk Steinke, says the study has positive implications for bird conservation efforts. He says his students have already begun looking at American Kestrels, a threatened bird of prey, to find out if there are clues in the nest communities via metabarcoding and if DNA can help scientists determine if lack of prey or increased parasitism could be among the causes of nestling mortalities.

Darwin’s finch, also called Galápagos finch. PHOTO BY CHRIS HO, CENTRE FOR BIODIVERSITY GENOMICS.

Galapagos finches are another species threatened by the avian vampire fly – a parasite that attacks nestlings – and treatments include pesticides. Steinke notes that one of his graduate students has begun using DNA metabarcoding in the finches’ nests to understand better the potential impact of pesticide treatment on the entire arthropod nest community.

Research article:

Levesque-Beaudin V, Steinke D, Böcker M, Thalinger B (2023) Unravelling bird nest arthropod community structure using metabarcoding. Metabarcoding and Metagenomics 7: e103279. https://doi.org/10.3897/mbmg.7.103279

News piece originally published by the Centre of Biodiversity Genomics. Republished with permission.

Taylor Swift, the millipede: Scientists name a new species after the singer

Scientists described a total of 17 new species from the Appalachian Mountains—now published in the open access journal ZooKeys.

Taylor Swift, U.S. singer-songwriter known for hits such as “Shake It Off” and “You Belong With Me”, has earned a new accolade—she now has a new species of millipede named in her honor.

Taylor Swift. Photo by Eva Rinaldi

The twisted-claw millipede Nannaria swiftae joins 16 other new species described from the Appalachian Mountains of the United States. These little-known invertebrates have a valuable role as decomposers: breaking down leaf litter, they release their nutrients into the ecosystem. They live on the forest floor, where they feed on decaying leaves and other plant matter, and in fact, they are somewhat tricky to catch, because they tend to remain buried in the soil, sometimes staying completely beneath the surface.

Her music helped me get through the highs and lows of graduate school, so naming a new millipede species after her is my way of saying thanks.

Derek Hennen

Scientists Derek Hennen, Jackson Means, and Paul Marek, at Virginia Tech, U.S., describe the new species in a research paper published in the open access journal ZooKeys. The research was funded by a National Science Foundation Advancing Revisionary Taxonomy and Systematics grant (DEB# 1655635).

The newly described twisted-claw millipede, Nannaria swiftae. Photo by Dr Derek Hennen

Because of their presence in museum collections, scientists long suspected that the twisted-claw millipedes included many new species, but these specimens went undescribed for decades. To fix this, the researchers began a multi-year project to collect new specimens throughout the eastern U.S. They traveled to 17 US states, checking under leaf litter, rocks, and logs to find species so that they could sequence their DNA and scientifically describe them.

Example of typical habitat for twisted-claw millipedes. Photo by Dr Derek Hennen

Looking at over 1800 specimens collected on their field study or taken from university and museum collections, the authors described 17 new species, including Nannaria marianae, which was named after Hennen’s wife. They discovered that the millipedes prefer to live in forested habitats near streams and are often found buried under the soil, exhibiting more cryptic behaviors than relatives.

The newly-described millipedes range between 18 and 38 mm long, have shiny caramel-brown to black bodies with white, red, or orange spots, and have white legs. The males have small, twisted and flattened claws on their anterior legs, which is the basis for their common name.

The lead author of the study, Derek Hennen, is a fan of Taylor Swift. 

“Her music helped me get through the highs and lows of graduate school, so naming a new millipede species after her is my way of saying thanks,” he says.

Research article:

Hennen DA, Means JC, Marek PE (2022) A revision of the wilsoni species group in the millipede genus Nannaria Chamberlin, 1918 (Diplopoda, Polydesmida, Xystodesmidae). ZooKeys 1096: 17-118. https://doi.org/10.3897/zookeys.1096.73485

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Decade-old photographs shared on social media give away a new species of pygmy grasshopper

While scrolling through iNaturalist – a social network where professional and citizen scientists share their photographs, in order to map biodiversity observations from across the globe – a group of students from Croatia discovered a couple of curious pictures, taken in 2008 in the Peruvian rainforest and posted in 2018. What they were looking at was a pygmy grasshopper sporting a unique pattern of lively colors. The motley insect was nothing they have so far encountered in the scientific literature.

While scrolling through iNaturalist – a social network where professional and citizen scientists share their photographs, in order to map biodiversity observations from across the globe – a group of students from Croatia discovered a couple of curious pictures, taken in 2008 in the Peruvian rainforest and posted in 2018. What they were looking at was a pygmy grasshopper sporting a unique pattern of lively colors. The motley insect was nothing they have so far encountered in the scientific literature.

The scientist and photographer Roberto Sindaco, Museo Civico di Storia naturale (Torino, Italy) graciously shared his camera roll with Niko Kasalo, Maks Deranja, and Karmela Adžić, graduate students under the mentorship of Josip Skejo, all currently affiliated with University of Zagreb, Faculty of Science, Croatia. Together, they published a paper describing the yet to be named insect in the open-access scientific journal Journal of Orthoptera Research.

Typically, new species are described from specimens collected from their natural habitats and then deposited in a museum to be preserved for future reference. The authors, possessing several high-quality photographs, decided to challenge the norm and name the new species based on photographs only. The paper was initially rejected, but a compromise was reached—it could be published with the species name removed.

The International Code of Zoological nomenclature is a document that contains regulations for proper scientific naming of animal species. It allows naming species from photographs, but the practice is generally looked down upon. Thus, the authors decided to use the nameless species to draw attention to this problem and bring more clarity. Names in zoology consist of two words: the genus name and the species name. As the species name was denied, the grasshopper is now mysteriously referred to as „the nameless Scaria“.

Another important message of this paper is how citizen science portals, such as iNaturalist, allow everybody interested in nature to contribute to ‘real’ scientific work by posting their findings online.

The authors believe that including laypeople in the scientific process can help bridge the communication gap between scientists and the general population, dissipating the growing suspicion towards science. The researchers urge everybody to engage with nature around them and capture its beauty with their camera lens. 

“Only by interacting with nature can we truly feel how much we might lose if we do not take care of it, and care is urgently needed,”

said the authors of the study.
Male of the nameless Scaria species
Photo by Roberto Sindaco

Original source:

Kasalo N, Deranja M, Adžić K, Sindaco R, Skejo J (2021) Discovering insect species based on photographs only: The case of a nameless species of the genus Scaria (Orthoptera: Tetrigidae). Journal of Orthoptera Research 30(2): 173-184. https://doi.org/10.3897/jor.30.65885

48 years of Australian collecting trips in one data package

From 1973 to 2020, Australian zoologist Dr Robert Mesibov kept careful records of the “where” and “when” of his plant and invertebrate collecting trips. Now, he has made those valuable biodiversity data freely and easily accessible via the Zenodo open-data repository, so that future researchers can rely on this “authority file” when using museum specimens collected from those events in their own studies. The new dataset is described in the open-access, peer-reviewed Biodiversity Data Journal.

While checking museum records, Dr Robert Mesibov found there were occasional errors in the dates and places for specimens he had collected many years before. He was not surprised.

“It’s easy to make mistakes when entering data on a computer from paper specimen labels”, said Mesibov. “I also found specimen records that said I was the collector, but I know I wasn’t!”

One solution to this problem was what librarians and others have long called an “authority file”.

“It’s an authoritative reference, in this case with the correct details of where I collected and when”, he explained.

“I kept records of almost all my collecting trips from 1973 until I retired from field work in 2020. The earliest records were on paper, but I began storing the key details in digital form in the 1990s.”

The 48-year record has now been made publicly available via the Zenodo open-data repository after conversion to the Darwin Core data format, which is widely used for sharing biodiversity information. With this “authority file”, described in detail in the open-access, peer-reviewed Biodiversity Data Journal, future researchers will be able to rely on sound, interoperable and easy to access data, when using those museum specimens in their own studies, instead of repeating and further spreading unintentional errors.

“There are 3829 collecting events in the authority file”, said Mesibov, “from six Australian states and territories. For each collecting event there are geospatial and date details, plus notes on the collection.”

Mesibov hopes the authority file will be used by museums to correct errors in their catalogues.

“It should also save museums a fair bit of work in future”, he explained. “No need to transcribe details on specimen labels into digital form in a database, because the details are already in digital form in the authority file.”

Mesibov points out that in the 19th and 20th centuries, lists of collecting events were often included in the reports of major scientific expeditions.

“Those lists were authority files, but in the pre-digital days it was probably just as easy to copy collection data from specimen labels.”

“In the 21st century there’s a big push to digitise museum specimen collections”, he said. “Museum databases often have lookup tables with scientific names and the names of collectors. These lookup tables save data entry time and help to avoid errors in digitising.”

“Authority files for collecting events are the next logical step,” said Mesibov. “They can be used as lookup tables for all the important details of individual collections: where, when, by whom and how.”

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Research paper:

Mesibov RE (2021) An Australian collector’s authority file, 1973–2020. Biodiversity Data Journal 9: e70463. https://doi.org/10.3897/BDJ.9.e70463

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Robert Mesibov’s webpage: https://www.datafix.com.au/mesibov.html

Robert Mesibov’s ORCID page: https://orcid.org/0000-0003-3466-5038

Dwarfs under dinosaur legs: 99-million-year-old millipede discovered in Burmese amber

A 3D reconstruction of the fossil allowed for the description of an entirely new suborder


The newly described millipede (Burmanopetalum inexpectatum) rendered using 3D X-ray microscopy. Image by Leif Moritz.

Even though we are led to believe that during the Cretaceous the Earth used to be an exclusive home for fearsome giants, including carnivorous velociraptors and arthropods larger than a modern adult human, it turns out that there was still room for harmless minute invertebrates measuring only several millimetres.

Such is the case of a tiny millipede of only 8.2 mm in length, recently found in 99-million-year-old amber in Myanmar. Using the latest research technologies, the scientists concluded that not only were they handling the first fossil millipede of the order (Callipodida) and also the smallest amongst its contemporary relatives, but that its morphology was so unusual that it drastically deviated from its contemporary relatives.

As a result, Prof. Pavel Stoev of the National Museum of Natural History (Bulgaria) together with his colleagues Dr. Thomas Wesener and Leif Moritz of the Zoological Research Museum Alexander Koenig (Germany) had to revise the current millipede classification and introduce a new suborder. To put it in perspective, there have only been a handful of millipede suborders erected in the last 50 years. The findings are published in the open-access journal ZooKeys.

To analyse the species and confirm its novelty, the scientists used 3D X-ray microscopy to ‘slice’ through the Cretaceous specimen and look into tiny details of its anatomy, which would normally not be preserved in fossils. The identification of the millipede also presents the first clue about the age of the order Callipodida, suggesting that this millipede group evolved at least some 100 million years ago. A 3D model of the animal is also available in the research article.

Curiously, the studied arthropod was far from the only one discovered in this particular amber deposit. On the contrary, it was found amongst as many as 529 millipede specimens, yet it was the sole representative of its order. This is why the scientists named it Burmanopetalum inexpectatum, where “inexpectatum” means “unexpected” in Latin, while the generic epithet (Burmanopetalum) refers to the country of discovery (Myanmar, formerly Burma).

Lead author Prof. Pavel Stoev says:

We were so lucky to find this specimen so well preserved in amber! With the next-generation micro-computer tomography (micro-CT) and the associated image rendering and processing software, we are now able to reconstruct the whole animal and observe the tiniest morphological traits which are rarely preserved in fossils. This makes us confident that we have successfully compared its morphology with those of the extant millipedes. It came as a great surprise to us that this animal cannot be placed in the current millipede classification. Even though their general appearance have remained unchanged in the last 100 million years, as our planet underwent dramatic changes several times in this period, some morphological traits in Callipodida lineage have evolved significantly.


The newly described millipede seen in amber. Image by Leif Moritz.

Co-author Dr. Thomas Wesener adds:

“We are grateful to Patrick Müller, who let us study his private collection of animals found in Burmese amber and dated from the Age of Dinosaurs. His is the largest European and the third largest in the world collection of the kind. We had the opportunity to examine over 400 amber stones that contain millipedes. Many of them are now deposited at the Museum Koenig in Bonn, so that scientists from all over the world can study them. Additionally, in our paper, we provide a high-resolution computer-tomography images of the newly described millipede. They are made public through MorphBank, which means anyone can now freely access and re-use our data without even leaving the desk.”

Leading expert in the study of fossil arthropods Dr. Greg Edgecombe (Natural History Museum, London) comments:

“The entire Mesozoic Era – a span of 185 million years – has until now only been sampled for a dozen species of millipedes, but new findings from Burmese amber are rapidly changing the picture. In the past few years, nearly all of the 16 living orders of millipedes have been identified in this 99-million-year-old amber. The beautiful anatomical data presented by Stoev et al. show that Callipodida now join the club.”

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Original source:

Stoev P, Moritz L, Wesener T (2019) Dwarfs under dinosaur legs: a new millipede of the order Callipodida (Diplopoda) from Cretaceous amber of Burma. ZooKeys 841: 79-96. https://doi.org/10.3897/zookeys.841.34991

New tarantula species from Angola distinct with a one-of-a-kind ‘horn’ on its back

A new to science species of tarantula with a peculiar horn-like protuberance sticking out of its back was recently identified from Angola, a largely underexplored country located at the intersection of several Afrotropical ecoregions.

Collected as part of the National Geographic Okavango Wilderness Project, which aims to uncover the undersampled biodiversity in the entire Okavango catchment of Angola, Namibia and Botswana, thereby paving the way for sustainable conservation in the area, the new arachnid is described in a paper published in the open-access journal African Invertebrates by the team of Drs John Midgley and Ian Engelbrecht.

Although the new spider (Ceratogyrus attonitifer sp.n.) belongs to a group known as horned baboon spiders, the peculiar protuberance is not present in all of these species. Moreover, in the other species – where it is – the structure is completely sclerotised, whereas the Angolan specimens demonstrate a soft and characteristically longer ‘horn’. The function of the curious structure remains unknown.

The new tarantula’s extraordinary morphology has also prompted its species name: C. attonitifer, which is derived from the Latin root attonit– (“astonishment” or “fascination”), and the suffix –fer (“bearer of” or “carrier”). It refers to the astonishment of the authors upon the discovery of the remarkable species.

“No other spider in the world possesses a similar foveal protuberance,” comment the authors of the paper.

Individual of the newly described species in defensive posture in its natural habitat. Photo by Kostadine Luchansky.

During a series of surveys between 2015 and 2016, the researchers collected several female specimens from the miombo forests of central Angola. To find them, the team would normally spend the day locating burrows, often hidden among grass tufts, but sometimes found in open sand, and excavate specimens during the night. Interestingly, whenever the researchers placed an object in the burrow, the spiders were quick and eager to attack it.

The indigenous people in the region provided additional information about the biology and lifestyle of the baboon spider. While undescribed and unknown to the experts until very recently, the arachnid has long been going by the name “chandachuly” among the local tribes. Thanks to their reports, information about the animal’s behaviour could also be noted. The tarantula tends to prey on insects and the females can be seen enlarging already existing burrows rather than digging their own. Also, the venom of the newly described species is said to not be dangerous to humans, even though there have been some fatalities caused by infected bites gone untreated due to poor medical access.

In conclusion, the researchers note that the discovery of the novel baboon spider from Angola does not only extend substantially the known distributional range of the genus, but can also serve as further evidence of the hugely unreported endemic fauna of the country:

“The general paucity of biodiversity data for Angola is clearly illustrated by this example with theraphosid spiders, highlighting the importance of collecting specimens in biodiversity frontiers.”

Apart from the described species, the survey produced specimens of two other potentially new to science species and range expansions for other genera. However, the available material is so far insufficient to formally diagnose and describe them.

The newly described baboon spider species (Ceratogyrus attonitifer), showing the peculiar soft and elongated horn-like protuberance sticking out of its back. Photo by Dr Ian Enelbrecht.

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Original source:

Midgley JM, Engelbrecht I (2019) New collection records for Theraphosidae (Araneae, Mygalomorphae) in Angola, with the description of a remarkable new species of Ceratogyrus. African Invertebrates 60(1): 1-13. https://doi.org/10.3897/afrinvertebr.60.32141

Biodiversity project in Azores delivers detailed abundance data for 286 arthropod species

In 1999, a long-term biodiversity project started at the Azores Islands (Portugal, Atlantic Ocean), the Biodiversity of Arthropods from the Laurisilva of the Azores (BALA) project (1999-2004). Its aim was to obtain detailed distributional and abundance data for a large fraction of arthropod fauna, living in all remaining native forests at seven of the Azores Islands.

After the first successful sampling of 100 sites at 18 native forest fragments over those five years, a second survey was accomplished in 2010-2011, where two sites per fragment were re-sampled. Now, Dr Paulo A.V. Borges and colleagues publish the complete list of the 286 species identified, including many species described as new to science in the open access journal Biodiversity Data Journal. They have also added detailed information on their distribution and abundance.

The resulting database has inspired the publication of many studies in the last ten years, including macroecological studies evaluating the abundance, spatial variance and occupancy of arthropods, the effects of disturbance and biotic integrity of the native forests on arthropod assemblages and the performance of species richness estimators.

image-2Moreover, these data allowed the ranking of conservation priorities for the fauna of the Azores, and allowed the estimation of extinction debt (the species likely to be wiped out because of past events) in the Azores. The present study has also inspired the development of the Azorean Biodiversity Portal and the Azores Island Lab.

The study stresses the need to expand the approaches applied in these projects to other habitats in the Azores, and, more importantly, to other less thoroughly surveyed taxonomic groups (e.g. Diptera and Hymenoptera).

“These steps are fundamental for getting a more accurate assessment of the biodiversity in the Azores archipelago, and we hope that can inspire similar biodiversity surveys at other islands,” say the authors.

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Original source:

Borges P, Gaspar C, Crespo L, Rigal F, Cardoso P, Pereira F, Rego C, Amorim I, Melo C, Aguiar C, André G, Mendonça E, Ribeiro S, Hortal J, Santos A, Barcelos L, Enghoff H, Mahnert V, Pita M, Ribes J, Baz A, Sousa A, Vieira V, Wunderlich J, Parmakelis A, Whittaker R, Quartau J, Serrano A, Triantis K (2016) New records and detailed distribution and abundance of selected arthropod species collected between 1999 and 2011 in Azorean native forests. Biodiversity Data Journal 4: e10948. https://doi.org/10.3897/BDJ.4.e10948

Flying jewels spell death for tarantulas: Study of a North American spider fly genus

Spider flies are usually a rarely encountered group of insects, except in Western North America, where the North American jewelled spider flies (the Eulonchus genus) can be locally abundant in mountainous areas such as the Sierra Nevada of California. The brilliantly coloured adults (also known as ‘sapphires’ and ’emeralds’) are important pollinators of flowers.

The North American jewelled spider flies typically have large rounded bodies covered with dense hairs and metallic green to blue or even purple colouration, giving them a jewel-like appearance. Together, the elongated mouthparts, the metallic coloration and the eyes, covered with soft hairs, immediately set these flies apart from any other group of tarantula fly. The mouthparts are greatly elongated to help them feed on nectar from the flowers of more than 25 different plant families and 80 species.

However, their larvae are more insidious, seeking out and inserting themselves into tarantula hosts and slowly eating away their insides until they mature and burst out of the abdomen, killing the spider, and leaving behind only the skin. Once they have emerged from the host, they pupate to develop into adults.

image-1In the present study, published in the open access journal ZooKeys, six species of the genus are recognized in North America, including one from the Smokey Mountains, and five from the West, ranging from Mexico to Canada. Drs Christopher J. Borkent and Shaun L. Winterton, and PhD student Jessica P. Gillung, all affiliated with the California State Collection of Arthropods, USA, have redescribed all of them using cybertaxonomic methods of natural language description. A phylogenetic tree of the relationships among the species is also presented.

The examined individuals include many from the collection amassed by the late Dr. Evert Schlinger (1928-2014) over the span of more than 60 years. Today, the collection resides at the California Academy of Sciences (CAS). “Dr. Evert I. Sclinger was a world renowned expert on spider fly taxonomy and biology,” write the authors in the paper, which they dedicate to the scientist and his legacy.

All of the studied flies are relatively widely distributed, and locally abundant, except for a single species (E. marialiciae), which is known from only a few specimens, collected within a small contiguous area in the Great Smoky Mountains. However, the scientists suggest that future studies are needed to explore whether this is actually their full range.

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Original source:

Borkent CJ, Gillung JP, Winterton SL (2016) Jewelled spider flies of North America: a revision and phylogeny of Eulonchus Gerstaecker (Diptera, Acroceridae). ZooKeys 619: 103-146. doi: 10.3897/zookeys.619.8249