Newly established Bulgarian Barcode of Life to support biodiversity conservation in the country

As the latest national node to join the International Barcode of Life Consortium (iBOL), its main task is to coordinate, support, and promote DNA barcoding research in Bulgaria.

On 27 September 2023, during a specialised symposium on DNA barcoding at the Bulgarian Academy of Sciences, the Bulgarian Barcode of Life (BgBOL), a Bulgarian DNA barcoding consortium, was founded. 

Logo of the Bulgarian Barcode of Life (BgBOL), a Bulgarian DNA barcoding consortium and the latest national node to join the International Barcode of Life Consortium (iBOL).

By becoming the latest national node to join the International Barcode of Life Consortium (iBOL), the main task before BgBOL will be to coordinate, support, and promote DNA barcoding research in Bulgaria, with a primary focus on the study and preservation of the country’s biodiversity.

“The Bulgarian Barcode of Life opens up new horizons and opportunities to study and understand the biodiversity in Bulgaria,”

says Dr Georgi Bonchev, Institute of Plant Physiology and Genetics at the Bulgarian Academy of Sciences (BAS).

DNA barcoding is a method to identify individual organisms based on nucleotide sequences captured from short, predefined and standardised segments of DNA.

Dr Georgi Bonchev explains the DNA barcoding method at the specialised symposium held on 27 September 2023 at the Bulgarian Academy of Sciences. 
Photo by the Bulgarian Academy of Sciences.

The formation of the BgBOL consortium is expected to strengthen the network of collaborations, ultimately contributing to the broader dissemination and popularisation of DNA barcoding research in the region.BgBOL was created by seven academic institutions: Institute of Plant Physiology and Genetics (BAS), Institute of Biodiversity and Ecosystem Research, National Museum of Natural History (BAS), Sofia University “St. Kliment Ohridski”, AgroBioInstitute (Agricultural Academy), University of Forestry, and Pensoft in its role of a scientific publisher and tech innovator well-known in the field of biodiversity science.

Prof. Lyubomir Penev joined the symposium with a talk on the publication, dissemination and management of DNA barcoding data. His presentation also touched on the relevant biodiversity data workflows and tools currently in development at Pensoft with the support of the Horizon 2020-funded project BiCIKL.
Photo by the Bulgarian Academy of Sciences.

As part of the event, Pensoft’s founder and CEO Prof. Lyubomir Penev led a discussion on the publication, dissemination and management of DNA barcoding data. His presentation also touched on the relevant biodiversity data workflows and tools currently in development at Pensoft with the support of the Horizon 2020-funded project BiCIKL (abbreviation for Biodiversity Community Integrated Knowledge Library).

“I’d like to congratulate everyone involved in the establishment of the Bulgarian Barcode of Life! This is a huge step forward in advancing DNA barcoding research in Bulgaria and, ultimately, the preservation of the country’s amazing biodiversity,”

comments Prof. Lyubomir Penev.

***

About the International Barcode of Life:

The International Barcode of Life Consortium is a research alliance undertaking the largest global biodiversity science initiative: create a digital identification system for life that is accessible to everyone.

iBOL is working to establish an Earth observation system that will discover species, reveal their interactions, and establish biodiversity baselines. The consortium is tracking ecosystems across the planet and exploring symbiomes – the distinct fungal, plant, and animal species associated with host organisms. Our goal is to complete this research and establish baseline data for science and society’s benefit.

Genetic study reveals that a captive-bred population could save endangered crocodile from extinction

Since this species is almost extinct in the wild, the news brings hope for the recovery of populations.

The Orinoco crocodile (Crocodylus intermedius) is a critically endangered species native to the Orinoco River basin in Colombia and Venezuela. It is one of the largest crocodilian species in the world, reaching lengths of up to seven meters. Despite its impressive size, it is also the most endangered and least-studied of the New World crocodilians.

Female Orinoco crocodile from the Roberto Franco Tropical Biological Station´s ex-situ population.

The species has faced a severe population decline due to commercial overexploitation of its skin, which was highly sought after by the fashion industry of Europe, the USA and Japan in the 20th century. As a result, the current estimated global population stands at less than 250 adult individuals.

Recognizing the critical status of the species, herpetologist Federico Medem established a captive breeding program for the Orinoco crocodile in 1971 at the Roberto Franco Tropical Biological Station (RFTBS) in Villavicencio. Currently, the RFTBS houses over 600 individuals, making it the largest stock of this species and the only one in Colombia. Remarkably, there might be more adult crocodiles kept there than in the wild. 

Despite the success of the captive breeding program, reintroduction of animals into the wild has been challenging. This is primarily due to the lack of a comprehensive genetic characterization that can determine whether the population is genetically viable and has no signs of inbreeding, which can result in reduced fitness at the individual and population level. To ensure the successful reintroduction of the species, it was crucial to have a robust and conclusive genetic assessment that confirms the population’s genetic health and viability.

“We felt a sense of urgency to determine the genetic viability of the population in order to proceed with the reintroduction of animals and establish new populations of the species in Colombia. Therefore, we conducted a comprehensive genetic characterization using fast-evolving molecular markers on a sample of 551 crocodiles,” explains Ana María Saldarriaga, a former researcher at the Universidad Nacional de Colombia who is currently pursuing a Ph.D. at Fordham University.

Female Orinoco crocodile from the Roberto Franco Tropical Biological Station´s ex-situ population.

“Our findings showed that the individuals within the population possess sufficient genetic diversity and are suitable for reintroduction efforts, as well as for maintaining and enhancing the genetic variability of the ex-situ population.”

“We demonstrated that molecular data could be used to improve the management of ex-situ conservation programs well beyond what could be achieved with pedigree information alone,” she and her colleagues write in a study just published in the journal Nature Conservation.

Female Orinoco crocodile from the Roberto Franco Tropical Biological Station´s ex-situ population.

Based on the findings of this study, the Colombian government, along with other public and private conservation institutions and agencies, can use the individuals identified in this research to initiate the establishment of new populations in regions where the species has been completely depleted.

Female Orinoco crocodile from the Roberto Franco Tropical Biological Station´s ex-situ population.

“Today, it is widely recognized that top predators, such as crocodiles, play fundamental roles in both aquatic and terrestrial ecosystems. They have a significant impact on the nutrient cycle, regulate fish populations, and contribute to important cross-ecosystem engineering processes,” stated Mario Vargas-Ramírez, professor at the Genetics Institute of the Universidad Nacional de Colombia and director of the RFTBS.

“Therefore, the reintroduction of the Orinoco crocodile to the Orinoco region is an urgent priority. Additionally, as the Orinoco crocodile is considered an umbrella species, its recovery and conservation efforts will have a positive cascading effect, protecting a large number of species that coexist in the same environment.” 

Research article:

Saldarriaga-Gómez AM, Ardila-Robayo MC, Medem F, Vargas-Ramírez M (2023) Hope is the last thing lost: Colombian captive-bred population of the critically endangered Orinoco crocodile (Crocodylus intermedius) is a genetic reservoir that could help to save the species from extinction. Nature Conservation 53: 85-103. https://doi.org/10.3897/natureconservation.53.104000

Photos by Mario Vargas-Ramírez.

Follow Nature Conservation on social media:

New way to browse interlinked biodiversity data: Biodiversity Knowledge Hub NOW ONLINE!

The Biodiversity Knowledge Hub is a one-stop portal that allows users to access FAIR and interlinked biodiversity data and services in a few clicks.

The Horizon 2020 BiCIKL Project is proud to announce that the Biodiversity Knowledge Hub (BKH) is now online.

BKH is a one-stop portal that allows users to access FAIR and interlinked biodiversity data and services in a few clicks. BKH was designed to support a new emerging community of users over time and across the entire biodiversity research cycle providing its services to anybody, anywhere and anytime.

The Knowledge Hub is the main product from our BiCIKL consortium, and we are delighted with the result!

BKH can easily be seen as the beginning of the major shift in the way we search interlinked biodiversity information.”

Biodiversity researchers, research infrastructures and publishers interested in fields ranging from taxonomy to ecology and bioinformatics can now freely use BKH as a compass to navigate the oceans of biodiversity data. BKH will do the linkages.

says Prof. Lyubomir Penev, BiCIKL’s Project coordinator and Founder of Pensoft Publishers
The BKH is designed to serve a new emerging community of users over time and across the entire biodiversity research cycle. 

We have invested our best energies and resources in the development of BKH and the Fair Data Place (FDP), which is the beating heart of the portal,”

BKH has been designed to support a new emerging community of users across the entire biodiversity research cycle.

Its purpose goes beyond the BiCIKL project itself: we are thrilled to say that BKH is meant to stay, aiming to reshape the way biodiversity knowledge is accessed and used.

says Dr Christos Arvanitidis, CEO of LifeWatch ERIC.

The BKH outlines how users can navigate and access the linked data, tools and services of the infrastructures cooperating in BiCIKL.

By revealing how they harvest, liberate and reuse data, these increasingly integrated sources enable researchers in the natural sciences to move more seamlessly between specimens and material samples, genomic and metagenomic data, scientific literature, and taxonomic names and units.

said Dr Joe Miller, Executive Secretary of GBIF—the Global Biodiversity Information Facility.

A training programme on how to best utilise the platform is currently being developed by the Consortium of European Taxonomic Facilities (CETAF), Pensoft PublishersPlaziMeise Botanic GardenEMBL’s European Bioinformatics Institute (EMBL-EBI), ELIXIR HubGBIF – the Global Biodiversity Information Facility, and LifeWatch ERIC and will be finalised in the coming months.

***

A detailed description of the BKH tools and services provided by its contributing organisations is available at: https://biodiversityknowledgehub.eu.

***

Find more information about the BiCIKL consortium partners on the project’s website.

***

Follow BiCIKL Project on Twitter and Facebook. Join the conversation on Twitter at #BiCIKL_H2020.

Lizards go north: Balkan wall lizard population found all the way in the Czech Republic

The northernmost population of the Balkan lizard, recently discovered in the Czech Republic, has proven to be genetically unique and variable.

The Czech Republic is a zoologically well-studied area, and its reptile fauna is not very rich. Therefore, the recent discovery of a new reptile species for the country, the Balkan wall lizard (Podarcis tauricus), came as a big surprise. This lizard inhabits areas of the Central and Western Balkans as far as Crimea, with isolated areas of occurrence in Hungary and northern Romania, so how did it get as far north as the Czech Republic? Fortunately, the genetics in much of the lizard’s range are relatively well-studied. Finding out where lizards from the Czech Republic fit genetically could reveal the origins of this northernmost population.

Podarcis tauricus in the wild – Váté písky near Bzenec, Czech Republic.

An analysis published by Czech herpetologists in the journal Biodiversity Data Journal shows that the lizards from the Czech population are genetically variable; therefore, the population was not established by the introduction of a single gravid female.

Geographical distribution of Podarcis tauricus. The green arrow shows the northernmost known locality (Váté písky, Czech Republic).

The population also has genetic “markers” not yet found elsewhere, although it is clearly related to populations from the Central and Western Balkans and Hungary. These findings suggest that this could be an original, possibly relict population.

Haplotype network, designed from 24 haplotypes of the cytb locus from 167 individuals of Podarcis tauricus and Podarcis gaigeae (Psonis et al. 2017; this study). Colours correspond to the country of the specimen’s geographical origin and each circle corresponds to a haplotype. The circle size is proportional to the number of individuals with the same haplotype. The number of individuals per haplotype is indicated. Due to the unequal size of cytb sequences from Psonis et al. (2017), only a fragment of 257 bp which was common for all 167 sequences was used for the haplotype network reconstruction. For this region of cytb locus, the sequences of our individuals from Czech Republic are identical to 18 individuals from Albania, Hungary, Kosovo and Serbia.

However, we cannot rule out recent introductions or spontaneous northward dispersal of the lizard associated with global climate change. Exotic species of animals and plants appear in the Czech Republic through various routes and tracing their origin is not always easy. Both intentional and unintentional introductions have been recorded for some reptiles, while some previously southern vertebrate and invertebrate species spread to the north spontaneously.

The first genetic data on the origin of the northernmost population of the Balkan wall lizard suggest that the lizard can spread to the north naturally; however, further investigations are needed to support this tentative conclusion. 

Research article:

Rehák I, Fischer D, Kratochvíl L, Rovatsos M (2022) Origin and haplotype diversity of the northernmost population of Podarcis tauricus (Squamata, Lacertidae): Do lizards respond to climate change and go north? Biodiversity Data Journal 10: e82156. https://doi.org/10.3897/BDJ.10.e82156

The EU not ready for the release of Gene drive organisms into the environment

Gene drive organisms (GDOs) have been suggested as an approach to solve some of the most pressing environmental and public health issues. Currently, it remains unclear what kind of regulations are to be used to cover the potential risks. In their study, published in the open-access journal BioRisk, scientists evaluate the options for an operational risk assessment of GDOs before their release into environments across the EU.

EU scientists are taking a closer look into the CRISPR/Cas-9-induced population-wide genetic modifications before introducing it into practice

Within the last decades, new genetic engineering tools for manipulating genetic material in plants, animals and microorganisms are getting large attention from the international community, bringing new challenges and possibilities. While genetically modified organisms (GMO) have been known and used for quite a while now, gene drive organisms (GDO) are yet at the consideration and evaluation stage. 

The difference between these two technologies, where both are meant to replace certain characters in animals or plants with ones that are more favourable for the human population, is that, even though in GDO there is also foreign “synthetic” DNA being introduced, the inheritance mode differs. In GDO, the genome’s original base arrangements are changed, using CRISPR/Cas-9 genome editing. Once the genome is changed, its alterations are carried down the organism’s offspring and subsequent generations. 

In their study, published in the open-access journal Biorisk, an international group of scientists led by Marion Dolezel from the Environment Agency Austria, discuss the potential risks and impacts on the environment. 

The research team also points to current regulations addressing invasive alien species and biocontrol agents, and finds that the GMO regulations are, in principle, also a useful starting point for GDO.

There are three main areas suggested to benefit from gene drive systems: public health (e.g. vector control of human pathogens), agriculture (e.g. weed and pest control), environmental protection and nature conservation (e.g. control of harmful non-native species).

In recent years, a range of studies have shown the feasibility of synthetic CRISPR-based gene drives in different organisms, such as yeast, the common fruit fly, mosquitoes and partly in mammals. 

Given the results of previous research, the gene drive approach can even be used as prevention for some zoonotic diseases and, hence, possible future pandemics. For example, laboratory tests showed that release of genetically modified mosquitoes can drastically reduce the number of malaria vectors. Nevertheless, potential environment and health implications, related to the release of GDO, remain unclear. Only a few potential applications have so far progressed to the research and development stage.

“The potential of GDOs for unlimited spread throughout wild populations, once released, and the apparently inexhaustible possibilities of multiple and rapid modifications of the genome in a vast variety of organisms, including higher organisms such as vertebrates, pose specific challenges for the application of adequate risk assessment methodologies”,

shares the lead researcher Mrs. Dolezel.

In the sense of genetic engineering being a fastly developing science, every novel feature must be taken into account, while preparing evaluations and guidances, and each of them provides extra challenges.

Today, the scientists present three key differences of gene drives compared to the classical GMO:

1. Introducing novel modifications to wild populations instead of “familiar” crop species, which is a major difference between “classic” GMOs and GDOs.

“The goal of gene drive applications is to introduce a permanent change in the ecosystem, either by introducing a phenotypic change or by drastically reducing or eradicating a local population or a species. This is a fundamental difference to GM crops for which each single generation of hybrid seed is genetically modified, released and removed from the environment after a relatively short period”,

shares Dolezel.

2. Intentional and potentially unlimited spread of synthetic genes in wild populations and natural ecosystems.

Gene flow of synthetic genes to wild organisms can have adverse ecological impact on the genetic diversity of the targeted population. It could change the weediness or invasiveness of certain plants, but also threaten with extinction the species in the wild.

3. Possibility for long-term risks to populations and ecosystems.

Key and unique features of GDOs are the potential long-term changes in populations and large-scale spread across generations. 

In summary, the research team points out that, most of all, gene drive organisms must be handled extremely carefully, and that the environmental risks related to their release must be assessed under rigorous scrutiny. The standard requirements before the release of GDOs need to also include close post-release monitoring and risk management measures.

It is still hard to assess with certainty the potential risks and impact of gene drive applications on the environment, human and animal health. That’s why highly important questions need to be addressed, and the key one is whether genetically driven organisms are to be deliberately released into the environment in the European Union. The High Level Group of the European Commission’s Scientific Advice Mechanism highlights that within the current regulatory frameworks those risks may not be covered.

The research group recommends the institutions to evaluate whether the regulatory oversight of GMOs in the EU is accomodate to cover the novel risks and challenges posed by gene drive applications.

“The final decision to release GDOs into the environment will, however, not be a purely scientific question, but will need some form of broader stakeholder engagement and the commitment to specific protection goals for human health and the environment”,

concludes  Dolezel.

***

Original source:
Dolezel M, Lüthi C, Gaugitsch H (2020) Beyond limits – the pitfalls of global gene drives for environmental risk assessment in the European Union. BioRisk 15: 1-29. https://doi.org/10.3897/biorisk.15.49297

Contact:
Marion Dolezel
Email: marion.dolezel@umweltbundesamt.at

Mosquito populations give a new insight into the role of Caucasus in evolution

We know that the Caucasus is a relatively large mountainous region, situated between Black and the Caspian seas. In its turn, it is divided into three subregions: Ciscaucasia, Greater Caucasus and Transcaucasia, also known as South Caucasus.

A closer look into the chromosome structure of mosquito larvae of a curious group of species (Chironomus “annularius” sensu Strenzke (1959)), collected from the three localities, has allowed Dr Mukhamed Karmokov of the Tembotov Institute of Ecology of Mountain territories at the Russian Academy of Science to figure out how the specificity of the Caucasian region has simultaneously unified its fauna geographically, yet has divided it evolutionarily. His paper is published in the open access journal Comparative Cytogenetics.

Having collected a sufficient amount of mosquito larvae, the researcher managed to study the chromosome structure, rearrangements and possible peculiarities of the separate Caucasian populations, in order to compare them.

Additionally, he analysed their relations to earlier known populations from Europe, Siberia, Kazakhstan and North America.

Amongst the curious peculiarities Karmokov identified in the chromosome structure of the studied larvae were some rearrangements which appear unique to Caucasus. Furthermore, he found that despite the close geographic proximity, the genetic distance between the Caucasian populations is quite significant, even While not enough to determine them as separate species, it could prove them as separate subspecies.

In conclusion, the scientist notes that the obtained data confirm that the Caucasian populations of the studied species have complex genetic structure and provide evidence for microevolution processes in the region.

###

Original source:

Karmokov MKh (2018) Karyotype characteristics and chromosomal polymorphism of Chironomus “annularius” sensu Strenzke (1959) (Diptera, Chironomidae) from the Caucasus region. Comparative Cytogenetics 12(3): 267-284. https://doi.org/10.3897/CompCytogen.v12i3.25832

New butterfly species discovered in Russia with an unusual set of 46 chromosomes

What looked like a population of a common butterfly species turned out to be a whole new organism, and, moreover – one with a very peculiar genome organisation.

Discovered by Vladimir Lukhtanov, entomologist and evolutionary biologist at the Zoological Institute in St. Petersburg, Russia, and Alexander Dantchenko, entomologist and chemist at the Moscow State University, the startling discovery was named South-Russian blue (Polyommatus australorossicus). It was found flying over the northern slopes of the Caucasus mountains in southern Russia. The study is published in the open access journal Comparative Cytogenetics.

“This publication is the long-awaited completion of a twenty-year history,” says Vladimir Lukhtanov.

In the mid-nineties, Vladimir Lukhtanov, together with his students and collaborators, started an exhaustive study of Russian butterflies using an array of modern and traditional research techniques. In 1997, Alexander Dantchenko who was mostly focused on butterfly ecology, sampled a few blue butterfly specimens from northern slopes of the Caucasus mountains. These blues looked typical at first glance and were identified as Azerbaijani blue (Polyommatus aserbeidschanus).

However, when the scientists looked at them under a microscope, it became clear that they had 46 chromosomes – a very unusual number for this group of the blue butterflies and exactly the same count as in humans.

Having spent twenty years studying the chromosomes of more than a hundred blue butterfly species and sequencing DNA from all closely related species, the researchers were ready to ascertain the uniqueness of the discovered butterfly and its chromosome set.

Throughout the years of investigation, it has become clear that caterpillars of genetically related species in the studied butterfly group feed on different, but similar plants. This discovery enables entomologists to not only discover new butterfly species with the help of botanic information, but also protect them.

“We are proud of our research,” says Vladimir Lukhtanov. “It contributes greatly to both the study of biodiversity and understanding the mechanisms of biological evolution.”

###

Original source:

Lukhtanov VA, Dantchenko AV (2017) A new butterfly species from south Russia revealed through chromosomal and molecular analysis of the Polyommatus (Agrodiaetus) damonides complex (Lepidoptera, Lycaenidae). Comparative Cytogenetics 11(4): 769-795. https://doi.org/10.3897/CompCytogen.v11i4.20072