Evolution of the interaction between mitochondrial and nuclear genomes in bumblebees (Hymenoptera, Apidae, Bombus): the importance of numts and heteroplasmy

Project Information

EVOBOMICS

Grant agreement ID: 101023351

DOI

10.3030/101023351

Project closed

EC signature date 9 March 2021

Start date 4 October 2021

End date 2 October 2025

Funded under

• EXCELLENT SCIENCE - Marie Skłodowska-Curie Actions

Total cost

€ 224 933,76

EU contribution

€ 224 933,76

Coordinated by

ROYAL HOLLOWAY AND BEDFORD NEW COLLEGE
United Kingdom

Periodic Reporting for period 1 - EVOBOMICS (Evolution of the interaction between mitochondrial and nuclear genomes in bumblebees (Hymenoptera, Apidae, Bombus): the importance of numts and heteroplasmy)

Reporting period: 2021-10-04 to 2023-10-03

Summary of the context and overall objectives of the project

Numts are non-functional copies of genes of mitochondrial origin present in the nuclear genome, and heteroplasmy is the presence of different mitochondrial genotypes in the same organism. Although they are completely distinct molecular phenomena, both can be at the same time obstacles and new tools for evolutionary studies. EVOBOMICS aims to investigate numts, heteroplasmy and genomes (nuclear and mitochondrial) at the same time and from an evolutionary perspective. Researchers will identify numts and heteroplasmy in bumblebees to understand their evolution and interaction.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

Work performed:
Standardising laboratory protocols to optimise DNA extraction
Sequencing four samples during a research trip to Brazil
Collecting bees on a field trip to Switzerland
Using DNA barcoding for species identification
Conducting genome sequencing with the PacBio platform


Bioinformatics and self-development training:
Foundations of Project Management (2025) - Coursera
The Conversation Media Training (2025) - RHUL
Project design: Designing your career in science (2024) - Marie Curie Alumni Association
Python for bioinformatics (2024) - NEOF NERC Environment
Phylogenomics (2024) - NEOF NERC Environment
R Primer for omics (2024) - NEOF NERC Environment
Introduction to Command Line Bioinformatics (2024) - NEOF NERC Environment
Eukaryote genome assembly (2024) - NEOF NERC Environment
Time management (2023) - RHUL
Leading collaboration (2023) - RHUL
Performance management (2023) - RHUL
Articulating & communicating skills (2023) - RHUL
Introduction to public engagement (2023) - RHUL
Unconscious bias (2023) - RHUL
Presentation skills (2022) - RHUL
Academic writing for researchers (2022) - RHUL
Bullying & harassment awareness (2022) - RHUL
Introduction to ethics (2022) - RHUL


Grants obtained:
2024 Marie Curie Alumni Association – Micro grant - €1,000
2023 NERC/NEOF Pilot Project Grants Competition – Early Career Researchers - £16,356.62
2022Visiting Researcher Award from Abroad (FAPESP 2022/06069-1) – R$11.970,00
Participation in events:
1. XXVII International Congress of Entomology, ICE (2024) Deciphering the puzzle of Tetragonula species from Australia: A tale of numts, rapid evolution, whole mitogenome duplication & rearrangements. Kyoto, Japan (congress). Oral presentation
2. IUSSI North-west European section (2023). Bristol, UK (meeting). Attendant
3. IUSSI Brazil (2023) Numts & heteroplasmy in bees. Online, Brazil (webinar, invited speaker)
4. IUSSI North-west European section (2022). London, UK (meeting). Attendant
5. IUSSI Brazil - Insetos Sociais em Rede (2021) Introduction to omics analysis in social insects. Online, Brazil (short course ministration)

Symposium organization
1. Organization of monthly IUSSI Brazil webinars (2023-2024)
2. Symposium organization (2024): Genetics & Genomics in Ecology and Evolution of Social Insects, XXVII International Congress of Entomology, Kyoto, Japan

Advising
2021-2024 Co-advising – Leonardo Tresoldi Gonçalves. Project: Mitonuclear interaction and niche adaptation of bumblebees (Hymenoptera: Apidae: Bombus). PhD candidate. UFRS, Brazil
2018-2023 Co-advising - Julia Colombelli. Project: Identity analysis of two nominal species of Xylocopa (Neoxylocopa) using morphological and molecular data. MSc candidate. Unila, Brazil

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

My results indicate that numts and heteroplasmy are common phenomena in bees, both with significant implications for species identification, genetics, and evolution. In the current genomic era, isolating and understanding these phenomena remain major challenges.
When analysing my genomes, I often recover dozens to hundreds of mitochondrial contigs, each displaying unusual characteristics. I believe this diversity of mitochondrial genomes may act as a fail-safe mechanism to retain genetic variation, providing the basis for coadaptation across evolutionary time and space.

Based on my findings, I propose that heteroplasmy plays a key role in species distribution, diversification, and speciation. I am eager to continue advancing this innovative research in the next stages of my work.

Heteroplasmy