The Portuguese genomics community teams up with iconic species to understand the destruction of biodiversity
Building a Portuguese Coalition for Biodiversity Genomics
Recommendation: posted 13 November 2023, validated 20 November 2023
Racimo, F. (2023) The Portuguese genomics community teams up with iconic species to understand the destruction of biodiversity. Peer Community in Genomics, 100257. 10.24072/pci.genomics.100257
This manuscript describes the ongoing work and plans of Biogenome Portugal: a new network of researchers in the Portuguese biodiversity genomics community. The aims of this network are to jointly train scientists in ecology and evolution, generate new knowledge and understanding of Portuguese biodiversity, and better engage with the public and with international researchers, so as to advance conservation efforts in the region. In collaboration across disciplines and institutions, they are also contributing to the European Reference Genome Atlas (ERGA): a massive scientific effort, seeking to eventually produce reference-quality genomes for all species in the European continent (Mc Cartney et al. 2023).
The manuscript centers around six iconic and/or severely threatened species, whose range extends across parts of what is today considered Portuguese territory. Via the Portugal chapter of ERGA (ERGA-Portugal), the researchers will generate high-quality genome sequences from these species. The species are the Iberian hare, the Azores laurel, the Black wheatear, the Portuguese crowberry, the Cave ground beetle and the Iberian minnowcarp. In ignorance of human-made political borders, some of these species also occupy large parts of the rest of the Iberian peninsula, highlighting the importance of transnational collaboration in biodiversity efforts. The researchers extracted samples from members of each of these species, and are building reference genome sequences from them. In some cases, these sequences will also be co-analyzed with additional population genomic data from the same species or genetic data from cohabiting species. The researchers aim to answer a variety of ecological and evolutionary questions using this information, including how genetic diversity is being affected by the destruction of their habitat, and how they are being forced to adapt as a consequence of the climate emergency.
The authors did a very good job in providing a justification for the choice of pilot species, a thorough methodological overview of current work, and well thought-out plans for future analyses once the genome sequences are available for study. The authors also describe plans for networking and training activities to foster a well-connected Portuguese biodiversity genomics community.
Applying a genomic analysis lens is important for understanding the ever faster process of devastation of our natural world. Governments and corporations around the globe are destroying nature at ever larger scales (Diaz et al. 2019). They are also destabilizing the climatic conditions on which life has existed for thousands of years (Trisos et al. 2020). Thus, genetic diversity is decreasing faster than ever in human history, even when it comes to non-threatened species (Exposito-Alonso et al. 2022), and these decreases are disrupting ecological processes worldwide (Richardson et al. 2023). This, in turn, is threatening the conditions on which the stability of our societies rest (Gardner and Bullock 2021). The efforts of Biogenome Portal and ERGA-Portugal will go a long way in helping us understand in greater detail how this process is unfolding in Portuguese territories.
Díaz, Sandra, et al. "Pervasive human-driven decline of life on Earth points to the need for transformative change." Science 366.6471 (2019): eaax3100. https://doi.org/10.1126/science.aax3100
Exposito-Alonso, Moises, et al. "Genetic diversity loss in the Anthropocene." Science 377.6613 (2022): 1431-1435. https://doi.org/10.1126/science.abn5642
Gardner, Charlie J., and James M. Bullock. "In the climate emergency, conservation must become survival ecology." Frontiers in Conservation Science 2 (2021): 659912. https://doi.org/10.3389/fcosc.2021.659912
Mc Cartney, Ann M., et al. "The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics." bioRxiv (2023): 2023-09, ver. 2 peer-reviewed and recommended by Peer Community in Genomics. https://doi.org/10.32942/X20W3Q
Richardson, Katherine, et al. "Earth beyond six of nine planetary boundaries." Science Advances 9.37 (2023): eadh2458. https://doi.org/10.1126/sciadv.adh2458
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The recommender in charge of the evaluation of the article and the reviewers declared that they have no conflict of interest (as defined in the code of conduct of PCI) with the authors or with the content of the article. The authors declared that they comply with the PCI rule of having no financial conflicts of interest in relation to the content of the article.
see acknowledgements section
Evaluation round #1
DOI or URL of the preprint: https://doi.org/10.32942/X20W3Q
Version of the preprint: 1
Author's Reply, 28 Oct 2023
Decision by Fernando Racimo, posted 31 Aug 2023, validated 31 Aug 2023
The manuscript by Marques et al. describe the Portuguese contribution to ERGA’s pilot effort, involving the sequencing and annotation of genomes of six Portuguese species that are endemic, iconic or endangered. The manuscript also presents a new Portuguese network of researchers working on biodiversity genomics, aiming to jointly train scientists, generate new knowledge and engage with the public about biodiversity efforts in the region.
The manuscript is generally well written, and I believe it needs no major revisions. Both reviewers agreed the text provides an extensive explanation behind the choice of species and methodological efforts underway. They both felt there was a bit of a need for enriching the manuscript with a brief statement about ongoing discoveries or concrete results that are emerging from the efforts described in the paper. I agree with them. I don't think this would have to go beyond one paragraph providing a taste of what is emerging from some of these sequencing studies, as I understand various manuscripts are also probably being prepared for each of the species. I also agree with anonymous reviewer 1 regarding the modification of Figure 2. A map detailing the locations of sampling (and perhaps species ranges?) would be a helpful addition.
Once these minor concerns are addressed, I would be happy to recommend this manuscript in PCI Genomics.