Vulnerable genomes of endangered species
We showed genomic patterns such as reduced genetic diversity, accumulation of deleterious variation, and a low proportion of duplicated genes, specific to the genome of endangered species. A species’ risk of extinction could be predicted by examining its genomic information.
Organisms inhabit various environments, but the habitat distribution varies greatly depending on the species. Species that inhabit a specific environment are greatly affected by environmental changes such as global warming, while species inhabiting diverse environments will adapt to new or fluctuating conditions. However, little is known about the mechanisms that allow organisms to adapt to more diverse environments. I have previously conducted researches on gene duplication, which can be considered a source of genetic diversity as it relates to the ability of organisms to adapt to their environment.
When gene duplication occurs in a genome, mutations will accumulate under relaxed functional constraints, resulting in the creation of a novel gene function. Therefore, I hypothesized that a species maintaining duplicated genes in its genome would have high environmental adaptability to survive in various environments. I found that the proportion of duplicated genes (PD) was positively correlated with habitat diversity for Drosophila1 and mammalian2. Additionally, I discovered that invasive alien species with high environmental adaptability had a higher PD than non-invasive species3.
Invasive aliens have adapted to their new environments and have expanded their habitat range, while the rapid extinction of species has continued worldwide. Further research is essential for conserving ecosystems more effectively and for halting the extinction of species. However, it is difficult to formulate an effective conservation approach because appropriate methods for assessing the risk of extinction for a species have not yet been established.
From my previous studies of duplicated genes, I hypothesized that endangered species with low environmental adaptability might have a low PD. I therefore attempted to apply genomic information to extinction risk assessments of endangered species. During these risk assessments, we not only focused on PD but also on genetic diversity and the accumulation of deleterious variations. I was inspired by the results of our recent work, which showed that domestic species (e.g., chicken, dog, and rice) with small population sizes had low genetic diversity and an elevated proportion of deleterious variations compared with their wild relatives4.
In this study, RNA was extracted from six endangered plants from four genera (Ajuga boninsimae, Crepidiastrum grandicollum, Crepidiastrum ameristophyllum, Crepidiastrum linguifolium, Calanthe hoshii, and Melastoma tetramerum) in the Ogasawara Islands where are registered as a UNESCO World Heritage site as well as from closely related non-endangered species in Japan. We then obtained their genetic variations via RNA-seq analysis. Genetic variation in an evolutionary conserved locus was estimated to be deleterious. The proportion of the duplicated genes in assembled transcripts was estimated as a PD. Our results showed that endangered plants had lower genetic diversity, a higher proportion of deleterious variations, and lower PD when compared with closely related non-endangered plants.
There are concerns that the number of extinct species will increase owing to human activity and future climate change, meaning that developing conservation plans for endangered species is critical. Knowing in advance which species are vulnerable to environmental changes is important when considering conservation priorities. Our results show that genomic information could be used as a possible indicator to measure the risk of extinction for species. We hope that this novel approach to species conservation will advance the scientific knowledge in this field.
1. Makino, T. & Kawata, M. Habitat variability correlates with duplicate content of Drosophila genomes. Mol. Biol. Evol. 29, 3169–3179 (2012).
2. Tamate, S. C., Kawata, M. & Makino, T. Contribution of nonohnologous duplicated genes to high habitat variability in mammals. Mol. Biol. Evol. 31, 1779–1786 (2014).
3. Makino, T. & Kawata, M. Invasive invertebrates associated with highly duplicated gene content. Mol. Ecol. 28, 1652-1663 (2019).
4. Makino, T., Rubin, C. J., Carneiro, M., Axelsson, E., Andersson, L. & Webster, M. T. Elevated proportions of deleterious genetic variation in domestic animals and plants. Genome. Biol. Evol. 10, 276-290 (2018).