Endangered island endemic plants have vulnerable genomes

Abstract

Loss of genetic diversity is known to decrease the fitness of species and is a critical factor that increases extinction risk. However, there is little evidence for higher vulnerability and extinction risk in endangered species based on genomic differences between endangered and non-endangered species. This is true even in the case of functional loci, which are more likely to relate to the fitness of species than neutral loci. Here, we compared the genome-wide genetic diversity, proportion of duplicated genes ( P D ), and accumulation of deleterious variations of endangered island endemic (EIE) plants from four genera with those of their non-endangered (NE) widespread congeners. We focused on exhaustive sequences of expressed genes obtained by RNA sequencing. Most EIE species exhibited significantly lower genetic diversity and P D than NE species. Additionally, all endangered species accumulated deleterious variations. Our findings provide new insights into the genomic traits of EIE species.

Island songbirds as windows into evolution in small populations

“…Previous taxon-specific studies have reported low Ne in a diverse range of island organisms (e.g., giant Galá pagos tortoises, 24 woolly mammoths, 25 island foxes, 26,27 and Corvus 28 ). Therefore, it is very likely that island species predominantly exhibit lower Ne than their more abundant, broadly distributed, mainland relatives, and this pattern may not be restricted to some specific animal clades such as birds or mammals but may also be true for a large range of taxa (e.g., Hamabata et al 29 for plants). More broadly, this result opens up new opportunities for using island species as models to understand the impact of Ne on genome evolution in natural populations, including genome size, or of natural selection on non-coding genomic regions.…”

Genome Sequencing of the Endangered Kingdonia uniflora (Circaeasteraceae, Ranunculales) Reveals Potential Mechanisms of Evolutionary Specialization

“…Shrinking habitats and low adaptive ability to new environments together lead some plants to endangered status. A recent study has shown that endangered species have more vulnerable genomes than that of congeneric non-endangered species (Hamabata et al, 2019); in fact, the endangered species exhibited significantly lower genetic diversity ll OPEN ACCESS and proportion of duplicated genes and accumulated more deleterious variations than non-endangered species. Owing to limited genomic studies, genomic changes of endangered plants are largely unknown.…”

“…Owing to limited genomic studies, genomic changes of endangered plants are largely unknown. To clarify which genetic factors contribute to vulnerability in endangered species, genome-wide genetic changes in functionality should be assessed (Hamabata et al, 2019).…”

Impacts by feral goats on critically endangered Crepidiastrum grandicollum (Compositae) endemic to the Ogasawara Islands

“…These factors suggest that immediate eradication of the moth is difficult. Moreover, accumulation of harmful genes is progressing in critically endangered species in Ogasawara, including in C. grandicollum (Hamabata et al, 2019), and decreased genetic diversity may lead to reduced defensive ability against herbivores (Sato, 2018). Although protection of the natural habitat is a basic method of species conservation, in the case of C. grandicollum , population restoration in novel habitats is necessary to avoid insect damage and to prevent erosion of genetic diversity (IUCN/SSC, 2013).…”