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.

Keywords: Conservation biology; Evolutionary ecology; Evolutionary genetics; Plant genetics.

Fig. 1

Map showing the distribution sites of the plant species used in this study a, and enlarged map of the Ogasawara Islands, where the six endangered plant species in this study are distributing b. Pictures boxed in red show the endangered island endemic (EIE) species with its classification in the Red List category (bottom left), and pictures boxed in white show the non-endangered (NE) species in each genus. Each painted island map on the right side of the picture of endangered species indicates its distribution; black-painted means distributing in the island, gray-painted means extinct in the island, and white-painted means not-distributing in the island. The number below the painted island map indicates the estimated current number of individuals of the endangered species. The Red List category is as follows; CR is Critically Endangered, EN is Endangered, and VU is Vulnerable. Distribution ranges of the non-endangered species are as follows; A. pygmaea in Kyushu and the Ryukyu Archipelago, A shikotanensis in Honshu, C. lanceolatam in Honshu, Korean Peninsula and Mainland China, C. keiskeanum in Honshu, Shikoku, Kyushu, Korean Peninsula and Mainland China, C. triplicata in Kyushu, the Ryukyu Archipelago, Taiwan, and Mainland China, and M. candidum the Ryukyu Archipelago, Taiwan, and Mainland China

Fig. 2

Mean values of the number of synonymous SNVs for heterozygous loci (counts per kb). The values compared between endangered island endemic (EIE) and non-endangered (NE) species within the same genus are connected by lines between species

Fig. 3

Mean values of the proportion of deleterious variations in non-synonymous SNVs on transcripts with heterozygous loci estimated by PROVEAN a, and the proportions of SNVs that varied by nonsense SNVs (loss-of-function SNVs) to total non-synonymous SNVs b. The values compared between EIE and NE species within the same genus are connected by lines between species

Fig. 4

Proportion of duplicated genes for endangered and non-endangered species. The values compared between EIE and NE species within the same genus are connected by lines between species