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 (PD), 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 PD than NE species. Additionally, all endangered species accumulated deleterious variations. Our findings provide new insights into the genomic traits of EIE species.

Highlights

  • Loss of genetic diversity is known to decrease the fitness of species and is a critical factor that increases extinction risk

  • We investigated whether the reduced efficacy of selection is evident in endangered island endemic (EIE) species based on the proportion of non-synonymous single-nucleotide variants (SNVs) in the total SNVs on the heterozygous loci of expressed genes

  • Samples for RNA extraction were collected from 15 individuals of six endemic plant species of four genera in Ogasawara: Ajuga boninsimae (n = 5), Crepidiastrum grandicollum (n = 4), Crepidiastrum ameristophyllum (n = 1), Crepidiastrum linguifolium (n = 2), Calanthe hoshii (n = 3), and Melastoma tetramerum (n = 3). These species are all classified as endangered by the List of Threatened and Endangered Wildlife Species of the Ministry of Environment, Japan, and were analyzed as EIE species in this study

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Summary

Introduction

Loss of genetic diversity is known to decrease the fitness of species and is a critical factor that increases extinction risk. Islands contribute to global biodiversity, insular species —oceanic island populations derived from a single individual in self-fertilizing species or a pair in non-self-fertilizing species—are generally expected to display low genetic diversity because of founder effects and lower subsequent population size[9]. Such species have few chances to recover genetic diversity owing to low immigration and gene flow in small, isolated populations on islands. There is little evidence that endangered island endemic (EIE) species experience the expected genomic changes: loss of genome-wide genetic diversity, or accumulation of deleterious mutations

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