Use of the nucleotide diversity in COI mitochondrial gene as an early diagnostic of conservation status of animal species

Natalia Petit‐Marty,Maite Vázquez‐Luis,Iris E Hendriks

doi:10.1111/conl.12756

Abstract

AbstractSpecies assessed as threatened by the International Union of Conservation of Nature (IUCN) show evidence of declining population sizes. Genetic diversity is lost by this decline, which reduces the adaptive potential of the species and increases its extinction risk in a changing environment. In this study, we collected an extensive dataset of nucleotide diversities in the COI (Cytochrome C Oxidase subunit I) mitochondrial gene for 4,363 animal species assessed by IUCN and found significantly reduced levels of diversity in threatened species of long‐lived animal classes. Then, we built up a comparative frame by acquiring the 95% confidence interval (CI) of mean values of COI nucleotide diversity in bootstrapped samples of nonthreatened species. Finally, we tested the comparative frame with data from the endangered bivalve species, Pinna nobilis. We conclude that nucleotide diversity in COI is a good proxy for a first evaluation of the conservation status of species populations, where previous knowledge is lacking and census is difficult to perform .

Highlights

The rate of species extinction and biodiversity loss has greatly increased in the past decades, obtaining information about the conservation status of populations of species has become a priority (Ceballos, Ehrlich, & Dirzo, 2017)
Estimates of nucleotide diversity of molecular markers could be especially useful because the decrease in population size produces a genomewide decrease of neutral genetic variation (Charlesworth, 2009), that can be investigated by contrasting the levels of nucleotide diversity against neutral expectations (π = Ne*μ, where π is the nucleotide diversity, Ne is the effective population size, and μ is the mutation rate; Kimura, 1983)
Because insects have on average a greater number of generations per year than the other animals studied here, and genetic diversity depends on the mutation rate by generation, we hypothesize that insects recover the mutation– drift equilibrium in shorter periods of time than longlived animals when population reductions are not too drastic

Summary

Introduction

The rate of species extinction and biodiversity loss has greatly increased in the past decades, obtaining information about the conservation status of populations of species has become a priority (Ceballos, Ehrlich, & Dirzo, 2017). Direct estimates for population sizes by census are difficult to get, inferences on changes in species population sizes can be obtained by using molecular markers (Bonebrake, Christensen, Boggs, & Ehrlich, 2010). Estimates of nucleotide diversity of molecular markers could be especially useful because the decrease in population size produces a genomewide decrease of neutral genetic variation (Charlesworth, 2009), that can be investigated by contrasting the levels of nucleotide diversity against neutral expectations (π = Ne*μ, where π is the nucleotide diversity, Ne is the effective population size, and μ is the mutation rate; Kimura, 1983). As genetic diversity is the raw material on which natural selection acts, loss of genetic diversity negatively affects the ability of the species to cope with environmental changes (e.g., global climate change, new or changed diseases, new predators, etc.) or in other words restricts their adaptive potential (Spielman et al, 2004; Willi, Van Buskirk, & Hoffmann, 2006)

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Results

Conclusion