Landscape Genomic Conservation Assessment of a Narrow-Endemic and a Widespread Morning Glory From Amazonian Savannas.

Éder C Lanes,Nelson M Carvalho Filho,Vera L Imperatriz-Fonseca,José O Siqueira,Rodolfo Jaffé,Pedro W Souza-Filho,Tereza C Giannini,Ana M Giulietti,Amanda R Silva,Santelmo Vasconcelos,Nathaniel S Pope,Waléria Monteiro,Guilherme Oliveira,Ronnie Alves

doi:10.3389/fpls.2018.00532

Abstract

Although genetic diversity ultimately determines the ability of organisms to adapt to environmental changes, conservation assessments like the widely used International Union for Conservation of Nature (IUCN) Red List Criteria do not explicitly consider genetic information. Including a genetic dimension into the IUCN Red List Criteria would greatly enhance conservation efforts, because the demographic parameters traditionally considered are poor predictors of the evolutionary resilience of natural populations to global change. Here we perform the first genomic assessment of genetic diversity, gene flow, and patterns of local adaptation in tropical plant species belonging to different IUCN Red List Categories. Employing RAD-sequencing we identified tens of thousands of single-nucleotide polymorphisms in an endangered narrow-endemic and a least concern widespread morning glory (Convolvulaceae) from Amazonian savannas, a highly threatened and under-protected tropical ecosystem. Our results reveal greater genetic diversity and less spatial genetic structure in the endangered species. Whereas terrain roughness affected gene flow in both species, forested and mining areas were found to hinder gene flow in the endangered plant. Finally we implemented environmental association tests and genome scans for selection, and identified a higher proportion of candidate adaptive loci in the widespread species. These mainly contained genes related to pathogen resistance and physiological adaptations to life in nutrient-limited environments. Our study emphasizes that IUCN Red List Criteria do not always prioritize species with low genetic diversity or whose genetic variation is being affected by habitat loss and fragmentation, and calls for the inclusion of genetic information into conservation assessments. More generally, our study exemplifies how landscape genomic tools can be employed to assess the status, threats and adaptive responses of imperiled biodiversity.

Highlights

Species conservation assessments have largely neglected measures of genetic diversity, even though genetic diversity determines the ability to adapt to environmental changes and underpins species long-term persistence (Reed and Frankham, 2003; Allendorf et al, 2012; Jamieson and Allendorf, 2012)
Willoughby et al (2015) gathered 1941 microsatellite datasets from wild populations of five vertebrate classes. They compared empirical estimates of heterozygosity and allelic richness between threatened and non-threatened species, and found that genetic diversity is generally reduced in threatened species. When they considered which of the International Union for Conservation of Nature (IUCN) Red List Criteria are most effective at identifying genetically depauperate species, they found that the existing criteria failed to systematically identify populations with low genetic diversity (Willoughby et al, 2015)
While heterozygosity and inbreeding levels were similar between I. cavalcantei and the analyzed populations of I. maurandioides, nucleotide diversity, Tajima’s D and effective population size were higher in I. cavalcantei (Table 1)

Summary

Introduction

Species conservation assessments have largely neglected measures of genetic diversity, even though genetic diversity determines the ability to adapt to environmental changes and underpins species long-term persistence (Reed and Frankham, 2003; Allendorf et al, 2012; Jamieson and Allendorf, 2012). Willoughby et al (2015) gathered 1941 microsatellite datasets from wild populations of five vertebrate classes They compared empirical estimates of heterozygosity and allelic richness between threatened and non-threatened species, and found that genetic diversity is generally reduced in threatened species. When they considered which of the IUCN Red List Criteria (including declining population size, species range extent, and the number of mature individuals) are most effective at identifying genetically depauperate species, they found that the existing criteria failed to systematically identify populations with low genetic diversity (Willoughby et al, 2015). The genetic consequences of habitat degradation and fragmentation in relation to the IUCN Red List Categories remain largely unexplored

Methods

Results

Conclusion