Conservation of biodiversity in the genomics era

Abstract

"Conservation genomics" encompasses the idea that genome-scale data will improve the capacity of resource managers to protect species. Although genetic approaches have long been used in conservation research, it has only recently become tractable to generate genome-wide data at a scale that is useful for conservation. In this Review, we discuss how genome-scale data can inform species delineation in the face of admixture, facilitate evolution through the identification of adaptive alleles, and enhance evolutionary rescue based on genomic patterns of inbreeding. As genomic approaches become more widely adopted in conservation, we expect that they will have a positive impact on management and policy decisions.

Fig. 1

Variation in evolutionary history due to admixture, using American bison as an example. a, b The two different evolutionary histories that are present in the genomes of bison from the Santa Catalina Island herd. c The autosomal tree (gray) with the two different mitochondrial trees superimposed (red and black). Examining autosomal markers, 99.4% of the population is represented by the unintrogressed tree. Examining mitochondrial markers, 55.1% of the population is represented by the unintrogressed tree (black), and 44.9% follow the introgressed tree (red). Data from Hedrick [23]

Fig. 2

Photos of a (a) gray wolf (photo by Derek Bakken), (b) an eastern wolf (photo by Christian Mehlführer), and (c) a coyote. Photos from Wikimedia Commons

Fig. 3

a Geographic cline of coyote ancestry in gray wolves. Coyote ancestry increases towards the eastern portion of the range, coincident with the increased persecution of wolves that reduced population densities, resulting in an increased probability of admixture with other canid species. Samples are labeled with the geographic location of collection. b The state or province of the sample collection (red). Data from vonHoldt et al. [52]

Fig. 4

Photos of a healthy (a) and a diseased (b) Tasmanian devil. Photos courtesy of the Save the Tasmanian Devil Program

Fig. 5

Manhattan plot of adjusted p values of the Tasmanian devil genome-wide association study (GWAS) comparing seven devils that recovered after infection with devil facial tumor disease (DFTD) to six devils that succumbed to the disease. Scaffolds are placed on chromosomes but are unordered. Circles indicate the five candidate SNPs, which are located on three scaffolds. Four of the candidate SNPs (on Chr3 and Chr6) remained significant after including additional samples. Data courtesy of Wright et al. [61]