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How massive sequencing helps endangered species

For a decade now, massive sequencing of environmental samples has been on the front lines of research in ecology-related studies. Some of the most notable work has focused on the analysis of microbial diversity in soil, while other studies that used NGS sequencing have enabled the analysis of old genomes, or the comparison of the microbiota of healthy individuals and patients, as described in a review published in Molecular Ecology. A lesser-known application of massive sequencing is its role in helping endangered species. The endangered species list for Spain includes the Iberian lynx, the North Atlantic right whale, the brown bear and the Mediterranean monk seal. The list of threatened or endangered species is growing, in most cases due to anthropogenic causes.

The greatest advantage of applying sequencing through NGS is the exponential increase in loci that can be studied, as opposed to classical techniques that only analyze microsatellites or SNP’s, according to a study published in the International Journal of Genomics. There is a growing body of studies that use massive sequencing to improve management of threatened or endangered populations, as shown by the annotation of genomes for species such as the Adriatic sturgeon and primates like the ring-tailed lemur. A recent research project, led by scientists from the Doñana Biological Station and the Centre for Genomic Regulation of Barcelona sequenced the genome of one of Spain’s most endangered species, the Iberian lynx. The study allowed researchers to decode the 21,000 genes of Candiles, a male lynx living in Sierra Morena, and compare his DNA with that of ten other specimens. The main purpose of the work was to improve the Iberian lynx conservation programs in consonance with projects underway in other regions to recover endangered species like the Tasmanian devil or the California condor.

Source: Iberian lynx ex-situ Conservation Program (Wikimedia)

The study, which annotated the complete genome of the Iberian lynx, was published in the journal Genome Biology. Its results have allowed researchers to determine the reduced genetic diversity and the high degree of erosion suffered by its DNA, two characteristics directly related with the limited margin of adaptation presented by the Iberian lynx. “We also describe several other aspects in which the genome of the Iberian lynx has been shaped by demographic declines. These include extended linkage disequilibrium, reduced GC-biased gene conversion, and high fixation rates of transposable elements, most notably in places where they can affect function (insertions in sense within genes), another signature of a less effective purifying selection”, said Dr. José A. Godoy, Principal Investigator of the study.

The Iberian lynx became significantly endangered in the second half of the 20th century, when the decimation of its main food source–rabbits–led to the disappearance of all but some 100 individuals, which remained in two isolated populations on the Iberian peninsula. The DNA analysis of the specimens now living in Sierra Morena and Doñana has determined that the individuals living in Doñana National Park have less genetic diversity than those inhabiting Sierra Morena. According to the experts, massive sequencing helps determine whether a species is recoverable. Fortunately, scientists believe the Iberian lynx has yet to reach the point of no return.

Source: Iberian lynx ex-situ Conservation Program (Wikimedia)

“Moreover, a large proportion of the variation that is observed in protein coding sequences is likely deleterious, meaning that they probably negatively affect the function of the corresponding proteins, and could thus be limiting survival and reproduction. These kinds of variants rarely become abundant in large populations due to natural selection, but this purifying process becomes less effective in small or bottlenecked populations”, stated Godoy. The approaches offered by genomics may lead to tools and data to maximize genetic diversity of endangered species, and reduce inbreeding with a view to improving crosses and diminishing the presence of genetic characters that limit its recovery. Among other traits, especially relevant are the juvenile epilepsy that affects the Iberian lynx or chondrodystrophy in the case of the Californian condor. Although much remains to be done in the application of genomic analysis to conservation biology, the initial studies are beginning to bear their fruits, with the aim of recovering species as extraordinary and iconic as the lynx.