A team of researchers in Spain has successfully sequenced and analyzed the genome of the Iberian lynx (Lynx pardinus), the world’s most endangered feline and a unique example of a species on the brink of extinction.
The Iberian lynx is one of the four extant lynx species that share a short bobbed tail, spotted coat, muscular body, long legs, and characteristic tufted ears and beard-resembling ruffs.
Also known as the Spanish lynx, this species is only about half the size of the Eurasian lynx (Lynx lynx) and is closer in size to the Canadian lynx (Lynx canadensis) and the bobcat (Lynx rufus).
The Iberian and Eurasian lynx are sister species and the two extant lynxes in Eurasia. In contrast to the large, generalist and widespread Eurasian lynx, the Iberian lynx is smaller and a habitat- and prey-specialist, being restricted to the Mediterranean region in the Iberian Peninsula where they prey almost exclusively on European rabbits (Oryctolagus cuniculus).
Supposed to be once fairly abundant and widely distributed across the Iberian Peninsula, a steep decline during the second half of the 20th century left less than 100 individuals (less than 62 mature) distributed in the two isolated populations of Doñana and Andújar (Sierra Morena) in Andalusia, southern Spain, leading to its recognition as the most endangered felid in the world and to its classification as ‘critically endangered’ in the 2002, 2006, and 2008 IUCN red lists.
According to a new genetic analysis published this week in the journal Genome Biology, the Iberian lynx has one of the least diverse genomes among mammals.
The study authors, headed by Dr. José Godoy, a researcher at the Doñana Biological Station of the Spanish National Research Council, sequenced, assembled, and annotated a draft genome of an Iberian male named Candiles, and re-sequenced another ten Iberian and one Eurasian lynx genomes.
In addition, to obtain gene expression data and to assist gene annotation they characterized the transcriptome of 11 lynx tissues.
“We managed to read and organize 2.4 billion letters of DNA from Candiles, a male lynx born in the Sierra Morena lynx population,” the authors said.
“To do so, we used new sequencing techniques and developed innovative procedures to generate a high-quality draft genome.”
A total of 21,257 genes were identified, a number similar to that of human beings and other mammals, and they have been compared to those of cats, tigers, cheetahs and dogs.
“Specifically, we compared the Iberian lynx genome with those of other species, attempting to identify genes that have lost their function because they have remained isolated and the existence of a small population of specimens of this species,” the scientists said.
They found evidence of modifications in genes related with the senses of hearing, sight and smell to facilitate the adaptation of the lynx to its environment, which have enabled them to become exceptional hunters specialized in rabbits as prey.
“With the aim of studying the history and genetic diversity of the species, analysis was conducted on the genomes of another ten Iberian lynxes from Doñana and Sierra Morena, the only two surviving populations on the Iberian Peninsula, which have been isolated from each other for decades,” the authors said.
The team also completed a comparative analysis with the European lynx, to discover the bonds between the two lynxes that inhabit Eurasia.
“The Iberian lynx began to diverge from its sister species some 300,000 years ago, and the two species became completely separated some 2,500 years ago,” the researchers said.
“Throughout that period, they continued to cross-breed and exchange genes, probably in the periods between glaciations, when the climatology allowed the species to spread and encounter each other on the Iberian Peninsula and in southern Europe.”
The scientists also identified a series of severe population bottlenecks in the history of the Iberian lynx that predate its known demographic decline during the 20th century and have greatly impacted its genome evolution.
“The demographic history of the Iberian lynx has been marked by three historic declines, the last of which took place some 300 years ago, decimating its population,” they explained. “In addition to this, there was a drastic drop in the number of specimens in the 20th century due to its persecution, the destruction of its habitat, and two major viral epidemics suffered by the rabbit, its main food source.”
The team interpreted these demographic drops as the cause of the low levels of diversity observed, and warns that this could impair the lynx’s capacity to adapt to changes in its environment.
“Furthermore, the existence of multiple potentially harmful genetic variants was confirmed, which could be contributing to the reduced survival and reproduction rates of the species,” they said.
“This genetic deterioration is especially marked in the Doñana population — smaller, and isolated for a longer period — which has half the genetic diversity of the Sierra Morena group.”
“Nevertheless, the study reflects the situation before the exchange between the two relict populations and their inter-breeding in captivity begun.”
“These measures, taken within the Iberian lynx conservation program, have led to improvement of the species’ genetic situation in recent years.”
Federico Abascal et al. 2016. Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx. Genome Biology 17: 251; doi: 10.1186/s13059-016-1090-1