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The endan­gered Iber­ian lynx, the species with least genetic diversity

pub­lished 19 Decem­ber 2016 | mod­i­fied 27 Decem­ber 2016

Iberian lynx with lambSpan­ish sci­en­tists have sequenced the genome of the Iber­ian lynx (Lynx par­di­nus), cur­rently one of the world’s most endan­gered felines. They have con­firmed the “extreme ero­sion” suf­fered by its DNA. The Iber­ian lynx has one of the least genetically-​diverse genomes. It is even less diverse than other endan­gered mam­mals, such as the chee­tah or Tas­man­ian devil, or birds like the crested ibis or osprey.

The study, pub­lished on 14 Decem­ber in the sci­en­tific jour­nal Genome Biol­ogy, has been coor­di­nated by sci­en­tists from the Doñana Bio­log­i­cal Sta­tion (CSIC). Span­ish researchers from The Cen­tre for Genomic Reg­u­la­tion (CRG) con­tributed to this project that deliv­ered the first mam­mal genome of ref­er­ence gen­er­ated entirely in Spain. The project involved the efforts of 50 sci­en­tists from research groups of 12 insti­tu­tions, two of them from out­side Spain, that cover a broad range of dis­ci­plines, includ­ing bioin­for­mat­ics, genomics, oncol­ogy, evo­lu­tion and conservation.

The method
The sci­en­tists have man­aged to read and organ­ise 2.4 bil­lion let­ters of DNA from Can­diles, a male lynx born in the Sierra Morena lynx pop­u­la­tion, who now forms part of a cap­tive breed­ing pro­gramme. To do so, they have used new sequenc­ing tech­niques and devel­oped inno­v­a­tive pro­ce­dures to gen­er­ate a high-​quality draft genome on a lim­ited budget.

The result
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, Toni Gabaldón’s group at the CRG in Barcelona has 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. Researchers have 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.

Con­ser­va­tion his­tory of the Iber­ian lynx
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. Researchers have also com­pleted a com­par­a­tive analy­sis with a Euro­pean lynx, to dis­cover the bonds between the two species of lynx that inhabit Eurasia.

The Iber­ian lynx began to diverge from its con­spe­cific, the Eurasian lynx (Lynx lynx) some 300,000 years ago, and the two species became com­pletely sep­a­rated about 2,500 years ago. 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.

Pop­u­la­tion decline
The demo­graphic his­tory of the Iber­ian lynx has been marked by three his­toric declines, the last of which took place approx­i­mately 300 years ago, dec­i­mat­ing its pop­u­la­tion. 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. Cur­rently the Iber­ian lynx is clas­si­fied as Endan­gered by the IUCN Red List of Threat­ened Species.

Sci­en­tists have inter­preted these demo­graphic drops as the cause of the low lev­els of diver­sity observed, and warn that this could impair the lynx’s capac­ity to adapt to changes in its envi­ron­ment (cli­mate, dis­ease, etc.). Fur­ther­more, exis­tence of mul­ti­ple poten­tially harm­ful genetic vari­ants has been con­firmed, which could be con­tribut­ing to the reduced sur­vival and repro­duc­tion rates of the species. 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.

Improve­ment mea­sures
Nev­er­the­less, the study reflects the sit­u­a­tion before the exchange between the two relict pop­u­la­tions and their inter­breed­ing in cap­tiv­ity were begun. These mea­sures, taken within the Iber­ian lynx con­ser­va­tion pro­gramme, have led to improve­ment of the species’ genetic sit­u­a­tion in recent years.

The use of new genomic resources, within the frame­work of the project, will con­tribute to opti­miz­ing man­age­ment aimed at pre­serv­ing the great­est genetic diver­sity, in addi­tion to dimin­ish­ing these pop­u­la­tions’ genetic defects as much as possible.

(Source: Cen­tre for Genomic Reg­u­la­tion press release, 14.12.2016)

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