SIMBA

Search for Innate Markers of Barbary Affinity

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 Obiettivo del progetto (Objective)

'Recent disparate studies on lion (Panthera leo) phylogeography have focused on both the mitochondrial cytochrome b gene and autosomal markers (SNP/Microsatellites) to produce a patchwork of results covering select regions of the lions range. The lack of an integrated approach to the question of lion evolutionary development has actively hindered conservation efforts, which rely on knowledge of the interrelationships between populations to effectively manage natural diversity. A major hurdle to achieving complete genetic coverage of lion populations throughout their modern range has been the very recent extinction of populations from North Africa (extinct ~1940) and the Middle East (extinct ~1957) and the rarity of lions representing the West African (P.l.senegalensis) and Central African (P.l.azandica) subspecies in the wild and in zoo populations. Recent advances in ancient DNA techniques now allow for the routine generation of sequence data in the range of millions of basepairs (MBP) from ancient material, opening up the possibility of recovering whole genomes (both mitochondrial and nuclear) from preserved remains. Application of cutting-edge aDNA techniques to the problems presented by lion phylogeography offers the means to produce a comprehensive study of lion evolution and expansion. To achieve these objective, the project will aim to: 1) Extract and enrich DNA from museum and modern P.leo samples representing rare and extinct populations, to produce high quality genomic libraries. 2) Generate complete mitochondrial genomes, the first to be sequenced from P.leo, and informative autosomal genes as well as a library of modern P.leo LINE elements 3) Generate a species level phylogeny covering complete range for modern lions using combined dataset of mtDNA and nuDNA, incorporating all previously published data. 4) Identify Barbary lion specific mtDNA SNPs, nuDNA SNPs and LINEs with which to screen zoo population.'

Introduzione (Teaser)

Recent extinction of regional populations and the rarity of certain subspecies have prevented scientists from achieving complete genetic coverage of lions through their modern range. An EU-funded project overcame these obstacles by extracting DNA from museum samples and rare subspecies of lions living in zoos.

Descrizione progetto (Article)

Greater understanding of the evolutionary development of lions and the interrelationship between populations is needed to effectively manage their natural diversity. Therefore, the 'Search for innate markers of Barbary affinity' (SIMBA) initiative built genomic libraries from ancient DNA and from extinct and endangered lion populations.

Project partners examined over 100 samples taken from museum and zoo collections of rare and extinct populations, and modern lions (Panthera leo). After initial tests, 75 were considered well-preserved enough to produce high-quality genomic libraries.

These libraries were then amplified, indexed and sequenced to generate sequences of mitochondrial DNA (mitogenome). Initial data was used to assemble complete mitogenomes for a number of specimens originating from North African, Cape, Gabonese, Iranian, Senegalese and Sudanese lion populations.

Researchers also used the best libraries to obtain nuclear DNA from key regions of the natural range of P. leo. This included the extinct North African, Iranian and Cape populations and the Pleistocene cave lion.

Results included the complete mitogenome from a Pleistocene cave lion (Panthera spelaea) and focused on phylogenetics within the Panthera genus. Phylogenetics is used to study evolutionary relationships between species and populations.

The evolutionary development within lion species was also studied using mitogenomes. This included the identification of useful DNA sequence variations known as single nucleotide polymorphisms to separate regional lion populations, such as the Barbary.

SIMBA's results have generated much discussion within lion conservation circles. This included collaboration with the African Lion Working Group to petition the International Union for Conservation of Nature (IUCN). The aim was to gain special protection for certain regional populations of lions.