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Pandascape: Applying Next Generation Sequencing To Conservation Problems

You can now add ‘panda conservation’ to your list of next-generation sequencing applications! Earlier this year in Nature Genetics, a team of Chinese and Danish researchers published new findings on genetic diversity and population structure for the giant panda (Ailuropoda melanoleuca), based on the genome sequences of dozens of wild pandas. Though the darling of Western conservationists and the star of over four decades of ‘panda diplomacy’, China’s favorite non-bear bear is in trouble. Wild population estimates don’t top 2,000. Giant pandas are wedded to their bamboo habitats (the trees make up over 90% of their decidedly un-bearlike diet), but rampant deforestation across central China has taken its toll.

All hands on deck

The Chinese government has invested heavily in conservation efforts, including opening over forty panda sanctuaries. Worldwide breeding programs through zoos (who receive giant pandas for decade-long loans through the aforementioned ‘panda diplomacy’) are also popular. But these efforts, though noble, run the risk of saving the giant panda at the cost of its genetic diversity.

Eroded genes

Ideally, conservation efforts would promote demographic recovery whilst preventing genetic bottlenecks. However, retrospective analyses of some successful conservation efforts show that randomly saving breeding pairs extracts a heavy cost in the loss of whole historical populations and severely eroded genetic diversity among the survivors, as shown recently for New Zealand’s little spotted kiwi.

Take into account

To prevent a similar fate for the giant panda, all conservation efforts and breeding programs should take into account both the panda’s population structure in its dwindling native range and the diversity within and between genetically distinct populations.  Zhao et al.’s report in Nature Genetics represents an important step in collecting these sorts of data.

Two become three

Their study subjects were 34 giant pandas (some 2% of the wild population), hailing from dozens of sites across three provinces. Blood and muscle samples yielded genomic DNA for whole-genome sequencing, with an overage of 10.5 Gb of mapped reads per individual (~4.67-fold coverage across the 2.25 Gb panda genome, if you’re curious). Among all 34 individuals, Zhao et al. reported over 13 million SNPs and three genetically-distinct population clusters. Previous estimates had suggested only two giant panda populations. Yet despite their small numbers, the giant panda’s genetic diversity rivals ours.

Trading meat for bamboo

Bayesian tests detected the signatures of selection in over 100 genes among panda populations, including taste and olfactory receptor genes. Researchers already knew of some changes in sensory system dynamics during in panda evolution (a prominent umami receptor gene went the way of the dodo when ancient pandas traded in meat for bamboo). But, the biological roles of these loci under selection are murky, at best.

Bitter herbs

At least two of these are bitter taste receptor genes and one of these, Tas2r49, is under positive selection in a population that consumes a large amount of alkaloid-rich bamboo leaves. Bitter herbs aside, conservationists would no doubt like to know the roles these genes might play in local adaptation, particularly as they choose release sites for sanctuary-bred pandas to fortify their numbers.

It was the best of times, it was the worst of times

Zhao et al. also used genome-wide SNP data for all three populations in statistical models to infer the giant panda’s population history over the past eight million years. Their models predict historic population dynamics that waxed and waned with the glaciers. In warmer times, their beloved bamboo forests expanded and giant pandas roamed swathes of ancient China and southeast Asia. Some 300,000 years ago the first group of extant giant pandas diverged from other panda populations. This troupe, a shadow of its former self, now hugs shrinking bamboo forests in Shaanxi Province’s Qin Mountains.

Deforestation

While glaciation shaped the destiny of their forbearers, for the past three millennia the giant panda’s fate has been intimately intertwined with human activity. The 3,000-year decline of Qin Mountain pandas coincides with road construction, urbanization, and agriculture-fuelled deforestation. Deforestation and road construction may have also established the two youngest giant panda populations some 2,800 years ago.

Lessons

While it’s too late to erase the footprints which humanity has stamped all over the panda’s bamboo realm, these whole-genome surveys should at least help conservationists target their limited resources toward efforts to increase panda numbers and preserve their rich genetic diversity, all without disrupting existing population structures or placing pandas in areas for which they are ill-adapted. Next-generation sequencing surveys like this could assist other conservation efforts for vulnerable or endangered species- especially by identifying cryptic population structures, establishing a baseline genetic diversity, and uncovering loci of potential importance to local adaptation. With over 17,000 species listed as vulnerable or endangered by the International Union for Conservation of Nature, there are plenty of targets to choose from, though most lack the panda’s diplomatic clout.

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