Old dogs, and ‘carnivorous’ pandas

It was a good fortnight for large mammals! Two recent studies attempt to date the emergence of modern canids, and offer insights into the gut microbiomes of giant pandas.

In retrospect, Po could quite possibly kick butt, and chomp on the Wolf Boss just as well…(Image courtesy: Kung Fu Panda 2)

Ancient Wolf Genome Reveals an Early Divergence of Domestic Dog Ancestors and Admixture into High-Latitude Breeds. Skoglund et al. (2015) Current Biology

Previous studies have dated the divergence of modern dogs and wolves to the LGM, and before using both fossil and genetic evidence.

Admixture history (model) fitted to the data. Branch lengths are proportional to drift. Image courtesy: Figure 2 of Skoglund et al. (2015)

Admixture history (model) fitted to the data. Branch lengths are proportional to drift. Image courtesy: Figure 2 of Skoglund et al. (2015)

Skoglund et al. (2015) in a new manuscript attempt to resolve the emergence of modern canids using the genome of an ancient wolf from the Taimyr peninsula in Siberia to suggest a much older divergence date (>35,000 ybp, consistent with carbon dating estimates). The authors (a) construct an mtDNA phylogeny which suggests that the Taimyr wolf comprises a distinct lineage from all modern dog lineages, (b) estimate divergence time between modern dogs, and the Taimyr wolf using D statistics (also called the ABBA-BABA statistics – see Patterson et al. (2012)) to be consistent with the ~35,000 ybp carbon-dating estimate by using a slower mutation rate, (c) estimate approximately 3.5% (1.4% – 27.3%) derived ancestry in modern canids from Greenland, suggesting recent divergence of wolves and modern canids from the Taimyr wolf’s lineage.

…we find that the ancestry of present-day dog breeds descends from more than a single domestication event, since high-latitude dog breeds such as the Siberian Husky and Greenland Sledge Dogs can trace part of their ancestry to the now-extinct Taimyr wolf lineage. This introgression could have provided early dogs in high latitudes with phenotypic variation beneficial for adaptation to a new challenging environment.

The Bamboo-Eating Giant Panda Harbors a Carnivore-Like Gut Microbiota, with Excessive Seasonal Variations. Xue et al. (2015) mBio

In another interesting find, Xue et al. (2015) report that the 16s rRNA gene-based profile of fecal microbiota of the strictly bamboo-eating giant panda (Ailuropoda melanoleuca) indicates a surprisingly ‘carnivorous’ microbiome (Enterobacteriacae, and Streptococcus), as against surmised microbiota that are seen in other herbivores (Clostridiales, Fibrobacterales, etc).

PCoA of gut microbiota structure of giant pandas and other herbivores, omnivores, and carnivores. Image courtesy: Figure 4 of Xue et al. (2015)

PCoA of gut microbiota structure of giant pandas and other herbivores, omnivores, and carnivores. Image courtesy: Figure 4 of Xue et al. (2015)

Using 121 fecal samples from adults, and cubs, bacterial 16s rRNA genes were sequenced and analyzed to study the compositional variation of microbiota in the giant panda. Findings suggest (a) relative abundance of Streptococcus, and Escherichia across all samples, (b) drastic seasonal and age-related variation with significantly reduced diversity in late autumnal samples, and (c) a comparison of microbiome diversity using a PCoA indicate similarities in variation (clustering) of fecal microbiomes of the giant panda, and other carnivores.

 

Unlike other mammalian species that have evolved gut microbiota (and also digestive system anatomies) optimized for their specific diets, the aberrant coevolution of the giant panda, its dietary preferences, and its gut microbiota remains enigmatic.

References

Skoglund, Pontus, et al. “Ancient Wolf Genome Reveals an Early Divergence of Domestic Dog Ancestors and Admixture into High-Latitude Breeds.” Current Biology (2015). DOI:  http://dx.doi.org/10.1016/j.cub.2015.04.019

Xue, Zhengsheng, et al. “The Bamboo-Eating Giant Panda Harbors a Carnivore-Like Gut Microbiota, with Excessive Seasonal Variations.” mBio 6.3 (2015): e00022-15. DOI: http://dx.doi.org/10.1128/mBio.00022-15

Patterson N, Moorjani P, Luo Y, Mallick S, Rohland N, Zhan Y, Genschoreck T, Webster T, Reich D. 2012. Ancient admixture in human history. Genetics 192:1065–1093. DOI: http://dx.doi.org/10.1534/genetics.112.145037

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About Arun Sethuraman

I am a computational biologist, and I build statistical models and tools for population genetics. I am particularly interested in studying the dynamics of structured populations, genetic admixture, and ancestral demography.
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