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August 27, 2018

Cave bears live on in brown bears, and were vegetarians (what!?!?!)

Filed under: Ancient DNA,cave bears,paleogenomics — Razib Khan @ 8:39 pm


Unless you’ve been asleep you are aware of another megafauna ancient DNA discover, Partial genomic survival of cave bears in living brown bears:

Although many large mammal species went extinct at the end of the Pleistocene epoch, their DNA may persist due to past episodes of interspecies admixture. However, direct empirical evidence of the persistence of ancient alleles remains scarce. Here, we present multifold coverage genomic data from four Late Pleistocene cave bears (Ursus spelaeus complex) and show that cave bears hybridized with brown bears (Ursus arctos) during the Pleistocene. We develop an approach to assess both the directionality and relative timing of gene flow. We find that segments of cave bear DNA still persist in the genomes of living brown bears, with cave bears contributing 0.9 to 2.4% of the genomes of all brown bears investigated. Our results show that even though extinction is typically considered as absolute, following admixture, fragments of the gene pool of extinct species can survive for tens of thousands of years in the genomes of extant recipient species.

A sad thing about this publication is that brought to my attention that these ancient cave bears were mostly herbivores. It makes me view The Clan of the Cave Bear differently!

I assume most readers of this weblog are not surprised. We know that various extant and extinct members of the elephant lineage have mixed. By a strange coincidence (or perhaps not?) the fraction of cave bear DNA in modern brown bears seems very similar to the fractions of Neanderthal DNA we seen in modern lineages. The authors infer that the gene flow may also have been bidirectional, so various bear lineages had multiple and complex interactions over hundreds of thousands of years. Something notable is that the divergence between cave and brown bears is considerably deeper than that between Neanderthals and modern humans. If the latter can be dated to around 750,000 years ago, with large intervals on either side, the bears apparently separated into separate species 1.2 to 1.4 million years ago.

The greater time depth is of interest to the authors. From The New York Times:

“We did not expect to find this at all because they’re really quite diverse in terms of their evolution,” Dr. Barlow said.

The team was also able to determine that the genes flowed both ways between species, with the cave bears also carrying some brown bear DNA. The most recent transfer of genes came from the cave bear to the brown, the study found.

Brown bears are more closely related to polar bears than they were to cave bears from whom they diverged more than a million years ago, he said. Cave bears were largely herbivores, while brown bears are meat-eaters and about 20 percent smaller than cave bears, with more delicate bones. A brown bear would probably have looked “wimpy” next to a cave bear, he said.

The expectation here is conditional on the idea that bears which occupy different ecological niches probably won’t hybridize even if they overlap in range.

All that being said, when Greg Cochran started talking about archaic admixture into modern lineages in 2005 I read up on the mammalian hybridization literature and came to the conclusion that a priori there was no reason why Neanderthals and modern (African) humans couldn’t have produced fertile offspring. Big mammals tend to occupy a lot of territory, and different big mammal lineages overlap. It seems rather common for gene flow to occur between them. There is evidence of jackal and coyote introgression into Eurasian wolves, for example.

So I  guess I’m not that surprised. And David Quammen’s new book, The Tangled Tree, presents a rather non-revolutionary message from where I stand. Though perhaps it hasn’t gotten out to the “public.” The complexity and multi-textured reality of the “species problem” is pretty clear to any biologist who work’s on population-level data.

Cave bears live on in brown bears, and were vegetarians (what!?!?!)

Filed under: Ancient DNA,cave bears,paleogenomics — Razib Khan @ 8:39 pm


Unless you’ve been asleep you are aware of another megafauna ancient DNA discover, Partial genomic survival of cave bears in living brown bears:

Although many large mammal species went extinct at the end of the Pleistocene epoch, their DNA may persist due to past episodes of interspecies admixture. However, direct empirical evidence of the persistence of ancient alleles remains scarce. Here, we present multifold coverage genomic data from four Late Pleistocene cave bears (Ursus spelaeus complex) and show that cave bears hybridized with brown bears (Ursus arctos) during the Pleistocene. We develop an approach to assess both the directionality and relative timing of gene flow. We find that segments of cave bear DNA still persist in the genomes of living brown bears, with cave bears contributing 0.9 to 2.4% of the genomes of all brown bears investigated. Our results show that even though extinction is typically considered as absolute, following admixture, fragments of the gene pool of extinct species can survive for tens of thousands of years in the genomes of extant recipient species.

A sad thing about this publication is that brought to my attention that these ancient cave bears were mostly herbivores. It makes me view The Clan of the Cave Bear differently!

I assume most readers of this weblog are not surprised. We know that various extant and extinct members of the elephant lineage have mixed. By a strange coincidence (or perhaps not?) the fraction of cave bear DNA in modern brown bears seems very similar to the fractions of Neanderthal DNA we seen in modern lineages. The authors infer that the gene flow may also have been bidirectional, so various bear lineages had multiple and complex interactions over hundreds of thousands of years. Something notable is that the divergence between cave and brown bears is considerably deeper than that between Neanderthals and modern humans. If the latter can be dated to around 750,000 years ago, with large intervals on either side, the bears apparently separated into separate species 1.2 to 1.4 million years ago.

The greater time depth is of interest to the authors. From The New York Times:

“We did not expect to find this at all because they’re really quite diverse in terms of their evolution,” Dr. Barlow said.

The team was also able to determine that the genes flowed both ways between species, with the cave bears also carrying some brown bear DNA. The most recent transfer of genes came from the cave bear to the brown, the study found.

Brown bears are more closely related to polar bears than they were to cave bears from whom they diverged more than a million years ago, he said. Cave bears were largely herbivores, while brown bears are meat-eaters and about 20 percent smaller than cave bears, with more delicate bones. A brown bear would probably have looked “wimpy” next to a cave bear, he said.

The expectation here is conditional on the idea that bears which occupy different ecological niches probably won’t hybridize even if they overlap in range.

All that being said, when Greg Cochran started talking about archaic admixture into modern lineages in 2005 I read up on the mammalian hybridization literature and came to the conclusion that a priori there was no reason why Neanderthals and modern (African) humans couldn’t have produced fertile offspring. Big mammals tend to occupy a lot of territory, and different big mammal lineages overlap. It seems rather common for gene flow to occur between them. There is evidence of jackal and coyote introgression into Eurasian wolves, for example.

So I  guess I’m not that surprised. And David Quammen’s new book, The Tangled Tree, presents a rather non-revolutionary message from where I stand. Though perhaps it hasn’t gotten out to the “public.” The complexity and multi-textured reality of the “species problem” is pretty clear to any biologist who work’s on population-level data.

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