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The evolutionary history of bears is characterized by gene flow across species
#1
Bears breed across species borders

Date: April 19, 2017
Source: Senckenberg Research Institute and Natural History Museum

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Brown bears may be intermediate hosts of genes between the geographically separated polar and sun bears because the brown bear distribution area overlaps with both of the species.
Credit: © Papa Bravo / Fotolia

Senckenberg scientists have sequenced the entire genomes of four bear species, making it now possible to analyze the evolutionary history of all bears at the genome level. It shows that gene flow, or gene exchange, between species by extensive hybridization, is possible between most bear species -- not only polar and brown bear. The DNA samples of different bear species came from different European zoos, underlining their importance not only for conservation, but also for research. The study published in Scientific Reports also questions the existing species concept in general, because other genome studies too have, frequently found gene flow among species.

Pizzly, grolars or "capuccino bears" are common names of the offspring resulting from the mating of grizzly bears (Ursus arctos) and polar bears (Ursus maritimus). "Such hybrids among bears are not as rare as we have hitherto assumed," says Prof. Dr. Axel Janke of the Senckenberg Biodiversity and Climate Research Center in Frankfurt. In a large-scale analysis, a team of scientists led by the German evolutionary geneticist has sequenced six complete bear genomes. Each genome is about 2.5 billion base pairs large. "With these new data of the sun bear, sloth bear, Asiatic black bear and spectacled bear, we now have the genomes of all known bear species," adds Janke.

It has previously been assumed that the number of hybrids between polar and brown bears is increasing due to climate change, because brown bears invade northern regions and polar bears move onto the sea ice later than usual. The new results show however that an abundant flow of genes among different bear species occurred to a good deal in the past. Hybrids are thus not necessarily linked to climate change. "Bears can form hybrids in different combinations," explains Janke, and adds: "We knew this from zoos. In the wild, so far this was only observed for polar bears and brown bear as well as Asiatic black and sun bear."

The new genomic data also show that there must have even been gene flow between the polar and sun bears. However, the two species live in geographically completely distinct areas and thus have never met. The researchers are able to explain this alleged contradiction by suggesting that an "intermediate host" or "vector species" has passed the genes on in various directions. The brown bear is an ideal candidate for this role as conveyor of genes: his geographic distribution overlaps with that of all other bear species and its genome contains polar bear genes. "By hybridization the brown bear could pass these polar bear genes on to other bear species in Asia," adds the Frankfurt scientist.

The detected gene flow among bears also questions the basic biological concept of a species. The biological species definition assumes that different species cannot produce offspring in the wild or that hybrid offspring are sterile. The best-known example of this is the mule -- a hybrid between a horse and a donkey. However, it has been observed that grolars, the hybrids between polar and grizzly bears, are often fertile. Janke: "We have to ask ourselves: Does the species concept still hold true, given there is evidence of gene flow not only in bears, but also in other animals? Therefore, what do we need to protect for the future -- species or genomic diversity? ."

It is certain that the amazing progress of genomics and its technology will also question other fundamental principles of biology and fuel research. "Evolution creates genetic differences and adaptations, whether we call these differences species or not, is less important. What we must preserve, however, is genetic variation to protect diversity and to allow adaptation to future environmental changes," Janke states.

Story Source: Senckenberg Research Institute and Natural History Museum. "Bears breed across species borders." ScienceDaily. www.sciencedaily.com/releases/2017/04/170419093151.htm (accessed April 24, 2017).




Journal Reference:
Vikas Kumar, Fritjof Lammers, Tobias Bidon, Markus Pfenninger, Lydia Kolter, Maria A. Nilsson, Axel Janke. The evolutionary history of bears is characterized by gene flow across species. Scientific Reports, 2017; 7: 46487 DOI: 10.1038/srep46487

Abstract
Bears are iconic mammals with a complex evolutionary history. Natural bear hybrids and studies of few nuclear genes indicate that gene flow among bears may be more common than expected and not limited to polar and brown bears. Here we present a genome analysis of the bear family with representatives of all living species. Phylogenomic analyses of 869 mega base pairs divided into 18,621 genome fragments yielded a well-resolved coalescent species tree despite signals for extensive gene flow across species. However, genome analyses using different statistical methods show that gene flow is not limited to closely related species pairs. Strong ancestral gene flow between the Asiatic black bear and the ancestor to polar, brown and American black bear explains uncertainties in reconstructing the bear phylogeny. Gene flow across the bear clade may be mediated by intermediate species such as the geographically wide-spread brown bears leading to large amounts of phylogenetic conflict. Genome-scale analyses lead to a more complete understanding of complex evolutionary processes. Evidence for extensive inter-specific gene flow, found also in other animal species, necessitates shifting the attention from speciation processes achieving genome-wide reproductive isolation to the selective processes that maintain species divergence in the face of gene flow.

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Figure 1: Approximate geographic distribution of extant bears according to IUCN data.

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Figure 2: A coalescent species tree and a split network analysis from 18,621 GF ML trees.
(A) In the coalescent species tree all branches receive 100% bootstrap support. The position of root and depicted branch lengths were calculated from coding sequence and 10 Mb of GF data respectively. (B) A split network with a 7% threshold level depicts the complex phylogenetic signal in bear genomes. As expected, the ABC-island brown bear (asterisk) shares alleles with polar bears; among other bears allele sharing is complex. Paintings by Jon Baldur Hlidberg (www.fauna.is).

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Figure 5: Phylogenomic estimates of divergence times.
The scale bar shows divergence times in million years and 95% confidence intervals for divergence times are shown as shadings (Supplementary Table 7). The tree is rooted with the panda genome (not shown).Attached to this post:[Image: attach.png] The_evolutionary_history_of_bears_is_characterized_by_gene_flow_across_species.pdf (1.27 MB)
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