Lindqvist provides insight into the evolutionary history of bears

Charlotte Lindqvist, associate professor, Department of Biological Sciences.

Charlotte Lindqvist, associate professor, Department of Biological Sciences

The Proceedings of the National Academy of Sciences published a study led by Charlotte Lindqvist that analyzed the genomes of 64 modern polar and brown bears, including several new genomes from Alaska, a state where both species are found. The team also produced a new, more complete genome for a polar bear that lived 115,000 to 130,000 years ago in Norway’s Svalbard archipelago. DNA for the ancient polar bear was extracted from a tooth attached to a subfossil jawbone, which is now housed at the Natural History Museum at the University of Oslo. Read the news story by Charlotte Hsu.

Research News

The tangled evolutionary histories of polar and brown bears

Zoom image: The subfossil jawbone of a polar bear that lived 115,000 to 130,000 years ago in Norway’s Svalbard archipelago. A genomic study includes an analysis of DNA extracted from a tooth attached to this jawbone, which is now housed at the Natural History Museum at the University of Oslo. Photo: Karsten Sund, Natural History Museum, University of Oslo The subfossil jawbone of a polar bear that lived 115,000 to 130,000 years ago in Norway’s Svalbard archipelago. A genomic study includes an analysis of DNA extracted from a tooth attached to this jawbone, which is now housed at the Natural History Museum at the University of Oslo. Credit: Photo by Karsten Sund, Natural History Museum (NHM), University of Oslo

The subfossil jawbone of a polar bear that lived 115,000 to 130,000 years ago in Norway’s Svalbard archipelago. A genomic study includes an analysis of DNA extracted from a tooth attached to this jawbone, which is now housed at the Natural History Museum at the University of Oslo. Photo: Karsten Sund, Natural History Museum, University of Oslo

By CHARLOTTE HSU

Published June 7, 2022

Print
Charlotte Lindqvist.
“The formation and maintenance of species can be a messy process. ”
Charlotte Lindqvist, associate professor
Department of Biological Sciences

A new study is providing an enhanced look at the intertwined evolutionary histories of polar bears and brown bears.

Becoming separate species did not completely stop these animals from mating with each other. Scientists have known this for some time, but the new research draws on an expanded data set — including DNA from an ancient polar bear tooth — to tease out more detail.

The story that emerges reveals complexities similar to those that complicate human evolutionary history.

“The formation and maintenance of species can be a messy process,” says Charlotte Lindqvist, associate professor of biological sciences, College of Arts and Sciences, and an expert on bear genetics. “What’s happened with polar bears and brown bears is a neat analog to what we’re learning about human evolution: that the splitting of species can be incomplete.

“As more and more ancient genomes have been recovered from ancient human populations, including Neanderthals and Denisovans, we’re seeing that there was multidirectional genetic mixing going on as different groups of archaic humans mated with ancestors of modern humans. Polar bears and brown bears are another system where you see this happening.

“We find evidence for interbreeding between polar bears and brown bears that predates an ancient polar bear we studied,” she says. “And, moreover, our results demonstrate a complicated, intertwined evolutionary history among brown and polar bears, with the main direction of gene flow going into polar bears from brown bears. This inverts a hypothesis suggested by other researchers that gene flow has been unidirectional and going into brown bears around the peak of the last ice age.”

Zoom image: A mother polar bear and her 2-year-old cubs in northwestern Greenland. Photo: Øystein Wiig A mother polar bear and her 2-year-old cubs in northwestern Greenland. Credit: Øystein Wiig

A mother polar bear and her 2-year-old cubs in northwestern Greenland. Photo: Øystein Wiig

The study was published June 6 in the Proceedings of the National Academy of Sciences. It was led by Lindqvist; Luis Herrera-Estrella at the National Laboratory of Genomics for Biodiversity (LANGEBIO) in Mexico and Texas Tech University; and Kalle Leppälä at the University of Oulu in Finland. Tianying Lan, a former UB postdoctoral researcher now at Daicel Arbor Biosciences, was co-first author with Leppälä.

The concept of Arctic-adapted polar bears capturing genetic material from brown bears, which are adapted to life in lower latitudes, is one of several findings of possible interest for scientists concerned with climate change impacts on threatened species.

As the world warms and Arctic sea ice declines, polar bears and brown bears may run into each other more frequently in places where their ranges overlap. This makes their shared evolutionary history a particularly intriguing subject of study, Lindqvist says.

Zoom image: An adult male polar bear in northwestern Greenland. Photo: Øystein Wiig An adult male polar bear in northwestern Greenland. Credit: Øystein Wiig

An adult male polar bear in northwestern Greenland. Photo: Øystein Wiig

Splitting of species can be messy process

As Lindqvist explains, scientists once thought modern humans and Neanderthals simply split into separate species after evolving from a common ancestor. Then, researchers found Neanderthal DNA in modern Eurasian people, implying that modern human populations received an influx of genes from Neanderthals at some point in their shared evolutionary history, she says.

Only later did scientists realize that this genetic intermingling also supplemented Neanderthal populations with modern human genes, Lindqvist adds. In other words, interbreeding can be complex, not necessarily a one-way street, she says.

The new study on bears reveals a remarkably similar story: The analysis finds evidence of hybridization in both polar bear and brown bear genomes, with polar bears in particular carrying a strong signature of an influx of DNA from brown bears, researchers say. Earlier research proposed the inverse pattern only, Lindqvist says.

“It’s exciting how DNA can help reveal ancient life history. Gene flow direction is harder to determine than merely its presence, but these patterns are vital to understanding how past adaptations have transferred among species to give modern animals their current features,” says Leppälä, postdoctoral researcher in the research unit of mathematical sciences at the University of Oulu.

“Population genomics is an increasingly powerful toolbox to study plant and animal evolution, and the effects of human activity and climate change on endangered species,” says Herrera-Estrella, President’s Distinguished Professor of Plant Genomics and director of the Institute of Genomics for Crop Abiotic Stress Tolerance in the Texas Tech Department of Plant and Soil Science. He is also a professor emeritus at LANGEBIO. “Bears don’t provide simple speciation stories any more than human evolution has. This new genomic research suggests that mammalian species groups can hide complicated evolutionary histories.”

Zoom image: The subfossil jawbone of a polar bear that lived 115,000 to 130,000 years ago in Norway’s Svalbard archipelago. Photo: Karsten Sund, Natural History Museum, University of Oslo The subfossil jawbone of a polar bear that lived 115,000 to 130,000 years ago in Norway’s Svalbard archipelago. A genomic study includes an analysis of DNA extracted from a tooth attached to this jawbone, which is now housed at the Natural History Museum at the University of Oslo. Credit: Photo by Karsten Sund, Natural History Museum (NHM), University of Oslo

The subfossil jawbone of a polar bear that lived 115,000 to 130,000 years ago in Norway’s Svalbard archipelago. Photo: Karsten Sund, Natural History Museum, University of Oslo

Evidence from modern bear genomes — and DNA from an ancient tooth

The study analyzed the genomes of 64 modern polar and brown bears, including several new genomes from Alaska, a state where both species are found.

The team also produced a new, more complete genome for a polar bear that lived 115,000 to 130,000 years ago in Norway’s Svalbard archipelago. DNA for the ancient polar bear was extracted from a tooth attached to a subfossil jawbone, which is now housed at the Natural History Museum at the University of Oslo.

Using this data set, researchers estimate that polar bears and brown bears started to become distinct species about 1.3 to 1.6 million years ago, updating prior assessments made by some of the same scientists. The age of the split has been and remains a topic of scientific debate, with past interbreeding and limited fossil evidence for ancient polar bears among factors that make the timing hard to pinpoint, Lindqvist says.

In any case, after becoming their own species, polar bears endured dramatic population decline and a prolonged genetic bottleneck, leaving these bears with much less genetic diversity than brown bears, the new study concludes. The findings confirm past research pointing to the same trends, and add evidence in support of this hypothesis.

Zoom image: Genomes analyzed in a new study on bears include that of this bear, pictured here in 1995 on Alaska's North Slope. Scientists had wondered if this bear might be a brown bear-polar bear hybrid, but the new research finds that, “This bear is not a hybrid, but simply a light-colored brown bear,” says UB biologist Charlotte Lindqvist. Photo: Richard Shideler, Division of Wildlife Conservation, Alaska Department of Fish and Game Genomes analyzed in a new study on bears include that of this bear, pictured here in 1995 on Alaska's North Slope. Scientists had wondered if this bear might be a brown bear-polar bear hybrid, but the new research finds that, “This bear is not a hybrid, but simply a light-colored brown bear,” says University at Buffalo biologist Charlotte Lindqvist. Credit: Richard Shideler, Division of Wildlife Conservation, Alaska Department of Fish and Game

Genomes analyzed in a new study on bears include that of this bear, pictured here in 1995 on Alaska's North Slope. Scientists had wondered if this bear might be a brown bear-polar bear hybrid, but the new research finds that, “This bear is not a hybrid, but simply a light-colored brown bear,” says UB biologist Charlotte Lindqvist. Photo: Richard Shideler, Division of Wildlife Conservation, Alaska Department of Fish and Game

Together with the analysis of gene flow, these findings are providing new insights into the messy, intertwined evolutionary history of polar bears and brown bears.

The international research team included scientists from UB, LANGEBIO, Texas Tech, the University of Oulu, the Far Northwestern Institute of Art and Science, the Alaska Department of Fish and Game, the Natural History Museum at the University of Oslo, Nanyang Technological University, University of Helsinki and Aarhus University.

The research was funded by the National Fish and Wildlife Foundation, U.S. National Science Foundation, Alaska Department of Fish and Game, and U.S. Geological Survey.

Faculty Profile

  • Charlotte Lindqvist

    PhD

    Charlotte Lindqvist.

    Charlotte Lindqvist

    PhD

    Charlotte Lindqvist

    PhD

    Research Interests

    Evolutionary biology; molecular phylogenetics and population genomics

    Education

    PhD University of Copenhagen, Denmark
    Postdoctoral Research at University of Oslo, Norway

    Research Summary

    Research in the Lindqvist Lab is broadly concerned with the evolutionary genetic basis of diversification in natural populations and environments to better understand the processes of speciation and the impact of hybridization/admixture, and responses to global environmental perturbations in both animals and plants. My research uses genetic/genomic and metagenomic analyses of modern and historical/ancient material (ancient DNA) to address longstanding questions in the evolutionary history of mammals and flowering plants. Current projects include paleogenetic surveys of Late Quaternary subfossil biodiversity and lake sediments in Southeast Alaska, evolutionary genomics of Arctic and boreal carnivore mammals (with a focus on ursine bears and mustelids), and population genomics/phylogenomics of several angiosperm radiations.

    Selected Publications

    • Lan, T., Leppälä, K., Tomlin, C., Talbot, S.L., Sage, G.K., Farley, S.D., Shideler, R.T., Bachmann, L., Wiig, Ø., Albert, V.A., Salojärvi, J., Mailund, T., Drautz-Moses, D.I., Schuster, S.C., Herrera-Estrella, L., Lindqvist, C. (2022). Insights into bear evolution from a Pleistocene polar bear genome. Proceedings of the National Academy of Sciences, USA 119 (24) e2200016119. https://doi.org/10.1073/pnas.2200016119
    • Kosintsev, P.A., Bocherens, H., Kirillova, I.V., Levchenko, V.A., Zazovskaya, E.P., Trofimova, S.S., Lan, T., Lindqvist, C.* (2022) Palaeoecological and genetic analyses of Late Pleistocene bears in Asiatic Russia. Boreas 51: 465–480. https://onlinelibrary.wiley.com/doi/10.1111/bor.12570
    • Colella JP, Lan T, Talbot SL, Lindqvist C, Cook JA. (2021) Whole‐genome resequencing reveals persistence of forest‐associated mammals in Late Pleistocene refugia along North America’s North Pacific Coast. Journal of Biogeography 48:1153-69. https://doi.org/10.1111/jbi.14068
    • da Silva Coelho FA, Gill S, Tomlin CM, Heaton TH, Lindqvist C. (2021) An early dog from southeast Alaska supports a coastal route for the first dog migration into the Americas. Proceedings of the Royal Society B 288(1945):20203103. https://doi.org/10.1098/rspb.2020.3103
    • Srivastava A, Kumar Sarsani V, Fiddes I, Sheehan SM, Seger RL, Barter ME, Neptune-Bear S, Lindqvist C, Korstanje R. (2019) Genome assembly and gene expression in the American black bear provides new insights into the renal response to hibernation. DNA Research 26(1):37-44. https://doi.org/10.1093/dnares/dsy036
    • Lindqvist, C. & Rajora, O.P. (Eds.) 2019. Paleogenomics. Genome-Scale Analysis of Ancient DNASpringer Nature.
    • Colella, J.P., Lan, T., Schuster, S.C., Talbot, S.L., Cook, J.A., Lindqvist, C. (2018) Whole-genome analysis of Mustela erminea finds that pulsed hybridization impacts evolution at high latitudes.   Communications Biology 1: 51. 
    • Lesnek, A.J., Briner, J.P., Lindqvist, C., Baichtal, J.F., Heaton, T.H. (2018). Deglaciation of the Pacific coastal corridor and the human colonization of the Americas. Science Advances 4: 5.
    • Lan, T., Gill, S., Bellemain, E., Bischof, R., Nawaz, M.A., Lindqvist, C. (2017). Evolutionary history of enigmatic bears in the Tibetan Plateau-Himalaya Region and the identity of the Yeti. Proceedings of the Royal Society B 284: 20171804.
    • Welch, A.J., Hofer, K., Ratan, A., Drautz, D., Schuster, S.C., Lindqvist, C. (2016) The quest to resolve recent radiations: Plastid phylogenomics of extinct and endangered Hawaiian endemic mints (Lamiaceae). Mol Phyl Evol 99: 16-33.
    • Roy, T., Cole, L.W., Chang, T.-H., Lindqvist, C. (2015). Untangling reticulate evolutionary relationships among New World and Hawaiian mints (Stachydeae, Lamiaceae). Mol Phyl Evol 89: 46-62.
    • Welch, A.J., Bedoya-Reina, O.C., Carretero-Paulet, L., Miller, W., Rode, K.D., Lindqvist, C. (2014). Polar bears exhibit genome-wide signatures of bioenergetic adaptation to life in the Arctic environment. Genome Biol Evol 6: 433-450.
    • Miller, W., Schuster, S.C., Welch, A.J., Ratan, A., Bedoya-Reina, O.C., Zhao, F., Kim, H.L., Burhans, R.C., Drautz, D.I., Wittekindt, N.E., Tomsho, L.P., Ibarra-Laclette, E., Herrera-Estrella, L., Peacock, E., Farley, S., Sage, G.K., Rode, K., Obbard, M., Montiel, R., Bachmann, L., Ingólfsson, Ó., Aars, J., Mailund, T., Wiig, Ø., Talbot, S.L., Lindqvist, C. (2012). Polar and brown bear genomes reveal ancient admixture and demographic footprints of past climate change. Proc Natl Acad Sci, USA 109(36): E2382-E2390.
    • Lindqvist, C., Schuster, S.C., Sun, Y., Talbot, S.L., Qi, J., Ratan, A. Tomsho, L.P., Kasson, L., Zeyl, E., Aars, J., Miller, W., Ingolfsson, O., Bachmann, L., Wiig, Ø (2010). Complete mitochondrial genome of a Pleistocene jawbone unveils the origin of polar bear. Proc Natl Acad Sci, USA 107: 5053-5057.
    • Lindqvist, C. & Rajora, O.P. (Eds.) 2019. Paleogenomics. Genome-Scale Analysis of Ancient DNA. Springer Nature.
    • Colella, J.P., Lan, T., Schuster, S.C., Talbot, S.L., Cook, J.A., Lindqvist, C. (2018) Whole-genome analysis of Mustela erminea finds that pulsed hybridization impacts evolution at high latitudes. Communications Biology 1: 51. 
    • Lesnek, A.J., Briner, J.P., Lindqvist, C., Baichtal, J.F., Heaton, T.H. (2018). Deglaciation of the Pacific coastal corridor and the human colonization of the Americas. Science Advances 4: 5.
    • Lan, T., Gill, S., Bellemain, E., Bischof, R., Nawaz, M.A., Lindqvist, C. (2017). Evolutionary history of enigmatic bears in the Tibetan Plateau-Himalaya Region and the identity of the Yeti. Proceedings of the Royal Society B 284: 20171804.
    • Welch, A.J., Hofer, K., Ratan, A., Drautz, D., Schuster, S.C., Lindqvist, C. (2016) The quest to resolve recent radiations: Plastid phylogenomics of extinct and endangered Hawaiian endemic mints (Lamiaceae). Mol Phyl Evol 99: 16-33.
    • Roy, T., Cole, L.W., Chang, T.-H., Lindqvist, C. (2015). Untangling reticulate evolutionary relationships among New World and Hawaiian mints (Stachydeae, Lamiaceae). Mol Phyl Evol 89: 46-62.
    • Welch, A.J., Bedoya-Reina, O.C., Carretero-Paulet, L., Miller, W., Rode, K.D., Lindqvist, C. (2014). Polar bears exhibit genome-wide signatures of bioenergetic adaptation to life in the Arctic environment. Genome Biol Evol 6: 433-450.
    • Miller, W., Schuster, S.C., Welch, A.J., Ratan, A., Bedoya-Reina, O.C., Zhao, F., Kim, H.L., Burhans, R.C., Drautz, D.I., Wittekindt, N.E., Tomsho, L.P., Ibarra-Laclette, E., Herrera-Estrella, L., Peacock, E., Farley, S., Sage, G.K., Rode, K., Obbard, M., Montiel, R., Bachmann, L., Ingólfsson, Ó., Aars, J., Mailund, T., Wiig, Ø., Talbot, S.L., Lindqvist, C. (2012). Polar and brown bear genomes reveal ancient admixture and demographic footprints of past climate change. Proc Natl Acad Sci, USA 109(36): E2382-E2390.
    • Lindqvist, C., Schuster, S.C., Sun, Y., Talbot, S.L., Qi, J., Ratan, A. Tomsho, L.P., Kasson, L., Zeyl, E., Aars, J., Miller, W., Ingolfsson, O., Bachmann, L., Wiig, Ø (2010). Complete mitochondrial genome of a Pleistocene jawbone unveils the origin of polar bear. Proc Natl Acad Sci, USA 107: 5053-5057.
    • Scheen, A.-C., Bendiksby, Ryding, O., , Mathiesen, C., Albert, V.A., Lindqvist, C. (2010). Molecular phylogenetics, character evolution, and suprageneric classification of Lamioideae (Lamiaceae). Annals Miss Bot Gard 97: 191-218.
    • Lindqvist, C., Albert, V.A. (2002). Origin of the Hawaiian endemic mints within North American Stachys (Lamiaceae). Am J Bot 89: 1709-1724.