Charlotte Lindqvist

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

• Low YW, Rajaraman S, Tomlin CM, Ahmad JA, Ardi WH, Armstrong K, Athen P, Berhaman A, Bone RE, Cheek M, Cho NRW, Choo LM, Cowie ID, Crayn D, Fleck SJ, Ford AJ, Forster PI, Girmansyah D, Goyder DJ, Gray B, Heatubun CD, Ibrahim A, Ibrahim B, Jayasinghe HD, Kalat MA, Kathriarachchi HS, Kintamani E, Koh SL, Lai JTK, Lee SML, Leong PKF, Lim WH, Lum SKY, Mahyuni R, McDonald WJF, Metali F, Mustaqim WA, Naiki A, Ngo KM, Niissalo M, Ranasinghe S, Repin R, Rustiami H, Simbiak VI, Sukri RS, Sunarti S, Trethowan LA, Trias-Blasi A, Vasconcelos TNC, Wanma JF, Widodo P, Wijesundara DSA, Worboys S, Yap JW, Yong KT, Khew GSW, Salojärvi J, Michael TP, Middleton DJ, Burslem DFRP, Lindqvist C, Lucas EJ, Albert VA. Genomic insights into rapid speciation within the world’s largest tree genus Syzygium. Nature Communications. 2022 Sep 12, 13(1):5031.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.