Finding unknown species in the genomes of extant species

Yan Li; Dong-Dong Wu

doi:10.1016/j.jgg.2021.05.013

Volume 48 Issue 10

Oct. 2021

Turn off MathJax

Article Contents

Article Navigation > Journal of Genetics and Genomics > 2021 > 48(10): 867-871

PDF( 740 KB)

Finding unknown species in the genomes of extant species

doi: 10.1016/j.jgg.2021.05.013

Yan Li^a,
Dong-Dong Wu^b,c

a. State Key Laboratory for Conservation and Utilization of Bio-resource in Yunnan and School of Life Science & School of Ecology and Environmental Science, Yunnan University, Kunming 650091, China;
b. State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China;
c. Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China

Funds:

We thank S.W. for suggestion on method summarization and H.B.X. and C.X. for providing pictures. Y.L. was supported by the Strategic Priority Research Program of the Chinese Academy of Sciences (XDA2004010302), the Second Tibetan Plateau Scientific Expedition and Research (STEP) Program (2019QZKK05010703), and the Young Academic and Technical Leagder Raising Foundation of Yunnan Province (2018HB033). D.-D.W. was supported by the National Natural Science Foundation of China (31822048 and 31621062) and Qinghai Department of Science and Technology Major Project.

Received Date: 2021-03-03
Accepted Date: 2021-05-23
Rev Recd Date: 2021-05-21
Publish Date: 2021-07-03

Abstract

Abstract

Although many species have gone extinct, their genetic components might exist in extant species because of ancient hybridization. Via advances in genome sequencing and development of modern population genetics, one can find the legacy of unknown or extinct species in the context of available genomes from extant species. Such discovery can be used as a strategy to search for hidden species or fossils in conservation biology and archeology, gain novel insight into complex evolutionary history, and provide the new sources of genetic variation for breeding and trait improvement in agriculture.
- Unknown species,
- Introgression,
- Extant species,
- Extinct species,
- Genetic legacy

FullText(HTML)

References(30)

References

Ai, H., Fang, X., Yang, B., Huang, Z., Chen, H., Mao, L., Zhang, F., Zhang, L., Cui, L., He, W., et al., 2015. Adaptation and possible ancient interspecies introgression in pigs identified by whole-genome sequencing. Nat. Genet. 47, 217-225.

Barlow, A., Cahill, J.A., Hartmann, S., Theunert, C., Xenikoudakis, G., Fortes, G.G., Paijmans, J.L.A., Rabeder, G., Frischauf, C., Grandal-d’Anglade, A., et al., 2018. Partial genomic survival of cave bears in living brown bears. Nat. Ecol. Evol. 2, 1563-1570.

Browning, S.R., Browning, B.L., Zhou, Y., Tucci, S., Akey, J.M., 2018. Analysis of human sequence data reveals two pulses of archaic denisovan admixture. Cell 173, 53-61.

Chen, F., Welker, F., Shen, C.C., Bailey, S.E., Bergmann, I., Davis, S., Xia, H., Wang, H., Fischer, R., Freidline, S.E., et al., 2019. A late middle pleistocene denisovan mandible from the Tibetan plateau. Nature 569, 409-412.

Chen, L., Wolf, A.B., Fu, W., Li, L., Akey, J.M., 2020. Identifying and interpreting apparent neanderthal ancestry in African individuals. Cell 180, 677-687. e616.

Cheng, H., Liu, J., Wen, J., Nie, X., Xu, L., Chen, N., Li, Z., Wang, Q., Zheng, Z., Li, M., et al., 2019. Frequent intra- and inter-species introgression shapes the landscape of genetic variation in bread wheat. Genome Biol. 20, 136.

de Manuel, M., Kuhlwilm, M., Frandsen, P., Sousa, V.C., Desai, T., Prado-Martinez, J., Hernandez-Rodriguez, J., Dupanloup, I., Lao, O., Hallast, P., et al., 2016. Chimpanzee genomic diversity reveals ancient admixture with bonobos. Science 354, 477-481.

Durvasula, A., Sankararaman, S., 2020. Recovering signals of ghost archaic introgression in African populations. Sci. Adv. 6, eaax5097.

Estrada, O., Breen, J., Richards, S.M., Cooper, A., 2018. Ancient plant DNA in the genomic era. Nat. Plants 4, 394-396.

Gopalakrishnan, S., Sinding, M.S., Ramos-Madrigal, J., Niemann, J., Samaniego Castruita, J.A., Vieira, F.G., Caroe, C., Montero, M.M., Kuderna, L., Serres, A., et al., 2018. Interspecific gene flow shaped the evolution of the genus Canis. Curr. Biol. 28, 3441-3449.

He, Z., Li, X., Yang, M., Wang, X., Zhong, C., Duke, N.C., Wu, C.I., Shi, S., 2019. Speciation with gene flow via cycles of isolation and migration: insights from multiple mangrove taxa. Natl. Sci. Rev. 6, 275-288.

Hubisz, M.J., Williams, A.L., Siepel, A., 2020. Mapping gene flow between ancient hominins through demography-aware inference of the ancestral recombination graph. PLoS Genet. 16, e1008895.

Huerta-Sanchez, E., Jin, X., Asan, Bianba, Z., Peter, B.M., Vinckenbosch, N., Liang, Y., Yi, X., He, M., Somel, M., et al., 2014. Altitude adaptation in Tibetans caused by introgression of Denisovan-like DNA. Nature 512, 194-197.

Kuhlwilm, M., Han, S., Sousa, V.C., Excoffier, L., Marques-Bonet, T., 2019. Ancient admixture from an extinct ape lineage into bonobos. Nat. Ecol. Evol. 3, 957-965.

Lachance, J., Vernot, B., Elbers, C.C., Ferwerda, B., Froment, A., Bodo, J.M., Lema, G., Fu, W., Nyambo, T.B., Rebbeck, T.R., et al., 2012. Evolutionary history and adaptation from high-coverage whole-genome sequences of diverse African hunter-gatherers. Cell 150, 457-469.

Martin, N.H., Bouck, A.C., Arnold, M.L., 2006. Detecting adaptive trait introgression between Iris fulva and I. Brevicaulis in highly selective field conditions. Genetics 172, 2481-2489.

Oziolor, E.M., Reid, N.M., Yair, S., Lee, K.M., Guberman VerPloeg, S., Bruns, P.C., Shaw, J.R., Whitehead, A., Matson, C.W., 2019. Adaptive introgression enables evolutionary rescue from extreme environmental pollution. Science 364, 455-457.

Plagnol, V., Wall, J.D., 2006. Possible ancestral structure in human populations. PLoS Genet. 2, e105.

Racimo, F., Sankararaman, S., Nielsen, R., Huerta-Sanchez, E., 2015. Evidence for archaic adaptive introgression in humans. Nat. Rev. Genet. 16, 359-371.

Sankararaman, S., Mallick, S., Dannemann, M., Prufer, K., Kelso, J., Paabo, S., Patterson, N., Reich, D., 2014. The genomic landscape of neanderthal ancestry in present-day humans. Nature 507, 354-357.

Skoglund, P., Ersmark, E., Palkopoulou, E., Dalen, L., 2015. Ancient wolf genome reveals an early divergence of domestic dog ancestors and admixture into highlatitude breeds. Curr. Biol. 25, 1515-1519.

Skov, L., Hui, R., Shchur, V., Hobolth, A., Scally, A., Schierup, M.H., Durbin, R., 2018. Detecting archaic introgression using an unadmixed outgroup. PLoS Genet. 14, e1007641.

Song, Y., Endepols, S., Klemann, N., Richter, D., Matuschka, F.R., Shih, C.H., Nachman, M.W., Kohn, M.H., 2011. Adaptive introgression of anticoagulant rodent poison resistance by hybridization between old world mice. Curr. Biol. 21, 1296-1301.

Svardal, H., Jasinska, A.J., Apetrei, C., Coppola, G., Huang, Y., Schmitt, C.A., Jacquelin, B., Ramensky, V., Muller-Trutwin, M., Antonio, M., et al., 2017. Ancient hybridization and strong adaptation to viruses across African vervet monkey populations. Nat. Genet. 49, 1705-1713.

Taylor, S.A., Larson, E.L., 2019. Insights from genomes into the evolutionary importance and prevalence of hybridization in nature. Nat. Ecol. Evol. 3, 170-177.

Vernot, B., Akey, J.M., 2014. Resurrecting surviving neandertal lineages from modern human genomes. Science 343, 1017-1021.

Wang, H., Vieira, F.G., Crawford, J.E., Chu, C., Nielsen, R., 2017. Asian wild rice is a hybrid swarm with extensive gene flow and feralization from domesticated rice. Genome Res. 27, 1029-1038.

Wang, M.S., Wang, S., Li, Y., Jhala, Y., Thakur, M., Otecko, N.O., Si, J.F., Chen, H.M., Shapiro, B., Nielsen, R., et al., 2020. Ancient hybridization with an unknown population facilitated high-altitude adaptation of canids. Mol. Biol. Evol. 37, 2616-2629.

Whitney, K.D., Randell, R.A., Rieseberg, L.H., 2006. Adaptive introgression of herbivore resistance traits in the weedy sunflower Helianthus annuus. Am. Nat. 167, 794-807.

Wu, D.D., Ding, X.D., Wang, S., Wojcik, J.M., Zhang, Y., Tokarska, M., Li, Y., Wang, M.S., Faruque, O., Nielsen, R., et al., 2018. Pervasive introgression facilitated domestication and adaptation in the bos species complex. Nat. Ecol. Evol. 2, 1139-1145.

Relative Articles

Supplements(0)

Cited By

Proportional views