Headshot of Dr.Melinda  Yang

Dr. Melinda Yang

Assistant Professor of Biology
Data Science Advisory Board Member
  • Profile

    In the last decade, the number of both ancient and present-day genomes sequenced has exploded, leading to new discoveries each year on the genetic history of different species. The work in my lab has two major components. The first is the application of computational population genetic tools to the study of the evolutionary history of many organisms, particularly our own species, H. sapiens. My postdoctoral work at the Molecular Paleontology Lab in the Institute of Vertebrate Paleontology and Paleoanthropology, Beijing, China focused on determining the genetic history of ancient humans in East Asia, including their relationship to present-day human populations. The second is the assessment and development of computational tools to determine and infer demographic relationships, especially with the inclusion of ancient DNA. My graduate work in the Department of Integrative Biology at UC Berkeley included the development of population genetic tools used to study admixture using ancient and present-day genome-wide data, as well assessment of these tools through simulation. The focus of my research is to synthesize these two directions, assessing the robustness of currently used population genetic tools applied to these data and uncovering more on genetic variation and history of different species, with a particular emphasis on humans. For more information, please see: https://melyang4.github.io/.

  • Publications
    Journal Articles

    Yang MA and Korsnack K. “Pairing a Bioinformatics-focused Course-Based Undergraduate Research Experience with Specifications Grading in an Introductory Biology classroom.” Biology Methods and Protocols. doi:10.1093/biomethods/bpae013

    Lopatto D, Key CS, Van Stry M, Siders J, Leung W, Sandlin K, Rele C, …, Yang MA, …, Croonquist P. 2023. “Supporting the democratization of science during a pandemic: Genomics Course-based Undergraduate Research Experiences (CUREs) as an effective remote learning strategy.” J Microbiology & Biology Education.  doi:10.1128/jmbe.00039-23

    Yang MA. 2022. “A genetic history of migration, diversification, and admixture in Asia.” Human Population Genetics and Genomics. doi: 10.47248/hpgg2202010001

    Wang H*, Yang MA*, Wangdue S, Lu H, Chen H, Li L, Dong G, Tsring T, Yuan H, He W, Ding M, Wu X, Li S, Tashi N, Yang T, Yang F, Tong Y, Chen Z, He Y, Cao P, Dai Q, Liu F, Feng X, Wang T, Yang R, Ping W, Zhang Z, Gao Y, Zhang M, Wang X, Zhang C, Yuan K, Ko AM, Aldenderfer M, Gao X, Xu S, Fu Q. 2023. “Human genetic history on the Tibetan Plateau in the past 5100 years.” Science Advances.  doi: 10.1126/sciadv.add5582 (*co-first authors)

    Zhang Z, Zhang Y, Wang Y, Zhao Z, Yang MA, Zhang L, Zhou B, Xu B, Zhang H, Chen T, Dai W, Zhou Y, Shi S, Nielsen R, Li SC, Li S. 2022. “The Tibetan-Yi region is both a corridor and a barrier for human gene flow.” Cell Reports. doi: 10.1016/j.celrep.2022.110720

    Wang T, Wang W, Xie G, Li Z, Fan X, Yang Q, Wu X, Cao P, Liu Y, Yang R, Liu F, Dai Q, Feng X, Wu X, Qin L, Li F, Ping W, Zhang L, Zhang M*, Liu Y, Chen X, Zhang D, Zhou Z, Wu Y, Shafiey H, Gao X, Curnoe D, Mao X, Bennett EA, Ji X, Yang MA*, Fu Q*. 2021. “Human population history at the crossroads of East and Southeast Asia since 11,000 years ago.” Cell. doi: 10.1016/j.cell.2021.05.018 (*co-corresponding authors)

    Zhang DJ, Xia H, Chen F, Li B, Slon V, Cheng T, Yang R, Jacobs Z, Dai Q, Massilani D, Shen X, Wang J, Feng X, Cao P, Yang MA, Yao J, Yang J, Madsen DB, Han Y, Ping W, Liu F, Perreault C, Chen XS, Meyer M, Kelso J, Pääbo S, Fu Q. 2020. “Denisovan DNA in Late Pleistocene sediments from Baishiya Karst Cave on the Tibetan Plateau.” Science. doi:10.1126/scienceabb6320

    Yang MA, Fan X, Sun B, Chen C, Lang J, Ko YC, Tsang CH, Chiu H, Wang T, Bao Q, Wu X, Hajdinjak M, Min-shan Ko A, Ding M, Cao P, Yang R, Liu F, Nickel B, Dai Q, Feng X, Zhang L, Sun C, Ning C, Zeng W, Zhao Y, Zhang M, Gao X, Cui Y, Reich D, Stoneking M, Fu Q. 2020. “Ancient DNA indicates human population shifts and admixture in northern and southern China.” Science. doi:10.1126/science.aba0909

    Zhang M, Sun G, Ren L, Yuan H, Dong G, Zhang L, Liu F, Cao P, Min-shan Ko A, Yang MA, Hu S, Wang GD, Fu Q. 2020. “Ancient DNA from China reveals the expansion of Pacific dogs.” Mol Biol Evol. doi:10.1093/molbev/msz311

    Ding M, Wang T, Min-shan Ko A, Chen H, Wang H, Dong G, Lu H, He W, Wangdue S, Yuan H, He Y, Cai L, Chen Z, Hou G, Zhang D, Zhang Z, Cao P, Dai Q, Feng X, Zhang M*, Wang H, Yang MA, Fu Q. 2020. “Ancient mitogenomes show plateau populations from last 5200 years partially contributed to present-day Tibetans.” Proc Roy Soc B. doi:10.1098/rspb.2019.2968

    de Boer E, Yang MA, Kawagoe A, Barnes GL. 2020. “Japan considered from the hypothesis of farmer/language spread.” Evolutionary Human Sciences. doi:10.1017/ehs.2020.7

    Wang X, Zhou BW, Yang MA, Yin TT, Chen FL, Ommeh SC, Esmailizadeh A, Turner MT, Poyarkov AD, Savolainen P, Wang GD, Fu Q, Zhang YP. 2019. “Canine transmissible venereal tumor genome reveals ancient introgression from coyotes to pre-contact dogs in North America.” Cell Research. doi:10.1038/s41422-019-0183-2

    Sikora M, Pitulko VV, Sousa VC, Allentoft ME, Vinner L, Rasmussen S, Margaryan A, de Barros Damgaard P, de la Fuente C, Renaud G, Yang MA, …, Nielsen R, Meltzer DJ, Excoffier L, Willerslev E (54 co-authors total). 2019. “The population history of northeastern Siberia since the Pleistocene.” Nature. doi:10.1038/s41586-019-1279-z

    Wang GD, Zhang M, Wang X, Yang MA, Cao P, Liu F, Lu H, Feng X, Skoglund P, Wang L, Fu Q, Zhang Y. 2019. “Genomic approaches reveal an endemic sub-population of gray wolves in Southern China.” Molecular Biology and Evolution. (under review)

    Liu S, Huang S, Chen F, Zhao L, Yuan Y, Starko Francis S, …, Yang MA, …, Wang J, Albrechsten A, Jin X, Nielsen R, Xu X (37 co-authors total). 2018. "Genomic analyses from non-invasive prenatal testing reveal genetic associations, patterns of viral infections, and Chinese population history.” Cell. doi:10.1016/j.cub.2018.05.008

    Min-Shan Ko A, Zhang Y, Yang MA, Hu, Y, Cao P, Feng X, Zhang L, Wei F, Fu Q. 2018. “Mitochondrial genome of a 22,000-year-old giant panda from southern China reveals a new panda lineage.” Current Biology. doi:10.1016/j.cell.2018.08.016

    Yang MA, Fu Q. 2018. “Insights into Modern Human Prehistory Using Ancient Genomes.” Trends in Genetics. doi:10.1016/j.tig.2017.11.008

    Yang MA, Gao X, Theunert C, Tong H, Aximu Petri A, Nickel B, Slatkin M, Meyer M, Pääbo S, Kelso J, Fu Q. 2017. “40,000-year-old individual from Asia provides insight into early population structure in Eurasia.” Current Biology. doi:10.1016/j.cub.2017.09.030

    Yang MA and Slatkin M. 2016. “Using ancient samples in projection analysis.” G3: Genes, Genomes, Genetics. doi:10.1534/g3.115.023788

    Librado P, Der Sarkissian C, Ermini L, Schubert M, Jonsson H, Albrechtsen A, Fumagalli M, Yang MA, Gambo C, Seguin-Orlando A, et al. 2015. “Tracking the origins of Yakutian horses and the genetic basis for their fast adaptation to subarctic environments.” Proc Nat Acad Sci. 112(50). doi:10.1073/pnas.1513696112

    Der Sarkissian C, Ermini L, Schubert M, Yang MA, Librado P, Fumagalli M, Jonsson H, Bar-Gal GK, Albrechtsen A, Vieira FG, et al. 2015. “Evolutionary genomics and conservation of the endangered Przewalski’s horse.” Current Biology. 25(19). doi:10.1016/j.cub.2015.08.032

    Yang MA, Harris K, and Slatkin M. 2014. “The projection of a test genome onto a reference population and applications to humans and archaic hominins.” Genetics. 198(4). doi:10.1534/genetics.112.145359

    Wall JD, Yang MA, Jay F, Kim SK, Durand EY, Stevison LS, Gignoux C, Woerner A, Hammer MF, and Slatkin M. 2013. “Higher levels of Neanderthal ancestry in East Asians that in Europeans.” Genetics. 194(1). doi:10.1534/genetics.112.148213

    Yang MA, Sapfo-Malaspinas A, Durand E, and Slatkin M. 2012. “Ancient structure in Africa unlikely to explain Neanderthal and non-African genetic similarity.” Mol Biol Evol. 29(10). doi:10.1093/molbev/mss117

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