Dr. Shanlin Liu is the Principal Investigator (PI) of the Adaptive Evolution and Ecological Interaction lab in Institute of Zoology (IOZ), Chinese Academy of Science. He has recognized by Chinese Academy of Sciences on its list of Talents Program. He obtained his bachelor’s and master’s degree in 2007 and 2010, respectively, in Hunan Normal University, China, and obtained his PhD of evolutionary genomics in 2018 in the Natural History Museum of Denmark, Copenhagen University. During 2019 to 2023, he worked in China Agricultural University as postdoc and associate professor. The main breakthroughs in his research work on the animal diversity and its response to global change have centered on the development of a series of innovative methods for the animal molecular taxonomy and applying which to accelerate the taxonomic identification and description of museum specimen collections, and to explore the evolutionary mechanism driving the formation of their biodiversity. He, as the first or corresponding author (including co-), has published research articles in high rank journals, such as Cell, Nucleic Acid Research, Food Chemistry, Bioinformatics, etc. Currently, his publications have >10,000 citations, with a personal H-index of 41. He is selected by Clarivate as one of the world’s most influential scientists (in the Highly Cited Researchers 2023 List). He is also editorial board member for journals of Ecological entomology, Zoological Research: Diversity and Distribution.

The group mainly focuses on the diversity of insect pollinators and their response to global change. To achieve this, we take advantage of molecular taxonomy and paleo-genomics to discover and document wildlife resources and explore the evolutionary and adaptive mechanisms in the process of species formation, as well as issues related to the maintenance of species diversity and ecological service functions. The research work will mainly focus on the following two directions:

1. Development of new technology for rapid identification of species diversity: using DNA barcoding, combined with high-throughput sequencing for rapid identification of biodiversity in mixed samples ("bio-soup") and environmental DNA (eDNA), to provide technical support for species discovery and taxonomic identification, and thus deepen our understanding on interspecific interactions, biodiversity fluctuation response to global change as well as its maintenance in terms of ecological services.

2. Inspecting phylogeny and adaptive evolution using historical museum specimens: cutting-edge molecular technologies enable us to obtain genomics big data for historical specimens collected in the museum, and thus provide us a valuable chance to look into the past genetically. By putting them together with the contemporary living samples, we aim to decipher the evolutionary history of focal taxonomic groups via phylogenetic relations between different species and the changes genetic diversity within species, which can elucidate the adaptive evolution of the focal species in the progress of speciation and extinction. This will further shed light on the modern comprehensive evolutionary theory.

Research Fields：

DNA barcoding, Conservation genomics, Paleo-genomics, Apiology

（*Corresponding author）

Evolutionary Biology related：

Qiu L, Dong J, Li X, Parey SH, Tan K, Orr M, Majeed A, Zhang X, Luo S, Zhou X, Zhu C, Ji T, Niu Q, Liu S*, Zhou X*. Defining honeybee subspecies in an evolutionary context warrants strategized conservation. Zool Res. 2023 May 18;44(3):483-493. doi: 10.24272/j.issn.2095-8137.2022.414.

Liu S*, Westbury MV, Dussex N, Mitchell KJ, Sinding MS, Heintzman PD, Duchêne DA, Kapp JD, von Seth J, Heiniger H, Sánchez-Barreiro F, Margaryan A, André-Olsen R, De Cahsan B, Meng G, Yang C, et al. Ancient and modern genomes unravel the evolutionary history of the rhinoceros family. Cell. 2021 Sep 16;184(19):4874-4885.e16. doi: 10.1016/j.cell.2021.07.032.

van der Valk T, Pe？nerová P, Díez-Del-Molino D, Bergstr？m A, Oppenheimer J, Hartmann S, Xenikoudakis G, Thomas JA, Dehasque M, Sa？l？can E, Fidan FR, Barnes I, Liu S, Somel M, et al., Million-year-old DNA sheds light on the genomic history of mammoths. Nature. 2021 Mar;591(7849):265-269. doi: 10.1038/s41586-021-03224-9.

Misof B*^#, Liu S^#, Meusemann K^#, Peters RS^#, Donath A^#, Mayer C^#, Frandsen PB^#, Ware J, Flouri T^#, Beutel RG^#, Niehuis O^#, Petersen M^#, Izquierdo-Carrasco F^#, Wappler T^#, Rust J^#, Aberer AJ, Asp？ck U, Asp？ck H, Bartel D, et al., Phylogenomics resolves the timing and pattern of insect evolution. Science. 2014 Nov 7;346(6210):763-7. doi: 10.1126/science.1257570. (^#Major contributors)

DNA Barcoding and Bioinformatics related：

Yang C, Zheng Y, Tan S, Meng G, Rao W, Yang C, Bourne DG, O'Brien PA, Xu J, Liao S, Chen A, Chen X, Jia X, Zhang AB*, Liu S*. Efficient COI barcoding using high throughput single-end 400？bp sequencing. BMC Genomics. 2020 Dec 4;21(1):862. doi: 10.1186/s12864-020-07255-w.

Lang D, Zhang S, Ren P, Liang F, Sun Z, Meng G, Tan Y, Li X, Lai Q, Han L, Wang D, Hu F, Wang W*, Liu S*. Comparison of the two up-to-date sequencing technologies for genome assembly: HiFi reads of Pacific Biosciences Sequel II system and ultralong reads of Oxford Nanopore. Gigascience. 2020 Dec 15;9(12):giaa123. doi: 10.1093/gigascience/giaa123.

Hu J, Fan J, Sun Z, Liu S*. NextPolish: a fast and efficient genome polishing tool for long-read assembly. Bioinformatics. 2020 Apr 1;36(7):2253-2255. doi: 10.1093/bioinformatics/btz891

Meng G, Li Y, Yang C, Liu S*. MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization. Nucleic Acids Res. 2019 Jun 20; 47 (11): e63. doi: 10.1093/nar/gkz173

Liu S^#, Yang C^#, Zhou C^#, Zhou X. Filling reference gaps via assembling DNA barcodes using high-throughput sequencing-moving toward barcoding the world. Gigascience. 2017 Dec 1;6(12):1-8. doi: 10.1093/gigascience/gix104.

Liu S, Li Y, Lu J, Su X, Tang M, Zhang R, Zhou L, et al. SOAPBarcode: revealing arthropod biodiversity through assembly of Illumina shotgun sequences of PCR amplicons. Methods in Ecology and Evolution. 2013. 4: 1142-1150.