Forums | HES 健康与环境科学

12 December 2025, 10:16

Speaker: Dr. Xiaoting Xu
Title: Efficient Data Mining for Multi-Dimensional Biodiversity Patterns
Date: 2025-12-12
Time: 14:00 -15:00 
Room: ES420
Host: Dr. Yaoqi Li
Tencent Meeting ID: 979-1135-5376

Abstract: 

This study presents a systematic overview of highly efficient software tools—UltraGBIF, PyNCBIminer, and CPminer—designed for processing large-scale species distribution data, DNA sequence data, and chloroplast genome data, using the Asteraceae (Sunflower) family as a compelling case study.
UltraGBIF is a high-performance R package capable of rapidly cleaning and curating approximately 1million GBIF occurrence records in 15 minutes. Concurrently, PyNCBIminer and CPminer automate the retrieval of relevant DNA sequences from GenBank and facilitate the construction of phylogenomic supermatrices, significantly enhancing the efficiency of building large-scale, robust phylogenetic trees.
By integrating these refined species distribution datasets with high-fidelity phylogenetic analyses, these tools enable in-depth exploration of both species diversity and evolutionary diversity (e.g., Phylogenetic Diversity and Evolutionary Distinctiveness). This approach provides crucial, data-driven support for spatial conservation planning and biodiversity protection research.

Bio:

Dr. Xiaoting Xu is an Associate Professor at the College of Life Sciences, Sichuan University. She graduated with a Ph.D. in Physical Geography from Peking University in 2013.
Dr. Xu’s primary research focuses on the origin, evolution, and conservation of angiosperm diversity. She integrates multidisciplinary approaches, including macroecology, biogeography, and bioinformatics, to address large-scale ecological and evolutionary questions.
She is a highly productive researcher, having authored over 60 papers in high-quality journals in the fields of Botany and Ecology, with nearly 2,000 citations. Her work has appeared in prestigious publications such as Nature Communications, Journal of Integrative Plant Biology, Conservation Biology, and Diversity and Distributions. She also serves as a Young Editorial Board Member for the journal Plant Diversity.