Species identification through deep learning and geometrical morphology in oaks (Quercus spp.): Pros and cons

Author:

Qi Min1,Du Fang K.1ORCID,Guo Fei2,Yin Kangquan3,Tang Jijun4

Affiliation:

1. School of Ecology and Nature Conservation Beijing Forestry University Beijing China

2. School of Computer Science and Engineering Central South University Changsha Hunan China

3. School of Grassland Science Beijing Forestry University Beijing China

4. Shenzhen Institute of Advanced Technology Chinese Academy of Sciences Shenzhen Guangdong China

Abstract

AbstractPlant phenotypic characteristics, especially leaf morphology of leaves, are an important indicator for species identification. However, leaf shape can be extraordinarily complex in some species, such as oaks. The great variation in leaf morphology and difficulty of species identification in oaks have attracted the attention of scientists since Charles Darwin. Recent advances in discrimination technology have provided opportunities to understand leaf morphology variation in oaks. Here, we aimed to compare the accuracy and efficiency of species identification in two closely related deciduous oaks by geometric morphometric method (GMM) and deep learning using preliminary identification of simple sequence repeats (nSSRs) as a prior. A total of 538 Asian deciduous oak trees, 16 Q. aliena and 23 Q. dentata populations, were firstly assigned by nSSRs Bayesian clustering analysis to one of the two species or admixture and this grouping served as a priori identification of these trees. Then we analyzed the shapes of 2328 leaves from the 538 trees in terms of 13 characters (landmarks) by GMM. Finally, we trained and classified 2221 leaf‐scanned images with Xception architecture using deep learning. The two species can be identified by GMM and deep learning using genetic analysis as a priori. Deep learning is the most cost‐efficient method in terms of time‐consuming, while GMM can confirm the admixture individuals' leaf shape. These various methods provide high classification accuracy, highlight the application in plant classification research, and are ready to be applied to other morphology analysis.

Funder

Key Laboratory of Forest Ecology and Environment

Fundamental Research Funds for the Central Universities

National Natural Science Foundation of China

Publisher

Wiley

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