Geometric morphometric methods for identification of oyster species based on morphology
Both genetic and environmental factors affect the morphology of oysters. Molecular identification is currently the primary means of species identification, but it is inconvenient and costly. In this research, we evaluated the effectiveness of geometric morphometric (GM) techniques in distinguishing...
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2024
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traditional morphometrics geometric morphometrics Pacific oyster |
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traditional morphometrics geometric morphometrics Pacific oyster Liu, Qian Guo, Yuepeng Yang, Yanzhuo Mao, Junxia Wang, Xubo Liu, Haijiao Tian, Ying Hao, Zhenlin Geometric morphometric methods for identification of oyster species based on morphology |
topic_facet |
traditional morphometrics geometric morphometrics Pacific oyster |
description |
Both genetic and environmental factors affect the morphology of oysters. Molecular identification is currently the primary means of species identification, but it is inconvenient and costly. In this research, we evaluated the effectiveness of geometric morphometric (GM) techniques in distinguishing between two oyster species, Crassostrea gigas and C. ariakensis . We used traditional morphometric and GM methods, including principal component analysis (PCA), thin-plate spline analysis (TPS) and canonical variable analysis (CVA), to identify specific features that distinguish the two species. We found that differences in shape can be visualised using GM methods. The Procrustes analysis revealed significant differences in shell morphology between C. gigas and C. ariakensis . The shells of C. ariakensis are more prominent at the widest point and are more scattered and have a greater variety of shapes. The shells of C. gigas are more oval in shape. PCA results indicated that PC1 explained 45.22%, PC2 explained 22.09% and PC3 explained 10.98% of the variation between the two species, which suggests that the main morphological differences are concentrated in these three principal components. Combining the TPS analysis function plots showed that the shell shape of C. ariakensis is mainly elongated and spindle-shaped, whereas the shell shape of C. gigas is more oval. The CVA results showed that the classification rate for the two species reached 100% which means that C. ariakensis and C. gigas have distinct differences in shell morphology and can be completely separated, based on morphological characteristics. Through these methods, a more comprehensive understanding of the morphological characteristics of different oyster populations can be obtained, providing a reference for oyster classification and identification. |
format |
Article in Journal/Newspaper |
author |
Liu, Qian Guo, Yuepeng Yang, Yanzhuo Mao, Junxia Wang, Xubo Liu, Haijiao Tian, Ying Hao, Zhenlin |
author_facet |
Liu, Qian Guo, Yuepeng Yang, Yanzhuo Mao, Junxia Wang, Xubo Liu, Haijiao Tian, Ying Hao, Zhenlin |
author_sort |
Liu, Qian |
title |
Geometric morphometric methods for identification of oyster species based on morphology |
title_short |
Geometric morphometric methods for identification of oyster species based on morphology |
title_full |
Geometric morphometric methods for identification of oyster species based on morphology |
title_fullStr |
Geometric morphometric methods for identification of oyster species based on morphology |
title_full_unstemmed |
Geometric morphometric methods for identification of oyster species based on morphology |
title_sort |
geometric morphometric methods for identification of oyster species based on morphology |
publisher |
Pensoft Publishers |
publishDate |
2024 |
url |
https://doi.org/10.3897/BDJ.12.e115019 |
genre |
Crassostrea gigas Pacific oyster |
genre_facet |
Crassostrea gigas Pacific oyster |
op_source |
Biodiversity Data Journal, 12, e115019, (2024-02-26) |
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ftzenodo:oai:zenodo.org:10721471 2024-09-15T18:03:17+00:00 Geometric morphometric methods for identification of oyster species based on morphology Liu, Qian Guo, Yuepeng Yang, Yanzhuo Mao, Junxia Wang, Xubo Liu, Haijiao Tian, Ying Hao, Zhenlin 2024-02-26 https://doi.org/10.3897/BDJ.12.e115019 unknown Pensoft Publishers https://doi.org/10.3897/BDJ.12.e115019.figure6 https://doi.org/10.3897/BDJ.12.e115019.figure2 https://doi.org/10.3897/BDJ.12.e115019.figure4 https://doi.org/10.3897/BDJ.12.e115019.figure5 https://doi.org/10.3897/BDJ.12.e115019.figure1 https://doi.org/10.3897/BDJ.12.e115019.figure3 https://doi.org/10.3897/BDJ.12.e115019.suppl3 https://doi.org/10.3897/BDJ.12.e115019.suppl1 https://doi.org/10.3897/BDJ.12.e115019.suppl2 https://doi.org/10.1080/11250000409356545 https://doi.org/10.3897/zookeys.1043.66992 https://doi.org/10.1360/972012-1561 https://doi.org/10.1016/j.aquaculture.2018.08.048 https://doi.org/10.2983/035.036.0301 https://doi.org/10.4002/040.052.0201 https://doi.org/10.2983/035.040.0107 https://doi.org/10.3969/j.issn.1000-3096.2004.04.014 https://doi.org/10.2983/035.037.0407 https://doi.org/10.2983/035.038.0210 https://doi.org/10.1093/bioinformatics/btp187 https://doi.org/10.2983/035.036.0208 https://doi.org/10.1080/10635150802554779 https://doi.org/10.1006/mpev.1994.1024 https://doi.org/10.12657/folmal.024.020 https://doi.org/10.1007/s10750-008-9332-1 https://doi.org/10.1007/s11692-009-9055-x https://doi.org/10.2307/2992207 https://doi.org/10.1080/00212210.1996.10688879 https://doi.org/10.1371/journal.pone.0108696 https://doi.org/10.11759/hykx20210427003 https://doi.org/10.13287/j.1001-9332.202107.001 https://doi.org/10.1007/s00227-010-1532-3 https://doi.org/10.1017/s1089332600001868 https://doi.org/10.1007/978-3-319-96776-9_2 https://doi.org/10.1016/B978-012778460-1/50019-3. https://zenodo.org/communities/biosyslit https://doi.org/10.3897/BDJ.12.e115019 oai:zenodo.org:10721471 info:eu-repo/semantics/openAccess Creative Commons Attribution 4.0 International https://creativecommons.org/licenses/by/4.0/legalcode Biodiversity Data Journal, 12, e115019, (2024-02-26) traditional morphometrics geometric morphometrics Pacific oyster info:eu-repo/semantics/article 2024 ftzenodo https://doi.org/10.3897/BDJ.12.e11501910.3897/BDJ.12.e115019.figure610.3897/BDJ.12.e115019.figure210.3897/BDJ.12.e115019.figure410.3897/BDJ.12.e115019.figure510.3897/BDJ.12.e115019.figure110.3897/BDJ.12.e115019.figure310.3897/BDJ.12.e115019.suppl310.3897/ 2024-07-26T19:12:03Z Both genetic and environmental factors affect the morphology of oysters. Molecular identification is currently the primary means of species identification, but it is inconvenient and costly. In this research, we evaluated the effectiveness of geometric morphometric (GM) techniques in distinguishing between two oyster species, Crassostrea gigas and C. ariakensis . We used traditional morphometric and GM methods, including principal component analysis (PCA), thin-plate spline analysis (TPS) and canonical variable analysis (CVA), to identify specific features that distinguish the two species. We found that differences in shape can be visualised using GM methods. The Procrustes analysis revealed significant differences in shell morphology between C. gigas and C. ariakensis . The shells of C. ariakensis are more prominent at the widest point and are more scattered and have a greater variety of shapes. The shells of C. gigas are more oval in shape. PCA results indicated that PC1 explained 45.22%, PC2 explained 22.09% and PC3 explained 10.98% of the variation between the two species, which suggests that the main morphological differences are concentrated in these three principal components. Combining the TPS analysis function plots showed that the shell shape of C. ariakensis is mainly elongated and spindle-shaped, whereas the shell shape of C. gigas is more oval. The CVA results showed that the classification rate for the two species reached 100% which means that C. ariakensis and C. gigas have distinct differences in shell morphology and can be completely separated, based on morphological characteristics. Through these methods, a more comprehensive understanding of the morphological characteristics of different oyster populations can be obtained, providing a reference for oyster classification and identification. Article in Journal/Newspaper Crassostrea gigas Pacific oyster Zenodo |