Species identification and population genetics in Scylla using morphological and molecular characters

Date of Publication


Document Type


Degree Name

Doctor of Philosophy in Biology

Subject Categories

Biology | Genetics


College of Science



Thesis Adviser

Ma. Carmen Ablan-Lagman

Defense Panel Chair

Gliceria Ramos

Defense Panel Member

Jose Santos Carandang, IV
Florencia G. Claveria
Rachel Rabago-Gotanco
Maria Rowena Eguia


The mud crab, Scylla spp., is an important marine natural resource and comprises a major national industry where the Philippines is 2nd only to China in production. Despite the country’s competitive position, research on the organism and industry practices would benefit from improved species identification in adults and early developmental stages, as well as in the determination of the population structure of the preferred species Scylla serrata. Differentiation of the four existing species, Scylla serrata, S. tranquebarica, S. olivacea and S. paramamosain, is problematic, with morphological markers primarily based on a dichotomous key derived from a wide geographical region with limited sampling intensity. It does not account for local variations in the morphology of a genus known for their plasticity with difficulties aggravated by individuals with ambiguous morphology. In this study, existing molecular methods for species identification, specifically the internal transcribed spaces region I (ITS-1) and the 16S rDNA markers, were used on 1,185 adult mud crabs from wild populations in 7 sites across the Philippines made possible the identification of an updated hierarchy of morphological markers for species identification with 97.8% accuracy. This study was also able to identify 27 morphologically ambiguous mud crabs with atypical ITS-1 markers indicating rare genetic reasons for morphological aberrations. For immature mud crabs, there is no existing diagnostic key for species identification. The overlapping ranges of the Scylla species in the Philippines makes any batch of captured crablets a heterozygous mix preventing the focused allotment of limited space and resources to the rearing of preferred species. Image analysis, using SHAPE, and multivariate analysis, using Principal Component analysis (PCA) and Discriminant analysis (DCA), on 177 wild immature mud crabs from Cagayan detected of subtle morphological similarities on their frontal lobe spines that correspond to differences in species as confirmed by genetic barcoding using ITS-1 and 16S rDNA. Accuracy of the static species diagnostic marker at the instar and juveniles stages were proven when 85.7% of 100 wild immature mud crabs from Bataan and 50 cultured immature mud crabs from Zambales were correctly identified to species using the image comparison program Resemble.js and genetic barcoding. The high demand for stock for the preferred species S. serrata all over the country requires management efforts to be guided by a clear knowledge of genetic structure in existing populations. In this study, the previously observed genetic panmixia in the populations along the Pacific coast of the Philippines was tested using 27 morphometric, 2 mitochondrial and 10 microsatellite markers on 356 S. serrata from Cagayan, Bicol, Quezon, Pangasinan, Bataan, Panay and Iligan. An East- West structure was seen with populations from the Inner Philippine Seas show greater morphological similarity with the populations from the West Philippine Sea that may be You attributed to climate. Molecular markers indicate a distinct West population diverging from the East populations, with Panay exhibiting admixture.

Abstract Format






Accession Number


Shelf Location

Archives, The Learning Commons, 12F Henry Sy Sr. Hall

Physical Description

1 computer optical disc, 4 3/4 in


Regeneration (Biology)—Morphological aspects; Species; Scylla (Crustacea); Morphology; Population genetics; Scylla serrata

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