Date of Award

Summer 2022

Document Type

Open Access Dissertation


Biological Sciences

First Advisor

Joseph Quattro


Chapter 1: The seas surrounding the Arabian Peninsula, which represent the northernmost portion of the Indian Ocean, are considered to have the highest aquatic biodiversity among the worlds marine regions. Seas that surround the Arabian Peninsula include the Red Sea, the Gulf of Aden, the Arabian Sea, the Gulf of Oman, and the Arabian Gulf. In aggregate, this area harbors a large number of endemic and more widespread marine species, including fishes, echinoderms, and corals.

There are unique challenges involved in grouper species identification in the Arabian region including ‘familiar’ Arabic species designations that are not standardized in the Arabic literature but, rather, based on local variants. This has led to confusion regarding species names and features that are inadequately defined and extremely varied. Previous research lists two pervasive issues with species identification, including differences in localized dialect and an almost complete lack of “informant knowledge” regarding species name variation and uses.

Because of widespread ambiguity in grouper species recognition, many recent systematic studies have instead relied on alternative recognition approaches that utilize molecular techniques, such as DNA sequencing, to identify individual species rather than relying on morphological characters alone.

Chapter 2. The Red Sea is a somewhat peculiar aquatic ecosystem in the world, both from a biological and geological perspective. The basin has seen several episodes of geological and climatic instability that resulted, eventually, in the formation of an incipient ocean with a noticeable degree of faunal endemism. Chapter 2 develops the case that the Red Sea endemic grouper Epinephelus summana is a genetic indicator of Pleistocene events that derived Red Sea fauna endemism. This is substantiated with a pilot investigation of endemism in the Red Sea groupers and Pleistocene-driven speciation of Epinephelus species.

Groupers (Serranidae:Perciformes) are reef-associated fishes of great ecological and economic importance. The Summane grouper Epinephelus summana is a species native only to the Red Sea and Western the Gulf of Aden. This work aimed to identify the genetic relationship between E. summana and the allopatric, but morphologically similar, species E. ongus. Also, we were keen to identify the period when species divergence took place. For this, eight grouper species were collected from the coasts of the Kingdom of Saudi Arabia on the Red Sea and the Arabian Gulf. The net results indicated a high degree of endemism in the Red Sea groupers, and a necessity for assessment of possible cryptic speciation within serranids in this area.

Chapter 3: Application of genetic markers for species identification gains crucial importance in the Saudi Arabian national economy because marine products contribute significantly to the Gross Domestic Product (GDP). The current massive increase in the size and outreach of international trade has increased the threats of food misrepresentation and fraud, especially in fish markets. This could be attributable to the insufficiency of classical species identification methodologies that are based only on morphology. The accuracy of these methodologies have been proven to be insufficient to expectations, which may contribute to trading of already endangered or overfished species. This directly leads to fisheries decline due to improper management of fisheries. The issue is becoming more complicated with the outbreak of unreported fishing, overfishing, and even fraudulence in fisheries markets through representation of low-priced, abundantly-caught fish species as more expensive ones.

In summary, we obtained the first record of Cephalopholis sonnerati in the the Red Sea near Jazan which is close to Gulf of Aden. Identified both Cephalopholis oligosticta and Epinephelus summana. based on morphologically and genetic investigation using 4 different gene markers 16S, 12S, TMO4, and H3. Both are endemic to the Red Sea. First study using morphology and genetics to confirm their related. Finally, the unknown Epinephelus species that was found in the Red Sea fresh fish landings showed greater than 98 percent identity with E. akaara, E. stictus, E. fasciatus, and E. anlogus.

Chapter 4: The identification of species constitutes the first basic step for biodiversity monitoring and conservation. Fish species identification mainly relies on morphometric and meristic characteristics. However, there are pitfalls in relying primarily on morphology when attempting to identify fishes during various stages of their development not considered in original treatments or when examining fragmentary, partial or processed remains.

It has been recently proposed that the use of DNA methods can circumvent such a problem. The reconstruction of phylogenetic relationships based on molecular data in addition to the classical methodologies has helped to resolve taxonomic uncertainties for fishes.


© 2022, Mohammad Saeed Al Jazza Alqahtani

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