The taxonomy and systematics of the coral genus Favia from Thai waters

Narinratana Kongjandtre (2010). The taxonomy and systematics of the coral genus Favia from Thai waters PhD Thesis, School of Biological Sciences, The University of Queensland.

       
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Author Narinratana Kongjandtre
Thesis Title The taxonomy and systematics of the coral genus Favia from Thai waters
School, Centre or Institute School of Biological Sciences
Institution The University of Queensland
Publication date 2010-12
Thesis type PhD Thesis
Supervisor Ove Hoegh-Guldberg
Tyrone Ridgway
Lyn Cook
Selina Ward
Mauricio Rodriguez-Lanetty
Total pages 229
Total colour pages 25
Total black and white pages 204
Subjects 06 Biological Sciences
Abstract/Summary There is unequivocal evidence that the current changes in the global climate, coupled with increasing anthropogenic disturbance on reefs, pose serious threats to the future of coral reefs. As such, much emphasis has recently been placed on reef resilience. Biodiversity, however, is an important component underpinning resilience and its study via taxonomy is central to our understanding of coral reef ecosystems. Stable and accurate taxonomies are critical to an understanding the biodiversity on coral reefs, yet our understanding of the taxonomy and systematics of reef building corals is beset with problems and ambiguities. The genus Favia (Cnidaria: Scleractinia) is a particularly problematic group of corals with previous studies finding it to be non-monophyletic, with the Atlantic Favia and Indo-Pacific Favia being genetically distinct and nested among other genera and families. This thesis focuses on the taxonomy and systematics of Favia (with para-septothecal walls) and uncovers major problems with, and inconsistencies in, genetic markers currently used for corals. The non-homology of mt-IGR (COI-trnM region) and multiple copies of ITS present a huge challenge for using DNA sequences alone to delineate species of Favia (Chapter 4). This study explored ways to resolve some of the major problems within this important group resulting in some new insights into the evolution of Favia. Southeast Asian Favia appear to be largely monophyletic, when non-homologous copies of COI-trnM are removed (with the exception of Barabattoia amicorum, which was included along with a likely erroneous sequence of Goniastrea aspera from Genbank). The ITS region also recovers the monophyly of Favia (with para-septothecal walls) albeit with Barabattoia not sampled. Bayesian phylogenetic analysis of COI-trnM found no support for monophyly of F. pallida, F. cf. pallida, F. cf. lizardensis and the F. favus species complex; they were distributed in four clades that are sister to F. truncatus. In the ITS phylogeny, the four morphospecies were paraphyletic and haplotypes from each of these morphospecies were distributed among four poorly-defined clusters which were also sister species to F. truncatus, however with no support. This thesis found little support for the current circumscription of many species, including F. pallida, F. cf. pallida, F. cf. lizardensis and members of the F. favus species complex. Even though current taxonomy is mostly based on morphology, analyses of morphological data also failed to recover the described species (Chapter 5). Application of a Phylogenetic Species Concept (PSC) failed to recover current species and provided little resolution for alternative taxonomies (Chapter 4). Similarly, if considered under a Biological Species Concept (BSC), current species could not be separated and there were no alternative groupings (Chapters 3, 6). Nontheless, there is conclusive genetic evidence to show that F. truncatus and F. cf. helianthoides each represent a well-supported monophyletic group in both ITS and COI-trnM DNA regions. In addition, they are each reproductively isolated from other species and are thus separate species under both the PSC and the BSC (Chapters 4, 6). Furthermore, using the hooded appearance of the corallite as a character, F. truncatus is further defined under a Morphological Species Concept (MSC). On the other hand, the morphology of F. cf. helianthoides often overlapped with the highly variable morphology of the F. favus species complex and could therefore not be resolved under the MSC (Chapter 5). Chapters 4 – 6 reveal evidence for the non-monophyly for four morphospecies of Favia. Favia pallida, F. cf. pallida, F. cf. lizardensis and the F. favus species complex spawned on the same nights with ability for inter-breeding and highly compatible gametes between morphospecies, although testing for the presence of any post-zygotic isolating barriers was not included in this study. Therefore, these morphospecies have been rejected by the PSC and the BSC. More flexible species concepts such as the ‘genotypic cluster’ concept allowed the delineation of polytypic species. Chapter 5 therefore tested the ‘genotypic cluster’ against the MSC by testing the hypothesis that morphospecies represent natural taxa and are congruent with species described under the ‘genotypic cluster’ concept. This thesis reveals that, whilst showing some merit, morphological methods alone are limited in their ability to accurately classify proposed unknown specimens (potential hybrids) when specimens were identified based on a priori species information using morphospecies and genotypic clusters (ITS and COI-trnM). A direct comparison between genetic and morphological information suggests that the ‘genotypic cluster’ concept is more robust at revealing species boundaries between Favia. The work embodied by this thesis has significantly expanded knowledge about the role of introgressive hybridization within the Southeast Asian Favia and provided a novel perspective of these important species within a number of species concepts. Inferring phylogenies from mitochondrial versus nuclear gene trees has allowed unknown specimens (potential hybrids) to be identified suggesting that this approach should be used in future studies. Significant genetic differentiation between F. pallida and the F. favus species complex, well separated using morphological characters and a small gap in spawning time between 18.30 – 20.00 hours (the F. favus species complex) and 20.30 – 21.30 hours (F. pallida) supported the hypothesis that the two species were once distinct biological species. However, the lack of genetic differentiation observed between F. cf. pallida and F. cf. lizardensis, high genetic connectivity, and gamete compatibility across morphospecies, provided evidence that there has been gene flow between morphospecies of Favia. The present thesis emphasizes the lack of pre-mating barriers for genetic exchange to maintain species boundaries within Favia. In summary, non-monophyly observed using ITS and COI-trnM DNA regions reflect syngameons that are capable of introgressive hybridization. This thesis also demonstrates the importance of using both life history and molecular studies across the broad geographic range of corals. Comparisons between multiple study sites have also been shown to be informative to define hybridization zones. This thesis recognizes some morphological characters such as septa teeth, septa size and thickness, number of septa and wall thickness as useful in distinguishing the morphospecies of Favia. Further study on septa details by the use of the scanning electron microscope may provide new insight into morphological traits in the species of Favia. Incorporating environmental parameters from each location and transplantation experiments would provide a better understanding of phenotypic plasticity among different genotypes and species.
Keyword Favia, coral, Scleractinian, phylogeny, systematics, morphology, spawning, hybridization, Thailand
Additional Notes Color page number (Total 25) Portrait p.9, 26, 67, 68, 82, 89, 131, 133, 137, 142-143, 191-192, 199, 217 Landscape p.85-88, 139-141, 189-190, 196, B&W (Total 204) B&W Landscape p.34-37, 69, 101-114, 155, 157-175, 204-211

 
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