Multi-Scale Phylogenomics of Gadiformes With Emphasis on Hakes (Merluccius, Merlucciidae)

• Main Author: Roa-Varon, Adela Y.
• Format: Text
• Language: English
• Published: W&M ScholarWorks 2018
• Subjects: Aquaculture and Fisheries; Genetics; Southern Ocean; Patagonia; Pacific; New Zealand
• Online Access: https://scholarworks.wm.edu/etd/1550153685; https://scholarworks.wm.edu/cgi/viewcontent.cgi?article=6531&context=etd

Gadiformes include some of the most important commercially harvested fishes in the world (e.g. cods, hakes, and grenadiers). Currently, different authors recognize anywhere between 11 and 14 families, approximately 84 genera, and over 600 species. The monophyly of the order has been supported by both morphological and molecular data, yet the relationships among families and subfamilies remain poorly understood and interpreting phylogenetic patterns to date has been difficult. My dissertation research on multi-scale phylogenetics of Gadiformes with emphasis on hakes (Merluccius, Merlucciidae) has three primary objectives: (1) to improve the understanding of the phylogenetic relationships among families of Gadiformes (Teleostei); (2) to analyze the phylogenetic relationships within the family Merlucciidae (Merluccius) and (3) to explore the evolution of the caudal skeleton using molecular, morphological and ecological data. in chapter two, a gene capture approach was used, targeting coding DNA sequences (CDS) from single-copy protein-coding genes to study the higher-level relationships (i.e., above the genus level) of Gadiformes. Matrices of 14,208 loci (~2.8 M bp) were generated from a total of 57 species representing all recognized Gadiformes families and subfamilies. Species tree and concatenated maximum likelihood analyses resolved a highly congruent and well-supported phylogeny at both shallow and deep levels that contributes towards stabilizing higher-level Gadiformes classification. in accordance with these results a revised classification of the group is provided in chapter two. in Chapter three the systematics, evolution, and taxonomy of a particularly problematic family, the hakes (Merluccius, Merlucciidae), using genomic data from 13,771 loci and 74 taxa were reassessed. This study resolved the controversy surrounding the taxonomic extent of Merlucciidae and the phylogenetic placement of the genera historically included within the family, based on complete taxonomic sampling at the family and subfamily levels among gadiforms. Additionally, the phylogenetic analysis confirmed an early separation of two lineages of Merluccius, the Old World and the New World clades. The Old World clade includes five well defined species and the New World clade includes three species and two complexes of species suggesting the presence of only one species in the eastern Pacific, as well as, one species in the Southern Ocean (Patagonia – New Zealand). Chapter four provided for the first time a description of the caudal skeleton for all the families among Gadiformes and explores the character evolution of 11 characters (morphological and ecological) mapped on a taxonomically robust phylogenetic hypothesis proposed in chapter two. The ancestral state reconstruction analyses suggest that the ancestral condition among gadiforms had a caudal fin and a pelagic origin. Its loss arose at least two times within Gadiformes resulting in two main phenotypes - the tailed and the tailless fishes, neither of which form a monophyletic grouping. This study is the most comprehensive phylogenomic study of Gadiformes to date. This dissertation used a novel molecular technique coupled with morphological and ecological data that resulted in a better understanding of the evolution of commercially and ecological valuable fishes, which is necessary for effective fisheries management and the preservation of reproductive and genetic diversity. Further steps, including morphological data of extant and extinct taxa, is essential to fully understand macroevolutionary patterns and processes in phenotypic evolution and lineage diversification of gadiforms.