Gobiarian fishes, exemplified by gobies, sleepers and cardinalfishes, have radiated across
coastal marine and aquatic habitats worldwide, yet the biological traits deemed responsible for
generating their great diversity, such as small body size, short generation times, and
ecomorphological specialization, have also hindered resolution of their phylogeny. The current
classification of Gobiaria is based on molecular phylogenetics, and while broad relationships
among major groups have largely been settled by independent investigations, the placement of
all higher taxa have not been verified with multilocus data. The root topology recovered from
different molecular datasets is contentious, with multilocus and phylogenomic studies resolving
nursery and cardinalfishes either in reciprocal or sequential sister clades to other gobiarians,
and this deep systematic controversy questions the current two-order classification. Here I used
two complementary approaches to resolve the phylogeny of Gobiaria. In my first study I mined
public databases to assemble a sparse supermatrix of 23 genes and construct a phylogenetic
tree with dense taxon sampling, comprised of approximately 30 percent of the more than 2,400
known gobiarian species. In my second study I generated new ultraconserved element
sequence data to assemble a phylogenomic matrix of 704 genes, construct a phylogenetic tree
with comprehensive sampling of higher taxa, and estimate a timescale for diversification under
the relaxed molecular clock. Overall my studies produced more evidence in support of the
current two-order classification of Gobiaria, and revealed the root uncertainty is a result of
ancient incomplete lineage sorting. I also discovered that collared wrigglers (Xenisthmus spp.)
form a monophyletic clade separate from sleepers (Eleotridae), and recommend recognizing
family Xenisthmidae in the clade-based classification of Gobiaria. I dated origination of Gobiaria
in the youngest age of the Early Cretaceous (104 Ma), found major clades of gobies, sleepers,
and cardinalfishes diverged in the early Eocene (~50 Ma), and placed goby lineage
diversification in the Oligocene and Miocene. In summary, my studies support the current
two-order classification placing nursery and cardinalfishes in Kurtiformes and the remaining
gobiarian fishes in Gobiiformes, confirm the clade-based phylogenetic classification of gobiarian
families, and advance evidence for recognizing collared wrigglers in family Xenisthmidae.
