In this dissertation I address how open ocean plankton
populations can diverge genetically, and ultimately form new
species. Research focuses on the oceanic calanoid copepod
family Eucalanidae. A global phylogenetic study of the
Eucalanidae revealed substantial cryptic diversity at the species
level. Genetic data from both mitochondrial and nuclear gene
loci support 13 new genetic lineages within the Eucalanidae.
These new lineages range from 1.6% to 23.2% divergent from
their closest relatives (16S rRNA, p-distances) suggesting that
although some diverged relatively recently, other represent quite
ancient speciation events. Rhincalanus nasutus was found to be
a cryptic species complex, with at least 7 genetically distinct,
predominantly allopatric populations worldwide. A molecular
phylogeny for the family supports monophyly of the
Eucalanidae, all four eucalanid genera, and the ‘pileatus’ and
‘subtenuis’ species groups.

A distinct genetic form of Eucalanus hyalinus s. l. was identified
in subtropical waters worldwide. The species name Eucalanus
spinifer T. Scott was removed from synonymy with E. hyalinus
and applied to the smaller form, elevating the number of species
in Eucalanus to a total of six. Adult females of the sister species
can be distinguished morphologically by morphometric, shape,
and size characters. Results suggest that species originally
identified through molecular markers will also be distinguishable
by morphological characters.

A global population genetic study of the sympatric sister species
Eucalanus hyalinus and E. spinifer demonstrated that oceanic
zooplankton species can be highly genetically structured on
macrogeographic spatial scales, despite experiencing extensive
gene flow within features of the large-scale ocean circulation.
Habitat discontinuities at the boundaries of subtropical gyres,
and continental landmasses, acted as effective barriers to gene
flow for both species. The sister species differed in their global
population genetic structures as well as in their oceanographic
distributions. Species-specific differences in habitat were an
important factor determining patterns of dispersal between
populations of each species worldwide.

Two unique spliceosomal introns were discovered in the nuclear
gene elongation factor 1-? in Rhincalanus and Eucalanus, and
the locus was found to have limited phylogenetic utility due to
difficulty in identifying orthologous, functional gene copies.