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Scholarly Works (4 results)

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Research Theses and Dissertations (2004)

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. I. 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-α in Rhincalanus and Eucalanus, and the locus was found to have limited phylogenetic utility due to difficulty in identifying orthologous, functional gene copies.

    Cover page: Speciation in the Open Ocean: The Phylogeography of the Oceanic Copepod Family Eucalanidae
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    • Peer Reviewed
    UC San Diego Previously Published Works (2010)
    Species range information forms the empirical data of pelagic biogeography. Early descriptions of canonical zooplankton distributions in the Pacific Ocean were based, in part, on distributional data from the planktonic copepod family Eucalanidae. A large-scale molecular survey of this group, covering Atlantic, Pacific, and Indian Oceans (1295 individuals), increased the total diversity from 24 to 39 evolutionarily significant units (ESUs). New biogeographies are presented here for 18 lineages within 10 described species in the genera Subeucalanus, Pareucalanus, and Rhincalanus. Integration of molecular and morphological data on diversity and distribution resulted in three primary outcomes: (1) the morphological species was confirmed to be valid, and the biogeographic distribution remains largely unchanged from prior reports, (2) the species was found to contain multiple ESUs, each of which has a more restricted distribution than the parent taxon, and (3) the species was found to contain multiple ESUs, whose biogeographic distributions remain unclear. Subeucalanus subtenuis, S. mucronatus, S. subcrassus, Pareucalanus attenuatus, P. langae, and P. parki are all valid genetic and morphological species, and prior distribution records from Fleminger (1973) and Lang (1965) are confirmed to be accurate. New records in the western Indian Ocean extend the biogeographic range of S. subtenuis, S. mucronatus, S. subcrassus, and P. langae. Subeucalanus pileatus, P. sewelli, and R. rostrifrons, all species with Indo-Pacific or circumglobal distributions, consist of genetically divergent, allopatric populations that subdivide the original biogeographic range. Subeucalanus crassus and Rhincalanus nasutus are species complexes containing 4-8 genetically divergent lineages, whose distributions are inadequately characterized. Although results suggest more restricted pelagic habitats for some eucalanid species, those habitats have been previously described for other zooplanktonic taxa and do not represent new pelagic distributional types. © 2010 Elsevier Ltd.
      Cover page: Integrated molecular and morphological biogeography of the calanoid copepod family Eucalanidae
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      UC San Diego Previously Published Works (2021)
      Metabarcoding of zooplankton communities is becoming more common, but molecular results must be interpreted carefully and validated with morphology-based analyses, where possible. To evaluate our metabarcoding approach within the California Current Ecosystem, we tested whether physical subsampling and PCR replication affects observed community composition; whether community composition resolved by metabarcoding is comparable to morphological analyses by digital imaging; and whether pH neutralization of ethanol with ammonium hydroxide affects molecular diversity. We found that (1) PCR replication was important to accurately resolve alpha diversity and that physical subsampling can decrease sensitivity to rare taxa; (2) there were significant correlations between relative read abundance and proportions of carbon biomass for most taxonomic groups analyzed, but such relationships showed better agreement for the more dominant taxonomic groups; and (3) ammonium hydroxide in ethanol had no effect on molecular diversity. Together, these results indicate that with appropriate replication, paired metabarcoding and morphological analyses can characterize zooplankton community structure and biomass, and that metabarcoding methods are to some extent indicative of relative community composition when absolute measures of abundance or biomass are not available.
        Cover page: Recommendations for interpreting zooplankton metabarcoding and integrating molecular methods with morphological analyses
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        • Peer Reviewed
        UC San Diego Previously Published Works (2017)
          Creative Commons 'BY' version 4.0 license
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