Date of Award


Degree Name

Master of Science


Biological Sciences


Elizabeth J. Walsh


1. Cryptic speciation in zooplankton is a phenomenon that has been recently gaining much attention. This is due in part to advances in molecular techniques which help in the identification of morphologically indistinct species. Organisms that have been traditionally believed to have cosmopolitan distributions are being found to be composed of cryptic species complexes with high levels of genetic divergence among lineages.

2. Epiphanes chihuahuaensis is a member in the Epiphanes senta species complex. In a previous study by Schröder & Walsh (2007), genetic data, along with morphological and reproductive isolation data were employed to help delineate four species within the complex. A more recent study based on DNA fingerprinting demonstrated the presence of two distinct lineages of Epiphanes chihuahuaensis coexisting within a site in the northern Chihuahuan Desert. Using genetic sequence data in combination with DNA fingerprinting and reproductive isolation, I investigated genetic population structure and differentiation in populations of Epiphanes chihuahuaensis to better understand the diversity of the E. senta cryptic species complex.

3. Individuals were collected from two sites in the northern Chihuahuan Desert separated by approximately 40 km. From these individuals, 47 COI gene (649 bp) and 43 ITS region (673 bp) sequences were obtained for phylogenetic analyses using Bayesian and Maximum Likelihood approaches. I also conducted a Bayesian phylogenetic analysis including other isolates from E. senta species complex obtained through GenBank. In addition, DNA fingerprints for some of these individuals were generated using 4 Randomly Amplified Polymorphic DNA (RAPD) primers for Bayesian population structure analysis. Cross-mating experiments were conducted to assess the level of reproductive isolation in the E. senta species complex.

4. Analyses of COI gene sequences demonstrated a high level of differentiation between populations of E. senta species complex occurring at the two sites in the northern Chihuahuan Desert. Mean COI sequence divergence between lineages from each site was 19.5%. Less divergence was seen in ITS region gene sequences with a mean of 4.3% between the two lineages. Phylogenetic analyses of COI gene and ITS region sequences produced two distinct monophyletic clusters with high clade support when using isolates from the northern Chihuahuan Desert only. When other isolates from the E. senta complex were included in a Bayesian phylogenetic analysis, two main clades were formed. One clade was formed by individuals from Hueco Tanks State Park and Historic Site, which corresponded to E. chihuahuaensis. The other clade was composed by the individuals from Rio Bosque Wetlands Park, a representative of E. hawaiiensis and isolates from the E. senta species complex obtained from GenBank. Within E. chihuahuaensis low levels of genetic divergence were found with 0-1.6% for the COI. For the ITS region, percent sequence differences were lower (0-0.4%). COI gene sequences of E. chihuahuaensis yielded 11 haplotypes and a haplotype diversity of 0.69 while 9 haplotypes and a haplotype diversity of 0.75 were detected based on ITS region sequences. Two distinct clusters with high levels of support were identified by Bayesian analysis of RAPD band patterns for individuals from Rio Bosque Wetlands Park and Hueco Tanks State Park and Historic Site. Cross-mating experiments between individuals from the two populations resulted in the occasional production of fertilized eggs. Only in 9% of cross-matings were diapausing eggs successfully produced. Viability of these embryos was not assessed.

5. The high levels of COI gene sequence divergence between E. senta lineages from this region are comparable to those of other rotifer species and aquatic zooplankton species. The low levels of genetic divergence within individuals from HTSPHS do not support the idea of further cryptic speciation in E. chihuahuaensis. Moreover, no coherent structure was found between the two populations sampled in this region by Analysis of Molecular Variation, again supporting the distinctness of the lineages studied here. Finally population structure analysis did not support cryptic speciation in E. chihuahuaensis but it detected the presence of two distinct lineages. Although reproductive isolation is incomplete among these populations of the E. senta species complex, it is presently unknown if the fertilized eggs are viable. As demonstrated in this study, the level of complexity underlying the diversity of these animals is just beginning to be understood. While there are some lineages having large scale distributions, other lineages have only been found in few localities in the region. Understanding the diversity of aquatic ecosystems is important as different species, even if morphologically undistinguishable as in the case of cryptic species, likely contribute differently to their habitats.




Received from ProQuest

File Size

81 pages

File Format


Rights Holder

Diego E. Reyes