Espinoza, Gloria Janelle (2020-07). Comparative Phylogeography, Historical Demography, and Population Genomics of Colonizing Fauna in Restored and Natural Spartina Salt Marshes Along the Northern Gulf of Mexico. Doctoral Dissertation. Thesis uri icon

abstract

  • Salt marshes provide vital ecosystem services to nearby coastal communities and have suffered accelerated rates of loss, worldwide. A number of biotic and abiotic factors contribute to the success of restoration projects, but restoration focuses primarily on hydrology and plant cover. Gulf Killifish (Fundulus grandis), daggerblade grass shrimp (Palaemon pugio; previously Palaemonetes pugio), and phloem-feeding planthoppers (Prokelisia marginata) are three ecologically important and abundant species in salt marshes, for which there is a paucity of data on population genetics or the effects of restoration projects on levels of genetic diversity. In this study I: 1) developed a short amplicon high resolution melting assay (SA-HRMA) for molecular identification of two morphologically similar planthopper species, Prokelisia marginata and Prokelisia dolus; 2) compared population structure and historical demography for the Gulf Killifish, daggerblade grass shrimp, and Prokelisia planthopper in the north and west Gulf of Mexico (Gulf) using mitochondrial DNA (mtDNA) sequences; and 3) investigated levels of genetic diversity of Gulf Killifish inhabiting a reference marsh compared with restored marshes of differing ages and distances from the reference in Galveston Bay, Texas, using mtDNA sequences and nuclear single nucleotide polymorphism (SNP) data generated via double digest restriction site associated DNA (ddRAD) sequencing. A 60 bp fragment of Cytochrome C Oxidase Subunit I (COI) was used in a SA-HRMA assay to differentiate P. marginata from P. dolus via a minimum separation of ~1.7?C between the melting peaks for each species. A high-throughput test (n=518) of the HRMA resulted in clearly diagnostic melting curves for species assignment of 213 P. dolus individuals and 296 P. marginata individuals, with only 9 (1.7%) amplification failures. Mitochondrial sequence data revealed high levels of haplotypic diversity, evidence of isolation by distance (IBD), and population structure at regional levels, along with two distinct phylogroup associations and concordant distinct historical demography characteristics for Gulf Killifish in the Gulf. Grass shrimp and planthoppers displayed low levels of haplotypic diversity, and evidence of population structure, but both appear to contain snapshots of the total potential diversity for these species in the Gulf. Gulf Killifish inhabiting restored and reference marshes in Galveston Bay displayed no evidence of population structure or IBD, but SNP data showed significantly (p < 0.05) lower levels of heterozygosity in the two youngest restored marshes compared to the reference, and a higher degree of inbreeding in the two young marshes. Overall, it was determined that levels of genetic diversity in Gulf Killifish inhabiting restored marshes are similar to that in a reference marsh, suggesting Gulf Killifish have enough dispersal potential for adequate gene flow between marshes up to 10km distant from each other.

publication date

  • July 2020