Conservation genetics of California abalone species

Over the past three decades, five species of abalone (genus Haliotis) in California waters have gone from harvestable resources to rare or even endangered species status. Both anthropogenic (overexploitation, habitat destruction) and natural (disease, predation) factors have contributed to the declines. This dissertation explores several aspects of abalone recovery and conservation along the coast of California through population genetic theory and techniques. Chapters I and II deal with the captive breeding of two California abalone species. Chapter I focuses on ensuring the specific purity of broodstock and maintaining genetic diversity in hatchery-bred progeny of the endangered white abalone (H. soreseni). Using DNA from these animals, genetic markers were developed, including five nuclear microsatellite loci and partial sequences of one nuclear (VERL) and two mitochondrial (COI and CytB) genes, to assess genetic variability in the species, aid in species identification (ergo prevent broodstock contamination), and potentially track the success of future outplanting of captive-reared animals in restocking operations. Chapter II quantifies the loss of genetic diversity resulting from the captive breeding of green abalone (H. fulgens). No change in overall heterozygosity was evident, but significant losses in allelic richness were found in the captive-bred green abalone versus that in wild populations. Chapters III, IV, and V center on inferring realized connectivity (gene flow) among natural populations of red (H. rufescens), black (H. cracherodii), and pink (H. corrugata) abalone. For red abalone (Chapter III), COI sequencing and microsatellite genotyping did not show significant genetic divergence among populations. In contrast, data from AFLPs became the first to suggest there is significant genetic differentiation among California red abalone populations. In black abalone (Chapter IV), data from AFLPs and one microsatellite locus showed significant divergence among multiple populations and exhibited a signal of isolation by distance consistent with a stepping-stone model of connectivity. Pink abalone (Chapter V) also showed evidence of restricted gene flow among populations. Finally, Chapters VI and VII focus on the fatal disease withering syndrome (WS). Chapter VI involves characterizing the post-esophageal microbiomes of red and black abalone with and without WS. Significant differences between the clone libraries isolated from healthy and diseased abalone suggested that WS has significant impact on the bacterial composition of the abalone post-esophageal microbiome, and specific membership of the microbiomes suggests that infection by Candidatus Xenohaliotis californiensis, the etiological agent of WS, may not be the sole cause of morbidity and mortality due to WS in abalone. Chapter VII is a preliminary study of genetic variation within C. X. californiensis samples from wild and captive-bred abalone species collected from multiple locations along the coast of California. Thus far, no variation has been found in partial sequences of either the 16S rDNA or recombinase A (recA) genes