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The San Diego fairy shrimp (Branchinecta sandiegonensis ) is listed as federally endangered as a result of large-scale urbanization and subsequent vernal pool habitat loss. When new pools are created for mitigation or disturbed pools are restored, sediment from existing pools may be used for inoculation. The success of these projects can depend on whether source material is taken from a gene pool that is differentially adapted from the destination. Previous studies have suggested that there are at least two regional gene pools of San Diego fairy shrimp within San Diego County. A putative contact zone between these gene pools occurs primarily on land owned by the Marine Corps Air Station at Miramar (MCAS Miramar). We collected adult fairy shrimp from 51 pools across MCAS Miramar and extracted DNA from 1752 individuals. Using the mitochondrial gene cytochrome oxidase I (COI) in conjunction with seven microsatellite loci, we delineated the gene pool boundary with greater precision than was previously known. We also tested for additional population structure within each of these regional gene pools, based on a variety of poolspecific and landscape features. Both COI and microsatellite results were largely concordant at our study site and showed two gene pools with a distinct geographic break. Undisturbed pools were fixed for one gene pool, but disturbed pools showed greater admixture between the two genetic groups. The distinct geographic break between the two gene pools coincided with a large canyon on our study site. Isolation by distance analyses supported the canyon as a barrier to gene flow after we controlled for geographic distance. In addition, landscape genetic analyses showed presence of roads as a barrier to gene flow between pools. We designated six management units on MCAS Miramar, which will allow us to maintain species integrity, maintain the two regional gene pools, and maintain the integrity of complexes that show unusually high divergence. To best ensure the continued success of this endangered species, we recommend that inoculation of new pools use soil from within the same management group. Electronic appendices accompanying this thesis can be found at the Media Center in Malcolm A. Love Library, San Diego State University.
Population genetic data are becoming an increasingly important tool in the conservation and management of endangered species. Statistical analysis of genetic data can inform agencies on population boundaries within a species, and help to infer processes that lead to genetic patterns, thereby influencing conservation decisions. This thesis examines population genetics in the endangered San Diego fairy shrimp, Branchinecta sandiegonensis, using multiple molecular markers. In order to quantify diversity and population structure, genetic data were collected from 50 pools from 23 pool complexes scattered throughout San Diego County at seven novel microsatellite loci. We tested the hypothesis that pool complex boundaries and geographic distance are important components of genetic structure. Microsatellite and mtDNA genetic patterns were compared to test for concordance between marker types. We also conducted preliminary tests for the effect of pool disturbance and hybridization on genetic diversity. Overall, results show that there is considerable microsatellite diversity within pools. In the preliminary tests, no significant change in genetic diversity in response to hybridization was detected. Disturbance may affect genetic diversity within pools, but it is unclear which component of disturbance is correlated with diversity. Overall, genetic differentiation among pool complexes is relatively strong. The hierarchical spatial arrangement of pools plays a significant role in genetic divergence among populations. Increasing geographic distances between sites is a significant gene flow barrier for this species, as has been found for other fairy shrimp species. Evidence of historical isolation between two divergent groups was also found. There is concordance among marker types, with some discrepancies. Population genetic structure in B. sandiegonensis across the study range is governed by gene flow restricted primarily to pool complexes. We recommend that pool complexes be treated as management units provided that pools are ecologically similar within them. Historical divergence among groups of pools should be taken into account as well, in order to maintain genetic variation and dispersal mechanisms across the species' range.
Wetlands are rapidly being lost from human impacts, and in California the effects are especially dramatic. Sensitive wetland habitats, like vernal pools, are at risk of being lost. Vernal pools are home to many endemic species, so the conservation of vernal pools is critical to maintaining California's biodiversity. Understanding the ecological, physiological, and genetic aspects of a species is important when implementing critical management for the persistence of endangered species. The longhorn fairy shrimp, Branchinecta longiantenna, is one of several endemic and endangered inhabitants of California's vernal pools. Longhorn fairy shrimp distribution is quite restricted, they are found in only three regions of California (Altamont Pass, Kesterson National Wildlife Refuge, and Carrizo Plains). Little is known about their ecology, physiology, and genetics. My research aimed to establish a framework of our genetic understanding of longhorn fairy shrimp throughout its range. I analyzed population genomic data for samples collected from each region to determine population structure and variation. I found evidence for phylogeographic structure associated with isolated regions from pairwise estimates of population differentiation, principal component analysis, and phylogenetics. Differentiation within regions was generally low, but much higher at Altamont Pass, which is likely due to differences in population size and dispersal. This is also reflected in levels of heterozygosity, which were much lower in the Altamont Pass pool than any other. These differences stress that management programs should use evolutionary significant units that distinguish longhorn fairy shrimp by their respective regions when developing conservation plans for this species.
Patterns of dispersal and gene-flow in freshwater invertebrates have often been difficult to interpret. Despite the assumed high potential for dispersal, populations of freshwater invertebrates display high genetic differentiation over small distances. There have been several explanations posed for this gene flow dispersal paradox, including strong priority effects or low realized dispersal. This study explores the spatial genetic structure of the freshwater invertebrate Branchinecta lynchi, a threatened vernal pool inhabitant, at two scales with a goal to determine the scale at which gene flow is important in shaping these patterns. Vernal pools were sampled at two different localities the San Luis National Wildlife Refuge Complex and a preserve adjacent to the University of California, Merced. Individuals were genotyped using both the mitochondrial cytochrome oxidase I subunit (COI) and nuclear amplified fragment length polymorphisms (AFLPs). Pairwise Fst values showed that genetic structure for this species was high, however, the only geographic pattern that emerged was isolation by distance at the local scale for the COI marker. Discrepancies between mitochondrial and AFLP markers may be explained several ways, including genotyping error, sex-biased dispersal and/or the longer time to equilibrium of the nuclear genome. These results suggest that gene flow is important at the local scale, at least for mitochondrial DNA, while historical colonization patterns are likely maintained at the regional scale by priority effects. I infer that maintaining connectivity among vernal pool complexes through local dispersal vectors should be a management priority.
Driven by landscape alteration and the introduction of non-natives through human activities, biotic homogenization is thought to be a significant threat to the survival of endemic taxa. Extensive urbanization in southern California, USA, has converted most of the native coastal vernal pool habitat prompting the conservation of native vernal pool species. Habitat alteration associated with urban expansion in this region has extirpated B. sandiegonensis from the majority of its historical habitat. In some artificial basins within the remaining vernal pool habitat, B. sandiegonensis hybridizes with B. lindahli. Hybrids can be identified through both morphology and newly developed genetic characters (Patel et al. 2017). By using both morphological and genomic hybrid indices, researchers and habitat managers will obtain a relatively holistic perspective on the hybridization process. This not only helps to identify populations where a large-scale introduction of B. lindahli has occurred, but also to perhaps predict the future trajectory of species and hybrid distributions.
This volume is a collection of papers concerning the biology of large branchiopod crustaceans: Anostraca, Conchostraca, and Notostraca. Many of the individual papers were first presented at the Third International Large Branchiopod Symposium (ILBS-3) held at the University of San Diego, CA, USA, July 15-18, 1996. Contributions on additional topics from participants at the symposium, and from colleagues not able to join us in San Diego, are also included. In addition, there is a supplement to the 1995 `Checklist of the Anostraca'. The theme of the ILBS-3 was `understanding and conserving large branchiopod diversity'. Researchers from around the world presented papers on a variety of topics related to conservation of large branchiopods, with contributions ranging from alpha-taxonomy and zoogeography to community structure and studies of ecology and evolution. One important issue developed in many of the papers in this volume is the need to advance our understanding of basic aspects of branchiopod biology throughout the world in order to enhance our efforts to conserve them. Although we have made important strides in understanding the biology of large branchiopods, we have, with few notable exceptions, made little progress in assuring the conservation of their diversity. We hope this volume will supply the reader with new ideas, and generate enthusiasm for research and public education efforts on behalf of branchiopod conservation.
The Tijuana River Valley Historical Ecology Investigation synthesizes hundreds of historical maps, photographs, and texts to reconstruct the ecological, hydrological, and geomorphic conditions of the Tijuana River valley prior to major European-American landscape modification. How did the valley look and function before there was the state of California, the city of Tijuana, or an international border? What habitat types and wildlife were found there? How have these habitat types and the physical processes that shaped them changed over time? And finally, what can the valley's ecological past tell us about its present and future? In answering these fundamental questions, this richly-illustrated study provides scientists, managers, and residents in the valley with information designed to support and inspire ongoing management and restoration activities.