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FINAL REPORT Development and Use of Genetic Methods for Assessing Aquatic Environmental Condition and Recruitment Dynamics of Native Stream Fishes on Pacific Islands

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FINAL REPORT Development and Use of Genetic Methods for Assessing Aquatic Environmental Condition and Recruitment Dynamics of Native Stream Fishes on Pacific Islands SERDP Project RC-1646 APRIL 2014 Michael J. Blum Tulane University James F. Gilliam North Carolina State University Peter B. McIntyre University of Wisconsin Distribution Statement A Table of Contents List of Tables ii List of Figures iii List of Acronyms v Keywords ix Acknowledgments x 1 Abstract 1 2 Objectives 3 3 Background 5 3.0 Oceanic Island Watersheds and Stream Ecosystems 5 3.1 Genetic Assessment of Aquatic Environmental Condition 8 3.2 Historical Colonization and Contemporary Connectivity 9 3.2.1 Genetic Analysis of Historical Colonization and Contemporary Connectivity 11 3.2.2 Use of Otolith Microchemistry for Estimating Contemporary Connectivity 12 3.2.3 Use of Oxygen Isotopes in Otoliths for Reconstructing Life History 14 3.2.4 Coupled Biophysical Modeling of Larval Dispersal 16 3.3 Genetic and Integrative Assessment of Pacific Island Watersheds 18 3.3.1 Among-Watershed Assessment of Environmental Condition 18 3.3.2 Within-Watershed Assessment of Environmental Condition 19 3.3.3 Mark-recapture Calibration of Snorkel Surveys 22 4 Materials and Methods 26 4.0 Historical Colonization and Contemporary Connectivity 26 4.0.1 Genetic Analysis of Historical Colonization and Contemporary Connectivity 26 4.0.2 Otolith Microchemistry Analysis of Contemporary Connectivity 32 4.0.3 Use of Oxygen Isotopes in Otoliths for Reconstructing Life History 38 4.0.4 Coupled Biophysical Modeling of Larval Dispersal 41 4.1 Genetic and Integrative Assessment of Pacific Island Watersheds 43 4.1.1 Among-Watershed Assessment of Environmental Condition 44 4.1.2 Within-Watershed Assessment of Environmental Condition 48 4.1.3 Mark-recapture Calibration of Snorkel Surveys 51 5 Results and Discussion 55 5.0 Historical Colonization and Contemporary Connectivity 55 5.0.1 Genetic Analysis of Historical Colonization 55 5.0.2 Genetic Analysis of Contemporary Connectivity 64 5.0.3 Otolith-based Analysis of Life History Variation and Movement Potential 74 5.0.4 Use of Oxygen Isotopes in Otoliths for Reconstructing Life History 82 5.0.5 Coupled Biophysical Modeling of Larval Dispersal 89 5.1 Genetic and Integrative Assessment of Pacific Island Watersheds 96 5.1.1 Among-Watershed Assessment of Environmental Variation 96 5.1.2 Sensitivity of Genetic, Population, & Community Metrics to 102 Among-Watershed Environmental Variation 5.1.3 Sensitivity of Genetic, Population, & Community Metrics to 129 Within-Watershed Environmental Variation 5.1.4 Mark-recapture Calibration of Snorkel Surveys 145 6 Conclusions and Implications for Future Research and Implementation 150 7 Literature Cited 156 8 Appendix A. Scientific and Technical Publications 179 i List of Tables Table 1: Specimens of Awaous stamineus and Sicyopterus stimpsoni sampled, sequenced 27 and genotyped per island. Table 2: Microsatellite loci developed for Sicyopterus stimpsoni in the Hawaiian Islands. 30 Table 3: The number of Awaous stamineus included in the study of otolith microchemistry 33 and the proportion of fishes that showed marine and freshwater larval chemistry. Table 4: The numbers of individuals encountered in visual surveys, batch mark-recapture 54 events, and individual mark-recapture events, per site. Table 5: The number and diversity of Awaous stamineus mtDNA haplotypes recovered on 57 Kauai, Oahu, Molokai, Maui and Hawaii. Table 6: Pair-wise values of ФST based on cytochrome b haplotype variation in Awaous 58 stamineus among islands. Table 7: Age and growth statistics for nine Awaous stamineus collected for otolith micro- 84 structure analysis. Table 8: Summary of postlarval (stream) chemistry for nine Awaous stamineus individuals 85 from five watersheds across the Hawaiian archipelago. Table 9: Stepwise regressions models of Awaous stamineus genetic diversity and population 113 density, as well as native, non-native, and total species richness among watersheds. Table 10:Stepwise regressions models of Awaous stamineus genetic diversity and population 114 density, as well as native, non-native, and total species richness among sites. Table 11:Stepwise regressions models of Sicyopterus stimpsoni genetic diversity and population 115 density among watersheds. Table 12:Stepwise regressions models of Sicyopterus stimpsoni genetic diversity and population 116 density among sites. Table 13:Site information and estimates of Awaous stamineus population characteristics. 131 Table 14:Site-specific estimates of native goby species richness, Awaous stamineus demographic 132 characteristics, as well as estimates of genetic diversity and effective population size. Table 15:Analysis of molecular variance for microsatellite allelic variation among watersheds 134 on Hawaii and Oahu. Table 16:Pairwise FST values for 4 watersheds on Hawaii and Oahu. 135 Table 17:Pairwise FST values for comparisons by month and elevation and across 4 watersheds 136 on Hawaii and Oahu. Table 18:Results of stepwise regression of Awaous stamineus genetic diversity for sites in 3 138 watersheds on Hawaii. Table 19:Results of stepwise regression of Awaous stamineus genetic diversity and density, 139 native goby density and species richness in 4 watersheds on Hawaii and Oahu. Table 20:General linear model results for Awaous stamineus genetic diversity and demography, 141 as well as total goby density, goby richness, and Poeciliid density. Table 21:Comparison of population density estimates from visual surveys, individual mark- 145 recapture, and batch mark-recapture for watersheds across the Hawaiian Islands. Table 22:Regression results for density estimates from visual survey versus mark-recapture. 146 Table 23:General linear models of y-axis residuals from the geometric mean regressions of 147 visual survey and individual mark-recapture data. Table 24:Statistical comparison of the observed size distributions from visual surveys and 148 individual mark-recapture. ii List of Figures Figure 1: Conceptual model of an oceanic island stream ecosystem. 6 Figure 2: Hypotheses of geographic structure and larval recruitment of native 11 amphidromous fishes in the Hawaiian Islands. Figure 3: Photos of the two study species, Awaous stamineus and Sicyopterus stimpsoni 12 Figure 4: Example of an otolith cross-section, resolution of daily growth rings, and 13 a transect analysis of an otolith cross section to reconstruct life history. Figure 5: Longitudinal distribution of native amphidromous species in a Hawaiian stream. 20 Figure 6: Watersheds where A. stamineus and/or S. stimpsoni were sampled in the Hawaiian 28 archipelago, categorized according to dominant land use or stewardship. Figure 7: Map of the Hawaiian archipelago, with the streams sampled for the study of 36 otolith microchemistry. Figure 8: Example of amphidromous and non-amphidromous otolith profiles. 37 Figure 9: Structure of the coupled biophysical model implemented to estimate larval dispersal 42 across the Hawaiian Islands. Figure 10: Stream mouth locations for release and settlement of virtual larvae across the five 43 Hawaiian Islands with perennial streams. Figure 11: The location of individual mark-recapture study watersheds on the north shore of 49 Oahu and along the Hamakua coast of Hawaii. Figure 12: Cytochrome b haplotype network for Awaous stamineus in Hawaii and 55 Awaous guamensis in Guam. Figure 13: Occurrence and prevalence of shared cytochrome b haplotypes in Awaous stamineus. 56 Figure 14: Cytochrome b haplotype network for Sicyopterus stimpsoni. 59 Figure 15: Cytochrome oxidase one haplotype network for Sicyopterus stimpsoni. 59 Figure 16: Bayesian population assignment results for Awaous stamineus across the Hawaiian 66 archipelago in 2009 and 2011. Figure 17: Genetic contour plots of larval dispersal between source and destination island populations 67 of Awaous stamineus in 2009 and 2011. Figure 18: Bayesian population assignment results for Sicyopterus stimpsoni across the Hawaiian 68 achipelago in 2009 and 2011. Figure 19: Genetic contour plots of larval dispersal between source and destination island populations of 69 S. stimpsoni in 2009 and 2011. Figure 20: Results of the Delta K information criterion for determining the “true” number of k 75 groups in the marine core otolith chemistry data. Figure 21: Sr:Ca ratios for adult and putatively freshwater larvae and marine larvae. 76 Figure 22: Principle components analysis (PC) showing the orientation of the different chemical 77 groupings in PC space. Figure 23: Correlations between adult and larval Cu:Ca concentrations. 78 Figure 24: Cumulative frequency curves illustrating development and growth differences between 79 amphidromous and non-amphidromous larvae. Figure 25: The daily growth profile for nine Awaous stamineus. 82 Figure 26: Early larval growth anomalies. 83 Figure 27: Correlation between early larval growth anomaly duration and late larval duration. 84 Figure 28: Otolith transect profiles of δ18O and Sr:Ca for five Awaous stamineus. 85 Figure 29: Correlation between Sr:Ca in the early larval growth periods and the duration of 86 the early larval growth anomaly. Figure 30: The proportion of successfully settled propagules according to their island of origin for 89 Kauai, Oahu, Molokai, Maui and Hawaii under conditions of short larval life duration and long larval life duration under constant spawning output. Figure 31: Connectivity matrix showing settlement probabilities for 51 streams on five islands in 90 the main Hawaiian
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