Project Funding: 2013 - 2018

NRA: 2012 NASA: Ecological Forecasting   

Funded by NASA

Abstract:
Understanding how species and habitats are likely to respond to climate warming is critical in developing effective conservation and management strategies for freshwater ecosystems. We propose to link high-resolution satellite remote sensing mapping of freshwater habitats with genetic and demographic data and spatially explicit hydrological and thermal model outputs to assess the vulnerability of salmon populations under current conditions and future climate scenarios. We will answer important conservation management questions regarding the distribution, abundance, physical complexity, and quality of freshwater habitats available to salmon and trout now and under projected climate change. We will train anglers (crowdsourcing) to collect images paired with DNA samples from fish to assess genomic diversity and connectivity (gene flow) among many streams and species across the Pacific Rim. This work will build upon an existing conservation decision support web system for wild salmon conservation (RAP: Riverscape Analysis Project; http://rap.ntsg.umt.edu), which includes spatially explicit mapping of salmonid physical freshwater habitats and predictions of potential salmon habitats, their relative quality, and potential vulnerability. We will enhance the RAP web system by implementing new satellite remote sensing measures of riparian zone habitat quality, and genetic and demographic indices of salmonid population vulnerability derived from landscape genetic and individual-based simulation models of population connectivity and abundance. We initially will focus on the Yukon and Columbia Rivers to assess new RAP metrics across spatial scales and because the best available time-series genetic and abundance exist for salmonids in these rivers (including endangered Chinook salmon, chum salmon, and threatened bull trout). In Years 2-4, we would assess new RAP metrics in >1500 Pacific Rim rivers. These activities will be used with decision makers to identify and assess vulnerable populations, species and ecosystems, design long-term monitoring programs, inform future research needs, and develop conservation delivery options in response to multiple environmental stressors.

Publications:

Ackerman, M. W., Hand, B. K., Waples, R. K., Luikart, G., Waples, R. S., Steele, C. A., Garner, B. A., McCane, J., Campbell, M. R. 2016. Effective number of breeders from sibship reconstruction: empirical evaluations using hatchery steelhead. Evolutionary Applications. 10(2), 146-160. DOI: 10.1111/eva.12433

Ali, F. N., Meehan, S. M., Pahl, E., Cohn, R. A. 2010. Native BK viral nephropathy in a pediatric heart transplant recipient. Pediatric Transplantation. 14(4), E38-E41. DOI: 10.1111/j.1399-3046.2008.01127.x

Amish, S. J., Ali, O., Peacock, M., Miller, M., Robinson, M., Smith, S., Luikart, G., Neville, H. 2019. Assessing thermal adaptation using family-based association and F ST outlier tests in a threatened trout species. Molecular Ecology. 28(10), 2573-2593. DOI: 10.1111/mec.15100

Andrews, K. R., Good, J. M., Miller, M. R., Luikart, G., Hohenlohe, P. A. 2016. Harnessing the power of RADseq for ecological and evolutionary genomics. Nature Reviews Genetics. 17(2), 81-92. DOI: 10.1038/nrg.2015.28

Benestan, L. M., Ferchaud, A., Hohenlohe, P. A., Garner, B. A., Naylor, G. J. P., Baums, I. B., Schwartz, M. K., Kelley, J. L., Luikart, G. 2016. Conservation genomics of natural and managed populations: building a conceptual and practical framework. Molecular Ecology. 25(13), 2967-2977. DOI: 10.1111/mec.13647

Cooper, D. K. C., Ekser, B., Burlak, C., Ezzelarab, M., Hara, H., Paris, L., Tector, A. J., Phelps, C., Azimzadeh, A. M., Ayares, D., Robson, S. C., Pierson, R. N. 2012. Clinical lung xenotransplantation - what donor genetic modifications may be necessary? Xenotransplantation. 19(3), 144-158. DOI: 10.1111/j.1399-3089.2012.00708.x

Forester, B. R., Landguth, E. L., Hand, B. K., Balkenhol, N. 2018. Landscape Genomics for Wildlife Research in: Population Genomics: Population Genomics: Wildlife. Springer International Publishing, 145-184. DOI: 10.1007/13836_2018_56

Garner, B. A., Hand, B. K., Amish, S. J., Bernatchez, L., Foster, J. T., Miller, K. M., Morin, P. A., Narum, S. R., O'Brien, S. J., Roffler, G., Templin, W. D., Sunnucks, P., Strait, J., Warheit, K. I., Seamons, T. R., Wenburg, J., Olsen, J., Luikart, G. 2016. Genomics in Conservation: Case Studies and Bridging the Gap between Data and Application. Trends in Ecology & Evolution. 31(2), 81-83. DOI: 10.1016/j.tree.2015.10.009

Grummer, J. A., Beheregaray, L. B., Bernatchez, L., Hand, B. K., Luikart, G., Narum, S. R., Taylor, E. B. 2019. Aquatic Landscape Genomics and Environmental Effects on Genetic Variation. Trends in Ecology & Evolution. 34(7), 641-654. DOI: 10.1016/j.tree.2019.02.013

Hand, B. K., Hether, T. D., Kovach, R. P., Muhlfeld, C. C., Amish, S. J., Boyer, M. C., O'rourke, S. M., Miller, M. R., Lowe, W. H., Hohenlohe, P. A., Luikart, G. 2015. Genomics and introgression: Discovery and mapping of thousands of species-diagnostic SNPs using RAD sequencing. Current Zoology. 61(1), 146-154. DOI: 10.1093/czoolo/61.1.146

Hand, B. K., Lowe, W. H., Kovach, R. P., Muhlfeld, C. C., Luikart, G. 2015. Landscape community genomics: understanding eco-evolutionary processes in complex environments. Trends in Ecology & Evolution. 30(3), 161-168. DOI: 10.1016/j.tree.2015.01.005

Hand, B. K., Muhlfeld, C. C., Wade, A. A., Kovach, R. P., Whited, D. C., Narum, S. R., Matala, A. P., Ackerman, M. W., Garner, B. A., Kimball, J. S., Stanford, J. A., Luikart, G. 2016. Climate variables explain neutral and adaptive variation within salmonid metapopulations: the importance of replication in landscape genetics. Molecular Ecology. 25(3), 689-705. DOI: 10.1111/mec.13517

Hendricks, S., Anderson, E. C., Antao, T., Bernatchez, L., Forester, B. R., Garner, B., Hand, B. K., Hohenlohe, P. A., Kardos, M., Koop, B., Sethuraman, A., Waples, R. S., Luikart, G. 2018. Recent advances in conservation and population genomics data analysis. Evolutionary Applications. 11(8), 1197-1211. DOI: 10.1111/eva.12659

Hohenlohe, P. A., Hand, B. K., Andrews, K. R., Luikart, G. 2018. Population Genomics Provides Key Insights in Ecology and Evolution in: Population Genomics. Springer International Publishing, 483-510. DOI: 10.1007/13836_2018_20

Jordan, S., Hand, B. K., Hotaling, S., Delvecchia, A. G., Malison, R., Nissley, C., Luikart, G., Stanford, J. A. 2019. Genomic data reveal similar genetic differentiation in aquifer species with different dispersal capabilities and life histories. Biological Journal of the Linnean Society. 129(2), 315-322. DOI: 10.1093/biolinnean/blz173

Kamath, P. L., Haroldson, M. A., Luikart, G., Paetkau, D., Whitman, C., Manen, F. T. 2015. Multiple estimates of effective population size for monitoring a long-lived vertebrate: an application to Y ellowstone grizzly bears. Molecular Ecology. 24(22), 5507-5521. DOI: 10.1111/mec.13398

Kovach, R. P., Luikart, G., Lowe, W. H., Boyer, M. C., Muhlfeld, C. C. 2016. Risk and efficacy of human-enabled interspecific hybridization for climate-change adaptation: response to Hamilton and Miller (2016). Conservation Biology. 30(2), 428-430. DOI: 10.1111/cobi.12678

Kovach, R. P., Muhlfeld, C. C., Boyer, M. C., Lowe, W. H., Allendorf, F. W., Luikart, G. 2015. Dispersal and selection mediate hybridization between a native and invasive species. Proceedings of the Royal Society B: Biological Sciences. 282(1799), 20142454. DOI: 10.1098/rspb.2014.2454

Kovach, R. P., Muhlfeld, C. C., Wade, A. A., Hand, B. K., Whited, D. C., DeHaan, P. W., Al-Chokhachy, R., Luikart, G. 2015. Genetic diversity is related to climatic variation and vulnerability in threatened bull trout. Global Change Biology. 21(7), 2510-2524. DOI: 10.1111/gcb.12850

Luikart, G., Kardos, M., Hand, B. K., Rajora, O. P., Aitken, S. N., Hohenlohe, P. A. 2018. Population Genomics: Advancing Understanding of Nature in: Population Genomics. Springer International Publishing, 3-79. DOI: 10.1007/13836_2018_60

Milligan, B. G., Archer, F. I., Ferchaud, A., Hand, B. K., Kierepka, E. M., Waples, R. S. 2018. Disentangling genetic structure for genetic monitoring of complex populations. Evolutionary Applications. 11(7), 1149-1161. DOI: 10.1111/eva.12622

Muhlfeld, C. C., McMahon, T. E., Boyer, M. C., Gresswell, R. E. 2011. Local Habitat, Watershed, and Biotic Factors Influencing the Spread of Hybridization between Native Westslope Cutthroat Trout and Introduced Rainbow Trout. Transactions of the American Fisheries Society. 138(5), 1036-1051. DOI: 10.1577/t08-235.1

Scribner, K. T., Lowe, W. H., Landguth, E., Luikart, G., Infante, D. M., Whelan, G. E., Muhlfeld, C. C. 2016. Applications of Genetic Data to Improve Management and Conservation of River Fishes and Their Habitats. Fisheries. 41(4), 174-188. DOI: 10.1080/03632415.2016.1150838

Wade, A. A., Hand, B. K., Kovach, R. P., Luikart, G., Whited, D. C., Muhlfeld, C. C. 2016. Accounting for adaptive capacity and uncertainty in assessments of species' climate-change vulnerability. Conservation Biology. 31(1), 136-149. DOI: 10.1111/cobi.12764

More details may be found in the following project profile(s):

• NASA Biological Diversity & Ecological Conservation (BDEC) Project Profile