Source: UNIVERSITY OF FLORIDA submitted to NRP
CONSERVATION GENOMICS OF SPECIES OF CONSERVATION AND MANAGEMENT CONCERN
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
COMPLETE
Funding Source
HATCH
Reporting Frequency
Annual
Accession No.
0233037
Grant No.
(N/A)
Cumulative Award Amt.
(N/A)
Proposal No.
(N/A)
Multistate No.
(N/A)
Project Start Date
Mar 1, 2013
Project End Date
Mar 1, 2018
Grant Year
(N/A)
Program Code
[(N/A)]- (N/A)
Recipient Organization
UNIVERSITY OF FLORIDA
G022 MCCARTY HALL
GAINESVILLE,FL 32611
Performing Department
Wildlife Ecology and Conservation
Non Technical Summary
A central challenge that faces both economically important species and species of conservation concern is identifying and understanding the genetic basis of adaptation to factors such as climate change and habitat conversion. Identifying the genes for ecologically relevant traits is now possible and this scientific endeavor has the potential to answer a large number of questions that have remained unanswerable until recently. Using next-generation sequencing tools together with computer intensive bioinformatics we can explore large portions of the genome and locate regions associated with traits of economic or biological interest. For example, understanding the genetics underlying high and increasing mortality of clam stocks as sea temperatures rise may help to improve yields and will provide insight into how species adapt to climate change.
Animal Health Component
(N/A)
Research Effort Categories
Basic
(N/A)
Applied
(N/A)
Developmental
(N/A)
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
1360810108010%
1360811108040%
1360830108025%
1360860108025%
Knowledge Area
136 - Conservation of Biological Diversity;

Subject Of Investigation
0810 - Finfish; 0830 - Wild animals; 0811 - Shellfish; 0860 - Endangered species;

Field Of Science
1080 - Genetics;
Goals / Objectives
The goals of the project are to increase our understanding of the genetic architecture of adaptively important traits in wildlife, as related to anthropogenic pressures (habitat loss/degradation, reduction in population size). Objectives: 1. The development of genomic tools and methods for the study of adaptation and landscape connectivity in non-model species. We conduct this research on a variety of organisms and ecosystems from marine (e.g., greater amberjack, hard clams) to freshwater (e.g., black bass) to terrestrial (e.g., rodents, amphibians) animals. 2. Determine the impact of captive management (P. polionotus trissyllepsis) and propagation (M. mercenaria) on the genetics of species, and the consequences of genetic introgression between captive-bred and released animals into natural systems. 3. Determine how different habitat uses, land-practices and environmental change impacts population genetic diversity in native wildlife communities.
Project Methods
To study the genetic architecture of potentially adaptive traits we will be incorporating various genomic tools the study of wildlife conservation. One approach will be to develop genome-wide markers through next-generation sequencing and applying these to objectives related to 1) determining the markers associated with adaptive traits, 2) the study of population structuring at large (continental) small (sub- and landscape level) geographic scales. Markers will be developed using next generation sequencing of genomic information, translated using bioinformatic tools and interpreted within the context of the study (e.g. genetic association studies of fitness traits in hard clams, pedigree analyses and genetic diversity analyses of captive mice and wild endangered species). This information will be targeted to various audiences (depending on the focal species) including fisheries managers, extension agents and fishermen, wildlife managers at the state and federal level, and the scientific community through peer-reviewed publications.

Progress 03/01/13 to 03/01/18

Outputs
Target Audience:State and federal wildlife resource managers. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?There have been 3 graduate students and 2 undergraduate students trained in relation to goals of this project. How have the results been disseminated to communities of interest?Publications listed in report. What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? During this project period were conducted large-scale range-wide genetic survey of a number of species including: Florida mouse, Florida Bonneted bat, Perdido Key beach mouse, and the insular cotton rat. These studies provided the Fish and Wildlife Service and the Florida Fish and Wildlife Conservation Commission with data on the genetic status, connectiviity, and degree of isolation (distinction), that was then able to be used to inform managemetn decisions. In addition the project contributed to the establishiment of a captive breeding program for Perdido Key beach mouse.

Publications


    Progress 10/01/16 to 09/30/17

    Outputs
    Target Audience:The majority of my target audience is professional scientists, wildlife and fisheries managers, and academics involved with conservation science within the state of Florida, nationally, and internationally. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?In 2017 we trained 3 undergraduate students in basic and more advanced molecular genetics. In addition, two graduate students completed their research projects and successfully graduated. How have the results been disseminated to communities of interest?In 2017 we shared results and progress on various projects with the US Fish and Wildlife Service, Florida Fish and Wildlife Conservation Commission, and National Oceanic and Atmospheric Administration. These events included meetings and participation in working groups to discuss genomic contributions to specific state and federal agency-funded projects. What do you plan to do during the next reporting period to accomplish the goals?In 2018 we are developing and applying genomic tools to advance conservation and wildlife management, including addtional research on endangered crayfish species, and endangered grasshopper sparrows, and spotted sea trout.

    Impacts
    What was accomplished under these goals? Researchers developed genomic markers for the purpose of research on endangered species including the Panama City Crayfish, Florida Bonneted Bat, and the beach mouse. These markers allow for a more detailed picture of genome-wide variation than traditional genetic markers. These genomic markers are useful in that they provide greater resolution for estimating past demographic parameters, a tool that allow for more informed conservation decisions in many cases. We have successfully used traditional markers to understand the impacts of angling practices on important freshwater game fishes, and the role that hatchery production can play in the genetic diversity of stocked fishes (e.g., black basses). Another example is the application of genetic tools to successfully evaluate intensive management practices such as reintroductions of endangered mammals to their native habitat.

    Publications

    • Type: Journal Articles Status: Published Year Published: 2017 Citation: Greene DU, Gore JA, Austin JD. 2017. The importance of demographic and genetic monitoring in conservation reintroductions: a case study on captive-born beach mice. Journal of Mammalogy 98: 513522
    • Type: Journal Articles Status: Published Year Published: 2017 Citation: Hargrove JS, Austin JD. 2017. Parentage and mating patterns in a Florida bass hatchery. Aquaculture Research 48: 3272-3277.
    • Type: Journal Articles Status: Published Year Published: 2017 Citation: Robertson EP, Fletcher RJ, Austin JD. 2017. The causes of dispersal and the cost of carryover effects for an endangered bird in a dynamic wetland landscape. Journal of Animal Ecology 86: 857865
    • Type: Journal Articles Status: Published Year Published: 2017 Citation: Trippel NA, Hargrove JS, Leone EH, Austin JD, Allen MS. 2017. Angling-induced impacts on recruitment and contributions to reproduction in Florida bass, Micropterus floridanus. Transactions of the American Fisheries Society 146: 871887.


    Progress 10/01/15 to 09/30/16

    Outputs
    Target Audience: Nothing Reported Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?Training of 7 new undergraduate, and graduate studetns, and 1 high school student occured during the reporting year. In addition, 5 undergraduate students from UF and 3 other US institutions were trained as part of the National Science Foundation, International Research experience for Students (NSF-IRES) program. How have the results been disseminated to communities of interest?Student reports from the NSF IRES have been published online at www.uf-ires.com. What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

    Impacts
    What was accomplished under these goals? In terms of objective 1, during the reporting period, we have developed and/or applied genetic tools toward understanding the impacts of habitat fragmentation in endngered species including Perdido Key beachmice, Everglades snail kites and Insular cotton rats. All of these species are of conservation concern and are listed or being considered for listing under the Endangered Species Act. FOr objective 2 we have been continuing to monitor the genetics of captive populations of Perdido Key beach mice that hare being maintained as "insurance populations" in case of catastrophic storm activity that could decimate the wild population of this endangered species. For objectie 3 we have initiated a NSF funded training project in Swaziland, through the NSF-IRES program. In 2016, 5 US students conducted research on the impacts of land use change on biodiversity in the lowveld savanna.

    Publications

    • Type: Journal Articles Status: Published Year Published: 2016 Citation: Saarinen EV, Reilly PF, Austin JD. 2016. Conservation genetics of an endangered grassland butterfly (Oarisma poweshiek) reveals historically high gene flow despite recent and rapid range loss. Insect Conservation and Diversity 9: 517-528.
    • Type: Journal Articles Status: Published Year Published: 2016 Citation: Stewart K, Austin JD, Zamudio KR, Lougheed SC. 2016. Contact zone dynamics during early stages of speciation in a chorus frog (Pseudacris crucifer). Heredity 116:239-247.
    • Type: Journal Articles Status: Published Year Published: 2016 Citation: Fletcher RJ Jr, Burrell NS, Reichart BE, Vasudev D, Austin JD. 2016. The effects of landscape connectivity: evidence, challenges, and opportunities. Current Landscape Ecology Reports 1: 67-79. Saarinen EV, Reilly PF, Austin JD. 2016. Conservation genetics of an endangered grassland butterfly (Oarisma poweshiek) reveals historically high gene flow despite recent and rapid range loss. Insect Conservation and Diversity 9: 517-528.
    • Type: Journal Articles Status: Published Year Published: 2016 Citation: Greenberg CH, Goodrick S, Austin JD, Parresol BR. 2016. Hydroregime Prediction Models for Ephemeral Groundwater-Driven Sinkhole Wetlands: A Planning Tool for Climate Change and Amphibian Conservation. Wetlands 35:899-911


    Progress 10/01/14 to 09/30/15

    Outputs
    Target Audience:During this reporting session I have trained 4 indiviuals in genetic data analyses. These were graduate students involved in projects at the University of Florida that required training in conservation genetics. In addition, 5 undergradutes were trained as interns. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?During this period I have trained two postdoctoral researchers through mentorship related to behavioral studies and genetic analyses. In addition, 4 graduate students havebeen involved in training. How have the results been disseminated to communities of interest? Nothing Reported What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

    Impacts
    What was accomplished under these goals? Genetic tools can provide researchers with a valuable approach to understandning the status of wildlife species, and the consequences of human activities on the long-term persistence of wildlife populations. Over the past year my research program has moved forward with four main initiatives that have contributed to our knowledge of regarding the consequences of habitat fragmentation (i.e., development, conversion to agriculture, resource extraction) on wildlife of Florida. First, our research has demonstrated how development in fragile coastal ecosystems (dunes) has impacted the connectivity of wildlife populations. Connectivity (the ability of animals and plant to move from one area to another and interbreed) is a central component of wildlife conservation. By using genetic markers, we have shown that Perdido Key beach mouse populations that have been highly fragmented for over 30 years, and unable re-colonize empty habitat due to development, have recently begun moving across this seemingly impermeable development matrix. We deduced that this change may have been a result of the re-establishment of vegetation along sand berms that were built to reduce beach erosion. Second, within the same study system we have been examining the effects of roads on the demographics (e.g., monthly survival, population growth, reproduction) and behavior (e.g., movement). This research is ongoing; however or preliminary data suggests that road lighting may play a greater roll in inhibiting movement by small rodents than does the road itself. Third, with respect to aquaculture breeding and reintroductions and stocking of fish and wildlife, we have been working with the North Carolina wildlife agency on their Lake Mattamuskeet bass stocking program. Our early results indicate that hatchery stocked fishes are surviving to year-1 fish. Fourth, with respect to captive bred endangered beach mice, we have found that captive bred mice released into the wild can survive and reproduce, offering a potential means of aiding in recovery of this and similar endangered species.

    Publications

    • Type: Journal Articles Status: Published Year Published: 2015 Citation: Hargrove JS, Sturmer L, Scarpa J, Austin JD. 2015. Assessment of genetic diversity in wild and aquacultured stocks of the hard clam Mercenaria mercenaria in Florida. Journal of Shellfish Research 34: 355-365
    • Type: Journal Articles Status: Accepted Year Published: 2015 Citation: Shirley M, Villanova VL, Vliet KA, Austin JD. 2015. Genetic barcoding facilitates captive and wild management of three cryptic African crocodile species complexes. Animal Conservation 18: 322-330.
    • Type: Journal Articles Status: Accepted Year Published: 2015 Citation: Austin JD, Gore JA, Greene DU, Gotteland C. 2015. Conspicuous genetic structure belies recent dispersal in an endangered beach mouse (Peromyscus polionotus trissyllepsis). Conservation Genetics 16: 915-928.
    • Type: Journal Articles Status: Accepted Year Published: 2015 Citation: Greenberg CH, Goodrick S, Austin JD, Parresol BR. 2015. Hydroregime prediction models for ephemoral groundwater-driven sinkhole wetlands: a planning tool for climate change and amphibian conservation


    Progress 10/01/13 to 09/30/14

    Outputs
    Target Audience: Nothing Reported Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided? Nothing Reported How have the results been disseminated to communities of interest? I have met with members of the hard clam industry and there has been considerable interest in the development of genomic markers that can be used to address future issues associated with heat stress and changes in salinity associated with regional climate fluctuations. What do you plan to do during the next reporting period to accomplish the goals? We will be completing the development of hard clam genomic resources and developing strategies for obtaining funding to further develop these goals. We are also beginning genomic work on additional wildlife species not associated with industry.

    Impacts
    What was accomplished under these goals? During the reporting period genomic markers for hard clams were in the process of being developed. This was accomplised using a University of Florida Faculty Enhancement Award.

    Publications


      Progress 03/01/13 to 09/30/13

      Outputs
      Target Audience: Nothing Reported Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided? I obtained funding from the Faculty Enhancement Opportunity Fund (FEO, Provost Offfice, UF) for a planned visit to the laboratory of Dennis Hedgecock at University of Southern California, Los Angeles. This FEO was awarded in July 2013 in anticipation for a training visitation to USC for the November 2013. How have the results been disseminated to communities of interest? Dessemination of any results did not occur during the reporting period as the project was in its initial 6 months. What do you plan to do during the next reporting period to accomplish the goals? I will be spending a period of my Faculty Development Leave (sabbatical) developming genome-wide markers for hard clams that can be used to create quantitative trait loci maps. I will alos be studying programing langualge (python) that will be necessary for large scale genomic project management. Continued training and development of genomic tools and methods during my sabbatical will be a major focus (Oct 2013-July 2014).

      Impacts
      What was accomplished under these goals? We initiated a pilot study of hard clams (Mercenaria mercenaria), by creating a family cross for the purpose of genotyping the family using genotype by sequencing methods for the following year. This family was spawned in May and raised at Cedar Key through October 2013. At this point it was collected in preparation for sequencing.

      Publications

      • Type: Book Chapters Status: Published Year Published: 2013 Citation: Greenberg CH, Perry RW, Franzreb KE, Loeb SC, Saenz D, Rudolph C, Winters E, Fucik EM, Kwiatkowski MA, Parresol BR, Austin JD, Tanner GW. 2013. Climate change and wildlife in the southern United States: potential effects and management options. In Vose JM, Klepzig KD, eds. Climate change adaptation and mitigation management options: A guide for natural resource managers in southern forest ecosystems. CRC Press.