DOCSLIB.ORG

Guidelines for Collecting and Maintaining Archives for Genetic Monitoring

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Guidelines for Collecting and Maintaining Archives for Genetic Monitoring Conservation Genet Resour DOI 10.1007/s12686-011-9545-x TECHNICAL REVIEW Guidelines for collecting and maintaining archives for genetic monitoring Jennifer A. Jackson • Linda Laikre • C. Scott Baker • Katherine C. Kendall • The Genetic Monitoring Working Group Received: 20 April 2011 / Accepted: 20 September 2011 Ó Springer Science+Business Media B.V. 2011 Abstract Rapid advances in molecular genetic tech- biological diversity and ecological analysis, helping to niques and the statistical analysis of genetic data have illuminate and define cryptic and poorly understood revolutionized the way that populations of animals, plants species and populations. Many of the detected biodiversity and microorganisms can be monitored. Genetic monitoring declines, changes in distribution and hybridization events is the practice of using molecular genetic markers to track have helped to drive changes in policy and management. changes in the abundance, diversity or distribution of Because a time series of samples is necessary to detect populations, species or ecosystems over time, and to follow trends of change in genetic diversity and species compo- adaptive and non-adaptive genetic responses to changing sition, archiving is a critical component of genetic moni- external conditions. In recent years, genetic monitoring has toring. Here we discuss the collection, development, become a valuable tool in conservation management of maintenance, and use of archives for genetic monitoring. This includes an overview of the genetic markers that facilitate effective monitoring, describes how tissue and The NCEAS/NESCent Working Group on Genetic Monitoring (GeM) is chaired by F. W. Allendorf, University of Montana, USA, and DNA can be stored, and provides guidelines for proper M. K. Schwartz, USDA Forest Service, USA. The other members are: practice. C. S. Baker (Oregon State University, USA), D. P. Gregovich (University of Alaska, USA), M. M. Hansen (Aarhus University, Keywords Conservation Á Museum DNA Á Biodiversity Á Denmark), J.A. Jackson (Oregon State University, USA), K. C. Kendall (US Geological Survey, USA), L. Laikre (Stockholm Molecular markers Á Biological collections University, Sweden), K. McKelvey (USDA Forest Service, USA), M. C. Neel (University of Maryland, USA), I. Olivieri (Universite´ de Montpellier II, France), N. Ryman (Stockholm University, Sweden), Since the origins of human societies, marine and terrestrial R. Short Bull (University of Montana, USA), J.B. Stetz (University of Montana, USA), D. A. Tallmon (University of Alaska, USA), plant and animal populations have been subject to a variety C. D. Vojta (US Forest Service, USA), D. M. Waller (University of of anthropogenic environmental impacts including loss of Wisconsin, USA) and R. S. Waples (National Marine Fisheries habitat, direct exploitation and encroachment of introduced Service, USA). C. S. Baker J. A. Jackson Marine Mammal Institute and Department of Fisheries Marine Mammal Institute, Oregon State University, and Wildlife, Oregon State University, 2030 SE Marine Science 2030 SE Marine Science Drive, Newport, OR 97365, USA Drive, Newport, OR 97365, USA e-mail: [email protected] Present Address: J. A. Jackson (&) C. S. Baker British Antarctic Survey, High Cross, Madingley Road, School of Biological Sciences, University of Auckland, Cambridge CB3 0ET, UK Auckland, New Zealand e-mail: [email protected] K. C. Kendall L. Laikre US Geological Survey, Northern Rocky Mountain Science Division of Population Genetics, Department of Zoology, Center, Glacier National Park, West Glacier, MT, USA Stockholm University, 10691 Stockholm, Sweden 123 Conservation Genet Resour species (including pathogens). Impacts on biodiversity individual level, genetic identification can enable estima- include changes in species abundance and distribution and tion of population abundance and vital rates within the loss of genetic diversity (Frankham 2005; Wright et al. framework of mark-recapture models. Genetic species 2008). Methods for assessing and monitoring these types of identification can be used to monitor changes in distribu- changes are necessary to assure conservation and sustain- tion through occupancy modeling that incorporates detec- able use of our remaining biodiversity. Various molecular tion probability (MacKenzie et al. 2006). Category II genetic techniques are now becoming affordable and reli- represents the use of genetic markers to monitor changes in able approaches in this respect (Schwartz et al. 2007). population genetic parameters, e.g., amount of genetic Genetic monitoring has been defined as ‘‘quantifying variation, degree of population divergence, rate of gene temporal changes in population genetic metrics or other flow, and effective population size (Ne). We focus on the population data generated using molecular markers’’ use of both modern and historical DNA archives for (Schwartz et al. 2007). Integral to genetic monitoring is the genetic monitoring but do not discuss the use of ancient interpretation of individual and population genetic data DNA, as this has been covered elsewhere (e.g., Leonard in the context of ecological and evolutionary processes, 2008;Pa¨a¨bo et al. 2004). particularly in human impacted environments. In addition, genetic monitoring can provide valuable baseline infor- mation to evaluate population responses to future global Construction of archives environmental changes, such as global warming. Genetic monitoring can be used to monitor population processes in The ability of archival time series to detect changes elusive and cryptic species that cannot be directly counted, depends on a combination of factors, including the gener- e.g., by using DNA obtained from feces, shed hair, feath- ation time of the species of interest relative to the age of the ers, skin and scales (Proctor et al. 2005; Boulanger et al. archival data, the number and distribution of individuals 2004; Piggott et al. 2006; Prugh et al. 2005), or from hunter sampled at each time point, the preservation of material for kills, market products or incidental mortality (e.g., fisheries DNA analysis, and the genetic marker types employed to by-catch, road-kills) (Pichler and Baker 2000; Bellinger perform the analysis. The success of genetic monitoring 2003; Baker 2008). ‘‘Resurrection’’ analyses of museum- thus crucially hinges on the quality, age, and size of the collected specimens or other artifacts (e.g., Austin and genetic archive available for the species or population of Melville 2006; Kelley Thomas et al. 1990; Groombridge interest. et al. 2000) can also provide an historical baseline for comparison with current estimates of species abundance. Marker types and their utility for genetic monitoring Genetic monitoring projects require a time series of archived genetic data, either in the form of specimen tissue, Genetic monitoring schemes that estimate abundance or extracted DNA, or records of previously obtained genetic monitor population changes require variable genetic markers information (e.g., DNA sequences or genotypic data). For that allow identification of individuals or population level the purposes of genetic monitoring, DNA and tissue diversity, in order to identify changes in the abundance or archives are spatially and temporally explicit, intentional diversity of individuals or populations through time. Com- collections of individuals from the population of interest, monly used genetic marker types include mitochondrial and with multiple samples obtained from each period of col- chloroplast DNA, nuclear introns, microsatellites, single lection. In contrast, the temporal or spatial spread of tra- nucleotide polymorphisms (SNPs) and amplified fragment ditional historical archives is often sporadic or unknown. length polymorphisms. Attributes of these markers and their Although methods of genetic monitoring have received utility in molecular ecology have been discussed elsewhere considerable attention, less attention has been given to the (Sunnucks 2000; Morin et al. 2004; Selkoe and Toonen archiving of samples required to detect trends over time. 2006). Here we review the techniques available for generating and The utility of different types of molecular markers for maintaining tissue and DNA archives for genetic moni- genetic monitoring depends on the quality and quantity of toring, discuss challenges facing archivists, geneticists, and DNA available for analysis. For example, large amounts of managers, and present a series of guidelines for archiving good quality DNA are required to amplify microsatellites material in order to facilitate genetic monitoring of wild and screen for SNPs. These markers can be used to esti- plants and animals. We consider archives that span both mate population size, bottlenecks and kinship and deter- genetic monitoring categories defined by Schwartz et al. mine sex and identity (Selkoe and Toonen 2006). (2007). Category I encompasses the use of genetic markers Microsatellite loci are prone to amplification errors when as identifiers of individuals, populations and species DNA quantity or quality is low, biasing amplification for traditional population monitoring purposes. At the toward shorter fragment lengths (Taberlet et al. 1999)orto 123 Conservation Genet Resour just one allele at a locus (i.e., allelic dropout). Furthermore, genetic analyses to complement traditional taxonomic microsatellite data are often difficult to compare between approaches to species identification. Such archives are laboratories and studies when
Load more

Recommended publications
  • Genetic Monitoring As a Promising Tool for Conservation and Management
    University of Nebraska - Lincoln DigitalCommons@University of Nebraska - Lincoln Publications, Agencies and Staff of the U.S. Department of Commerce U.S. Department of Commerce 9-2006 Genetic monitoring as a promising tool for conservation and management Michael K. Schwartz USDA Forest Service, [email protected] Gordon Luikart University of Montana, [email protected] Robin Waples NOAA, [email protected] Follow this and additional works at: https://digitalcommons.unl.edu/usdeptcommercepub Schwartz, Michael K.; Luikart, Gordon; and Waples, Robin, "Genetic monitoring as a promising tool for conservation and management" (2006). Publications, Agencies and Staff of the U.S. Department of Commerce. 482. https://digitalcommons.unl.edu/usdeptcommercepub/482 This Article is brought to you for free and open access by the U.S. Department of Commerce at DigitalCommons@University of Nebraska - Lincoln. It has been accepted for inclusion in Publications, Agencies and Staff of the U.S. Department of Commerce by an authorized administrator of DigitalCommons@University of Nebraska - Lincoln. Review TRENDS in Ecology and Evolution Vol.22 No.1 Genetic monitoring as a promising tool for conservation and management Michael K. Schwartz1, Gordon Luikart2,3 and Robin S. Waples4 1 USDA Forest Service, Rocky Mountain Research Station, 800 E. Beckwith Avenue, Missoula, MT 59801, USA 2 Center for Investigation of Biodiversity and Genetic Resources, University of Porto, Campus Agra`rio de Vaira˜ o 4485-661, Portugal 3 Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA 4 National Marine Fisheries Service, Northwest Fisheries Science Center, 2725 Montlake Boulevard East, Seattle, WA 98112, USA In response to ever-increasing anthropogenic changes to markets [8].
    [Show full text]
  • Genetic Diversity, Population Structure, and Effective Population Size in Two Yellow Bat Species in South Texas
    Genetic diversity, population structure, and effective population size in two yellow bat species in south Texas Austin S. Chipps1, Amanda M. Hale1, Sara P. Weaver2,3 and Dean A. Williams1 1 Department of Biology, Texas Christian University, Fort Worth, TX, United States of America 2 Biology Department, Texas State University, San Marcos, TX, United States of America 3 Bowman Consulting Group, San Marcos, TX, United States of America ABSTRACT There are increasing concerns regarding bat mortality at wind energy facilities, especially as installed capacity continues to grow. In North America, wind energy development has recently expanded into the Lower Rio Grande Valley in south Texas where bat species had not previously been exposed to wind turbines. Our study sought to characterize genetic diversity, population structure, and effective population size in Dasypterus ega and D. intermedius, two tree-roosting yellow bats native to this region and for which little is known about their population biology and seasonal movements. There was no evidence of population substructure in either species. Genetic diversity at mitochondrial and microsatellite loci was lower in these yellow bat taxa than in previously studied migratory tree bat species in North America, which may be due to the non-migratory nature of these species at our study site, the fact that our study site is located at a geographic range end for both taxa, and possibly weak ascertainment bias at microsatellite loci. Historical effective population size (NEF) was large for both species, while current estimates of Ne had upper 95% confidence limits that encompassed infinity. We found evidence of strong mitochondrial differentiation between the two putative subspecies of D.
    [Show full text]
  • Inbreeding in the Natterjack Toad (Epidalea Calamita)
    The importance of long-term genetic monitoring of reintroduced populations: inbreeding in the natterjack toad (Epidalea calamita) Item Type Article Authors Muir, Anna P.; Phillips, Susanna; Geary, Matt; Allmark, Matthew; Bennett, Sarah; Norman, Kim; Ball, Rachel J; Peters, Catherine Citation Phillips, S., Geary, M., Allmark, M., Bennett, S., Norman, K., Ball, R., Peters, C., Muir, A.P. (2020). The importance of long-term genetic monitoring of reintroduced populations: inbreeding in the natterjack toad (Epidalea calamita). The Herpetological Journal, 30(3), 159-167. DOI 10.33256/hj30.3.159167 Publisher British Herpetological Society Journal The Herpetological Journal Rights Attribution-NonCommercial-NoDerivatives 4.0 International Download date 26/09/2021 09:59:29 Item License http://creativecommons.org/licenses/by-nc-nd/4.0/ Link to Item http://hdl.handle.net/10034/623500 The importance of long-term genetic monitoring of reintroduced populations: inbreeding in the natterjack toad (Epidalea calamita) Susanna Phillips1, Matthew Geary1, Matthew Allmark2, Sarah Bennett2, Kim Norman3, Rachel J. Ball1, Catherine M. Peters1, Anna P. Muir1* 1Conservation Biology Research Group, University of Chester, Chester, CH1 4BJ, UK. 2Cheshire Wildlife Trust, Bickley Hall Farm, Bickley, Malpas, Cheshire, SY14 8EF, UK. 3Eni UK Ltd, Liverpool Bay, Point of Ayr, Station Road, Talacre, Flintshire, CH8 9RD, UK. Running title: Inbreeding in reintroduced natterjack toads Key words Reintroduction, amphibian, inbreeding, conservation, natterjack, genetics. *Author for correspondence: [email protected]; Conservation Biology Research Group, University of Chester, Chester, CH1 4BJ, UK. 1 Abstract Genetic monitoring is an important, but frequently lacking, component of management actions to support long-term persistence in reintroduced populations.
    [Show full text]
  • Monitoring Changes in Genetic Diversity
    Chapter 5 Monitoring Changes in Genetic Diversity Michael W. Bruford, Neil Davies, Mohammad Ehsan Dulloo, Daniel P. Faith and Michele Walters Abstract DNA is the most elemental level of biodiversity, drives the process of speciation, and underpins other levels of biodiversity, including functional traits, species and ecosystems. Until recently biodiversity indicators have largely over- looked data from the molecular tools that are available for measuring variation at the DNA level. More direct analysis of trends in genetic diversity are now feasible and are ready to be incorporated into biodiversity monitoring. This chapter explores the current state-of-the-art in genetic monitoring, with an emphasis on new molecular tools and the richness of data they provide to supplement existing approaches. We also briefly consider proxy approaches that may be useful for many-species, global scale monitoring cases. Keywords Biodiversity Á Molecular tools Á Genetic diversity Á Variation Á Monitoring M.W. Bruford (&) School of Biosciences and Sustainable Places Institute, Cardiff University, Cardiff, Wales CF10 3AX, UK e-mail: [email protected] N. Davies Richard P Gump South Pacific Research Station, University of California Berkeley, Moorea, French Polynesia e-mail: [email protected] M.E. Dulloo Biodiversity International, Maccarese, 00054 Fiumicino, Italy e-mail: [email protected] D.P. Faith The Australian Museum Research Institute, The Australian Museum, Sydney, Australia e-mail: [email protected] M. Walters Natural Resources and Environment, Council for Scientific and Industrial Research, PO Box 395, Pretoria 0001, South Africa e-mail: [email protected] M. Walters Centre for Wildlife Management, University of Pretoria, Pretoria 0002, South Africa © The Author(s) 2017 107 M.
    [Show full text]
  • Genetic and Genomic Monitoring with Minimally Invasive Sampling Methods
    Genetic and genomic monitoring with minimally invasive sampling methods E. L. Carroll1, M. W. Bruford2, J. A. DeWoody3, G. Leroy4, A. Strand5, L. Waits6, J. Wang7 1. Scottish Oceans Institute and School of Biology, University of St Andrews, St Andrews, Fife, Scotland, UK, [email protected] 2. Cardiff School of Biosciences and Sustainable Places Research Institute, Cardiff University, Cardiff, Wales, UK, [email protected] 3. Department of Forestry and Natural Resources and Department of Biological Sciences, Purdue University, West Lafayette, IN, USA, [email protected], ORCID ID: 0000-0002- 7315-5631 4. Food and Agriculture Organization of the United Nations, Animal Production and Health Division, Viale delle Terme de Caracalla, 00153, Rome, Italy, [email protected], ORCID ID: 0000-0003-2588-4431 5. Department of Biology, Grice Marine Laboratory, College of Charleston, Charleston, SC, USA, [email protected] 6. Department of Fish and Wildlife Sciences, University of Idaho, Moscow, ID, USA, [email protected] 7. Institute of Zoology, Zoological Society of London, London, UK, [email protected] PeerJ Preprints | https://doi.org/10.7287/peerj.preprints.3209v1 | CC BY 4.0 Open Access | rec: 30 Aug 2017, publ: 30 Aug 2017 Abstract Emerging genomic technologies are reshaping the field of molecular ecology. However, many modern genomic approaches (e.g., RAD-seq) require large amounts of high quality template DNA. This poses a problem for an active branch of conservation biology: genetic monitoring using minimally invasive sampling (MIS) methods. Without handling or even observing an animal, MIS methods (e.g. collection of hair, skin, faeces) can provide genetic information on individuals or populations.
    [Show full text]
  • The Interplay Between Forest Management Practices, Genetic Monitoring, and Other Long-Term Monitoring Systems
    Review The Interplay between Forest Management Practices, Genetic Monitoring, and Other Long-Term Monitoring Systems Darius Kavaliauskas 1,*, Barbara Fussi 1, Marjana Westergren 2, Filippos Aravanopoulos 3, Domen Finzgar 2, Roland Baier 1, Paraskevi Alizoti 3 ID , Gregor Bozic 2 ID , Evangelia Avramidou 3, Monika Konnert 1 and Hojka Kraigher 2 1 Bavarian Office for Forest Seeding and Planting, Forstamtsplatz 1, 83317 Teisendorf, Germany; [email protected] (B.F.); [email protected] (R.B.); [email protected] (M.K.) 2 Slovenian Forestry Institute, Vecna Pot 2, Ljubljana 1000, Slovenia; [email protected] (M.W.); domen.fi[email protected] (D.F.); [email protected] (G.B.); [email protected] (H.K.) 3 Aristotle University of Thessaloniki, University Campus, 541 24 Thessaloniki, Greece; [email protected] (F.A.); [email protected] (P.A.); [email protected] (E.A.) * Correspondence: [email protected]; Tel.: +49-8666-988-350 Received: 31 January 2018; Accepted: 7 March 2018; Published: 10 March 2018 Abstract: The conservation and sustainable use of forests and forest genetic resources (FGR) is a challenging task for scientists and foresters. Forest management practices can affect diversity on various levels: genetic, species, and ecosystem. Understanding past natural disturbance dynamics and their level of dependence on human disturbances and management practices is essential for the conservation and management of FGR, especially in the light of climate change. In this review, forest management practices and their impact on genetic composition are reviewed, synthesized, and interpreted in the light of existing national and international forest monitoring schemes and concepts from various European projects.
    [Show full text]
  • Bobcat Movement Study – Megan Jennings • American Badger Study – Cheryl Brehme • Underpass/Linkage Study – Carlton Rochester
    Connectivity Strategic Plan for Western San Diego County Science Session Workshop Materials Workshop materials include: 1. Agenda with attendees list, background, purpose, and schedule………………......…2 2. Completed or ongoing project information…………………………………....……….....5 a. 1-3 page summaries of each project……………………….........................…...5 b. CSP objective list with a brief description of related projects…….............….30 3. Workshop Map Handouts..........................................................................................39 4. Breakout group information……………………………….................………........…….43 a. Background and guiding questions i. Large Animals……………………………………………........................44 ii. Small Animals………………………………………….....................…...46 iii. Pollinators………………………………………………....................…...49 b. Notes from each session i. Large Animals……………………………………......................………..52 ii. Small Animals…………………………………………....................…....54 iii. Pollinators…………………………………………..................……….....55 Connectivity Strategic Plan for Western San Diego County Science Session Agenda Date: Tuesday, July 1, 2014 Time: 8:30 am – 4:30 pm Location: USGS Conference Room 103, 4165 Spruance Rd, San Diego, CA 92101 Meeting Organizers: Yvonne C. Moore, Coordinator ([email protected]) Ron Rempel, Administrator ([email protected]) Dr. Kris Preston, Ecologist ([email protected]) Emily Perkins, GIS Manager ([email protected]) Invitees & Group Assignments: Group Last Name First Name Affiliation Large Animals Bohonak
    [Show full text]
  • Next‐Generation Conservation Genetics and Biodiversity Monitoring
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Online Research @ Cardiff Received: 7 May 2018 | Revised: 1 June 2018 | Accepted: 4 June 2018 DOI: 10.1111/eva.12661 PERSPECTIVE Next-­generation­conservation­genetics­and­biodiversity­ monitoring Margaret­E.­Hunter1 | Sean­M.­Hoban2 | Michael­W.­Bruford3 | ­ Gernot­Segelbacher4 | Louis­Bernatchez5 1U.S. Geological Survey, Wetland and Aquatic Research Center, Gainesville, Florida Abstract 2The Morton Arboretum, Lisle, Illinois This special issue of Evolutionary Applications consists of 10 publications investigating 3Cardiff School of Biosciences and the use of next- generation tools and techniques in population genetic analyses and Sustainable Places Institute, Cardiff biodiversity assessment. The special issue stems from a 2016 Next Generation University, Cardiff, UK 4Wildlife Ecology and Management, Genetic Monitoring Workshop, hosted by the National Institute for Mathematical University Freiburg, Freiburg, Germany and Biological Synthesis (NIMBioS) in Tennessee, USA. The improved accessibility of 5 GIROQ, Département de Biologie, next- generation sequencing platforms has allowed molecular ecologists to rapidly Université Laval, Ste-Foy, Québec, QC, Canada produce large amounts of data. However, with the increased availability of new genomic markers and mathematical techniques, care is needed in selecting appropri- Correspondence Margaret E. Hunter, U.S. Geological Survey, ate study designs, interpreting results in light of conservation concerns, and deter- Wetland and Aquatic Research Center, 7920 mining appropriate management actions. This special issue identifies key attributes NW 71st Street, Gainesville, FL 32653. Email: [email protected] of successful genetic data analyses in biodiversity evaluation and suggests ways to improve analyses and their application in current population and conservation genet- Funding­information National Institute for Mathematical and ics research.
    [Show full text]
  • South Texas Wildlife
    SOUTH TEXAS WILDLIFE J. R. THOMASSON A publication of the Caesar Kleberg Wildlife Research Institute Spring 2018 at Texas A&M University-Kingsville Volume 22, No. 1 the effects of habitat fragmentation. Genetic methods are ideal because ecological disturbances that affect multiple generations are reflected in patterns of genetic diversity. Genetic diversity is essential for a population to avoid the effects of inbreeding, limit susceptibility to disease, and adapt to environmental change. We compared genetic differen- tiation and diversity from bobcats sampled in fragmented areas to bobcats sampled in contiguous rangeland habitats. Bobcats often defecate on roads or trails as a means of scent-marking and communica- tion to other cats. DNA extracted from the scats is an efficient way to © Larry Ditto study bobcat populations. We used DNA extracted from bobcat scat to BOBCATS OF THE farming have left only small patches genetically confirm 68 individuals at BORDERLANDS of wildlife habitat scattered across sampling sites within the Lower Rio the landscape. This fragmentation of Grande Valley. by Dan Taylor, Randy DeYoung, habitat is an issue of concern for the Our genetic data revealed sig- and Michael Tewes future persistence of native wildlife nificant evidence for restricted in this unique region. movement and dispersal of bob- Some of the highest rates of Bobcats are among the many cats in fragmented habitat patches human population growth and land- species of wildlife native to the use changes in the U.S. are cur- Lower Rio Grande Valley. Bobcats This Issue rently taking place in the Lower are capable of living in small habitat Bobcats and Genetics..................1 Rio Grande Valley of South Texas.
    [Show full text]
  • Evaluating Noninvasive Genetic Sampling Techniques to Estimate Large Carnivore Abundance
    See discussions, stats, and author profiles for this publication at: https://www.researchgate.net/publication/272515587 Evaluating noninvasive genetic sampling techniques to estimate large carnivore abundance Article in Molecular Ecology Resources · February 2015 DOI: 10.1111/1755-0998.12390 · Source: PubMed CITATIONS READS 8 382 5 authors, including: Matthew A Mumma Todd Fuller University of Northern British Columbia University of Massachusetts Amherst 8 PUBLICATIONS 107 CITATIONS 175 PUBLICATIONS 4,633 CITATIONS SEE PROFILE SEE PROFILE Lisette P Waits University of Idaho 364 PUBLICATIONS 11,284 CITATIONS SEE PROFILE Some of the authors of this publication are also working on these related projects: Project done to obtain PhD degree at University of Massachusetts, Amherst, USA, 2000-2004. View project Migration ecology and conservation of Mongolian wild ungulates View project All content following this page was uploaded by Todd Fuller on 23 March 2015. The user has requested enhancement of the downloaded file. Molecular Ecology Resources (2015) doi: 10.1111/1755-0998.12390 Evaluating noninvasive genetic sampling techniques to estimate large carnivore abundance MATTHEW A. MUMMA,* CHRIS ZIEMINSKI,† TODD K. FULLER,† SHANE P. MAHONEY‡1 and LISETTE P. WAITS* *Department of Fish and Wildlife Sciences, University of Idaho, Moscow, ID 83844, USA, †Department of Environmental Conservation, University of Massachusetts, Amherst, MA 01003, USA, ‡Sustainable Development and Strategic Science, Department of Environment and Conservation, Government of Newfoundland and Labrador, Sir Brian Dunfield Bldg., St. John’s, A1B 4J6 NL, Canada Abstract Monitoring large carnivores is difficult because of intrinsically low densities and can be dangerous if physical cap- ture is required. Noninvasive genetic sampling (NGS) is a safe and cost-effective alternative to physical capture.
    [Show full text]
  • Genetic Composition and Evaluation of Effective Population Size in Temperate Coastal Fish Species
    Time matters: genetic composition and evaluation of effective population size in temperate coastal fish species Sara M. Francisco and Joana I. Robalo MARE—Marine and Environmental Sciences Centre, ISPA—Instituto Universitário, Lisbon, Portugal ABSTRACT Background. Extensive knowledge on the genetic characterization of marine organisms has been assembled, mainly concerning the spatial distribution and structuring of populations. Temporal monitoring assesses not only the stability in genetic composition but also its trajectory over time, providing critical information for the accurate forecast of changes in genetic diversity of marine populations, particularly important for both fisheries and endangered species management. We assessed fluctuations in genetic composition among different sampling periods in the western Portuguese shore in three fish species. Methods. White seabream Diplodus sargus, sand smelt Atherina presbyter and shanny Lipophrys pholis were chosen, because of their genetic patterns in distinct ecological environments, insight into historical and contemporary factors influencing population effective size (Ne), and degree of commercial exploitation. Samples were obtained near Lisbon between 2003 and 2014 and screened for genetic variation with mitochondrial and nuclear markers. Analyses included genealogies, genetic diversities, temporal structures and contemporary Ne. Results. For mtDNA no temporal structure was detected, while for nDNA significant differences were recorded between some sampling periods for the shanny and
    [Show full text]
  • Connectivity Monitoring Strategic Plan for the San Diego Preserve System
    Connectivity Monitoring Strategic Plan For the San Diego Preserve System Prepared for the San Diego Environmental Mitigation Program Working Group January 11, 2011 Connectivity Monitoring Strategic Plan for the San Diego Preserve System CONNECTIVITY MONITORING STRATEGIC PLAN “The ongoing biodiversity crisis is primarily driven by the loss and fragmentation of natural habitats” (Burdett et al. 2010) 1. Background Purpose of Strategic Plan In San Diego County, two large conservation plans, the Multiple Species Conservation Program (MSCP) and the Multiple Habitats Conservation Program (MHCP) are being implemented and two additional large-scale plans (North County and East County MSCP) are in preparation. These plans, in aggregate, are intended to contribute to the preservation of the biological diversity of southern California (MSCP 1998), a world-wide biological diversity hot spot. All four plans anticipate achieving their conservation goals (including species-specific and biodiversity goals), through the conservation and adaptive management of core habitat areas that are functionally connected for a wide variety of species including Covered Species identified in each plan. The MSCP and MHCP plans and supporting and subsequent documents include information regarding the importance of functionally linked core areas in meeting preserve system goals, linkages goals, and the need for monitoring to evaluate linkage function (see Appendix 2 for key portions of these documents). Based on the MSCP, MHCP, and supporting and subsequent documents, the overarching and interrelated goals of connectivity amongst core conserved habitat areas are: (1) ensuring the persistence of species across the preserve system and (2) preserving ecosystem functions across the landscape. This Connectivity Monitoring Strategic Plan (CMSP) provides direction for connectivity monitoring that helps assess if these dual goals are being achieved, and for identifying and informing adaptive management actions to maintain, restore or improve connectivity between conserved core areas in San Diego County.
    [Show full text]