DOCSLIB.ORG

Applications of Landscape Genetics to Connectivity Research in Terrestrial Animals

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Applications of Landscape Genetics to Connectivity Research in Terrestrial Animals Chapter 12 APPLICATIONS OF LANDSCAPE GENETICS TO CONNECTIVITY RESEARCH IN TERRESTRIAL ANIMALS 1 2 3 Lisette P. Waits, Samuel A. Cushman, and Steve F. Spear 1 Fish and Wildlife Sciences, University of Idaho, USA 2 Forest and Woodlands Ecosystems Program, Rocky Mountain Research Station, United States Forest Service, USA 3 The Orianne Society, USA 12.1 INTRODUCTION heterogeneous landscapes. Finally, we end the chapter with future directions and current knowledge gaps for This chapter focuses on applications of landscape terrestrial animal landscape genetic studies. genetics for understanding connectivity of terrestrial animal populations. We start with a general introduc­ tion covering unique characteristics and challenges of 12.2 GENERAL OVERVIEW the terrestrial study system, followed by an overview of OF TERRESTRIAL ANIMAL STUDY common research questions addressed in terrestrial SYSTEMS AND RESEARCH animals using neutral markers in landscape genetics. CHALLENGES These common research questions include detecting and defining barriers, identifying corridors, examining Landscape genetic studies have focused on terrestrial source-sink dynamics, and detecting and predicting animals more than any other taxonomic group (Storfer animal responses to environmental change. Based on et al. 2010). This is not surprising given the inclusion of this overview, we highlight limitations of current “land” in the name of the discipline and the usefulness research approaches and present case studies that of landscape genetics as a method to infer animal have specifically dealt with some of these limitations movement, a key process in ecology and conservation. when testing ecological hypotheses about gene flow in Many aspects of landscape genetic studies are well Landscape Genetics: Concepts, Methods, Applications, First Edition. Edited by Niko Balkenhol, Samuel A. Cushman, Andrew T. Storfer, and Lisette P. Waits. © 2016 John Wiley & Sons, Ltd. Published 2016 by John Wiley & Sons, Ltd. 200 Applications of landscape genetics to connectivity research in terrestrial animals suited for applications related to terrestrial animals. dynamics also are very different between typical terrestrial Landscape genetics usually requires a model of the and aquatic systems. Functional connectivity in terrestrial continuous environment, and such GIS models are environments is often more constrained, occurs at a finer most widely available for terrestrial systems (Chap­ scale, and changes at a slower rate than connectivity ter 2). This has allowed for a more realistic representa­ across marine environments (Carr et al. 2003; also see tion of the heterogeneity present in terrestrial Chapter 13). In many ways, this can make it easier to landscapes, whereas it is much more difficult to repre­ develop strong statistical models in terrestrial landscape sent the heterogeneity in aquatic systems using typical genetic studies if sufficient spatial data are available, as remote sensing methods. The ability to incorporate the scale of sampling is more likely to match the scale of existing GIS data into studies of animal population the gene flow process. In contrast, studies of seascape connectivity has benefited researchers greatly. In addi­ genetics often have detected very little genetic structure tion, landscape genetics has enabled effective research across broad areas (Selkoe et al. 2010; Schunter et al. on animals that are secretive or difficult to study using 2011), due in part to the combination of long-distance traditional mark-recapture or radio telemetry methods transport of gametes and larva by currents and temporal (e.g., Schwartz et al. 2009). Furthermore, landscape dynamics that are rapid relative to population turnover. In genetic studies provide some of the best case studies of the terrestrial system, the dynamics of landscape change how contemporary habitat alteration is affecting pop­ are generally slower than population processes, enabling ulation processes such as connectivity in terrestrial the effects of landscape change to be recorded in changes species, ranging from insects (e.g., Keyghobadi et al. in the genetic structure of populations. However, in many 2005a), amphibians (e.g., Funk et al. 2005; Murphy instances rates of change in terrestrial landscapes exceeds et al. 2010a, 2010b; Spear et al. 2012), reptiles (e.g., the equilibration time of population genetic processes, Stow et al. 2001; Clark et al. 2010), birds (e.g., Pav­ requiring non-equilibrium methods to analyze current lacky et al. 2009), and mammals (e.g., Epps et al. 2005; rates of gene flow. Vignieri et al. 2005; Wasserman et al. 2012). The vast scales, high-frequency dynamics, and typi­ cally immense numbers of gametes and larva in marine systems create processes that are essentially “large 12.2.1 Comparison of terrestrial animal number problems” in the sense of statistical mechanics studies with other systems and the Boltzmann equation (Boltzmann 1872), in which the overall statistical behavior of the entire system Landscape genetics research focused on terrestrial ani­ is highly predictable as the outcome of millions of micro- mals has a number of unique aspects compared to scale interactions. Terrestrial systems, however, are aquatic systems or terrestrial plant species. The terres­ more often in the range of “middle number problems”, trial landscape can be depicted as a combination of linear where there are often too many interacting individuals elements, mosaics of categorical patch types (Forman and entities to effectively model the mechanistic inter­ 1995), and gradients of continuously varying ecological actions of the entire system, but too few to average away factors (McGarigal and Cushman 2005; Chapter 2). The the individual interactions in a statistical mechanics patterns of these factors interact with organism behavior approach, and dynamics are too slow to collapse them to affect population processes, such as mating and as “noise” and too frequent to ignore and model as a dispersal. The functional connectivity of a landscape static system. As a result, terrestrial landscape genetic depends on how the pattern of the environment interacts analysis is often a “complex systems” problem, in which with behavioral responses and movement abilities of the researchers attempt to reduce complexity by adopting species to drive population processes. spatially-explicit approaches to represent the location, Terrestrial systems are generally depicted as two-dimen­ movement, and interactions of individuals within popu­ sional patterns, which is in contrast to many marine and lations as functions of the spatial structure of the land­ lacustrine systems, in which hydrodynamic fluxes occur scape. This presents a number of conceptual and in three dimensions, and riverine systems, which are often technical challenges for analysis. For instance, a depicted as networks of one-dimensional links. This in researcher using resistance modeling (see Chapter 8) principle can make analysis of terrestrial landscapes sim­ typically has to parameterize a multivariate resistance pler than marine systems and more complicated than surface in a terrestrial system, whereas following ocean­ riverine networks, simply as a function of the dimension­ ographic currents or stream lengths may be sufficient in ality of the pattern–process relationships. Temporal an aquatic system (although many aquatic systems do General overview of terrestrial animal study systems and research challenges 201 have multiple environmental influences; Chapter 13). often more strongly affected by land conversion, roads, Finally, the slower rate of change in functional connec­ and other forms of habitat fragmentation (e.g., Stow et al. tivity in the terrestrial environment introduces the chal­ 2001; Proctor et al. 2005; Amos et al. 2014; Paquette lenge of accounting for temporal lags. et al. 2014; Elliot et al. 2014a, 2014b). Animals and plants also differ with respect to landscape The complex, often indirect, relationship of animal influence on genetic structure in several ways (also see movement with gene flow is another challenge (Boho­ Chapter 11). The most obvious difference is that individ­ nak 1999). Animal movement occurs for multiple rea­ ual plants are stationary whereas animals are mobile. sons, many of which are not related to gene flow. Thus, The second major difference is that gene flow in terres­ models used to account for landscape influence in a trial animals occurs through the transport of gametes genetic study must recognize that only a subset of by the individual, whereas movement of gametes in movements are relevant when using empirical move­ plants typically occurs independent of the individual ment data to identify key landscape variables (see plant through seed and pollen. Therefore, modeling plant Chapter 8). Furthermore, genetic data may not always gene flow might require a simultaneously modeling of be appropriate to direct conservation actions such as both gametes. On the other hand, the field of adaptive movement corridors if the types of movement the actions landscape genetics is much more amenable to plants due need to facilitate are not tied to mating or reproduction to their sessile nature (see Chapter 9). (i.e. migration). These concerns highlight the impor­ tance of understanding the study system and conducting landscape genetic studies with well-designed objectives 12.2.2 Methodological and study that can investigate multiple processes. design challenges often faced by When analyses are based on individuals, another
Load more

Recommended publications
  • Spatial Population Genetics: It's About Time
    Spatial Population Genetics: It's About Time Gideon S. Bradburd1a and Peter L. Ralph2 May 13, 2019 1Ecology, Evolutionary Biology, and Behavior Group, Department of Inte- grative Biology, Michigan State University, East Lansing, MI, USA, 48824 2Institute of Ecology and Evolution, Departments of Mathematics and Bi- ology, University of Oregon, Eugene, OR 97403 [email protected] Abstract Many questions that we have about the history and dynamics of organisms have a geographical component: How many are there, and where do they live? How do they move and interbreed across the land- scape? How were they moving a thousand years ago, and where were the ancestors of a particular individual alive today? Answers to these questions can have profound consequences for our understanding of his- tory, ecology, and the evolutionary process. In this review, we discuss how geographic aspects of the distribution, movement, and reproduc- tion of organisms are reflected in their pedigree across space and time. Because the structure of the pedigree is what determines patterns of relatedness in modern genetic variation, our aim is to thus provide in- tuition for how these processes leave an imprint in genetic data. We also highlight some current methods and gaps in the statistical toolbox arXiv:1904.09847v2 [q-bio.PE] 10 May 2019 of spatial population genetics. 1 Contents 1 Introduction 3 2 The spatial pedigree 4 2.1 Peeking at the spatial pedigree . 6 2.2 Simulating spatial pedigrees . 6 2.3 Estimating \effective" parameters from the spatial pedigree . 7 3 Things we want to know 8 3.1 Where are they? .
    [Show full text]
  • Effective Population Size Is Strongly Correlated with Breeding Pond Size in the Endangered California Tiger Salamander, Ambystoma Californiense
    Conserv Genet (2011) 12:911–920 DOI 10.1007/s10592-011-0194-0 RESEARCH ARTICLE Effective population size is strongly correlated with breeding pond size in the endangered California tiger salamander, Ambystoma californiense Ian J. Wang • Jarrett R. Johnson • Benjamin B. Johnson • H. Bradley Shaffer Received: 19 October 2010 / Accepted: 31 January 2011 / Published online: 18 February 2011 Ó The Author(s) 2011. This article is published with open access at Springerlink.com Abstract Maintaining genetic diversity and population breeding habitat for A. californiense. We found no cor- viability in endangered and threatened species is a primary relation between pond area and heterozygosity or allelic concern of conservation biology. Genetic diversity diversity, but we identified a strong positive relationship depends on population connectivity and effective popula- between breeding pond area and Ne, particularly for vernal tion size (Ne), both of which are often compromised in pools. Our results provide some of the first empirical endangered taxa. While the importance of population evidence that variation in breeding habitat can be associ- connectivity and gene flow has been well studied, inves- ated with differences in Ne and suggest that a more tigating effective population sizes in natural systems has complete understanding of the environmental features that received far less attention. However, Ne plays a prominent influence Ne is an important component of conservation role in the maintenance of genetic diversity, the preven- genetics and management. tion of inbreeding depression, and in determining the probability of population persistence. In this study, we Keywords Effective population size Á Landscape examined the relationship between breeding pond char- genetics Á Dispersal Á Bottleneck Á Population structure Á acteristics and Ne in the endangered California tiger sal- Microsatellite amander, Ambystoma californiense.
    [Show full text]
  • A Longitudinal Genetic Survey Identifies Temporal Shifts in the Population
    Heredity (2016) 117, 259–267 & 2016 Macmillan Publishers Limited, part of Springer Nature. All rights reserved 0018-067X/16 www.nature.com/hdy ORIGINAL ARTICLE A longitudinal genetic survey identifies temporal shifts in the population structure of Dutch house sparrows L Cousseau1, M Husemann2, R Foppen3,4, C Vangestel1,5 and L Lens1 Dutch house sparrow (Passer domesticus) densities dropped by nearly 50% since the early 1980s, and similar collapses in population sizes have been reported across Europe. Whether, and to what extent, such relatively recent demographic changes are accompanied by concomitant shifts in the genetic population structure of this species needs further investigation. Therefore, we here explore temporal shifts in genetic diversity, genetic structure and effective sizes of seven Dutch house sparrow populations. To allow the most powerful statistical inference, historical populations were resampled at identical locations and each individual bird was genotyped using nine polymorphic microsatellites. Although the demographic history was not reflected by a reduction in genetic diversity, levels of genetic differentiation increased over time, and the original, panmictic population (inferred from the museum samples) diverged into two distinct genetic clusters. Reductions in census size were supported by a substantial reduction in effective population size, although to a smaller extent. As most studies of contemporary house sparrow populations have been unable to identify genetic signatures of recent population declines, results of this study underpin the importance of longitudinal genetic surveys to unravel cryptic genetic patterns. Heredity (2016) 117, 259–267; doi:10.1038/hdy.2016.38; published online 8 June 2016 INTRODUCTION demographic population growth and increased genetic variation as Rapid land use changes, most severely the loss or fragmentation of a result of gene flow (Hanski and Gilpin, 1991; Clobert et al.,2001).
    [Show full text]
  • Impact of Landscape on Host–Parasite Genetic Diversity and Distribution Using the Puumala Orthohantavirus–Bank Vole System
    microorganisms Article Impact of Landscape on Host–Parasite Genetic Diversity and Distribution Using the Puumala orthohantavirus–Bank Vole System Maria Razzauti 1,* , Guillaume Castel 1 and Jean-François Cosson 2 1 CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, Université Montpellier, 34000 Montpellier, France; [email protected] 2 UMR BIPAR, Animal Health Laboratory, ANSES, INRAE, Ecole Nationale Vétérinaire d’Alfort, Université Paris-Est, 94700 Maisons-Alfort, France; [email protected] * Correspondence: [email protected] Abstract: In nature, host specificity has a strong impact on the parasite’s distribution, prevalence, and genetic diversity. The host’s population dynamics is expected to shape the distribution of host-specific parasites. In turn, the parasite’s genetic structure is predicted to mirror that of the host. Here, we study the tandem Puumala orthohantavirus (PUUV)–bank vole system. The genetic diversity of 310 bank voles and 33 PUUV isolates from 10 characterized localities of Northeast France was assessed. Our findings show that the genetic diversity of both PUUV and voles, was positively correlated with forest coverage and contiguity of habitats. While the genetic diversity of voles was weakly structured in space, that of PUUV was found to be strongly structured, suggesting that the dispersion of voles was not sufficient to ensure a broad PUUV dissemination. Genetic diversity of PUUV was mainly shaped by purifying selection. Genetic drift and extinction events were better Citation: Razzauti, M.; Castel, G.; reflected than local adaptation of PUUV. These contrasting patterns of microevolution have important Cosson, J.-F. Impact of Landscape on consequences for the understanding of PUUV distribution and epidemiology.
    [Show full text]
  • Current Status, Future Opportunities, and Remaining Challenges in Landscape Genetics
    Chapter 14 CURRENT STATUS, FUTURE OPPORTUNITIES, AND REMAINING CHALLENGES IN LANDSCAPE GENETICS 1 2 3 4 Niko Balkenhol, Samuel A. Cushman, Lisette P. Waits, and Andrew Storfer 1 Department of Wildlife Sciences, University of Göttingen, Germany 2 Forest and Woodlands Ecosystems Program, Rocky Mountain Research Station, United States Forest Service, USA 3 Fish and Wildlife Sciences, University of Idaho, USA 4 School of Biological Sciences, Washington State University, USA 14.1 INTRODUCTION essentially replaced the isolation-by-distance paradigm with spatially explicit tests of effects of landscape varia- Just over a decade ago, advances in geographic informa- bles on genetic population structure. More generally, tion systems and genetic methodology helped usher in landscape genetics has advanced the field of evolution- the field of landscape genetics, an amalgamation of ary ecology by providing a direct focus on relationships landscape ecology, population genetics, and spatial sta- between landscape patterns and population processes, tistics aimed at testing how landscape heterogeneity such as gene flow, selection, and genetic drift. shapes patterns of spatial genetic variation. It is clear Since the inception of landscape genetics, there have that the tools developed in landscape genetics have been many calls for: (1) better communication among shaped a new paradigm for conducting empirical popu- spatial statisticians, landscape ecologists, and population lation genetics studies; although population genetics geneticists (Storfer et al. 2007; Balkenhol et al. 2009a); theory itself remains largely unchanged, the majority (2) more rigorous hypothesis testing (Storfer et al. 2007, of empirical studies of spatial genetic structure now 2010; Cushman & Landguth 2010; Segelbacher et al. include spatially explicit tests of landscape influences 2010; Manel & Holderegger 2013); (3) increased con- on gene flow.
    [Show full text]
  • Using Landscape Genetics to Assess Population Connectivity in a Habitat Generalist
    University of Central Florida STARS Electronic Theses and Dissertations, 2004-2019 2010 Using Landscape Genetics To Assess Population Connectivity In A Habitat Generalist Tyler Duncan Hether University of Central Florida Part of the Biology Commons, and the Natural Resources and Conservation Commons Find similar works at: https://stars.library.ucf.edu/etd University of Central Florida Libraries http://library.ucf.edu This Masters Thesis (Open Access) is brought to you for free and open access by STARS. It has been accepted for inclusion in Electronic Theses and Dissertations, 2004-2019 by an authorized administrator of STARS. For more information, please contact [email protected]. STARS Citation Hether, Tyler Duncan, "Using Landscape Genetics To Assess Population Connectivity In A Habitat Generalist" (2010). Electronic Theses and Dissertations, 2004-2019. 1567. https://stars.library.ucf.edu/etd/1567 USING LANDSCAPE GENETICS TO ASSESS POPULATION CONNECTIVITY IN A HABITAT GENERALIST by TYLER DUNCAN HETHER B.S. University of Central Florida, 2006 A thesis submitted in partial fulfillment of the requirements for the degree of Master of Science in the Department of Biological Sciences in the College of Sciences at the University of Central Florida Orlando, Florida Summer Term 2010 Major Professor: Eric A. Hoffman © 2010 Tyler Hether ii ABSTRACT Understanding the nature of genetic variation in natural populations is an underlying theme of population genetics. In recent years population genetics has benefited from the incorporation of landscape and environmental data into pre-existing models of isolation by distance (IBD) to elucidate features influencing spatial genetic variation. Many of these landscape genetics studies have focused on populations separated by discrete barriers (e.g., mountain ridges) or species with specific habitat requirements (i.e., habitat specialists).
    [Show full text]
  • Contemporary and Historic Factors Influence Differently Genetic
    Heredity (2015) 115, 216–224 & 2015 Macmillan Publishers Limited All rights reserved 0018-067X/15 www.nature.com/hdy ORIGINAL ARTICLE Contemporary and historic factors influence differently genetic differentiation and diversity in a tropical palm C da Silva Carvalho1,2, MC Ribeiro2, MC Côrtes2, M Galetti2 and RG Collevatti1 Population genetics theory predicts loss in genetic variability because of drift and inbreeding in isolated plant populations; however, it has been argued that long-distance pollination and seed dispersal may be able to maintain gene flow, even in highly fragmented landscapes. We tested how historical effective population size, historical migration and contemporary landscape structure, such as forest cover, patch isolation and matrix resistance, affect genetic variability and differentiation of seedlings in a tropical palm (Euterpe edulis) in a human-modified rainforest. We sampled 16 sites within five landscapes in the Brazilian Atlantic forest and assessed genetic variability and differentiation using eight microsatellite loci. Using a model selection approach, none of the covariates explained the variation observed in inbreeding coefficients among populations. The variation in genetic diversity among sites was best explained by historical effective population size. Allelic richness was best explained by historical effective population size and matrix resistance, whereas genetic differentiation was explained by matrix resistance. Coalescence analysis revealed high historical migration between sites within landscapes and constant historical population sizes, showing that the genetic differentiation is most likely due to recent changes caused by habitat loss and fragmentation. Overall, recent landscape changes have a greater influence on among-population genetic variation than historical gene flow process. As immediate restoration actions in landscapes with low forest amount, the development of more permeable matrices to allow the movement of pollinators and seed dispersers may be an effective strategy to maintain microevolutionary processes.
    [Show full text]
  • Habitat Fragmentation Reduces Genetic Diversity and Connectivity of the Mexican Spotted Owl: a Simulation Study Using Empirical Resistance Models
    G C A T T A C G G C A T genes Article Habitat Fragmentation Reduces Genetic Diversity and Connectivity of the Mexican Spotted Owl: A Simulation Study Using Empirical Resistance Models Ho Yi Wan 1,* ID , Samuel A. Cushman 2 and Joseph L. Ganey 2 1 School of Earth Sciences and Environmental Sustainability, Northern Arizona University, Flagstaff, AZ 86011, USA 2 USDA Forest Service Rocky Mountain Research Station, 2500 S. Pine Knoll, Flagstaff, AZ 86001, USA; [email protected] (S.A.C.); [email protected] (J.L.G.) * Corresponding: [email protected] Received: 24 July 2018; Accepted: 7 August 2018; Published: 10 August 2018 Abstract: We evaluated how differences between two empirical resistance models for the same geographic area affected predictions of gene flow processes and genetic diversity for the Mexican spotted owl (Strix occidentalis lucida). The two resistance models represented the landscape under low- and high-fragmentation parameters. Under low fragmentation, the landscape had larger but highly concentrated habitat patches, whereas under high fragmentation, the landscape had smaller habitat patches that scattered across a broader area. Overall habitat amount differed little between resistance models. We tested eight scenarios reflecting a factorial design of three factors: resistance model (low vs. high fragmentation), isolation hypothesis (isolation-by-distance, IBD, vs. isolation-by-resistance, IBR), and dispersal limit of species (200 km vs. 300 km). Higher dispersal limit generally had a positive but small influence on genetic diversity. Genetic distance increased with both geographic distance and landscape resistance, but landscape resistance displayed a stronger influence. Connectivity was positively related to genetic diversity under IBR but was less important under IBD.
    [Show full text]
  • Preferred Habitat and Effective Population Size Drive the Landscape
    Downloaded from rspb.royalsocietypublishing.org on September 25, 2013 Preferred habitat and effective population size drive landscape genetic patterns in an endangered species Byron V. Weckworth, Marco Musiani, Nicholas J. DeCesare, Allan D. McDevitt, Mark Hebblewhite and Stefano Mariani Proc. R. Soc. B 2013 280, 20131756, published 4 September 2013 Supplementary data "Data Supplement" http://rspb.royalsocietypublishing.org/content/suppl/2013/08/29/rspb.2013.1756.DC1.h tml References This article cites 49 articles, 8 of which can be accessed free http://rspb.royalsocietypublishing.org/content/280/1769/20131756.full.html#ref-list-1 This article is free to access Subject collections Articles on similar topics can be found in the following collections ecology (1431 articles) genetics (83 articles) Receive free email alerts when new articles cite this article - sign up in the box at the top Email alerting service right-hand corner of the article or click here To subscribe to Proc. R. Soc. B go to: http://rspb.royalsocietypublishing.org/subscriptions Preferred habitat and effective population size drive landscape genetic patterns in an endangered species rspb.royalsocietypublishing.org Byron V. Weckworth1,5,7, Marco Musiani1, Nicholas J. DeCesare2,6, Allan D. McDevitt3, Mark Hebblewhite2 and Stefano Mariani3,4 1Faculties of Environmental Design and Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada T2N 1N4 2Wildlife Biology Program, Department of Ecosystem and Conservation Sciences College of Forestry and Research Conservation, University of Montana, Missoula, MT 59812, USA 3School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Republic of Ireland Cite this article: Weckworth BV, Musiani M, 4School of Environment and Life Sciences, University of Salford, Salford M5 4WT, UK DeCesare NJ, McDevitt AD, Hebblewhite M, 5College of Life Sciences, Peking University, Beijing 100871, People’s Republic of China 6 Mariani S.
    [Show full text]
  • Margaret E. Hunter1, Kimberly Pause Tucker2, Robert K. Bonde1
    Margaret E. Hunter1, Kimberly Pause Tucker2, Robert K. Bonde1 1Southeast Ecological Science Center, U.S. Geological Survey, Gainesville, FL 2Department of Mathematics and Natural Sciences, College of Coastal Georgia, Brunswick, GA U.S. Department of the Interior U.S. Geological Survey Florida manatee • Endangered • Census size – 1200 (1991) – 4800 (2011) • Threats – 25% deaths due to water craft (1970’s-today) – Perinatal, Red tide, Cold stress • 2010: 766 deaths; 282 CS Southwest MU: Everglades region • 10,000 Islands to Florida Bay • Ocean, estuaries, and inland creeks Modeling Manatee Response to Restoration in the Ten Thousand Islands and Everglades National Park. Bradley M. Stith, James P. Reid, and Susan M. Butler , First National Conference on Ecosystem Restoration (NCER), 2004, Orlando, Florida Southwest region • Most difficult to quantify population size and estimate survival rates – Demographic data are lacking for the Everglades region – Population decline over time and 11.9% extinction probability within 100 years (Runge et al. 2007) • High mortality rate (Red tide) • Loss of warm water effluents Langtimm, C.A., Swain, E.D., Stith, B.M., and others, 2009, Integrated Science: Florida Manatees and Everglades Hydrology: U.S. Geological Survey Fact Sheet 2009-3002 Florida manatee conservation genetics tools • Genetic diversity – bottlenecks and inbreeding • Effective population size – the number of genetically effective breeders in a population • Landscape genetics – determining genetic connectivity and dispersal Genetic diversity • Genetic diversity is the raw material of evolution • Small, isolated populations have low diversity • Threat to long-term population viability Population Size vs. Genetic Diversity Diversity 0 Time 1 Microsatellite genetic diversity Heterozygosity Ave # of Alleles Healthy 0.6-0.7 8.8 mammalian* Disturbed 0.5-0.6 6.9 mammalian* Florida# 0.480 4.8 Puerto Rico$ 0.447 3.9 Belize+ 0.455 3.4 *DIBATTISTA, 2007; #PAUSE AND HUNTER ET AL.
    [Show full text]
  • Ten Years of Landscape Genetics
    TREE-1709; No. of Pages 8 Review Ten years of landscape genetics 1,2 3,4 Ste´ phanie Manel and Rolf Holderegger 1 Laboratoire LPED ‘‘Population Environnement, De´ veloppement’’ - UMR151 - Aix Marseille University - IRD Marseille, France 2 UMR Botanique et BioinforMatique de l’Architecture des Plantes, CIRAD, TA A51/PS2 34398 Montpellier Cedex 5, France 3 WSL Swiss Federal Research Institute, Zu¨ rcherstrasse 111, CH-8903 Birmensdorf, Switzerland 4 Institute of Integrative Biology, ETH Zu¨ rich, Universita¨ tsstrasse 16, CH-8092 Zu¨ rich, Switzerland Landscape genetics is now ten years old. It has stimu- discipline with a particular focus on potential applications lated research into the effect of landscapes on evolution- in terms of adaptation to global change and the conserva- ary processes. This review describes the main topics that tion of natural resources. have contributed most significantly to the progress of landscape genetics, such as conceptual and methodo- Glossary logical developments in spatial and temporal patterns of Adaptation: the process by which a population or a species globally or locally gene flow, seascape genetics, and landscape genomics. adapts to its environment. Adaptation refers to both the current state of being We then suggest perspectives for the future, investigat- adapted and the dynamic evolutionary process that leads to adaptation. Adaptive genetic variation: variation at loci that are under selection. ing what the field will contribute to the assessment of Covariance structure: incorporating a matrix of pairwise covariances of data into global change and conservation in general and to the a model allows researchers to statistically account for the autocorrelation of data.
    [Show full text]
  • Population Structure and Landscape Genetics of Two Endangered Frog Species of Genus Odorrana: Different Scenarios on Two Islands
    Heredity (2013) 110, 46–56 & 2013 Macmillan Publishers Limited All rights reserved 0018-067X/13 www.nature.com/hdy ORIGINAL ARTICLE Population structure and landscape genetics of two endangered frog species of genus Odorrana: different scenarios on two islands TIgawa1, S Oumi2, S Katsuren3 and M Sumida1 Isolation by distance and landscape connectivity are fundamental factors underlying speciation and evolution. To understand how landscapes affect gene flow and shape population structures, island species provide intrinsic study objects. We investigated the effects of landscapes on the population structure of the endangered frog species, Odorrana ishikawae and O. splendida, which each inhabit an island in southwest Japan. This was done by examining population structure, gene flow and demographic history of each species by analyzing 12 microsatellite loci and exploring causal environmental factors through ecological niche modeling (ENM) and the cost-distance approach. Our results revealed that the limited gene flow and multiple-population structure in O. splendida and the single-population structure in O. ishikawae were maintained after divergence of the species through ancient vicariance between islands. We found that genetic distance correlated with geographic distance between populations of both species. Our landscape genetic analysis revealed that the connectivity of suitable habitats influences gene flow and leads to the formation of specific population structures. In particular, different degrees of topographical complexity between islands are the major determining factor for shaping contrasting population structures of two species. In conclusion, our results illustrate the diversification mechanism of organisms through the interaction with space and environment. Our results also present an ENM approach for identifying the key factors affecting demographic history and population structures of target species, especially endangered species.
    [Show full text]