1
|
Savary P, Foltête JC, Moal H, Vuidel G, Garnier S. Inferring landscape resistance to gene flow when genetic drift is spatially heterogeneous. Mol Ecol Resour 2023; 23:1574-1588. [PMID: 37332161 DOI: 10.1111/1755-0998.13821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 05/12/2023] [Accepted: 05/24/2023] [Indexed: 06/20/2023]
Abstract
In connectivity models, land cover types are assigned cost values characterizing their resistance to species movements. Landscape genetic methods infer these values from the relationship between genetic differentiation and cost distances. The spatial heterogeneity of population sizes, and consequently genetic drift, is rarely included in this inference although it influences genetic differentiation. Similarly, migration rates and population spatial distributions potentially influence this inference. Here, we assessed the reliability of cost value inference under several migration rates, population spatial patterns and degrees of population size heterogeneity. Additionally, we assessed whether considering intra-population variables, here using gravity models, improved the inference when drift is spatially heterogeneous. We simulated several gene flow intensities between populations with varying local sizes and spatial distributions. We then fit gravity models of genetic distances as a function of (i) the 'true' cost distances driving simulations or alternative cost distances, and (ii) intra-population variables (population sizes, patch areas). We determined the conditions making the identification of the 'true' costs possible and assessed the contribution of intra-population variables to this objective. Overall, the inference ranked cost scenarios reliably in terms of similarity with the 'true' scenario (cost distance Mantel correlations), but this 'true' scenario rarely provided the best model goodness of fit. Ranking inaccuracies and failures to identify the 'true' scenario were more pronounced when migration was very restricted (<4 dispersal events/generation), population sizes were most heterogeneous and some populations were spatially aggregated. In these situations, considering intra-population variables helps identify cost scenarios reliably, thereby improving cost value inference from genetic data.
Collapse
Affiliation(s)
- Paul Savary
- ARP-Astrance, Paris, France
- UMR 6049 Thé MA, Université de Franche-Comté, CNRS, Besançon Cedex, France
- UMR 6282 Biogéosciences, Université Bourgogne Franche-Comté, CNRS, Dijon, France
| | | | | | - Gilles Vuidel
- UMR 6049 Thé MA, Université de Franche-Comté, CNRS, Besançon Cedex, France
| | - Stéphane Garnier
- UMR 6282 Biogéosciences, Université Bourgogne Franche-Comté, CNRS, Dijon, France
| |
Collapse
|
2
|
Maier PA, Vandergast AG, Ostoja SM, Aguilar A, Bohonak AJ. Landscape genetics of a sub-alpine toad: climate change predicted to induce upward range shifts via asymmetrical migration corridors. Heredity (Edinb) 2022; 129:257-272. [PMID: 36076071 PMCID: PMC9613655 DOI: 10.1038/s41437-022-00561-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 08/24/2022] [Accepted: 08/25/2022] [Indexed: 11/08/2022] Open
Abstract
Climate change is expected to have a major hydrological impact on the core breeding habitat and migration corridors of many amphibians in the twenty-first century. The Yosemite toad (Anaxyrus canorus) is a species of meadow-specializing amphibian endemic to the high-elevation Sierra Nevada Mountains of California. Despite living entirely on federal lands, it has recently faced severe extirpations, yet our understanding of climatic influences on population connectivity is limited. In this study, we used a previously published double-digest RADseq dataset along with numerous remotely sensed habitat features in a landscape genetics framework to answer two primary questions in Yosemite National Park: (1) Which fine-scale climate, topographic, soil, and vegetation features most facilitate meadow connectivity? (2) How is climate change predicted to influence both the magnitude and net asymmetry of genetic migration? We developed an approach for simultaneously modeling multiple toad migration paths, akin to circuit theory, except raw environmental features can be separately considered. Our workflow identified the most likely migration corridors between meadows and used the unique cubist machine learning approach to fit and forecast environmental models of connectivity. We identified the permuted modeling importance of numerous snowpack-related features, such as runoff and groundwater recharge. Our results highlight the importance of considering phylogeographic structure, and asymmetrical migration in landscape genetics. We predict an upward elevational shift for this already high-elevation species, as measured by the net vector of anticipated genetic movement, and a north-eastward shift in species distribution via the network of genetic migration corridors across the park.
Collapse
Affiliation(s)
- Paul A Maier
- Department of Biology, San Diego State University, 5500 Campanile Dr., San Diego, CA, 92182, USA.
- FamilyTreeDNA, Gene by Gene, 1445 N Loop W, Houston, TX, 77008, USA.
| | - Amy G Vandergast
- U.S. Geological Survey, Western Ecological Research Center, San Diego Field Station, San Diego, CA, 92101, USA
| | - Steven M Ostoja
- USDA California Climate Hub, Agricultural Research Service, John Muir Institute of the Environment, University of California, Davis, 1 Shields Ave., Davis, CA, 95616, USA
| | - Andres Aguilar
- Department of Biological Sciences, California State University, Los Angeles, 5151 State University Dr., Los Angeles, CA, 90032, USA
| | - Andrew J Bohonak
- Department of Biology, San Diego State University, 5500 Campanile Dr., San Diego, CA, 92182, USA
| |
Collapse
|
3
|
Valverde J, Perfectti F, Gómez JM. Pollination effectiveness in a generalist plant: adding the genetic component. THE NEW PHYTOLOGIST 2019; 223:354-365. [PMID: 30761538 DOI: 10.1111/nph.15743] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 02/05/2019] [Indexed: 06/09/2023]
Abstract
The pollination effectiveness of a flower visitor has traditionally been measured as the product of a quantity component that depends on the frequency of interaction and a quality component that measures the per-visit effects on plant reproduction. We propose that this could be complemented with a genetic component informing about each pollinator's contribution to the genetic diversity and composition of the plant progeny. We measured the quantity and quality components of effectiveness of most pollinator functional groups of the generalist herb Erysimum mediohispanicum. We used 10 microsatellite markers to calculate the genetic component as the diversity of sires among siblings and included it into the calculation of the pollination effectiveness. Functional groups varied in the quantity and quality components, which were shown to be decoupled. Functional groups also differed in the genetic component. This component changed the estimates of pollination effectiveness, increasing the differences between some functional groups and modifying the pollination effectiveness landscape. We demonstrate that including the genetic component in the calculation of the pollination effectiveness may allow a more complete quantification of the contribution of each pollinator to the reproductive success of a plant, providing information on its mating patterns and long-term fitness.
Collapse
Affiliation(s)
- Javier Valverde
- Departamento de Ecología, Universidad de Granada, ES-18071, Granada, Spain
| | - Francisco Perfectti
- Departamento de Genética and Unidad de Excelencia 'Modeling Nature', Universidad de Granada, ES-18071, Granada, Spain
| | - José María Gómez
- Departamento de Ecología Funcional y Evolutiva, Estación Experimental de Zonas Áridas (EEZA-CSIC), ES-04120, Almería, Spain
| |
Collapse
|
4
|
DiLeo MF, Husby A, Saastamoinen M. Landscape permeability and individual variation in a dispersal-linked gene jointly determine genetic structure in the Glanville fritillary butterfly. Evol Lett 2018; 2:544-556. [PMID: 30564438 PMCID: PMC6292703 DOI: 10.1002/evl3.90] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 10/22/2018] [Accepted: 10/29/2018] [Indexed: 12/14/2022] Open
Abstract
There is now clear evidence that species across a broad range of taxa harbor extensive heritable variation in dispersal. While studies suggest that this variation can facilitate demographic outcomes such as range expansion and invasions, few have considered the consequences of intraspecific variation in dispersal for the maintenance and distribution of genetic variation across fragmented landscapes. Here, we examine how landscape characteristics and individual variation in dispersal combine to predict genetic structure using genomic and spatial data from the Glanville fritillary butterfly. We used linear and latent factor mixed models to identify the landscape features that best predict spatial sorting of alleles in the dispersal-related gene phosphoglucose isomerase (Pgi). We next used structural equation modeling to test if variation in Pgi mediated gene flow as measured by Fst at putatively neutral loci. In a year when the population was recovering following a large decline, individuals with a genotype associated with greater dispersal ability were found at significantly higher frequencies in populations isolated by water and forest, and these populations showed lower levels of genetic differentiation at neutral loci. These relationships disappeared in the next year when metapopulation density was high, suggesting that the effects of individual variation are context dependent. Together our results highlight that (1) more complex aspects of landscape structure beyond just the configuration of habitat can be important for maintaining spatial variation in dispersal traits and (2) that individual variation in dispersal plays a key role in maintaining genetic variation across fragmented landscapes.
Collapse
Affiliation(s)
- Michelle F. DiLeo
- Organismal and Evolutionary Biology Research ProgrammeUniversity of HelsinkiPO Box 6500014Finland
| | - Arild Husby
- Organismal and Evolutionary Biology Research ProgrammeUniversity of HelsinkiPO Box 6500014Finland
- Department of Evolutionary Biology, EBCUppsala UniversityNorbyvägen 18D75236UppsalaSweden
| | - Marjo Saastamoinen
- Organismal and Evolutionary Biology Research ProgrammeUniversity of HelsinkiPO Box 6500014Finland
| |
Collapse
|
5
|
Miller MP, Davis RJ, Forsman ED, Mullins TD, Haig SM. Isolation by distance versus landscape resistance: Understanding dominant patterns of genetic structure in Northern Spotted Owls (Strix occidentalis caurina). PLoS One 2018; 13:e0201720. [PMID: 30071083 PMCID: PMC6072037 DOI: 10.1371/journal.pone.0201720] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 07/21/2018] [Indexed: 11/25/2022] Open
Abstract
Landscape genetics investigations examine how the availability and configuration of habitat influence genetic structure of plants and animals. We used landscape genetics to evaluate the role that forest connectivity plays in determining genetic structure of the federally-threatened Northern Spotted Owl (Strix occidentalis caurina) using genotypes of 339 Northern Spotted Owls obtained for 10 microsatellite loci. Spatial clustering analyses identified a distinct genetic cluster at the southern extent of the region examined. This cluster could not be linked to landscape connectivity patterns and suggested that post-Pleistocene processes were involved with its development rather than contemporary landscape configuration. We also compared matrices of pairwise inter-individual genetic distances with resistance distances derived from a circuit-theory based framework. Resistance distances were obtained for an idealized raster map that reflected continuous unimpeded dispersal habitat across the landscape along with five empirically-derived raster maps reflecting the 1870’s, 1940’s, 1986, 1994, and 2012. Resistance distances from the idealized map served as surrogates for linear geographic distances. Relative to idealized conditions, resistance distances were ~250% higher in the 1940’s and ~200% higher from 1986 onward. Resistance distances from the 1870’s were ~40% higher than idealized conditions. Inter-individual genetic distances were most highly correlated with resistance distances from the idealized map rather than any of the empirical maps. Two hypotheses explain our results. First, our results may reflect temporal lags between the onset of large-scale habitat alterations and their novel effects on genetic structure in long-lived species such as Northern Spotted Owls. Second, because Northern Spotted Owls disperse over long distances, our results may indicate that forest habitat has never been sufficiently fragmented to the point where connectivity was disrupted. The second hypothesis could indicate that forest management practices mandated by the Northwest Forest Plan succeeded with one of its primary goals. However, our results do not represent a complete portrayal of the status of Northern Spotted Owls given detection of significant population declines and bottlenecks in other studies. Future investigations based on computer simulations may help distinguish between hypotheses.
Collapse
Affiliation(s)
- Mark P. Miller
- U.S. Geological Survey, Forest and Rangeland Ecosystem Science Center, Corvallis, Oregon, United States of America
- * E-mail:
| | - Raymond J. Davis
- U.S. Department of Agriculture Forest Service, Pacific Northwest Region, Corvallis, Oregon, United States of America
| | - Eric D. Forsman
- U.S. Department of Agriculture Forest Service, Pacific Northwest Region, Corvallis, Oregon, United States of America
| | - Thomas D. Mullins
- U.S. Geological Survey, Forest and Rangeland Ecosystem Science Center, Corvallis, Oregon, United States of America
| | - Susan M. Haig
- U.S. Geological Survey, Forest and Rangeland Ecosystem Science Center, Corvallis, Oregon, United States of America
| |
Collapse
|
6
|
Inter-annual maintenance of the fine-scale genetic structure in a biennial plant. Sci Rep 2016; 6:37712. [PMID: 27883087 PMCID: PMC5121606 DOI: 10.1038/srep37712] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 11/02/2016] [Indexed: 11/13/2022] Open
Abstract
Within plant populations, space-restricted gene movement, together with environmental heterogeneity, can result in a spatial variation in gene frequencies. In biennial plants, inter-annual flowering migrants can homogenize gene frequencies between consecutive cohorts. However, the actual impact of these migrants on spatial genetic variation remains unexplored. Here, we used 10 nuclear microsatellite and one plastid genetic marker to characterize the spatial genetic structure within two consecutive cohorts in a population of the biennial plant Erysimum mediohispanicum (Brassicaceae). We explored the maintenance of this structure between consecutive flowering cohorts at different levels of complexity, and investigated landscape effects on gene flow. We found that cohorts were not genetically differentiated and showed a spatial genetic structure defined by a negative genetic-spatial correlation at fine scale that varied in intensity with compass directions. This spatial genetic structure was maintained when comparing plants from different cohorts. Additionally, genotypes were consistently associated with environmental factors such as light availability and soil composition, but to a lesser extent compared with the spatial autocorrelation. We conclude that inter-annual migrants, in combination with limited seed dispersal and environmental heterogeneity, play a major role in shaping and maintaining the spatial genetic structure among cohorts in this biennial plant.
Collapse
|
7
|
|
8
|
Moracho E, Moreno G, Jordano P, Hampe A. Unusually limited pollen dispersal and connectivity of Pedunculate oak (Quercus robur) refugial populations at the species' southern range margin. Mol Ecol 2016; 25:3319-31. [DOI: 10.1111/mec.13692] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Revised: 04/12/2016] [Accepted: 05/03/2016] [Indexed: 01/15/2023]
Affiliation(s)
- E. Moracho
- Integrative Ecology Group; Estación Biológica de Doñana; Consejo Superior de Investigaciones Científicas (CSIC); Avenida Americo Vespucio s/n Sevilla E-41092 Spain
| | - G. Moreno
- Forest Research Group; Universidad de Extremadura; Plasencia 10600 Spain
| | - P. Jordano
- Integrative Ecology Group; Estación Biológica de Doñana; Consejo Superior de Investigaciones Científicas (CSIC); Avenida Americo Vespucio s/n Sevilla E-41092 Spain
| | - A. Hampe
- UMR 1202 BIOGECO; INRA; Cestas F-33610 France
- UMR 1202 BIOGECO; University of Bordeaux; Pessac F-33615 France
| |
Collapse
|
9
|
Miller MD. The Modifiable Conceptual Unit Problem demonstrated using pollen and seed dispersal. Glob Ecol Conserv 2016. [DOI: 10.1016/j.gecco.2016.02.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
|
10
|
Dyer RJ. Population Graphs and Landscape Genetics. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2015. [DOI: 10.1146/annurev-ecolsys-112414-054150] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Rodney J. Dyer
- Department of Biology and Center for Environmental Studies, Virginia Commonwealth University, Richmond, Virginia 23284-2012;
| |
Collapse
|
11
|
Dyer RJ. Is there such a thing as landscape genetics? Mol Ecol 2015; 24:3518-28. [DOI: 10.1111/mec.13249] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 04/20/2015] [Accepted: 04/21/2015] [Indexed: 01/13/2023]
Affiliation(s)
- Rodney J. Dyer
- Department of Biology & Center for Environmental Studies; Virginia Commonwealth University; 1000 West Cary Street Richmond VA 23284-2012 USA
| |
Collapse
|
12
|
Koen EL, Bowman J, Wilson PJ. Node-based measures of connectivity in genetic networks. Mol Ecol Resour 2015; 16:69-79. [PMID: 25917123 DOI: 10.1111/1755-0998.12423] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Revised: 04/22/2015] [Accepted: 04/23/2015] [Indexed: 11/30/2022]
Abstract
At-site environmental conditions can have strong influences on genetic connectivity, and in particular on the immigration and settlement phases of dispersal. However, at-site processes are rarely explored in landscape genetic analyses. Networks can facilitate the study of at-site processes, where network nodes are used to model site-level effects. We used simulated genetic networks to compare and contrast the performance of 7 node-based (as opposed to edge-based) genetic connectivity metrics. We simulated increasing node connectivity by varying migration in two ways: we increased the number of migrants moving between a focal node and a set number of recipient nodes, and we increased the number of recipient nodes receiving a set number of migrants. We found that two metrics in particular, the average edge weight and the average inverse edge weight, varied linearly with simulated connectivity. Conversely, node degree was not a good measure of connectivity. We demonstrated the use of average inverse edge weight to describe the influence of at-site habitat characteristics on genetic connectivity of 653 American martens (Martes americana) in Ontario, Canada. We found that highly connected nodes had high habitat quality for marten (deep snow and high proportions of coniferous and mature forest) and were farther from the range edge. We recommend the use of node-based genetic connectivity metrics, in particular, average edge weight or average inverse edge weight, to model the influences of at-site habitat conditions on the immigration and settlement phases of dispersal.
Collapse
Affiliation(s)
- Erin L Koen
- Biology Department, Trent University, 2140 East Bank Drive, Peterborough, ON, K9J 7B8, Canada
| | - Jeff Bowman
- Wildlife Research & Monitoring Section, Ontario Ministry of Natural Resources and Forestry, Trent University DNA Building, 2140 East Bank Drive, Peterborough, ON, K9J 7B8, Canada
| | - Paul J Wilson
- Biology Department, Trent University, 2140 East Bank Drive, Peterborough, ON, K9J 7B8, Canada
| |
Collapse
|
13
|
Robledo-Arnuncio JJ, Klein EK, Muller-Landau HC, Santamaría L. Space, time and complexity in plant dispersal ecology. MOVEMENT ECOLOGY 2014; 2:16. [PMID: 25709828 PMCID: PMC4337469 DOI: 10.1186/s40462-014-0016-3] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Accepted: 07/24/2014] [Indexed: 05/09/2023]
Abstract
Dispersal of pollen and seeds are essential functions of plant species, with far-reaching demographic, ecological and evolutionary consequences. Interest in plant dispersal has increased with concerns about the persistence of populations and species under global change. We argue here that advances in plant dispersal ecology research will be determined by our ability to surmount challenges of spatiotemporal scales and heterogeneities and ecosystem complexity. Based on this framework, we propose a selected set of research questions, for which we suggest some specific objectives and methodological approaches. Reviewed topics include multiple vector contributions to plant dispersal, landscape-dependent dispersal patterns, long-distance dispersal events, spatiotemporal variation in dispersal, and the consequences of dispersal for plant communities, populations under climate change, and anthropogenic landscapes.
Collapse
Affiliation(s)
- Juan J Robledo-Arnuncio
- />Department of Forest Ecology & Genetics, INIA-CIFOR, Ctra. de la Coruña km 7.5, 28040 Madrid, Spain
| | - Etienne K Klein
- />INRA, UR546 Biostatistique et Processus Spatiaux (BioSP), Avignon, France
| | - Helene C Muller-Landau
- />Smithsonian Tropical Research Institute, Apartado Postal 0843-03092 Panamá, Republica de Panamá
| | - Luis Santamaría
- />Spatial Ecology Group, Doñana Biological Station (EBD-CSIC), Sevilla, Spain
| |
Collapse
|