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Sletvold N, Joffard N, Söderquist L. Fine-scale genetic structure in the orchid Gymnadenia conopsea is not associated with local density of flowering plants. AMERICAN JOURNAL OF BOTANY 2024; 111:e16273. [PMID: 38290971 DOI: 10.1002/ajb2.16273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 11/16/2023] [Accepted: 11/16/2023] [Indexed: 02/01/2024]
Abstract
PREMISE Density-dependent pollinator visitation can lead to density-dependent mating patterns and within-population genetic structure. In Gymnadenia conopsea, individuals in low-density patches receive more self pollen than individuals in high-density patches, suggesting higher relatedness at low density. Ongoing fragmentation is also expected to cause more local matings, potentially leading to biparental inbreeding depression. METHODS To evaluate whether relatedness decreases with local density, we analyzed 1315 SNP loci in 113 individuals within two large populations. We quantified within-population genetic structure in one of the populations, recorded potential habitat barriers, and visualized gene flow using estimated effective migration surfaces (EEMS). We further estimated the magnitude of biparental inbreeding depression that would result from matings restricted to within 5 m. RESULTS There was no significant relationship between local density and relatedness in any population. We detected significant fine-scale genetic structure consistent with isolation by distance, with positive kinship coefficients at distances below 10 m. Kinship coefficients were low, and predicted biparental inbreeding depression resulting from matings within the closest 5 m was a modest 1-3%. The EEMS suggested that rocks and bushes may act as barriers to gene flow within a population. CONCLUSIONS The results suggest that increased self-pollen deposition in sparse patches does not necessarily cause higher selfing rates or that inbreeding depression results in low establishment success of inbred individuals. The modest relatedness suggests that biparental inbreeding depression is unlikely to be an immediate problem following fragmentation of large populations. The results further indicate that habitat structure may contribute to governing fine-scale genetic structure in G. conopsea.
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Affiliation(s)
- Nina Sletvold
- Plant Ecology and Evolution, Department of Ecology and Genetics, EBC, Uppsala University, SE-752 36 Uppsala, Sweden
| | - Nina Joffard
- Plant Ecology and Evolution, Department of Ecology and Genetics, EBC, Uppsala University, SE-752 36 Uppsala, Sweden
- UMR 8198 -Evo-Eco-Paleo, University of Lille, Lille, France
| | - Linus Söderquist
- Plant Ecology and Evolution, Department of Ecology and Genetics, EBC, Uppsala University, SE-752 36 Uppsala, Sweden
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2
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Smith TB, Weissman DB. Isolation by distance in populations with power-law dispersal. G3 (BETHESDA, MD.) 2023; 13:jkad023. [PMID: 36718551 PMCID: PMC10085794 DOI: 10.1093/g3journal/jkad023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 01/07/2023] [Indexed: 02/01/2023]
Abstract
Limited dispersal of individuals between generations results in isolation by distance, in which individuals further apart in space tend to be less related. Classic models of isolation by distance assume that dispersal distances are drawn from a thin-tailed distribution and predict that the proportion of the genome that is identical by descent between a pair of individuals should decrease exponentially with the spatial separation between them. However, in many natural populations, individuals occasionally disperse over very long distances. In this work, we use mathematical analysis and coalescent simulations to study the effect of long-range (power-law) dispersal on patterns of isolation by distance. We find that it leads to power-law decay of identity-by-descent at large distances with the same exponent as dispersal. We also find that broad power-law dispersal produces another, shallow power-law decay of identity-by-descent at short distances. These results suggest that the distribution of long-range dispersal events could be estimated from sequencing large population samples taken from a wide range of spatial scales.
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Affiliation(s)
- Tyler B Smith
- Department of Physics, Emory University, Atlanta, Georgia 30322, USA
| | - Daniel B Weissman
- Corresponding author: Department of Physics, Emory University, Atlanta, Georgia 30322, USA.
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3
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Saillant EA, Luque PL, Short E, Antoni L, Reynal L, Pau C, Arocha F, Roque P, Hazin F. Population structure of blackfin tuna (Thunnus atlanticus) in the western Atlantic Ocean inferred from microsatellite loci. Sci Rep 2022; 12:9830. [PMID: 35701584 PMCID: PMC9198023 DOI: 10.1038/s41598-022-13857-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Accepted: 05/30/2022] [Indexed: 11/30/2022] Open
Abstract
The blackfin tuna, Thunnus atlanticus, is a small tropical tuna exploited by recreational and commercial fisheries in various parts of its range. Information on stock structure is needed to develop management plans for this species but is currently lacking. In this work, 470 blackfin tuna from nine geographic populations were assayed at 13 homologous microsatellite markers to provide a first assessment of stock structure across the species range. The overall divergence among locality samples was very low (overall FST = 0.0004) indicating high connectivity of blackfin tuna across their range. No clear grouping of localities in differentiated units was inferred but structuring followed a weak isolation by distance pattern (r = 0.16, P = 0.032). Pairwise exact tests and spatial analysis of molecular variance suggested divergence of the sample collected offshore Baía Formosa (Brazil) possibly reflecting reproductive isolation of Brazilian populations from those in the Caribbean region and further north. Further study of the status of Brazilian populations and the transition between this region and the Caribbean is warranted. Cryptic subdivision within the Northern Hemisphere part of the range is possible and should be evaluated using increased marker density and a more comprehensive geographic coverage.
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Affiliation(s)
- Eric A Saillant
- School of Ocean Science and Engineering, Gulf Coast Research Laboratory, University of Southern Mississippi, Ocean Springs, MS, 39564, USA.
| | - Patricia L Luque
- School of Ocean Science and Engineering, Gulf Coast Research Laboratory, University of Southern Mississippi, Ocean Springs, MS, 39564, USA.,AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Pasaia, Gipuzkoa, Spain
| | - Emily Short
- School of Ocean Science and Engineering, Gulf Coast Research Laboratory, University of Southern Mississippi, Ocean Springs, MS, 39564, USA
| | - Luca Antoni
- School of Ocean Science and Engineering, Gulf Coast Research Laboratory, University of Southern Mississippi, Ocean Springs, MS, 39564, USA
| | - Lionel Reynal
- IFREMER Délégation de Martinique, 97231, Le Robert, La Martinique, France
| | - Cedric Pau
- IFREMER Délégation de Martinique, 97231, Le Robert, La Martinique, France
| | - Freddy Arocha
- Instituto Oceanográfico de Venezuela, Universidad de Oriente, Cumana, 6101, Venezuela
| | - Pollyana Roque
- UFRPE-Universidade Federal Rural de Pernambuco, Rua Dois Irmãos, s/n, Recife, PE, Brazil
| | - Fabio Hazin
- UFRPE-Universidade Federal Rural de Pernambuco, Rua Dois Irmãos, s/n, Recife, PE, Brazil
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4
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The evolution of altruism and the serial rediscovery of the role of relatedness. Proc Natl Acad Sci U S A 2020; 117:28894-28898. [PMID: 33139540 DOI: 10.1073/pnas.2013596117] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The genetic evolution of altruism (i.e., a behavior resulting in a net reduction of the survival and/or reproduction of an actor to benefit a recipient) once perplexed biologists because it seemed paradoxical in a Darwinian world. More than half a century ago, W. D. Hamilton explained that when interacting individuals are genetically related, alleles for altruism can be favored by selection because they are carried by individuals more likely to interact with other individuals carrying the alleles for altruism than random individuals in the population ("kin selection"). In recent decades, a substantial number of supposedly alternative pathways to altruism have been published, leading to controversies surrounding explanations for the evolution of altruism. Here, we systematically review the 200 most impactful papers published on the evolution of altruism and identify 43 evolutionary models in which altruism evolves and where the authors attribute the evolution of altruism to a pathway other than kin selection and/or deny the role of relatedness. An analysis of these models reveals that in every case the life cycle assumptions entail local reproduction and local interactions, thereby leading to interacting individuals being genetically related. Thus, contrary to the authors' claims, Hamilton's relatedness drives the evolution to altruism in their models. The fact that several decades of investigating the evolution to altruism have resulted in the systematic and unwitting rediscovery of the same mechanism is testament to the fundamental importance of positive relatedness between actor and recipient for explaining the evolution of altruism.
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5
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Battey CJ, Ralph PL, Kern AD. Space is the Place: Effects of Continuous Spatial Structure on Analysis of Population Genetic Data. Genetics 2020; 215:193-214. [PMID: 32209569 PMCID: PMC7198281 DOI: 10.1534/genetics.120.303143] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 03/12/2020] [Indexed: 12/14/2022] Open
Abstract
Real geography is continuous, but standard models in population genetics are based on discrete, well-mixed populations. As a result, many methods of analyzing genetic data assume that samples are a random draw from a well-mixed population, but are applied to clustered samples from populations that are structured clinally over space. Here, we use simulations of populations living in continuous geography to study the impacts of dispersal and sampling strategy on population genetic summary statistics, demographic inference, and genome-wide association studies (GWAS). We find that most common summary statistics have distributions that differ substantially from those seen in well-mixed populations, especially when Wright's neighborhood size is < 100 and sampling is spatially clustered. "Stepping-stone" models reproduce some of these effects, but discretizing the landscape introduces artifacts that in some cases are exacerbated at higher resolutions. The combination of low dispersal and clustered sampling causes demographic inference from the site frequency spectrum to infer more turbulent demographic histories, but averaged results across multiple simulations revealed surprisingly little systematic bias. We also show that the combination of spatially autocorrelated environments and limited dispersal causes GWAS to identify spurious signals of genetic association with purely environmentally determined phenotypes, and that this bias is only partially corrected by regressing out principal components of ancestry. Last, we discuss the relevance of our simulation results for inference from genetic variation in real organisms.
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Affiliation(s)
- C J Battey
- Institute of Ecology Evolution, Department of Biology, University of Oregon, Eugene, Oregon
| | - Peter L Ralph
- Institute of Ecology Evolution, Department of Biology, University of Oregon, Eugene, Oregon
| | - Andrew D Kern
- Institute of Ecology Evolution, Department of Biology, University of Oregon, Eugene, Oregon
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6
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Bachmann JC, Jansen van Rensburg A, Cortazar-Chinarro M, Laurila A, Van Buskirk J. Gene Flow Limits Adaptation along Steep Environmental Gradients. Am Nat 2020; 195:E67-E86. [DOI: 10.1086/707209] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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7
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Bradburd GS, Ralph PL. Spatial Population Genetics: It's About Time. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2019. [DOI: 10.1146/annurev-ecolsys-110316-022659] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Many important questions 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 landscape? 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 history, ecology, and the evolutionary process. In this review, we discuss how geographic aspects of the distribution, movement, and reproduction 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 intuition for how these processes leave an imprint in genetic data. We also highlight some current methods and gaps in the statistical toolbox of spatial population genetics.
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Affiliation(s)
- Gideon S. Bradburd
- Ecology, Evolutionary Biology, and Behavior Group, Department of Integrative Biology, Michigan State University, East Lansing, Michigan 48824, USA
| | - Peter L. Ralph
- Institute of Ecology and Evolution, Department of Biology, University of Oregon, Eugene, Oregon 97403, USA
- Department of Mathematics, University of Oregon, Eugene, Oregon 97403, USA
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8
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Furstenau TN, Cartwright RA. The impact of self-incompatibility systems on the prevention of biparental inbreeding. PeerJ 2017; 5:e4085. [PMID: 29188143 PMCID: PMC5703146 DOI: 10.7717/peerj.4085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 11/02/2017] [Indexed: 12/05/2022] Open
Abstract
Inbreeding in hermaphroditic plants can occur through two different mechanisms: biparental inbreeding, when a plant mates with a related individual, or self-fertilization, when a plant mates with itself. To avoid inbreeding, many hermaphroditic plants have evolved self-incompatibility (SI) systems which prevent or limit self-fertilization. One particular SI system-homomorphic SI-can also reduce biparental inbreeding. Homomorphic SI is found in many angiosperm species, and it is often assumed that the additional benefit of reduced biparental inbreeding may be a factor in the success of this SI system. To test this assumption, we developed a spatially-explicit, individual-based simulation of plant populations that displayed three different types of homomorphic SI. We measured the total level of inbreeding avoidance by comparing each population to a self-compatible population (NSI), and we measured biparental inbreeding avoidance by comparing to a population of self-incompatible plants that were free to mate with any other individual (PSI). Because biparental inbreeding is more common when offspring dispersal is limited, we examined the levels of biparental inbreeding over a range of dispersal distances. We also tested whether the introduction of inbreeding depression affected the level of biparental inbreeding avoidance. We found that there was a statistically significant decrease in autozygosity in each of the homomorphic SI populations compared to the PSI population and, as expected, this was more pronounced when seed and pollen dispersal was limited. However, levels of homozygosity and inbreeding depression were not reduced. At low dispersal, homomorphic SI populations also suffered reduced female fecundity and had smaller census population sizes. Overall, our simulations showed that the homomorphic SI systems had little impact on the amount of biparental inbreeding in the population especially when compared to the overall reduction in inbreeding compared to the NSI population. With further study, this observation may have important consequences for research into the origin and evolution of homomorphic self-incompatibility systems.
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Affiliation(s)
- Tara N. Furstenau
- The Biodesign Institute and School of Life Sciences, Arizona State University, Tempe, AZ, United States of America
- The School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ, United States of America
| | - Reed A. Cartwright
- The Biodesign Institute and School of Life Sciences, Arizona State University, Tempe, AZ, United States of America
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9
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Ringbauer H, Coop G, Barton NH. Inferring Recent Demography from Isolation by Distance of Long Shared Sequence Blocks. Genetics 2017; 205:1335-1351. [PMID: 28108588 PMCID: PMC5340342 DOI: 10.1534/genetics.116.196220] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2016] [Accepted: 01/13/2017] [Indexed: 12/12/2022] Open
Abstract
Recently it has become feasible to detect long blocks of nearly identical sequence shared between pairs of genomes. These identity-by-descent (IBD) blocks are direct traces of recent coalescence events and, as such, contain ample signal to infer recent demography. Here, we examine sharing of such blocks in two-dimensional populations with local migration. Using a diffusion approximation to trace genetic ancestry, we derive analytical formulas for patterns of isolation by distance of IBD blocks, which can also incorporate recent population density changes. We introduce an inference scheme that uses a composite-likelihood approach to fit these formulas. We then extensively evaluate our theory and inference method on a range of scenarios using simulated data. We first validate the diffusion approximation by showing that the theoretical results closely match the simulated block-sharing patterns. We then demonstrate that our inference scheme can accurately and robustly infer dispersal rate and effective density, as well as bounds on recent dynamics of population density. To demonstrate an application, we use our estimation scheme to explore the fit of a diffusion model to Eastern European samples in the Population Reference Sample data set. We show that ancestry diffusing with a rate of [Formula: see text] during the last centuries, combined with accelerating population growth, can explain the observed exponential decay of block sharing with increasing pairwise sample distance.
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Affiliation(s)
- Harald Ringbauer
- Institute of Science and Technology Austria, A-3400 Klosterneuburg, Austria
| | - Graham Coop
- Department of Evolution and Ecology, University of California, Davis, California 95616
- Center for Population Biology, University of California, Davis, California 95616
| | - Nicholas H Barton
- Institute of Science and Technology Austria, A-3400 Klosterneuburg, Austria
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10
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Smith AL, Landguth EL, Bull CM, Banks SC, Gardner MG, Driscoll DA. Dispersal responses override density effects on genetic diversity during post-disturbance succession. Proc Biol Sci 2016; 283:20152934. [PMID: 27009225 DOI: 10.1098/rspb.2015.2934] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 02/26/2016] [Indexed: 11/12/2022] Open
Abstract
Dispersal fundamentally influences spatial population dynamics but little is known about dispersal variation in landscapes where spatial heterogeneity is generated predominantly by disturbance and succession. We tested the hypothesis that habitat succession following fire inhibits dispersal, leading to declines over time in genetic diversity in the early successional gecko Nephrurus stellatus We combined a landscape genetics field study with a spatially explicit simulation experiment to determine whether successional patterns in genetic diversity were driven by habitat-mediated dispersal or demographic effects (declines in population density leading to genetic drift). Initial increases in genetic structure following fire were likely driven by direct mortality and rapid population expansion. Subsequent habitat succession increased resistance to gene flow and decreased dispersal and genetic diversity inN. stellatus Simulated changes in population density alone did not reproduce these results. Habitat-mediated reductions in dispersal, combined with changes in population density, were essential to drive the field-observed patterns. Our study provides a framework for combining demographic, movement and genetic data with simulations to discover the relative influence of demography and dispersal on patterns of landscape genetic structure. Our results suggest that succession can inhibit connectivity among individuals, opening new avenues for understanding how disturbance regimes influence spatial population dynamics.
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Affiliation(s)
- Annabel L Smith
- Fenner School of Environment and Society, Australian National University, Fenner Building 141, Linnaeus Way, Canberra, Australian Capital Territory 2601, Australia
| | - Erin L Landguth
- Division of Biological Sciences, University of Montana, 32 Campus Drive, Missoula, MT 59812, USA
| | - C Michael Bull
- School of Biological Sciences, Flinders University, GPO Box 2100, Adelaide, South Australia 5001, Australia
| | - Sam C Banks
- Fenner School of Environment and Society, Australian National University, Fenner Building 141, Linnaeus Way, Canberra, Australian Capital Territory 2601, Australia
| | - Michael G Gardner
- School of Biological Sciences, Flinders University, GPO Box 2100, Adelaide, South Australia 5001, Australia Evolutionary Biology Unit, South Australian Museum, North Terrace, Adelaide, South Australia 5000, Australia
| | - Don A Driscoll
- Fenner School of Environment and Society, Australian National University, Fenner Building 141, Linnaeus Way, Canberra, Australian Capital Territory 2601, Australia School of Life and Environmental Sciences, Deakin University Geelong, 221 Burwood Highway, Burwood, Victoria 3125, Australia
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11
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Lion S. Moment equations in spatial evolutionary ecology. J Theor Biol 2016; 405:46-57. [DOI: 10.1016/j.jtbi.2015.10.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 10/06/2015] [Accepted: 10/08/2015] [Indexed: 11/28/2022]
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12
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Individual spatial aggregation correlates with between-population variation in fine-scale genetic structure of Silene ciliata (Caryophyllaceae). Heredity (Edinb) 2015; 116:417-23. [PMID: 26604191 DOI: 10.1038/hdy.2015.102] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Revised: 09/29/2015] [Accepted: 10/13/2015] [Indexed: 11/08/2022] Open
Abstract
Fine-scale genetic structure (FSGS) can vary among populations within species depending on multiple demographic and environmental factors. Theoretical models predict that FSGS should decrease in high-density populations and increase in populations where individuals are spatially aggregated. However, few empirical studies have compared FSGS between populations with different degrees of individual spatial aggregation and microhabitat heterogeneity. In this work, we studied the relationship between spatial and genetic structure in five populations of alpine specialist Silene ciliata Poiret (Caryophyllaceae). We mapped all individuals in each population and genotyped 96 of them using 10 microsatellite markers. We found significant FSGS consistent with an isolation-by-distance process in three of the five populations. The intensity of FSGS was positively associated with individual spatial aggregation. However, no association was found between FSGS and global population density or microhabitat heterogeneity. Overall, our results support theoretical studies indicating that stronger spatial aggregation tends to increase the magnitude of FSGS. They also highlight the relevance of characterizing local plant distribution and microhabitat to better understand the mechanisms that generate intraspecific variation in FSGS across landscapes.
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van Strien MJ, Holderegger R, Van Heck HJ. Isolation-by-distance in landscapes: considerations for landscape genetics. Heredity (Edinb) 2015; 114:27-37. [PMID: 25052412 PMCID: PMC4815601 DOI: 10.1038/hdy.2014.62] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Revised: 05/13/2014] [Accepted: 05/27/2014] [Indexed: 11/08/2022] Open
Abstract
In landscape genetics, isolation-by-distance (IBD) is regarded as a baseline pattern that is obtained without additional effects of landscape elements on gene flow. However, the configuration of suitable habitat patches determines deme topology, which in turn should affect rates of gene flow. IBD patterns can be characterized either by monotonically increasing pairwise genetic differentiation (for example, FST) with increasing interdeme geographic distance (case-I pattern) or by monotonically increasing pairwise genetic differentiation up to a certain geographical distance beyond which no correlation is detectable anymore (case-IV pattern). We investigated if landscape configuration influenced the rate at which a case-IV pattern changed to a case-I pattern. We also determined at what interdeme distance the highest correlation was measured between genetic differentiation and geographic distance and whether this distance corresponded to the maximum migration distance. We set up a population genetic simulation study and assessed the development of IBD patterns for several habitat configurations and maximum migration distances. We show that the rate and likelihood of the transition of case-IV to case-I FST-distance relationships was strongly influenced by habitat configuration and maximum migration distance. We also found that the maximum correlation between genetic differentiation and geographic distance was not related to the maximum migration distance and was measured across all deme pairs in a case-I pattern and, for a case-IV pattern, at the distance where the FST-distance curve flattens out. We argue that in landscape genetics, separate analyses should be performed to either assess IBD or the landscape effects on gene flow.
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Affiliation(s)
- M J van Strien
- Planning of Landscape and Urban Systems, ETH Zurich, Stefano-Franscini-Platz 5, Zurich, Switzerland
- WSL Swiss Federal Research Institute, Zürcherstrasse 111, Birmensdorf, Switzerland
| | - R Holderegger
- WSL Swiss Federal Research Institute, Zürcherstrasse 111, Birmensdorf, Switzerland
- Department of Environmental System Sciences, ETH Zurich, Universitätsstrasse 16, Zurich, Switzerland
| | - H J Van Heck
- Earth and Ocean Sciences, Cardiff University, Main Building, Park Place, Cardiff, UK
- Institute of Earth Sciences, Utrecht University, Budapestlaan 4, Utrecht, The Netherlands
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14
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Shirk AJ, Cushman SA. Spatially-explicit estimation of Wright's neighborhood size in continuous populations. Front Ecol Evol 2014. [DOI: 10.3389/fevo.2014.00062] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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15
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Lotterhos KE, Dick SJ, Haggarty DR. Evaluation of rockfish conservation area networks in the United States and Canada relative to the dispersal distance for black rockfish (Sebastes melanops). Evol Appl 2013; 7:238-59. [PMID: 24567745 PMCID: PMC3927886 DOI: 10.1111/eva.12115] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Accepted: 09/09/2013] [Indexed: 11/30/2022] Open
Abstract
Marine reserves networks are implemented as a way to mitigate the impact of fishing on marine ecosystems. Theory suggests that a reserve network will function synergistically when connected by dispersal, but the scale of dispersal is often unknown. On the Pacific coast of the United States and Canada, both countries have recently implemented a number of rockfish conservation areas (RCAs) to protect exploited rockfish species, but no study has evaluated the connectivity within networks in each country or between the two countries. We used isolation-by-distance theory to estimate the scale of dispersal from microsatellite data in the black rockfish, Sebastes melanops, and compared this estimate with the distance between RCAs that would protect this species. Within each country, we found that the distance between RCAs was generally within the confidence intervals of mean dispersal per generation. The distance between these two RCA networks, however, was greater than the average dispersal per generation. The data were also consistent with a genetic break between southern Oregon and central Oregon. We discuss whether additional nearshore RCAs in southern Oregon and Washington would help promote connectivity between RCA's for shallow-water rockfishes.
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Affiliation(s)
- Katie E Lotterhos
- Department of Zoology, University of British Columbia Vancouver, BC, Canada
| | - Stefan J Dick
- Department of Zoology, University of British Columbia Vancouver, BC, Canada
| | - Dana R Haggarty
- Department of Zoology, University of British Columbia Vancouver, BC, Canada
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16
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Rousset F, Leblois R. Likelihood-based inferences under isolation by distance: two-dimensional habitats and confidence intervals. Mol Biol Evol 2011; 29:957-73. [PMID: 22016575 DOI: 10.1093/molbev/msr262] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Likelihood-based methods of inference of population parameters from genetic data in structured populations have been implemented but still little tested in large networks of populations. In this work, a previous software implementation of inference in linear habitats is extended to two-dimensional habitats, and the coverage properties of confidence intervals are analyzed in both cases. Both standard likelihood and an efficient approximation are considered. The effects of misspecification of mutation model and dispersal distribution, and of spatial binning of samples, are considered. In the absence of model misspecification, the estimators have low bias, low mean square error, and the coverage properties of confidence intervals are consistent with theoretical expectations. Inferences of dispersal parameters and of the mutation rate are sensitive to misspecification or to approximations inherent to the coalescent algorithms used. In particular, coalescent approximations are not appropriate to infer the shape of the dispersal distribution. However, inferences of the neighborhood parameter (or of the product of population density and mean square dispersal rate) are generally robust with respect to complicating factors, such as misspecification of the mutation process and of the shape of the dispersal distribution, and with respect to spatial binning of samples. Likelihood inferences appear feasible in moderately sized networks of populations (up to 400 populations in this work), and they are more efficient than previous moment-based spatial regression method in realistic conditions.
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Affiliation(s)
- François Rousset
- Institut des Sciences de l'Evolution (UM2-CNRS), Université Montpellier 2, Montpellier, France.
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17
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Rieux A, Halkett F, de Lapeyre de Bellaire L, Zapater MF, Rousset F, Ravigne V, Carlier J. Inferences on pathogenic fungus population structures from microsatellite data: new insights from spatial genetics approaches. Mol Ecol 2011; 20:1661-74. [PMID: 21410575 DOI: 10.1111/j.1365-294x.2011.05053.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Landscape genetics, which combines population genetics, landscape ecology and spatial statistics, has emerged recently as a new discipline that can be used to assess how landscape features or environmental variables can influence gene flow and spatial genetic variation. We applied this approach to the invasive plant pathogenic fungus Mycosphaerella fijiensis, which causes black leaf streak disease of banana. Around 880 isolates were sampled within a 50 × 50 km area located in a fragmented banana production zone in Cameroon that includes several potential physical barriers to gene flow. Two clustering algorithms and a new F(ST) -based procedure were applied to define the number of genetic entities and their spatial domain without a priori assumptions. Two populations were clearly delineated, and the genetic discontinuity appeared sharp but asymmetric. Interestingly, no landscape features matched this genetic discontinuity, and no isolation by distance (IBD) was found within populations. Our results suggest that the genetic structure observed in this production area reflects the recent history of M. fijiensis expansion in Cameroon rather than resulting from contemporary gene flow. Finally, we discuss the influence of the suspected high effective population size for such an organism on (i) the absence of an IBD signal, (ii) the characterization of contemporary gene-flow events through assignation methods of analysis and (iii) the evolution of the genetic discontinuity detected in this study.
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Affiliation(s)
- A Rieux
- CIRAD, UMR BGPI, Campus international de Baillarguet, TA A-54K, F-34398 Montpellier Cedex 5, France
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