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Huang S, Feigs JT, Holzhauer SIJ, Kramp K, Brunet J, Decocq G, De Frenne P, Diekmann M, Liira J, Spicher F, Vangansbeke P, Vanneste T, Verheyen K, Naaf T. Limited effects of population age on the genetic structure of spatially isolated forest herb populations in temperate Europe. Ecol Evol 2024; 14:e10971. [PMID: 38414568 PMCID: PMC10897356 DOI: 10.1002/ece3.10971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 12/06/2023] [Accepted: 01/30/2024] [Indexed: 02/29/2024] Open
Abstract
Due to multiple land-cover changes, forest herb populations residing in forest patches embedded in agricultural landscapes display different ages and, thus, experience differences in genetic exchange, mutation accumulation and genetic drift. The extent of divergence in present-day population genetic structure among these populations of different ages remains unclear, considering their diverse breeding systems and associated pollinators. Answering this question is essential to understand these species' persistence, maintenance of evolutionary potential and adaptability to changing environments. We applied a multi-landscape setup to compare the genetic structure of forest herb populations across forest patches of different ages (18-338 years). We studied the impact on three common slow-colonizer herb species with distinct breeding systems and associated pollinators: Polygonatum multiflorum (outcrossing, long-distance pollinators), Anemone nemorosa (outcrossing, short-distance pollinators) and Oxalis acetosella (mixed breeding). We aimed to assess if in general older populations displayed higher genetic diversity and lower differentiation than younger ones. We also anticipated that P. multiflorum would show the smallest while O. acetosella the largest difference, between old and young populations. We found that older populations had a higher observed heterozygosity (H o) but a similar level of allelic richness (A r) and expected heterozygosity (H e) as younger populations, except for A. nemorosa, which exhibited higher A r and H e in younger populations. As populations aged, their pairwise genetic differentiation measured by D PS decreased independent of species identity while the other two genetic differentiation measures showed either comparable levels between old and young populations (G" ST) or inconsistency among three species (cGD). The age difference of the two populations did not explain their genetic differentiation. Synthesis: We found restricted evidence that forest herb populations with different ages differ in their genetic structure, indicating that populations of different ages can reach a similar genetic structure within decades and thus persist in the long term after habitat disturbance. Despite their distinct breeding systems and associated pollinators, the three studied species exhibited partly similar genetic patterns, suggesting that their common characteristics, such as being slow colonizers or their ability to propagate vegetatively, are important in determining their long-term response to land-cover change.
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Affiliation(s)
- Siyu Huang
- Leibniz Centre for Agricultural Landscape Research (ZALF)MünchebergGermany
| | - Jannis Till Feigs
- Leibniz Centre for Agricultural Landscape Research (ZALF)MünchebergGermany
| | | | - Katja Kramp
- Leibniz Centre for Agricultural Landscape Research (ZALF)MünchebergGermany
| | - Jörg Brunet
- Southern Swedish Forest Research CentreSwedish University of Agricultural SciencesLommaSweden
| | - Guillaume Decocq
- Research Unit Ecology and Dynamics of Anthropized SystemsUniversity of Picardie Jules VerneAmiens CedexFrance
| | - Pieter De Frenne
- Forest & Nature Lab, Department of EnvironmentGhent UniversityGontrodeBelgium
| | - Martin Diekmann
- Vegetation Ecology and Conservation Biology, Institute of Ecology, FB 2University of BremenBremenGermany
| | - Jaan Liira
- Institute of Ecology and Earth ScienceUniversity of TartuTartuEstonia
| | - Fabien Spicher
- Research Unit Ecology and Dynamics of Anthropized SystemsUniversity of Picardie Jules VerneAmiens CedexFrance
| | - Pieter Vangansbeke
- Forest & Nature Lab, Department of EnvironmentGhent UniversityGontrodeBelgium
| | - Thomas Vanneste
- Forest & Nature Lab, Department of EnvironmentGhent UniversityGontrodeBelgium
| | - Kris Verheyen
- Forest & Nature Lab, Department of EnvironmentGhent UniversityGontrodeBelgium
| | - Tobias Naaf
- Leibniz Centre for Agricultural Landscape Research (ZALF)MünchebergGermany
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2
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Cossu P, Mura L, Dedola GL, Lai T, Sanna D, Scarpa F, Azzena I, Fois N, Casu M. Detection of Genetic Patterns in Endangered Marine Species Is Affected by Small Sample Sizes. Animals (Basel) 2022; 12:ani12202763. [PMID: 36290149 PMCID: PMC9597844 DOI: 10.3390/ani12202763] [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: 09/16/2022] [Revised: 10/10/2022] [Accepted: 10/11/2022] [Indexed: 11/05/2022] Open
Abstract
Knowledge of Genetic diversity and its spatial distribution is crucial to improve conservation plans for endangered species. Genetic tools help ensure species' long-term persistence by unraveling connectivity patterns and evolutionary trajectories of populations. Here, microsatellite genotypes of individuals from populations of Patella ferruginea are used to assess the effect of sample size on metrics of within-and between-population genetic diversity by combining empirical and simulated data. Within-population metrics are slightly to moderately affected by small sample size, albeit the magnitude of the bias is proportional to the effective population size and gene flow. The power of detecting genetic differentiation among populations increases with sample size, albeit the gain of increasing the number of sampled individuals tends to be negligible between 30 and 50. Our results line up with those of previous studies and highlight that small sample sizes are not always a hindrance to investigating genetic patterns in endangered marine species. Caution is needed in interpreting genetic patterns based on small sample sizes when the observed genetic differentiation is weak. This study also highlights the importance of carrying out genetic monitoring in seemingly well-preserved but potentially isolated populations.
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Affiliation(s)
- Piero Cossu
- Department of Sciences for Nature and Environmental Resources, University of Sassari, 07100 Sassari, Italy
- Department of Veterinary Medicine, University of Sassari, 07100 Sassari, Italy
- Correspondence: ; Tel.: +39-079-2280924
| | - Laura Mura
- Dipartimento per la Ricerca nelle Produzioni Animali, Agris Sardegna, 07040 Olmedo, Italy
| | - Gian Luca Dedola
- Department of Sciences for Nature and Environmental Resources, University of Sassari, 07100 Sassari, Italy
| | - Tiziana Lai
- Department of Sciences for Nature and Environmental Resources, University of Sassari, 07100 Sassari, Italy
| | - Daria Sanna
- Department of Sciences for Nature and Environmental Resources, University of Sassari, 07100 Sassari, Italy
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy
| | - Fabio Scarpa
- Department of Sciences for Nature and Environmental Resources, University of Sassari, 07100 Sassari, Italy
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy
| | - Ilenia Azzena
- Department of Veterinary Medicine, University of Sassari, 07100 Sassari, Italy
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy
| | - Nicola Fois
- Dipartimento per la Ricerca nelle Produzioni Animali, Agris Sardegna, 07040 Olmedo, Italy
| | - Marco Casu
- Department of Sciences for Nature and Environmental Resources, University of Sassari, 07100 Sassari, Italy
- Department of Veterinary Medicine, University of Sassari, 07100 Sassari, Italy
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3
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Applying novel connectivity networks to wood turtle populations to provide comprehensive conservation management strategies for species at risk. PLoS One 2022; 17:e0271797. [PMID: 35960725 PMCID: PMC9374220 DOI: 10.1371/journal.pone.0271797] [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: 08/25/2021] [Accepted: 07/07/2022] [Indexed: 11/25/2022] Open
Abstract
Genetic diversity within and among populations is frequently used in prioritization processes to rank populations based on their vulnerability or distinctiveness, however, connectivity and gene flow are rarely considered within these frameworks. Using a wood turtle (Glyptemys insculpta) population graph, we introduce BRIDES as a new tool to evaluate populations for conservation purpose without focusing solely on individual nodes. BRIDES characterizes different types of shortest paths among the nodes of a subgraph and compares the shortest paths among the same nodes in a complete network. The main objectives of this study were to (1) introduce a BRIDES selection process to assist conservation biologists in the prioritization of populations, and (2) use different centrality indices and node removal statistics to compare BRIDES results and assess gene flow among wood turtle populations. We constructed six population subgraphs and used a stepwise selection algorithm to choose the optimal number of additional nodes, representing different populations, required to maximize network connectivity under different weighting schemes. Our results demonstrate the robustness of the BRIDES selection process for a given scenario, while inconsistencies were observed among node-based metrics. Results showed repeated selection of certain wood turtle populations, which could have not been predicted following only genetic diversity and distinctiveness estimation, node-based metrics and node removal analysis. Contrary to centrality measures focusing on static networks, BRIDES allowed for the analysis of evolving networks. To our knowledge, this study is the first to apply graph theory for turtle conservation genetics. We show that population graphs can reveal complex gene flow dynamics and population resiliency to local extinction. As such, BRIDES offers an interesting complement to node-based metrics and node removal to better understand the global processes at play when addressing population prioritization frameworks.
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4
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Savary P, Foltête JC, Moal H, Vuidel G, Garnier S. Analysing landscape effects on dispersal networks and gene flow with genetic graphs. Mol Ecol Resour 2021; 21:1167-1185. [PMID: 33460526 DOI: 10.1111/1755-0998.13333] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 01/08/2021] [Accepted: 01/12/2021] [Indexed: 12/16/2022]
Abstract
Graph-theoretic approaches have relevant applications in landscape genetic analyses. When species form populations in discrete habitat patches, genetic graphs can be used (a) to identify direct dispersal paths followed by propagules or (b) to quantify landscape effects on multi-generational gene flow. However, the influence of their construction parameters remains to be explored. Using a simulation approach, we constructed genetic graphs using several pruning methods (geographical distance thresholds, topological constraints, statistical inference) and genetic distances to weight graph links (FST , DPS , Euclidean genetic distances). We then compared the capacity of these different graphs to (a) identify the precise topology of the dispersal network and (b) to infer landscape resistance to gene flow from the relationship between cost-distances and genetic distances. Although not always clear-cut, our results showed that methods based on geographical distance thresholds seem to better identify dispersal networks in most cases. More interestingly, our study demonstrates that a sub-selection of pairwise distances through graph pruning (thereby reducing the number of data points) can counter-intuitively lead to improved inferences of landscape effects on dispersal. Finally, we showed that genetic distances such as the DPS or Euclidean genetic distances should be preferred over the FST for landscape effect inference as they respond faster to landscape changes.
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Affiliation(s)
- Paul Savary
- ARP-Astrance, 9 Avenue Percier, Paris, 75008, France.,ThéMA, UMR 6049 CNRS, Université Bourgogne-Franche-Comté, 32 Rue Mégevand, Besançon Cedex, 25030, France.,Biogéosciences, UMR 6282 CNRS, Université Bourgogne-Franche-Comté, 6 Boulevard Gabriel, Dijon, 21000, France
| | - Jean-Christophe Foltête
- ThéMA, UMR 6049 CNRS, Université Bourgogne-Franche-Comté, 32 Rue Mégevand, Besançon Cedex, 25030, France
| | - Hervé Moal
- ARP-Astrance, 9 Avenue Percier, Paris, 75008, France
| | - Gilles Vuidel
- ThéMA, UMR 6049 CNRS, Université Bourgogne-Franche-Comté, 32 Rue Mégevand, Besançon Cedex, 25030, France
| | - Stéphane Garnier
- Biogéosciences, UMR 6282 CNRS, Université Bourgogne-Franche-Comté, 6 Boulevard Gabriel, Dijon, 21000, France
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5
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Lang AR, Boveng P, Quakenbush L, Robertson K, Lauf M, Rode KD, Ziel H, Taylor BL. Re-examination of population structure in Arctic ringed seals using DArTseq genotyping. ENDANGER SPECIES RES 2021. [DOI: 10.3354/esr01087] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Although Arctic ringed seals Phoca hispida hispida are currently abundant and broadly distributed, their numbers are projected to decline substantially by the year 2100 due to climate warming. While understanding population structure could provide insight into the impact of environmental changes on this subspecies, detecting demographically important levels of exchange can be difficult in taxa with high abundance. We used a next-generation sequencing approach (DArTseq) to genotype ~5700 single nucleotide polymorphisms in 79 seals from 4 Pacific Arctic regions. Comparison of the 2 most geographically separated strata (eastern Bering vs. northeastern Chukchi-Beaufort Seas) revealed a statistically significant level of genetic differentiation (FST = 0.001, p = 0.005) that, while small, was 1 to 2 orders of magnitude greater than expected based on divergence estimated for similarly sized populations connected by low (1% yr-1) dispersal. A relatively high proportion (72 to 88%) of individuals within these strata could be genetically assigned to their stratum of origin. These results indicate that demographically important structure may be present among Arctic ringed seals breeding in different areas, increasing the risk that declines in the number of seals breeding in areas most negatively affected by environmental warming could occur.
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Affiliation(s)
- AR Lang
- Ocean Associates, Inc., Arlington, VA 22207, USA, under contract to the Southwest Fisheries Science Center, NOAA Fisheries, La Jolla, CA 92037, USA
| | - P Boveng
- Marine Mammal Laboratory, Alaska Fisheries Science Center, NOAA Fisheries, Seattle, WA 98115, USA
| | - L Quakenbush
- Arctic Marine Mammal Program, Alaska Department of Fish and Game, Fairbanks, AK 99701, USA
| | - K Robertson
- Marine Mammal and Turtle Division, Southwest Fisheries Science Center, NOAA Fisheries, La Jolla, CA 92037, USA
| | - M Lauf
- Ocean Associates, Inc., Arlington, VA 22207, USA, under contract to the Southwest Fisheries Science Center, NOAA Fisheries, La Jolla, CA 92037, USA
| | - KD Rode
- Alaska Science Center, US Geological Survey, Anchorage, AK 99508, USA
| | - H Ziel
- Marine Mammal Laboratory, Alaska Fisheries Science Center, NOAA Fisheries, Seattle, WA 98115, USA
| | - BL Taylor
- Marine Mammal and Turtle Division, Southwest Fisheries Science Center, NOAA Fisheries, La Jolla, CA 92037, USA
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6
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Homola JJ, Loftin CS, Kinnison MT. Landscape genetics reveals unique and shared effects of urbanization for two sympatric pool-breeding amphibians. Ecol Evol 2019; 9:11799-11823. [PMID: 31695889 PMCID: PMC6822048 DOI: 10.1002/ece3.5685] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Revised: 08/26/2019] [Accepted: 08/30/2019] [Indexed: 01/05/2023] Open
Abstract
Metapopulation-structured species can be negatively affected when landscape fragmentation impairs connectivity. We investigated the effects of urbanization on genetic diversity and gene flow for two sympatric amphibian species, spotted salamanders (Ambystoma maculatum) and wood frogs (Lithobates sylvaticus), across a large (>35,000 km2) landscape in Maine, USA, containing numerous natural and anthropogenic gradients. Isolation-by-distance (IBD) patterns differed between the species. Spotted salamanders showed a linear and relatively high variance relationship between genetic and geographic distances (r = .057, p < .001), whereas wood frogs exhibited a strongly nonlinear and lower variance relationship (r = 0.429, p < .001). Scale dependence analysis of IBD found gene flow has its most predictable influence (strongest IBD correlations) at distances up to 9 km for spotted salamanders and up to 6 km for wood frogs. Estimated effective migration surfaces revealed contrasting patterns of high and low genetic diversity and gene flow between the two species. Population isolation, quantified as the mean IBD residuals for each population, was associated with local urbanization and less genetic diversity in both species. The influence of geographic proximity and urbanization on population connectivity was further supported by distance-based redundancy analysis and multiple matrix regression with randomization. Resistance surface modeling found interpopulation connectivity to be influenced by developed land cover, light roads, interstates, and topography for both species, plus secondary roads and rivers for wood frogs. Our results highlight the influence of anthropogenic landscape features within the context of natural features and broad spatial genetic patterns, in turn supporting the premise that while urbanization significantly restricts interpopulation connectivity for wood frogs and spotted salamanders, specific landscape elements have unique effects on these two sympatric species.
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Affiliation(s)
| | - Cynthia S. Loftin
- Maine Cooperative Fish and Wildlife Research UnitU.S. Geological SurveyOronoMEUSA
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7
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Bouchard C, Tessier N, Lapointe FJ. Watersheds influence the wood turtle’s (Glyptemys insculpta) genetic structure. CONSERV GENET 2019. [DOI: 10.1007/s10592-019-01169-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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8
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Miles LS, Dyer RJ, Verrelli BC. Urban hubs of connectivity: contrasting patterns of gene flow within and among cities in the western black widow spider. Proc Biol Sci 2018; 285:rspb.2018.1224. [PMID: 30068686 DOI: 10.1098/rspb.2018.1224] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Accepted: 07/10/2018] [Indexed: 12/20/2022] Open
Abstract
As urbanization drastically alters the natural landscape and generates novel habitats within cities, the potential for changes to gene flow for urban-dwelling species increases. The western black widow spider (Latrodectus hesperus) is a medically relevant urban adapter pest species, for which we have previously identified population genetic signatures consistent with urbanization facilitating gene flow, likely due to human-mediated transport. Here, in an analysis of 1.9 million genome-wide SNPs, we contrast broad-scale geographical analyses of 10 urban and 11 non-urban locales with fine-scale within-city analyses including 30 urban locales across the western USA. These hierarchical datasets enable us to test hypotheses of how urbanization impacts multiple urban cities and their genetic connectivity at different spatial scales. Coupled fine-scale and broad-scale analyses reveal contrasting patterns of high and low genetic differentiation among locales within cities as a result of low and high genetic connectivity, respectively, of these cities to the overall population network. We discuss these results as they challenge the use of cities as replicates of urban eco-evolution, and have implications for conservation and human health in a rapidly growing urban habitat.
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Affiliation(s)
- Lindsay S Miles
- Center for Life Sciences Education, Virginia Commonwealth University, Richmond, VA, USA.,Integrative Life Sciences Doctoral Program, Virginia Commonwealth University, Richmond, VA, USA
| | - Rodney J Dyer
- Center for Environmental Studies, Virginia Commonwealth University, Richmond, VA, USA
| | - Brian C Verrelli
- Center for Life Sciences Education, Virginia Commonwealth University, Richmond, VA, USA .,Department of Biology, Virginia Commonwealth University, Richmond, VA, USA
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9
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Cross TB, Schwartz MK, Naugle DE, Fedy BC, Row JR, Oyler‐McCance SJ. The genetic network of greater sage-grouse: Range-wide identification of keystone hubs of connectivity. Ecol Evol 2018; 8:5394-5412. [PMID: 29938061 PMCID: PMC6010832 DOI: 10.1002/ece3.4056] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 03/09/2018] [Accepted: 03/13/2018] [Indexed: 12/02/2022] Open
Abstract
Genetic networks can characterize complex genetic relationships among groups of individuals, which can be used to rank nodes most important to the overall connectivity of the system. Ranking allows scarce resources to be guided toward nodes integral to connectivity. The greater sage-grouse (Centrocercus urophasianus) is a species of conservation concern that breeds on spatially discrete leks that must remain connected by genetic exchange for population persistence. We genotyped 5,950 individuals from 1,200 greater sage-grouse leks distributed across the entire species' geographic range. We found a small-world network composed of 458 nodes connected by 14,481 edges. This network was composed of hubs-that is, nodes facilitating gene flow across the network-and spokes-that is, nodes where connectivity is served by hubs. It is within these hubs that the greatest genetic diversity was housed. Using indices of network centrality, we identified hub nodes of greatest conservation importance. We also identified keystone nodes with elevated centrality despite low local population size. Hub and keystone nodes were found across the entire species' contiguous range, although nodes with elevated importance to network-wide connectivity were found more central: especially in northeastern, central, and southwestern Wyoming and eastern Idaho. Nodes among which genes are most readily exchanged were mostly located in Montana and northern Wyoming, as well as Utah and eastern Nevada. The loss of hub or keystone nodes could lead to the disintegration of the network into smaller, isolated subnetworks. Protecting both hub nodes and keystone nodes will conserve genetic diversity and should maintain network connections to ensure a resilient and viable population over time. Our analysis shows that network models can be used to model gene flow, offering insights into its pattern and process, with application to prioritizing landscapes for conservation.
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Affiliation(s)
- Todd B. Cross
- USDA Forest ServiceNational Genomics Center for Wildlife and Fish ConservationRocky Mountain Research StationMissoulaMontana
- College of Forestry and ConservationUniversity of MontanaMissoulaMontana
| | - Michael K. Schwartz
- USDA Forest ServiceNational Genomics Center for Wildlife and Fish ConservationRocky Mountain Research StationMissoulaMontana
| | - David E. Naugle
- College of Forestry and ConservationUniversity of MontanaMissoulaMontana
| | - Brad C. Fedy
- School of Environment, Resources and SustainabilityUniversity of WaterlooWaterlooONCanada
| | - Jeffrey R. Row
- School of Environment, Resources and SustainabilityUniversity of WaterlooWaterlooONCanada
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10
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van Strien MJ. Consequences of population topology for studying gene flow using link-based landscape genetic methods. Ecol Evol 2017; 7:5070-5081. [PMID: 28770047 PMCID: PMC5528204 DOI: 10.1002/ece3.3075] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 03/29/2017] [Accepted: 04/25/2017] [Indexed: 12/20/2022] Open
Abstract
Many landscape genetic studies aim to determine the effect of landscape on gene flow between populations. These studies frequently employ link‐based methods that relate pairwise measures of historical gene flow to measures of the landscape and the geographical distance between populations. However, apart from landscape and distance, there is a third important factor that can influence historical gene flow, that is, population topology (i.e., the arrangement of populations throughout a landscape). As the population topology is determined in part by the landscape configuration, I argue that it should play a more prominent role in landscape genetics. Making use of existing literature and theoretical examples, I discuss how population topology can influence results in landscape genetic studies and how it can be taken into account to improve the accuracy of these results. In support of my arguments, I have performed a literature review of landscape genetic studies published during the first half of 2015 as well as several computer simulations of gene flow between populations. First, I argue why one should carefully consider which population pairs should be included in link‐based analyses. Second, I discuss several ways in which the population topology can be incorporated in response and explanatory variables. Third, I outline why it is important to sample populations in such a way that a good representation of the population topology is obtained. Fourth, I discuss how statistical testing for link‐based approaches could be influenced by the population topology. I conclude the article with six recommendations geared toward better incorporating population topology in link‐based landscape genetic studies.
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Affiliation(s)
- Maarten J van Strien
- Planning of Landscape and Urban Systems (PLUS) Institute for Spatial and Landscape Planning ETH Zurich Zürich Switzerland
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11
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Bertrand P, Bowman J, Dyer RJ, Manseau M, Wilson PJ. Sex-specific graphs: Relating group-specific topology to demographic and landscape data. Mol Ecol 2017; 26:3898-3912. [PMID: 28488269 DOI: 10.1111/mec.14174] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 04/24/2017] [Accepted: 04/25/2017] [Indexed: 02/01/2023]
Abstract
Sex-specific genetic structure is a commonly observed pattern among vertebrate species. Facing differential selective pressures, individuals may adopt sex-specific life history traits that ultimately shape genetic variation among populations. Although differential dispersal dynamics are commonly detected in the literature, few studies have used genetic structure to investigate sex-specific functional connectivity. The recent use of graph theoretic approaches in landscape genetics has demonstrated network capacities to describe complex system behaviours where network topology represents genetic interaction among subunits. Here, we partition the overall genetic structure into sex-specific graphs, revealing different male and female dispersal dynamics of a fisher (Pekania [Martes] pennanti) metapopulation in southern Ontario. Our analyses based on network topologies supported the hypothesis of male-biased dispersal. Furthermore, we demonstrated that the effect of the landscape, identified at the population level, could be partitioned among sex-specific strata. We found that female connectivity was negatively correlated with snow depth, whereas connectivity among males was not. Our findings underscore the potential of conducting sex-specific analysis by identifying landscape elements or configuration that differentially promotes or impedes functional connectivity between sexes, revealing processes that may otherwise remain cryptic. We propose that the sex-specific graph approach would be applicable to other vagile species where differential sex-specific processes are expected to occur.
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Affiliation(s)
- Philip Bertrand
- Département de Biologie, Chimie & Géographie, Université du Québec à Rimouski, Rimouski, QC, Canada
| | - Jeff Bowman
- Wildlife Research & Monitoring Section, Ontario Ministry of Natural Resources and Forestry, Trent University, Peterborough, ON, Canada
| | - Rodney J Dyer
- Center for Environmental Studies, Virginia Commonwealth University, Richmond, VA, USA
| | - Micheline Manseau
- Office of the Chief Ecosystem Scientist, Gatineau, QC, Canada.,Natural Resources Institute, University of Manitoba, Winnipeg, MB, Canada
| | - Paul J Wilson
- Biology Department, Trent University, Peterborough, ON, Canada
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12
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Marrotte RR, Bowman J, Brown MG, Cordes C, Morris KY, Prentice MB, Wilson PJ. Multi-species genetic connectivity in a terrestrial habitat network. MOVEMENT ECOLOGY 2017; 5:21. [PMID: 29043084 PMCID: PMC5629812 DOI: 10.1186/s40462-017-0112-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2017] [Accepted: 09/26/2017] [Indexed: 05/05/2023]
Abstract
BACKGROUND Habitat fragmentation reduces genetic connectivity for multiple species, yet conservation efforts tend to rely heavily on single-species connectivity estimates to inform land-use planning. Such conservation activities may benefit from multi-species connectivity estimates, which provide a simple and practical means to mitigate the effects of habitat fragmentation for a larger number of species. To test the validity of a multi-species connectivity model, we used neutral microsatellite genetic datasets of Canada lynx (Lynx canadensis), American marten (Martes americana), fisher (Pekania pennanti), and southern flying squirrel (Glaucomys volans) to evaluate multi-species genetic connectivity across Ontario, Canada. RESULTS We used linear models to compare node-based estimates of genetic connectivity for each species to point-based estimates of landscape connectivity (current density) derived from circuit theory. To our knowledge, we are the first to evaluate current density as a measure of genetic connectivity. Our results depended on landscape context: habitat amount was more important than current density in explaining multi-species genetic connectivity in the northern part of our study area, where habitat was abundant and fragmentation was low. In the south however, where fragmentation was prevalent, genetic connectivity was correlated with current density. Contrary to our expectations however, locations with a high probability of movement as reflected by high current density were negatively associated with gene flow. Subsequent analyses of circuit theory outputs showed that high current density was also associated with high effective resistance, underscoring that the presence of pinch points is not necessarily indicative of gene flow. CONCLUSIONS Overall, our study appears to provide support for the hypothesis that landscape pattern is important when habitat amount is low. We also conclude that while current density is proportional to the probability of movement per unit area, this does not imply increased gene flow, since high current density tends to be a result of neighbouring pixels with high cost of movement (e.g., low habitat amount). In other words, pinch points with high current density appear to constrict gene flow.
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Affiliation(s)
- Robby R. Marrotte
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, Canada
| | - Jeff Bowman
- Wildlife Research and Monitoring Section, Ontario Ministry of Natural Resources and Forestry, Peterborough, Canada
| | - Michael G.C. Brown
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, Canada
| | - Chad Cordes
- Wildlife Research and Monitoring Section, Ontario Ministry of Natural Resources and Forestry, Peterborough, Canada
| | - Kimberley Y. Morris
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, Canada
| | - Melanie B. Prentice
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, Canada
| | - Paul J. Wilson
- Biology Department, Trent University, Peterborough, Canada
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Richardson JL, Brady SP, Wang IJ, Spear SF. Navigating the pitfalls and promise of landscape genetics. Mol Ecol 2016; 25:849-63. [PMID: 26756865 DOI: 10.1111/mec.13527] [Citation(s) in RCA: 122] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2015] [Revised: 12/12/2015] [Accepted: 01/07/2016] [Indexed: 12/17/2022]
Abstract
The field of landscape genetics has been evolving rapidly since its emergence in the early 2000s. New applications, techniques and criticisms of techniques appear like clockwork with each new journal issue. The developments are an encouraging, and at times bewildering, sign of progress in an exciting new field of study. However, we suggest that the rapid expansion of landscape genetics has belied important flaws in the development of the field, and we add an air of caution to this breakneck pace of expansion. Specifically, landscape genetic studies often lose sight of the fundamental principles and complex consequences of gene flow, instead favouring simplistic interpretations and broad inferences not necessarily warranted by the data. Here, we describe common pitfalls that characterize such studies, and provide practical guidance to improve landscape genetic investigation, with careful consideration of inferential limits, scale, replication, and the ecological and evolutionary context of spatial genetic patterns. Ultimately, the utility of landscape genetics will depend on translating the relationship between gene flow and landscape features into an understanding of long-term population outcomes. We hope the perspective presented here will steer landscape genetics down a more scientifically sound and productive path, garnering a field that is as informative in the future as it is popular now.
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Affiliation(s)
- Jonathan L Richardson
- Department of Biology, Providence College, 1 Cunningham Square, Providence, RI, 02918, USA
| | - Steven P Brady
- Department of Biological Sciences, Dartmouth College, Hanover, NH, 03755, USA
| | - Ian J Wang
- Department of Environmental Science, Policy & Management, University of California, Berkeley, CA, 94720, USA
| | - Stephen F Spear
- The Orianne Society, 100 Phoenix Rd., Athens, GA, 30605, USA
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14
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Peterman WE, Ousterhout BH, Anderson TL, Drake DL, Semlitsch RD, Eggert LS. Assessing modularity in genetic networks to manage spatially structured metapopulations. Ecosphere 2016. [DOI: 10.1002/ecs2.1231] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- William E. Peterman
- Division of Biological Sciences; University of Missouri; Columbia Missouri 65211 USA
| | | | - Thomas L. Anderson
- Division of Biological Sciences; University of Missouri; Columbia Missouri 65211 USA
| | - Dana L. Drake
- Division of Biological Sciences; University of Missouri; Columbia Missouri 65211 USA
| | - Raymond D. Semlitsch
- Division of Biological Sciences; University of Missouri; Columbia Missouri 65211 USA
| | - Lori S. Eggert
- Division of Biological Sciences; University of Missouri; Columbia Missouri 65211 USA
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15
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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;
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16
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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.
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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
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17
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Peterman WE, Anderson TL, Ousterhout BH, Drake DL, Semlitsch RD, Eggert LS. Differential dispersal shapes population structure and patterns of genetic differentiation in two sympatric pond breeding salamanders. CONSERV GENET 2014. [DOI: 10.1007/s10592-014-0640-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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18
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Tobler U, Garner TWJ, Schmidt BR. Genetic attributes of midwife toad (Alytes obstetricans) populations do not correlate with degree of species decline. Ecol Evol 2013; 3:2806-19. [PMID: 24101974 PMCID: PMC3790531 DOI: 10.1002/ece3.677] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2012] [Revised: 05/27/2013] [Accepted: 06/11/2013] [Indexed: 11/10/2022] Open
Abstract
Genetic diversity is crucial for long-term population persistence. Population loss and subsequent reduction in migration rate among the most important processes that are expected to lead to a reduction in genetic diversity and an increase in genetic differentiation. While the theory behind this is well-developed, empirical evidence from wild populations is inconsistent. Using microsatellite markers, we compared the genetic structure of populations of an amphibian species, the midwife toad (Alytes obstetricans), in four Swiss regions where the species has suffered variable levels of subpopulation extirpation. We also quantified the effects of several geographic factors on genetic structure and used a model selection approach to ascertain which of the variables were important for explaining genetic variation. Although subpopulation pairwise F ST-values were highly significant even over small geographic scales, neither any of the geographic variables nor loss of subpopulations were important factors for predicting spatial genetic structure. The absence of a signature of subpopulation loss on genetic differentiation may suggest that midwife toad subpopulations function as relatively independent units.
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Affiliation(s)
- Ursina Tobler
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich Winterthurerstrasse 190, CH-8057, Zurich, Switzerland ; KARCH Passage Maximilien-de-Meuron 6, CH-2000, Neuchâtel, Switzerland
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