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Delph LF, Brown KE, Ríos LD, Kelly JK. Sex‐specific natural selection on SNPs in
Silene latifolia. Evol Lett 2022; 6:308-318. [PMID: 35937470 PMCID: PMC9346077 DOI: 10.1002/evl3.283] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 02/24/2022] [Accepted: 03/13/2022] [Indexed: 01/15/2023] Open
Affiliation(s)
- Lynda F. Delph
- Department of Biology Indiana University Bloomington Indiana USA
| | - Keely E. Brown
- Department of Ecology and Evolutionary Biology University of Kansas Lawrence Kansas USA
| | - Luis Diego Ríos
- Department of Biology Indiana University Bloomington Indiana USA
| | - John K. Kelly
- Department of Ecology and Evolutionary Biology University of Kansas Lawrence Kansas USA
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2
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Lee KM, Ranta P, Saarikivi J, Kutnar L, Vreš B, Dzhus M, Mutanen M, Kvist L. Using genomic information for management planning of an endangered perennial, Viola uliginosa. Ecol Evol 2020; 10:2638-2649. [PMID: 32185008 PMCID: PMC7069310 DOI: 10.1002/ece3.6093] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 12/17/2019] [Accepted: 01/21/2020] [Indexed: 11/11/2022] Open
Abstract
Species occupying habitats subjected to frequent natural and/or anthropogenic changes are a challenge for conservation management. We studied one such species, Viola uliginosa, an endangered perennial wetland species typically inhabiting sporadically flooded meadows alongside rivers/lakes. In order to estimate genomic diversity, population structure, and history, we sampled five sites in Finland, three in Estonia, and one each in Slovenia, Belarus, and Poland using genomic SNP data with double-digest restriction site-associated DNA sequencing (ddRAD-seq). We found monophyletic populations, high levels of inbreeding (mean population F SNP = 0.407-0.945), low effective population sizes (N e = 0.8-50.9), indications of past demographic expansion, and rare long-distance dispersal. Our results are important in implementing conservation strategies for V. uliginosa, which should include founding of seed banks, ex situ cultivations, and reintroductions with individuals of proper origin, combined with continuous population monitoring and habitat management.
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Affiliation(s)
- Kyung Min Lee
- Ecology and Genetics Research UnitUniversity of OuluOuluFinland
| | - Pertti Ranta
- Faculty of Biological and Environmental SciencesUniversity of HelsinkiHelsinkiFinland
| | - Jarmo Saarikivi
- Faculty of Biological and Environmental SciencesUniversity of HelsinkiHelsinkiFinland
| | - Lado Kutnar
- Department of Forest EcologySlovenian Forestry InstituteLjubljanaSlovenia
| | - Branko Vreš
- Jovan Hadži Institute of BiologyZRC SAZULjubljanaSlovenia
| | - Maxim Dzhus
- Department of BotanyBelarusian State UniversityMinskBelarus
| | - Marko Mutanen
- Ecology and Genetics Research UnitUniversity of OuluOuluFinland
| | - Laura Kvist
- Ecology and Genetics Research UnitUniversity of OuluOuluFinland
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Wu Z, Sloan DB. Recombination and intraspecific polymorphism for the presence and absence of entire chromosomes in mitochondrial genomes. Heredity (Edinb) 2019; 122:647-659. [PMID: 30356223 PMCID: PMC6461862 DOI: 10.1038/s41437-018-0153-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 09/08/2018] [Accepted: 09/25/2018] [Indexed: 11/09/2022] Open
Abstract
Although mitochondrial genomes are typically thought of as single circular molecules, these genomes are fragmented into multiple chromosomes in many eukaryotes, raising intriguing questions about inheritance and (in)stability of mtDNA in such systems. A previous comparison of mitochondrial genomes from two different individuals of the angiosperm species Silene noctiflora found variation in the presence of entire mitochondrial chromosomes. Here, we expand on this work with a geographically diverse sampling of 25 S. noctiflora populations and the closely related species S. turkestanica and S. undulata. Using a combination of deep sequencing and PCR-based screening for the presence of 22 different mitochondrial chromosomes, we found extensive variation in the complement of chromosomes across individuals. Much of this variation could be attributed to recent chromosome loss events, suggesting that the massively expanded and fragmented mitochondrial genomes of S. noctiflora may have entered a phase of genome reduction in which they are losing entire chromosomes at a rapid rate. Sequence analysis of mitochondrial and plastid genomes revealed genealogical differences both between these organelles and within the mitochondrial genome, indicating a history of recombination. Evidence that recombination has generated novel combinations of alleles was more frequent between loci on different mitochondrial chromosomes than it was within chromosomes. Therefore, the fragmentation of mitochondrial genomes and the assortment of chromosomes during mitochondrial inheritance appears to have contributed to a history of sexual-like recombination in the mtDNA of this species.
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Affiliation(s)
- Zhiqiang Wu
- Department of Biology, Colorado State University, Fort Collins, CO, 80523, USA.
| | - Daniel B Sloan
- Department of Biology, Colorado State University, Fort Collins, CO, 80523, USA
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Schrieber K, Wolf S, Wypior C, Höhlig D, Keller SR, Hensen I, Lachmuth S. Release from natural enemies mitigates inbreeding depression in native and invasive Silene latifolia populations. Ecol Evol 2019; 9:3564-3576. [PMID: 30962911 PMCID: PMC6434559 DOI: 10.1002/ece3.4990] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 01/12/2019] [Accepted: 01/26/2019] [Indexed: 01/01/2023] Open
Abstract
Inbreeding and enemy infestation are common in plants and can synergistically reduce their performance. This inbreeding ×environment (I × E) interaction may be of particular importance for the success of plant invasions if introduced populations experience a release from attack by natural enemies relative to their native conspecifics. Here, we investigate whether inbreeding affects plant infestation damage, whether inbreeding depression in growth and reproduction is mitigated by enemy release, and whether this effect is more pronounced in invasive than native plant populations. We used the invader Silene latifolia and its natural enemies as a study system. We performed two generations of experimental out- and inbreeding within eight native (European) and eight invasive (North American) populations under controlled conditions using field-collected seeds. Subsequently, we exposed the offspring to an enemy exclusion and inclusion treatment in a common garden in the species' native range to assess the interactive effects of population origin (range), breeding treatment, and enemy treatment on infestation damage, growth, and reproduction. Inbreeding increased flower and leaf infestation damage in plants from both ranges, but had opposing effects on fruit damage in native versus invasive plants. Inbreeding significantly reduced plant fitness; whereby, inbreeding depression in fruit number was higher in enemy inclusions than exclusions. This effect was equally pronounced in populations from both distribution ranges. Moreover, the magnitude of inbreeding depression in fruit number was lower in invasive than native populations. These results support that inbreeding has the potential to reduce plant defenses in S. latifolia, which magnifies inbreeding depression in the presence of enemies. However, future studies are necessary to further explore whether enemy release in the invaded habitat has actually decreased inbreeding depression and thus facilitated the persistence of inbred founder populations and invasion success.
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Affiliation(s)
- Karin Schrieber
- Department of Chemical Ecology, Faculty of BiologyBielefeld UniversityBielefeldGermany
- Geobotany & Botanical Garden, Institute of BiologyMartin‐Luther‐University Halle‐WittenbergHalle (Saale)Germany
| | - Sabrina Wolf
- Geobotany & Botanical Garden, Institute of BiologyMartin‐Luther‐University Halle‐WittenbergHalle (Saale)Germany
| | - Catherina Wypior
- Geobotany & Botanical Garden, Institute of BiologyMartin‐Luther‐University Halle‐WittenbergHalle (Saale)Germany
| | - Diana Höhlig
- Geobotany & Botanical Garden, Institute of BiologyMartin‐Luther‐University Halle‐WittenbergHalle (Saale)Germany
| | | | - Isabell Hensen
- Geobotany & Botanical Garden, Institute of BiologyMartin‐Luther‐University Halle‐WittenbergHalle (Saale)Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐LeipzigLeipzigGermany
| | - Susanne Lachmuth
- Geobotany & Botanical Garden, Institute of BiologyMartin‐Luther‐University Halle‐WittenbergHalle (Saale)Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐LeipzigLeipzigGermany
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Antonovics J, Abbate JL, Bruns EL, Fields PD, Forrester NJ, Gilbert KJ, Hood ME, Park T, Taylor DR. Effect of the anther-smut fungus Microbotryum on the juvenile growth of its host Silene latifolia. AMERICAN JOURNAL OF BOTANY 2018; 105:1088-1095. [PMID: 29995339 DOI: 10.1002/ajb2.1114] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Accepted: 03/21/2018] [Indexed: 06/08/2023]
Abstract
PREMISE OF THE STUDY Plant pathogens that form persistent systemic infections within plants have the potential to affect multiple plant life history traits, yet we tend to focus only on visible symptoms. Anther smut of Silene latifolia caused by the fungus Microbotryum lychnidis-dioicae induces the anthers of its host to support fungal spore production instead of pollen, and the pathogen is primarily transmitted among flowering plants by pollinators. Nevertheless, most of its life cycle is spent in the asymptomatic vegetative phase, and spores falling on seedlings or nonflowering plants can also infect the host. The purpose of this study was to ask whether the fungus also had an effect on its host plant in the juvenile vegetative phase before flowering as this is important for the disease dynamics in species where infection of seedlings is commonplace. METHODS Leaf length and leaf number of inoculated and uninoculated juvenile plants were compared in greenhouse experiments, and in one experiment, disease status of the plants at flowering was determined. KEY RESULTS Inoculated plants had shorter but more leaves, and reduced root mass at the early juvenile (preflowering) stage. Some of these effects were detectable in plants that were inoculated but showed no disease symptoms at flowering. CONCLUSIONS These results show that pathogenic fungi can have endophyte-like effects even in the total absence of their typical and more charismatic symptoms, and conversely that the assessment of endophyte effects on the fitness of their hosts should include all stages of the host life cycle.
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Affiliation(s)
- Janis Antonovics
- Department of Biology, University of Virginia, Charlottesville, VA, 22904, USA
| | - Jessica L Abbate
- Department of Biology, University of Virginia, Charlottesville, VA, 22904, USA
| | - Emily L Bruns
- Department of Biology, University of Virginia, Charlottesville, VA, 22904, USA
| | - Peter D Fields
- Department of Biology, University of Virginia, Charlottesville, VA, 22904, USA
| | | | | | - Michael E Hood
- Biology Department, Amherst College, Amherst, MA, 01003, USA
| | - Timothy Park
- Department of Biology, University of Virginia, Charlottesville, VA, 22904, USA
| | - Douglas R Taylor
- Department of Biology, University of Virginia, Charlottesville, VA, 22904, USA
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Pilger TJ, Gido KB, Propst DL, Whitney JE, Turner TF. River network architecture, genetic effective size and distributional patterns predict differences in genetic structure across species in a dryland stream fish community. Mol Ecol 2017; 26:2687-2697. [PMID: 28247452 DOI: 10.1111/mec.14079] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 02/15/2017] [Accepted: 02/21/2017] [Indexed: 01/18/2023]
Abstract
Dendritic ecological network (DEN) architecture can be a strong predictor of spatial genetic patterns in theoretical and simulation studies. Yet, interspecific differences in dispersal capabilities and distribution within the network may equally affect species' genetic structuring. We characterized patterns of genetic variation from up to ten microsatellite loci for nine numerically dominant members of the upper Gila River fish community, New Mexico, USA. Using comparative landscape genetics, we evaluated the role of network architecture for structuring populations within species (pairwise FST ) while explicitly accounting for intraspecific demographic influences on effective population size (Ne ). Five species exhibited patterns of connectivity and/or genetic diversity gradients that were predicted by network structure. These species were generally considered to be small-bodied or habitat specialists. Spatial variation of Ne was a strong predictor of pairwise FST for two species, suggesting patterns of connectivity may also be influenced by genetic drift independent of network properties. Finally, two study species exhibited genetic patterns that were unexplained by network properties and appeared to be related to nonequilibrium processes. Properties of DENs shape community-wide genetic structure but effects are modified by intrinsic traits and nonequilibrium processes. Further theoretical development of the DEN framework should account for such cases.
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Affiliation(s)
- Tyler J Pilger
- Department of Biology and Museum of Southwestern Biology, MSC 03-2020, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Keith B Gido
- Division of Biology, Kansas State University, 116 Ackert Hall, Manhattan, KS, 66506, USA
| | - David L Propst
- Department of Biology and Museum of Southwestern Biology, MSC 03-2020, University of New Mexico, Albuquerque, NM, 87131, USA
| | - James E Whitney
- Department of Biology, Pittsburg State University, Heckert-Wells Hall 223, Pittsburg, KS, 66762, USA
| | - Thomas F Turner
- Department of Biology and Museum of Southwestern Biology, MSC 03-2020, University of New Mexico, Albuquerque, NM, 87131, USA
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Colautti RI, Alexander JM, Dlugosch KM, Keller SR, Sultan SE. Invasions and extinctions through the looking glass of evolutionary ecology. Philos Trans R Soc Lond B Biol Sci 2017; 372:20160031. [PMID: 27920376 PMCID: PMC5182427 DOI: 10.1098/rstb.2016.0031] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/30/2016] [Indexed: 11/12/2022] Open
Abstract
Invasive and endangered species reflect opposite ends of a spectrum of ecological success, yet they experience many similar eco-evolutionary challenges including demographic bottlenecks, hybridization and novel environments. Despite these similarities, important differences exist. Demographic bottlenecks are more transient in invasive species, which (i) maintains ecologically relevant genetic variation, (ii) reduces mutation load, and (iii) increases the efficiency of natural selection relative to genetic drift. Endangered species are less likely to benefit from admixture, which offsets mutation load but also reduces fitness when populations are locally adapted. Invading species generally experience more benign environments with fewer natural enemies, which increases fitness directly and also indirectly by masking inbreeding depression. Adaptive phenotypic plasticity can maintain fitness in novel environments but is more likely to evolve in invasive species encountering variable habitats and to be compromised by demographic factors in endangered species. Placed in an eco-evolutionary context, these differences affect the breadth of the ecological niche, which arises as an emergent property of antagonistic selection and genetic constraints. Comparative studies of invasions and extinctions that apply an eco-evolutionary perspective could provide new insights into the environmental and genetic basis of ecological success in novel environments and improve efforts to preserve global biodiversity.This article is part of the themed issue 'Human influences on evolution, and the ecological and societal consequences'.
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Affiliation(s)
- Robert I Colautti
- Department of Biology, Queen's University, 116 Barrie Street, Kingston, Ontario, Canada K7L 3N6
| | - Jake M Alexander
- Institute of Integrative Biology, Department of Environmental Systems Science, ETH Zurich, Universitätsstrasse 16, 8092 Zürich, Switzerland
| | - Katrina M Dlugosch
- Department of Ecology and Evolutionary Biology, University of Arizona, PO Box 210088, Tucson, AZ 85721, USA
| | - Stephen R Keller
- Department of Plant Biology, University of Vermont, 111 Jeffords Hall, Burlington, VT 05405, USA
| | - Sonia E Sultan
- Department of Biology, Wesleyan University, 237 Church Street, Middletown, CT 06459, USA
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Nelson-Tunley M, Morgan-Richards M, Trewick SA. Genetic diversity and gene flow in a rare New Zealand skink despite fragmented habitat in a volcanic landscape. Biol J Linn Soc Lond 2016. [DOI: 10.1111/bij.12807] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Moniqua Nelson-Tunley
- Ecology Group; Institute of Agriculture and Environment; Massey University; Private Bag 11-222 Palmerston North New Zealand
| | - Mary Morgan-Richards
- Ecology Group; Institute of Agriculture and Environment; Massey University; Private Bag 11-222 Palmerston North New Zealand
| | - Steven A. Trewick
- Ecology Group; Institute of Agriculture and Environment; Massey University; Private Bag 11-222 Palmerston North New Zealand
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Sanna D, Scarpa F, Lai T, Cossu P, Falautano M, Castriota L, Andaloro F, Follesa MC, Francalacci P, Curini-Galletti M, Casu M. Fistularia commersonii(Teleostea: Fistulariidae): walking through the Lessepsian paradox of mitochondrial DNA. ACTA ACUST UNITED AC 2015. [DOI: 10.1080/11250003.2015.1046958] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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