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Leonhardt F, Arranz Aveces C, Müller A, Angin B, Jegu M, Haynes P, Ernst R. Low genetic diversity in a widespread whistling alien: A comparison of Eleutherodactylus johnstonei Barbour, 1914 (Eleutherodactylidae) and congeners in native and introduced ranges. NEOBIOTA 2022. [DOI: 10.3897/neobiota.79.86778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
There is no clear empirical evidence to support the general assumption that genetic diversity favours successful invasions. Many invading species disperse and establish successfully despite low genetic diversity, a phenomenon known as the genetic paradox of biological invasion. Model systems that allow comparison of genetic patterns between exotic and native source populations are still scarce. This is particularly true for amphibians. Here we compare genetic patterns of the widely introduced Johnstone’s Whistling Frog, Eleutherodactylus johnstonei, with its successful alien congener E. antillensis and the single island endemic E. portoricensis. Genetic diversity and population differentiation in native and introduced populations of the three taxa were inferred from mitochondrial D-loop sequences (235 bp). Our results reveal that exotic populations of the two alien taxa, E. johnstonei and E. antillensis, are not only genetically impoverished due to founder effects, but that, moreover, their native range source-populations exhibit low genetic diversity and inter-population differentiation in the first place. Populations of the endemic E. portoricensis, on the other hand, are genetically more diverse and show marked inter-population differentiation. These observed genetic patterns are consistent with geological processes and invasion histories. We argue that the establishment success of the alien taxa in our model system is better explained by ecological factors and anthropogenic drivers than by genetic diversity. As these factors provide more parsimonious explanations, they should be given priority in management decisions. However, molecular studies with higher resolution are needed to fully test possible genetic and epigenetic components that could promote the invasion process.
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Lemmen KD, Verhoeven KJF, Declerck SAJ. Experimental evidence of rapid heritable adaptation in the absence of initial standing genetic variation. Funct Ecol 2021. [DOI: 10.1111/1365-2435.13943] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Kimberley D. Lemmen
- Department of Aquatic Ecology Netherlands Institute of Ecology (NIOO‐KNAW) Wageningen The Netherlands
- Department of Evolutionary Biology and Environmental Studies University of Zurich Zurich Switzerland
| | - Koen J. F. Verhoeven
- Department of Terrestrial Ecology Netherlands Institute of Ecology (NIOO‐KNAW) Wageningen The Netherlands
| | - Steven A. J. Declerck
- Department of Aquatic Ecology Netherlands Institute of Ecology (NIOO‐KNAW) Wageningen The Netherlands
- Department of Biology Laboratory of Aquatic Ecology, Evolution and Conservation KULeuven Leuven Belgium
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3
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Moran KL, Shlyakhtina Y, Portal MM. The role of non-genetic information in evolutionary frameworks. Crit Rev Biochem Mol Biol 2021; 56:255-283. [PMID: 33970731 DOI: 10.1080/10409238.2021.1908949] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The evolution of organisms has been a subject of paramount debate for hundreds of years and though major advances in the field have been made, the precise mechanisms underlying evolutionary processes remain fragmentary. Strikingly, the majority of the core principles accepted across the many fields of biology only consider genetic information as the major - if not exclusive - biological information carrier and thus consider it as the main evolutionary avatar. However, the real picture appears far more complex than originally anticipated, as compelling data suggest that nongenetic information steps up when highly dynamic evolutionary frameworks are explored. In light of recent evidence, we discuss herein the dynamic nature and complexity of nongenetic information carriers, and their emerging relevance in the evolutionary process. We argue that it is possible to overcome the historical arguments which dismissed these carriers, and instead consider that they are indeed core to life itself as they support a sustainable, continuous source of rapid adaptation in ever-changing environments. Ultimately, we will address the intricacies of genetic and non-genetic networks underlying evolutionary models to build a framework where both core biological information concepts are considered non-negligible and equally fundamental.
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Affiliation(s)
- Katherine L Moran
- Cell Plasticity & Epigenetics Lab, Cancer Research UK - Manchester Institute, The University of Manchester, Manchester, UK
| | - Yelyzaveta Shlyakhtina
- Cell Plasticity & Epigenetics Lab, Cancer Research UK - Manchester Institute, The University of Manchester, Manchester, UK
| | - Maximiliano M Portal
- Cell Plasticity & Epigenetics Lab, Cancer Research UK - Manchester Institute, The University of Manchester, Manchester, UK
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Fabricante JR, Targino de Araújo KC, Almeida TS, Bispo Santos JP, Oliveira Reis D. Invasive alien plants in Sergipe, north-eastern Brazil. NEOTROPICAL BIOLOGY AND CONSERVATION 2021. [DOI: 10.3897/neotropical.16.e56427] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Biological invasions are considered one of the greatest threats to global biodiversity. In addition, they cause substantial economic impacts. However, studies about the subject in Brazil are still scarce. The aim of the present study was to prepare an inventory of non-native flora with invasive potential from Sergipe, Brazil. The inventory was carried out along the entire length of the sites. The species with potential invaders were grouped according to the biome/ecosystem and classified according to their habit and origin. Eighty-five species with invasive potential were sampled, 43 in the Caatinga, 75 in the Atlantic Forest, 36 in Sandbank and 22 in Mangrove. From these species, 17 were inventoried in all the biomes/ecosystems and 36 were observed in only one of them, six in the Caatinga, 27 in the Atlantic Forest and three in Sandbank. The number of potentially-invasive species sampled in Sergipe is alarming. The present study showed nearly twice the species listed by other authors for the entire northeast Brazil. This high number of taxa may be a consequence of facilitating the transfer of these species and the conservation conditions of the ecosystems studied in Sergipe. Another very worrying factor is that many of the species sampled are extremely aggressive and cause a series of impacts.
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Huanel OR, Nelson WA, Robitzch V, Mauger S, Faugeron S, Preuss M, Zuccarello GC, Guillemin ML. Comparative phylogeography of two Agarophyton species in the New Zealand archipelago. JOURNAL OF PHYCOLOGY 2020; 56:1575-1590. [PMID: 32609871 DOI: 10.1111/jpy.13046] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Accepted: 06/23/2020] [Indexed: 06/11/2023]
Abstract
Molecular studies have reported the coexistence of two species of Agarophyton in New Zealand: the newly described A.transtasmanicum with an apparently restricted distribution to some sites in the North Island, and the more widespread A.chilense. Here, we compared the distribution, genetic diversity, and structure of both Agarophyton species throughout the archipelago using sequences of the nuclear Internal Transcribed Spacer 2 (ITS2) marker. Agarophyton chilense's distribution was continuous and extensive along the North and South Islands, Stewart Island, and Chatham Island, and the genetic clusters were mostly concordant with boundaries between biogeographic regions. In contrast, specimens of A.transtasmanicum were collected in four sites broadly distributed in both the North and South Islands, with no clear spatial structure of the genetic diversity. Populations, where the species co-occurred, tended to display similar levels in genetic diversity for the two species. Demographic inferences supported a postglacial demographic expansion for two A.chilense genetic clusters, one present in the South Island and the eastern coast of the North Island, and the other present in northern South Island. A third genetic cluster located on the western coast of the North Island had a signature of long-term demographic stability. For A.transtasmanicum, the skyline plot also suggested a postglacial demographic expansion. Last, we developed a new molecular tool to quickly and easily distinguish between the two Agarophyton species, which could be used to ease future fine-scale population studies, especially in areas where the two species coexist.
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Affiliation(s)
- Oscar R Huanel
- Departamento de Ecología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Casilla 114-D, Santiago, Chile
- CNRS, Sorbonne Université, UMI 3614, Evolutionary Biology and Ecology of Algae, Station Biologique de Roscoff, CS 90074, Place G. Tessier, 296888, Roscoff, France
| | - Wendy A Nelson
- National Institute of Water and Atmospheric Research, Wellington, 6021, New Zealand
- School of Biological Sciences, University of Auckland, Auckland, 1142, New Zealand
| | - Vanessa Robitzch
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Casilla 567, Valdivia, Chile
| | - Stéphane Mauger
- CNRS, Sorbonne Université, UMI 3614, Evolutionary Biology and Ecology of Algae, Station Biologique de Roscoff, CS 90074, Place G. Tessier, 296888, Roscoff, France
| | - Sylvain Faugeron
- Departamento de Ecología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Casilla 114-D, Santiago, Chile
- CNRS, Sorbonne Université, UMI 3614, Evolutionary Biology and Ecology of Algae, Station Biologique de Roscoff, CS 90074, Place G. Tessier, 296888, Roscoff, France
| | - Maren Preuss
- School of Biological Sciences, Victoria University of Wellington, Wellington, 6140, New Zealand
| | - Giuseppe C Zuccarello
- School of Biological Sciences, Victoria University of Wellington, Wellington, 6140, New Zealand
| | - Marie-Laure Guillemin
- CNRS, Sorbonne Université, UMI 3614, Evolutionary Biology and Ecology of Algae, Station Biologique de Roscoff, CS 90074, Place G. Tessier, 296888, Roscoff, France
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Casilla 567, Valdivia, Chile
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Eckert S, Herden J, Stift M, Joshi J, van Kleunen M. Manipulation of cytosine methylation does not remove latitudinal clines in two invasive goldenrod species in Central Europe. Mol Ecol 2020; 30:222-236. [PMID: 33150604 DOI: 10.1111/mec.15722] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 10/03/2020] [Accepted: 10/23/2020] [Indexed: 12/23/2022]
Abstract
Invasive species frequently differentiate phenotypically in novel environments within a few generations, often even with limited genetic variation. For the invasive plants Solidago canadensis and S. gigantea, we tested whether such differentiation might have occurred through heritable epigenetic changes in cytosine methylation. In a 2-year common-garden experiment, we grew plants from seeds collected along a latitudinal gradient in their non-native Central European range to test for trait differentiation and whether differentiation disappeared when seeds were treated with the demethylation agent zebularine. Microsatellite markers revealed no population structure along the latitudinal gradient in S. canadensis, but three genetic clusters in S. gigantea. Solidago canadensis showed latitudinal clines in flowering phenology and growth. In S. gigantea, the number of clonal offspring decreased with latitude. Although zebularine had a significant effect on early growth, probably through effects on cytosine methylation, latitudinal clines remained (or even got stronger) in plants raised from seeds treated with zebularine. Thus, our experiment provides no evidence that epigenetic mechanisms by selective cytosine methylation contribute to the observed phenotypic differentiation in invasive goldenrods in Central Europe.
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Affiliation(s)
- Silvia Eckert
- Biodiversity Research/Systematic Botany, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Jasmin Herden
- Ecology, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Marc Stift
- Ecology, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Jasmin Joshi
- Biodiversity Research/Systematic Botany, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany.,Institute for Landscape and Open Space, Eastern Switzerland University of Applied Sciences, Rapperswil, Switzerland.,Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
| | - Mark van Kleunen
- Ecology, Department of Biology, University of Konstanz, Konstanz, Germany.,Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, China
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Latombe G, Essl F, McGeoch MA. The effect of cross-boundary management on the trajectory to commonness in biological invasions. NEOBIOTA 2020. [DOI: 10.3897/neobiota.62.52708] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The number of alien species introduced and undergoing range expansion in novel environments is steadily increasing, with important consequences for native ecosystems. The efficacy of management planning and decision making to limit such invasions can be improved by understanding how interventions will impact the population dynamics of recently introduced species. To do so, here we expand on a typological framework that enables the classification of populations over time into 10 categories of commonness, and apply it to a spatially discrete metapopulation with heterogeneous abundance across spatial units (patches). We use this framework to assess the effect of cross-boundary management on the capacity of a metapopulation with different demographic and dispersal characteristics, including time lags in population growth, to become common. We demonstrate this framework by simulating a simple theoretical metapopulation model capable of exploring a range of environments, species characteristics, and management actions. Management can vary in the efficacy of propagule interception between patches, and in the synchronisation of the implementation of these measures across patches (i.e. if management is implemented simultaneously across patches). Simulations show that poor interception efficacy that only modestly reduces the number of propagules entering a given spatial unit cannot be compensated for by strong management synchronisation between spatial units. Management synchronisation will nonetheless result in a reduction in rates of spread once a critical threshold of interception efficacy has been met. Finally, time lags in population growth that may result in delayed spread are an important aspect to be considered in management as they can amplify the efficacy of management. Our results demonstrate how a typological framework of categories of commonness can be used to provide practical insights for the management of biological invasions.
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Population structure and genetic diversity in red clover (Trifolium pratense L.) germplasm. Sci Rep 2020; 10:8364. [PMID: 32433569 PMCID: PMC7239897 DOI: 10.1038/s41598-020-64989-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 04/22/2020] [Indexed: 01/29/2023] Open
Abstract
Red clover (Trifolium pratense L.) is a highly adaptable forage crop for temperate livestock agriculture. Genetic variation can be identified, via molecular techniques, and used to assess diversity among populations that may otherwise be indistinguishable. Here we have used genotyping by sequencing (GBS) to determine the genetic variation and population structure in red clover natural populations from Europe and Asia, and varieties or synthetic populations. Cluster analysis differentiated the collection into four large regional groups: Asia, Iberia, UK, and Central Europe. The five varieties clustered with the geographical area from which they were derived. Two methods (BayeScan and Samβada) were used to search for outlier loci indicating signatures of selection. A total of 60 loci were identified by both methods, but no specific genomic region was highlighted. The rate of decay in linkage disequilibrium was fast, and no significant evidence of any bottlenecks was found. Phenotypic analysis showed that a more prostrate and spreading growth habit was predominantly found among populations from Iberia and the UK. A genome wide association study identified a single nucleotide polymorphism (SNP) located in a homologue of the VEG2 gene from pea, associated with flowering time. The identification of genetic variation within the natural populations is likely to be useful for enhancing the breeding of red clover in the future.
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Hudson J, Johannesson K, McQuaid CD, Rius M. Secondary contacts and genetic admixture shape colonization by an amphiatlantic epibenthic invertebrate. Evol Appl 2020; 13:600-612. [PMID: 32431738 PMCID: PMC7045719 DOI: 10.1111/eva.12893] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 08/30/2019] [Accepted: 10/16/2019] [Indexed: 01/03/2023] Open
Abstract
Research on the genetics of invasive species often focuses on patterns of genetic diversity and population structure within the introduced range. However, a growing body of literature is demonstrating the need to study how native genotypes affect both ecological and evolutionary mechanisms within the introduced range. Here, we used genotyping-by-sequencing to study both native and introduced ranges of the amphiatlantic marine invertebrate Ciona intestinalis. A previous study using microsatellites analysed samples collected along the Swedish west coast and showed the presence of genetically distinct lineages in deep and shallow waters. Using 1,653 single nucleotide polymorphisms (SNPs) from newly collected samples (285 individuals), we first confirmed the presence of this depth-defined genomic divergence along the Swedish coast. We then used approximate Bayesian computation to infer the historical relationship among sites from the North Sea, the English Channel and the northwest Atlantic and found evidence of ancestral divergence between individuals from deep waters off Sweden and individuals from the English Channel. This divergence was followed by a secondary contact that led to a genetic admixture between the ancestral populations (i.e., deep Sweden and English Channel), which originated the genotypes found in shallow Sweden. We then revealed that the colonization of C. intestinalis in the northwest Atlantic was as a result of an admixture between shallow Sweden and the English Channel genotypes across the introduced range. Our results showed the presence of both past and recent genetic admixture events that together may have promoted the successful colonizations of C. intestinalis. Our study suggests that secondary contacts potentially reshape the evolutionary trajectories of invasive species through the promotion of intraspecific hybridization and by altering both colonization patterns and their ecological effects in the introduced range.
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Affiliation(s)
- Jamie Hudson
- School of Ocean and Earth ScienceNational Oceanography Centre SouthamptonUniversity of SouthamptonSouthamptonUK
| | - Kerstin Johannesson
- Department of Marine SciencesTjärnö Marine LaboratoryUniversity of GothenburgStrömstadSweden
| | - Christopher D. McQuaid
- Department of Zoology and EntomologyCoastal Research GroupRhodes UniversityGrahamstownSouth Africa
| | - Marc Rius
- School of Ocean and Earth ScienceNational Oceanography Centre SouthamptonUniversity of SouthamptonSouthamptonUK
- Department of ZoologyCentre for Ecological Genomics and Wildlife ConservationUniversity of JohannesburgAuckland ParkSouth Africa
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Ji SX, Wang XD, Shen XN, Liang L, Liu WX, Wan FH, Lü ZC. Using RNA Interference to Reveal the Function of Chromatin Remodeling Factor ISWI in Temperature Tolerance in Bemisia tabaci Middle East-Asia Minor 1 Cryptic Species. INSECTS 2020; 11:insects11020113. [PMID: 32050711 PMCID: PMC7074109 DOI: 10.3390/insects11020113] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 01/19/2020] [Accepted: 01/20/2020] [Indexed: 12/29/2022]
Abstract
Invasive species often encounter rapid environmental changes during invasions and only the individuals that successfully overcome environmental stresses can colonize and spread. Chromatin remodeling may be essential in environmental adaptation. To assess the functions of imitation switch (ISWI) in invasive Bemisia tabaci Middle East-Asia Minor 1 (MEAM1) cryptic species, we cloned and characterized the MEAM1 BtISWI gene and determined its functions in response to thermal stress. The full-length cDNA of BtISWI was 3712 bp, with a 3068 bp open reading frame (ORF) encoding a 118.86 kDa protein. BtISWI mRNA expression was significantly up-regulated after exposure to heat shock or cold shock conditions, indicating that BtISWI expression can be induced by thermal stress. After feeding double-stranded RNA (dsRNA), specifically for BtISWI, resistance to both heat and cold decreased significantly, suggesting that BtISWI may function directly in the thermal tolerance of MEAM1. Moreover, the preferred temperature of MEAM1 adults fed dsRNA was 1.9-3.5 °C higher than the control groups. Taken together, our findings highlight the importance of epigenetic gene regulation in the thermal response or thermal adaptation of invasive Bemisia tabaci (B. tabaci), and provide a new potential target for establishing sustainable control strategies for B. tabaci.
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Affiliation(s)
- Shun-Xia Ji
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (S.-X.J.); (X.-D.W.); (X.-N.S.); (L.L.); (W.-X.L.); (F.-H.W.)
| | - Xiao-Di Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (S.-X.J.); (X.-D.W.); (X.-N.S.); (L.L.); (W.-X.L.); (F.-H.W.)
| | - Xiao-Na Shen
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (S.-X.J.); (X.-D.W.); (X.-N.S.); (L.L.); (W.-X.L.); (F.-H.W.)
| | - Lin Liang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (S.-X.J.); (X.-D.W.); (X.-N.S.); (L.L.); (W.-X.L.); (F.-H.W.)
| | - Wan-Xue Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (S.-X.J.); (X.-D.W.); (X.-N.S.); (L.L.); (W.-X.L.); (F.-H.W.)
| | - Fang-Hao Wan
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (S.-X.J.); (X.-D.W.); (X.-N.S.); (L.L.); (W.-X.L.); (F.-H.W.)
- Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Zhi-Chuang Lü
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (S.-X.J.); (X.-D.W.); (X.-N.S.); (L.L.); (W.-X.L.); (F.-H.W.)
- Correspondence: ; Tel.: +86-10-8210-9572
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Wang J, Gaughan S, Lamer JT, Deng C, Hu W, Wachholtz M, Qin S, Nie H, Liao X, Ling Q, Li W, Zhu L, Bernatchez L, Wang C, Lu G. Resolving the genetic paradox of invasions: Preadapted genomes and postintroduction hybridization of bigheaded carps in the Mississippi River Basin. Evol Appl 2020; 13:263-277. [PMID: 31993075 PMCID: PMC6976960 DOI: 10.1111/eva.12863] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 06/07/2019] [Accepted: 07/15/2019] [Indexed: 12/23/2022] Open
Abstract
The genetic paradox of biological invasions is complex and multifaceted. In particular, the relative role of disparate propagule sources and genetic adaptation through postintroduction hybridization has remained largely unexplored. To add resolution to this paradox, we investigate the genetic architecture responsible for the invasion of two invasive Asian carp species, bighead carp (Hypophthalmichthys nobilis) and silver carp (H. molitrix) (bigheaded carps) that experience extensive hybridization in the Mississippi River Basin (MRB). We sequenced the genomes of bighead and silver carps (~1.08G bp and ~1.15G bp, respectively) and their hybrids collected from the MRB. We found moderate-to-high heterozygosity in bighead (0.0021) and silver (0.0036) carps, detected significantly higher dN/dS ratios of single-copy orthologous genes in bigheaded carps versus 10 other species of fish, and identified genes in both species potentially associated with environmental adaptation and other invasion-related traits. Additionally, we observed a high genomic similarity (96.3% in all syntenic blocks) between bighead and silver carps and over 90% embryonic viability in their experimentally induced hybrids. Our results suggest intrinsic genomic features of bigheaded carps, likely associated with life history traits that presumably evolved within their native ranges, might have facilitated their initial establishment of invasion, whereas ex-situ interspecific hybridization between the carps might have promoted their range expansion. This study reveals an alternative mechanism that could resolve one of the genetic paradoxes in biological invasions and provides invaluable genomic resources for applied research involving bigheaded carps.
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Affiliation(s)
- Jun Wang
- Department of BiologyUniversity of Nebraska at OmahaOmahaUSA
- Key Laboratory of Freshwater Fisheries Germplasm ResourcesMinistry of AgricultureNational Demonstration Center for Experimental Fisheries ScienceEducation/Shanghai Engineering Research Center of AquacultureShanghai Ocean UniversityShanghaiChina
| | - Sarah Gaughan
- Department of BiologyUniversity of Nebraska at OmahaOmahaUSA
| | - James T. Lamer
- Department of Biological SciencesWestern Illinois UniversityMacombILUSA
| | - Cao Deng
- DNA Stories Bioinformatics CenterChengduChina
| | - Wanting Hu
- College of Life of SciencesNanjing Normal UniversityNanjingChina
| | | | | | - Hu Nie
- DNA Stories Bioinformatics CenterChengduChina
| | - Xiaolin Liao
- Institute of HydroecologyMinistry of Water Resources & Chinese Academy of SciencesWuhanChina
| | - Qufei Ling
- Department of BiologyUniversity of Nebraska at OmahaOmahaUSA
- Aquaculture InstituteSchool of Biology and Basic Medical SciencesSoochow UniversitySuzhouChina
| | - Weitao Li
- Institute of HydroecologyMinistry of Water Resources & Chinese Academy of SciencesWuhanChina
| | - Lifeng Zhu
- College of Life of SciencesNanjing Normal UniversityNanjingChina
| | - Louis Bernatchez
- IBIS (Institut de Biologie Intégrative et des Systèmes)Université LavalQuébecQCCanada
| | - Chenghui Wang
- Key Laboratory of Freshwater Fisheries Germplasm ResourcesMinistry of AgricultureNational Demonstration Center for Experimental Fisheries ScienceEducation/Shanghai Engineering Research Center of AquacultureShanghai Ocean UniversityShanghaiChina
| | - Guoqing Lu
- Department of BiologyUniversity of Nebraska at OmahaOmahaUSA
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Brandão ML, Fernandes AMTDA, Gonçalves-de-Freitas E. Male and female cichlid fish show cognitive inhibitory control ability. Sci Rep 2019; 9:15795. [PMID: 31673023 PMCID: PMC6823373 DOI: 10.1038/s41598-019-52384-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 10/14/2019] [Indexed: 12/13/2022] Open
Abstract
Inhibitory control is a way to infer cognitive flexibility in animals by inhibiting a behavioral propensity to obtain a reward. Here we tested whether there are differences in inhibitory control between females and males of the fish Nile tilapia owing to their distinct reproductive roles. Individuals were tested under a detour-reaching paradigm, consisting of training fish to feed behind an opaque barrier and, thereafter, testing them with a transparent one. Fish is expected to avoid trying to cross through the transparent barrier to achieve food (reward), thus showing inhibitory control by recovering the learned detour with the opaque apparatus. Both males and females learned to detour the transparent barrier with similar scores of correct responses, whereas females reached the food faster. This result is probably associated to their different sex roles in reproduction: females care for the eggs and fry inside their mouth (thus requiring a high inhibitory control not to swallow them), whereas males have to stay inside the territory defending it against intruder males, which also demands some inhibitory ability not to leave the spawning site and take the risk of losing it. Furthermore, this evidence of cognitive flexibility can enable social fish to deal with unpredictable interactions.
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Affiliation(s)
- Manuela Lombardi Brandão
- Departamento de Zoologia e Botânica, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista (UNESP), Cristóvão Colombo, 2265, 15054-000, São José do Rio Preto, SP, Brazil
| | - Ana Marina Tabah de Almeida Fernandes
- Departamento de Zoologia e Botânica, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista (UNESP), Cristóvão Colombo, 2265, 15054-000, São José do Rio Preto, SP, Brazil
| | - Eliane Gonçalves-de-Freitas
- Departamento de Zoologia e Botânica, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista (UNESP), Cristóvão Colombo, 2265, 15054-000, São José do Rio Preto, SP, Brazil.
- Centro de Aquicultura da UNESP, São José do Rio Preto, SP, Brasil.
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Epigenetic patterns associated with an ascidian invasion: a comparison of closely related clades in their native and introduced ranges. Sci Rep 2019; 9:14275. [PMID: 31582771 PMCID: PMC6776620 DOI: 10.1038/s41598-019-49813-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Accepted: 08/29/2019] [Indexed: 12/12/2022] Open
Abstract
Environmentally induced epigenetic modifications have been proposed as one mechanism underlying rapid adaptive evolution of invasive species. Didemnum vexillum is an invasive colonial ascidian that has established in many coastal waters worldwide. Phylogenetic analyses have revealed that D. vexillum populations consist of two distinct clades; clade B appears to be restricted to the native range (Japan), whereas clade A is found in many regions throughout the world, including New Zealand. The spread of D. vexillum clade A suggests that it might be intrinsically more invasive than clade B, despite low levels of genetic diversity compared to populations from the native region. This study investigated whether D. vexillum clade A exhibits epigenetic signatures (specifically differences in DNA methylation) associated with invasiveness. Global DNA methylation patterns were significantly different between introduced clade A colonies, and both clades A and B in the native range. Introduced colonies also showed a significant reduction in DNA methylation levels, which could be a mechanism for increasing phenotypic plasticity. High levels of DNA methylation diversity were maintained in the introduced population, despite reduced levels of genetic diversity, which may allow invasive populations to respond quickly to changes in new environments. Epigenetic changes induced during the invasion process could provide a means for rapid adaptation despite low levels of genetic variation in introduced populations.
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14
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Birzu G, Matin S, Hallatschek O, Korolev KS. Genetic drift in range expansions is very sensitive to density dependence in dispersal and growth. Ecol Lett 2019; 22:1817-1827. [DOI: 10.1111/ele.13364] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 04/25/2019] [Accepted: 07/16/2019] [Indexed: 12/21/2022]
Affiliation(s)
- Gabriel Birzu
- Department of Physics Boston University Boston MA02215USA
| | - Sakib Matin
- Department of Physics Boston University Boston MA02215USA
| | - Oskar Hallatschek
- Departments of Physics and Integrative Biology University of California Berkeley CA94720USA
| | - Kirill S. Korolev
- Department of Physics and Graduate Program in Bioinformatics Boston University Boston MA02215USA
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15
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Banerjee AK, Guo W, Huang Y. Genetic and epigenetic regulation of phenotypic variation in invasive plants – linking research trends towards a unified framework. NEOBIOTA 2019. [DOI: 10.3897/neobiota.49.33723] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Phenotypic variation in the introduced range of an invasive species can be modified by genetic variation, environmental conditions and their interaction, as well as stochastic events like genetic drift. Recent studies found that epigenetic modifications may also contribute to phenotypic variation being independent of genetic changes. Despite gaining profound ecological insights from empirical studies, understanding the relative contributions of these molecular mechanisms behind phenotypic variation has received little attention for invasive plant species in particular.
This review therefore aimed at summarizing and synthesizing information on the genetic and epigenetic basis of phenotypic variation of alien invasive plants in the introduced range and their evolutionary consequences. Transgenerational inheritance of epigenetic modifications was highlighted focusing on its influence on microevolution of the invasive plant species. We presented a comprehensive account of epigenetic regulation of phenotypic variation and its role in plant invasion in the presence of reduced standing genetic variation, inbreeding depression and associated genomic events which have often been observed during introduction and range expansion of an invasive alien species. Finally, taking clues from the studies conducted so far, we proposed a unified framework of future experimental approaches to understand ecological and evolutionary aspects of phenotypic variation. This holistic approach, being aligned to the invasion process in particular (introduction-establishment-spread), was intended to understand the molecular mechanisms of phenotypic variation of an invasive species in its introduced range and to disentangle the effects of standing genetic variation and epigenetic regulation of phenotypic variation.
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16
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Mitotic Recombination and Rapid Genome Evolution in the Invasive Forest Pathogen Phytophthora ramorum. mBio 2019; 10:mBio.02452-18. [PMID: 30862749 PMCID: PMC6414701 DOI: 10.1128/mbio.02452-18] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Alien species are often successful invaders in new environments, despite the introduction of a few isolates with a reduced genetic pool. This is called the genetic paradox of invasion. We found two mechanisms by which the invasive forest pathogen causing sudden oak and sudden larch death can evolve. Extensive mitotic recombination producing runs of homozygosity generates genotypic diversity even in the absence of sexual reproduction, and rapid turnover of genes in the non-core, or nonessential portion of genome not shared by all isolates, allows pathogenicity genes to evolve rapidly or be eliminated while retaining essential genes. Mitotic recombination events occur in genomic hot spots, resulting in similar ROH patterns in different isolates or groups; one ROH, independently generated in two different groups, was enriched in pathogenicity genes and may be a target for selection. This provides important insights into the evolution of invasive alien pathogens and their potential for adaptation and future persistence. Invasive alien species often have reduced genetic diversity and must adapt to new environments. Given the success of many invasions, this is sometimes called the genetic paradox of invasion. Phytophthora ramorum is invasive, limited to asexual reproduction within four lineages, and presumed clonal. It is responsible for sudden oak death in the United States, sudden larch death in Europe, and ramorum blight in North America and Europe. We sequenced the genomes of 107 isolates to determine how this pathogen can overcome the invasion paradox. Mitotic recombination (MR) associated with transposons and low gene density has generated runs of homozygosity (ROH) affecting 2,698 genes, resulting in novel genotypic diversity within the lineages. One ROH enriched in effectors was fixed in the NA1 lineage. An independent ROH affected the same scaffold in the EU1 lineage, suggesting an MR hot spot and a selection target. Differences in host infection between EU1 isolates with and without the ROH suggest that they may differ in aggressiveness. Non-core regions (not shared by all lineages) had signatures of accelerated evolution and were enriched in putative pathogenicity genes and transposons. There was a striking pattern of gene loss, including all effectors, in the non-core EU2 genome. Positive selection was observed in 8.0% of RxLR and 18.8% of Crinkler effector genes compared with 0.9% of the core eukaryotic gene set. We conclude that the P. ramorum lineages are diverging via a rapidly evolving non-core genome and that the invasive asexual lineages are not clonal, but display genotypic diversity caused by MR.
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17
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Eyer PA, Matsuura K, Vargo EL, Kobayashi K, Yashiro T, Suehiro W, Himuro C, Yokoi T, Guénard B, Dunn RR, Tsuji K. Inbreeding tolerance as a pre-adapted trait for invasion success in the invasive ant Brachyponera chinensis. Mol Ecol 2018; 27:4711-4724. [PMID: 30368959 DOI: 10.1111/mec.14910] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 10/03/2018] [Accepted: 10/08/2018] [Indexed: 01/17/2023]
Abstract
Identifying traits that facilitate species introductions and successful invasions of ecosystems represents a key issue in ecology. Following their establishment into new environments, many non-native species exhibit phenotypic plasticity with post-introduction changes in behaviour, morphology or life history traits that allow them to overcome the presumed loss of genetic diversity resulting in inbreeding and reduced adaptive potential. Here, we present a unique strategy in the invasive ant Brachyponera chinensis (Emery), in which inbreeding tolerance is a pre-adapted trait for invasion success, allowing this ant to cope with genetic depletion following a genetic bottleneck. We report for the first time that inbreeding is not a consequence of the founder effect following introduction, but it is due to mating between sister queens and their brothers that pre-exists in native populations which may have helped it circumvent the cost of invasion. We show that a genetic bottleneck does not affect the genetic diversity or the level of heterozygosity within colonies and suggest that generations of sib-mating in native populations may have reduced inbreeding depression through purifying selection of deleterious alleles. This work highlights how a unique life history may pre-adapt some species for biological invasions.
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Affiliation(s)
- Pierre-André Eyer
- Department of Entomology, 2143 TAMU, Texas A&M University, College Station, Texas
| | - Kenji Matsuura
- Laboratory of Insect Ecology, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Edward L Vargo
- Department of Entomology, 2143 TAMU, Texas A&M University, College Station, Texas
| | - Kazuya Kobayashi
- Laboratory of Insect Ecology, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Toshihisa Yashiro
- Molecular Ecology, Evolution, and Phylogenetics (MEEP) laboratory School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia
| | - Wataru Suehiro
- Laboratory of Insect Ecology, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Chihiro Himuro
- Laboratory of Insect Ecology, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Tomoyuki Yokoi
- Laboratory of Conservation Ecology, University of Tsukuba, Tsukuba, Japan
| | - Benoit Guénard
- School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, Hong Kong
| | - Robert R Dunn
- Department of Applied Ecology, North Carolina State University, Raleigh, North Carolina.,German Centre for Integrative Biodiversity Research (iDiv), Leipzig, Germany.,Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, Copenhagen Ø, Denmark
| | - Kazuki Tsuji
- Faculty of Agriculture, University of the Ryukyus, Nishihara, Okinawa, Japan
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18
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Kilvitis HJ, Ardia DR, Thiam M, Martin LB. Corticosterone is correlated to mediators of neural plasticity and epigenetic potential in the hippocampus of Senegalese house sparrows (Passer domesticus). Gen Comp Endocrinol 2018; 269:177-183. [PMID: 30257180 DOI: 10.1016/j.ygcen.2018.09.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 09/19/2018] [Accepted: 09/21/2018] [Indexed: 10/28/2022]
Abstract
Our previous research on range-expanding house sparrows in Kenya revealed that (i) range-edge birds released more corticosterone (CORT) in response to a stressor than range-core birds, ii) that range-edge birds were more exploratory than range-core birds, and that (iii) all birds exhibited extensive variation in genome-wide DNA methylation among individuals, regardless of their position along the range expansion. Within the hippocampus, mediators of neural plasticity such as brain-derived neurotrophic factor (BDNF), can influence and be influenced by CORT, hippocampus-associated behaviors and regulatory epigenetic modification enzymes. Here, we investigated whether individuals and populations colonizing a new geographic range, Senegal, vary in the expression of BDNF and DNA methyltransferases (DNMTs) within the hippocampus and the release of CORT in response to a stressor. DNMT expression is an important mediator of epigenetic potential, the propensity of a genome to capacitate phenotypic variation via mechanisms such as DNA methylation. We surveyed three populations across Senegal, predicting that hippocampal BDNF and DNMT expression would be highest at the range-edge, and that BDNF and DNMT would be inversely related to one another, but would each positively covary with CORT within individuals. We found a nonlinear relationship between CORT and BDNF expression within individuals. Moreover, we found that CORT positively covaried with DNMT1 expression in a more recently established population, while the reverse was true in the oldest population (i.e. at the range-core). Our study is among the first to explore whether and how variation in CORT regulation contributes to variation in mediators of neural plasticity and epigenetic potential within the hippocampus of a range-expanding vertebrate.
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Affiliation(s)
- Holly J Kilvitis
- University of South Florida, Department of Integrative Biology, Tampa, FL, USA.
| | - Daniel R Ardia
- Franklin & Marshall College, Department of Biology, Lancaster, PA, USA
| | - Massamba Thiam
- Universite Cheikh Anta Diop, Department of Biology, Dakar, Senegal
| | - Lynn B Martin
- University of South Florida, Department of Global Health, Tampa, FL, USA
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19
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Hawes NA, Tremblay LA, Pochon X, Dunphy B, Fidler AE, Smith KF. Effects of temperature and salinity stress on DNA methylation in a highly invasive marine invertebrate, the colonial ascidian Didemnum vexillum. PeerJ 2018; 6:e5003. [PMID: 29967721 PMCID: PMC6022722 DOI: 10.7717/peerj.5003] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 05/29/2018] [Indexed: 12/27/2022] Open
Abstract
Environmentally induced epigenetic changes may contribute to phenotypic plasticity, increase adaptive potential in changing environments, and play a key role in the establishment and spread of invasive species in new habitats. In this study, we used methylation-sensitive amplified polymorphism (MSAP) to assess environmentally induced DNA methylation changes in a globally invasive clonal ascidian, Didemnum vexillum. We tested the effect of increasing temperature (19, 25 and 27 °C) and decreasing salinity (34, 32, 30, 28 and 26 practical salinity units (PSU)) on global DNA methylation, growth and survival rates. Exposure to 27 °C resulted in significant changes in DNA methylation over time. Growth also decreased in colonies exposed to high temperatures, suggesting they were under thermal stress. In contrast, no differences in growth nor DNA methylation patterns were observed in colonies exposed to a decreasing salinity gradient, potentially due to prior adaptation. The results of this study show that environmental stress can induce significant global DNA methylation changes in an invasive marine invertebrate on very rapid timescales, and that this response varies depending on the type, magnitude, and duration of the stressor. Changes in genomic DNA methylation and the rate of growth may act to ‘buy survival time’ under stressful conditions, expanding the distribution limits of this globally invasive species.
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Affiliation(s)
- Nicola A Hawes
- Institute of Marine Science, University of Auckland, Auckland, New Zealand.,Cawthron Institute, Nelson, New Zealand
| | - Louis A Tremblay
- Cawthron Institute, Nelson, New Zealand.,School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Xavier Pochon
- Institute of Marine Science, University of Auckland, Auckland, New Zealand.,Cawthron Institute, Nelson, New Zealand
| | - Brendon Dunphy
- Institute of Marine Science, University of Auckland, Auckland, New Zealand.,School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Andrew E Fidler
- Institute of Marine Science, University of Auckland, Auckland, New Zealand
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20
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Beal A, Rodriguez-Casariego J, Rivera-Casas C, Suarez-Ulloa V, Eirin-Lopez JM. Environmental Epigenomics and Its Applications in Marine Organisms. ACTA ACUST UNITED AC 2018. [DOI: 10.1007/13836_2018_28] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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21
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Hawes NA, Fidler AE, Tremblay LA, Pochon X, Dunphy BJ, Smith KF. Understanding the role of DNA methylation in successful biological invasions: a review. Biol Invasions 2018. [DOI: 10.1007/s10530-018-1703-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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22
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Kilvitis HJ, Hanson H, Schrey AW, Martin LB. Epigenetic Potential as a Mechanism of Phenotypic Plasticity in Vertebrate Range Expansions. Integr Comp Biol 2018; 57:385-395. [PMID: 28859411 DOI: 10.1093/icb/icx082] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
SYNOPSIS During range expansions, organisms are often exposed to multiple pressures, including novel enemies (i.e., predators, competitors and/or parasites) and unfamiliar or limited resources. Additionally, small propagule sizes at range edges can result in genetic founder effects and bottlenecks, which can affect phenotypic diversity and thus selection. Despite these obstacles, individuals in expanding populations often thrive at the periphery of a range, and this success may be mediated by phenotypic plasticity. Increasing evidence suggests that epigenetic mechanisms may underlie such plasticity because they allow for more rapid phenotypic responses to novel environments than are possible via the accumulation of genetic variation. Here, we review how molecular epigenetic mechanisms could facilitate plasticity in range-expanding organisms, emphasizing the roles of DNA methylation and other epigenetic marks in the physiological regulatory networks that drive whole-organism performance. We focus on the hypothalamic-pituitary-adrenal (HPA) axis, arguing that epigenetically-mediated plasticity in the regulation of glucocorticoids in particular might strongly impact range expansions. We hypothesize that novel environments release and/or select for epigenetic potential in HPA variation and hence organismal performance and ultimately fitness.
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Affiliation(s)
- Holly J Kilvitis
- Department of Integrative Biology, University of South Florida, Tampa, FL 33620, USA
| | - Haley Hanson
- Department of Integrative Biology, University of South Florida, Tampa, FL 33620, USA
| | - Aaron W Schrey
- Department of Biology, Armstrong State University, Savannah, GA 31419, USA
| | - Lynn B Martin
- Department of Integrative Biology, University of South Florida, Tampa, FL 33620, USA
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23
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Ma K, Sun L, Cheng T, Pan H, Wang J, Zhang Q. Epigenetic Variance, Performing Cooperative Structure with Genetics, Is Associated with Leaf Shape Traits in Widely Distributed Populations of Ornamental Tree Prunus mume. FRONTIERS IN PLANT SCIENCE 2018; 9:41. [PMID: 29441078 PMCID: PMC5797549 DOI: 10.3389/fpls.2018.00041] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 01/09/2018] [Indexed: 05/23/2023]
Abstract
Increasing evidence shows that epigenetics plays an important role in phenotypic variance. However, little is known about epigenetic variation in the important ornamental tree Prunus mume. We used amplified fragment length polymorphism (AFLP) and methylation-sensitive amplified polymorphism (MSAP) techniques, and association analysis and sequencing to investigate epigenetic variation and its relationships with genetic variance, environment factors, and traits. By performing leaf sampling, the relative total methylation level (29.80%) was detected in 96 accessions of P. mume. And the relative hemi-methylation level (15.77%) was higher than the relative full methylation level (14.03%). The epigenetic diversity (I∗ = 0.575, h∗ = 0.393) was higher than the genetic diversity (I = 0.484, h = 0.319). The cultivated population displayed greater epigenetic diversity than the wild populations in both southwest and southeast China. We found that epigenetic variance and genetic variance, and environmental factors performed cooperative structures, respectively. In particular, leaf length, width and area were positively correlated with relative full methylation level and total methylation level, indicating that the DNA methylation level played a role in trait variation. In total, 203 AFLP and 423 MSAP associated markers were detected and 68 of them were sequenced. Homologous analysis and functional prediction suggested that the candidate marker-linked genes were essential for leaf morphology development and metabolism, implying that these markers play critical roles in the establishment of leaf length, width, area, and ratio of length to width.
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Affiliation(s)
- Kaifeng Ma
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Lidan Sun
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Tangren Cheng
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Huitang Pan
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Jia Wang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Qixiang Zhang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, China
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
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24
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Bansal R, Michel A. Expansion of cytochrome P450 and cathepsin genes in the generalist herbivore brown marmorated stink bug. BMC Genomics 2018; 19:60. [PMID: 29347977 PMCID: PMC5774168 DOI: 10.1186/s12864-017-4281-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 11/03/2017] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND The brown marmorated stink bug (Halyomorpha halys) is an invasive pest in North America which causes severe economic losses on tree fruits, ornamentals, vegetables, and field crops. The H. halys is an extreme generalist and this feeding behaviour may have been a major contributor behind its establishment and successful adaptation in invasive habitats of North America. To develop an understanding into the mechanism of H. halys' generalist herbivory, here we specifically focused on genes putatively facilitating its adaptation on diverse host plants. RESULTS We generated over 142 million reads via sequencing eight RNA-Seq libraries, each representing an individual H. halys adult. The de novo assembly contained 79,855 high quality transcripts, totalling 39,600,178 bases. Following a comprehensive transcriptome analysis, H. halys had an expanded suite of cytochrome P450 and cathepsin-L genes compared to other insects. Detailed characterization of P450 genes from the CYP6 family, known for herbivore adaptation on host plants, strongly hinted towards H. halys-specific expansions involving gene duplications. In subsequent RT-PCR experiments, both P450 and cathepsin genes exhibited tissue-specific or distinct expression patterns which supported their principal roles of detoxification and/or digestion in a particular tissue. CONCLUSIONS Our analysis into P450 and cathepsin genes in H. halys offers new insights into potential mechanisms for understanding generalist herbivory and adaptation success in invasive habitats. Additionally, the large-scale transcriptomic resource developed here provides highly useful data for gene discovery; functional, population and comparative genomics as well as efforts to assemble and annotate the H. halys genome.
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Affiliation(s)
- Raman Bansal
- Department of Entomology, Ohio Agricultural Research and Development Center, The Ohio State University, 1680 Madison Avenue, Wooster, OH 44691 USA
| | - Andy Michel
- Department of Entomology, Ohio Agricultural Research and Development Center, The Ohio State University, 1680 Madison Avenue, Wooster, OH 44691 USA
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25
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King M, Sardella B. The effects of acclimation temperature, salinity, and behavior on the thermal tolerance of Mozambique tilapia (Oreochromis mossambicus). JOURNAL OF EXPERIMENTAL ZOOLOGY PART 2017; 327:417-422. [PMID: 29356426 DOI: 10.1002/jez.2113] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 09/03/2017] [Accepted: 09/11/2017] [Indexed: 12/30/2022]
Abstract
Mozambique tilapia have been shown to be incredibly stress tolerant with respect to environmental salinity, hypoxia, and ammonia concentrations. Temperature challenges to this species have shown that they have difficulty with cold acclimation. The purpose of this study was to measure the effects of acclimation temperature and salinity on the thermal tolerance of Mozambique tilapia as assessed by critical thermal maxima (CTMax) and critical thermal minima (CTMin). We also monitored fish behavior and quantified ventilation rate. To our knowledge, this study was the first to investigate upper and lower thermal tolerances, and the effect of environmental salinity in this physiologically impressive species. Using predictive regression analyses of the thermal limits, thermal tolerance polygons were constructed and total areas were calculated 678.9°C2 for freshwater (FW)-acclimated tilapia, and 739.4°C2 seawater (SW)-acclimated tilapia. During the thermal challenges, we observed two novel behaviors in response to thermal challenge, ventilation cessation behavior (VCB) and aquatic surface respiration (ASR), and we conclude that the use of these behaviors extended the thermal limits of these fish in both FW and two-thirds SW by limiting the exposure of the gill epithelium to the changing environment.
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Affiliation(s)
- Mallory King
- Department of Biological Sciences, California State University, Stanislaus, Turlock, California, USA
| | - Brian Sardella
- Department of Biological Sciences, California State University, Stanislaus, Turlock, California, USA
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26
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Dai TM, Lü ZC, Liu WX, Wan FH, Hong XY. The homology gene BtDnmt1 is Essential for Temperature Tolerance in Invasive Bemisia tabaci Mediterranean Cryptic Species. Sci Rep 2017; 7:3040. [PMID: 28596581 PMCID: PMC5465089 DOI: 10.1038/s41598-017-03373-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 04/27/2017] [Indexed: 02/07/2023] Open
Abstract
The Bemisia tabaci Mediterranean (MED) cryptic species has been rapidly invading most parts of the world owing to its strong ecological adaptability, particularly its strong resistance to temperature stress. Epigenetic mechanisms play important roles in mediating ecological plasticity. In particular, DNA methylation has been the focus of attempts to understand the mechanism of phenotypic plasticity. The relationship between temperature and DNA methylation and how it affects the adaptability of invasive insects remain unknown. To investigate the temperature resistance role of DNA methyltransferase 1 (Dnmt1) in MED, we cloned and sequenced BtDnmt1 homology and identified its functions under various temperature conditions. The full-length cDNA of MED BtDnmt1 homology was 5,958 bp and has a 4,287 bp open reading frame that encodes a 1,428-amino-acid protein. BtDnmt1 mRNA expression levels were significantly down-regulated after feeding with dsRNA. Furthermore, after feeding with dsBtDnmt1, the MED adults exhibited significantly higher mortality under temperature stress conditions than the controls, suggesting that MED BtDnmt1 homology plays an essential role in the temperature tolerance capacity of MED. Our data improve our understanding of the temperature resistance and temperature adaptability mechanisms that have allowed the successful invasion and colonization of various environments by this alien species.
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Affiliation(s)
- Tian-Mei Dai
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, 100193, Beijing, 100193, P.R. China
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, P.R. China
| | - Zhi-Chuang Lü
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, 100193, Beijing, 100193, P.R. China
| | - Wan-Xue Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, 100193, Beijing, 100193, P.R. China
| | - Fang-Hao Wan
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, 100193, Beijing, 100193, P.R. China.
- Center for Management of Invasive Alien Species, Ministry of Agriculture, Beijing, 100193, China.
| | - Xiao-Yue Hong
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, P.R. China
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27
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Epigenetic signatures of invasive status in populations of marine invertebrates. Sci Rep 2017; 7:42193. [PMID: 28205577 PMCID: PMC5311950 DOI: 10.1038/srep42193] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 01/06/2017] [Indexed: 12/27/2022] Open
Abstract
Epigenetics, as a DNA signature that affects gene expression and enables rapid reaction of an organism to environmental changes, is likely involved in the process of biological invasions. DNA methylation is an epigenetic mechanism common to plants and animals for regulating gene expression. In this study we show, for the first time in any marine species, significant reduction of global methylation levels during the expansive phase of a pygmy mussel (Xenostrobus securis) recent invasion in Europe (two-year old), while in older introductions such epigenetic signature of invasion was progressively reduced. Decreased methylation was interpreted as a rapid way of increasing phenotypic plasticity that would help invasive populations to thrive. This epigenetic signature of early invasion was stronger than the expected environmental signature of environmental stress in younger populations sampled from ports, otherwise detected in a much older population (>90 year old) of the also invasive tubeworm Ficopomatus enigmaticus established in similar locations. Higher epigenetic than genetic diversity found in X. securis was confirmed from F. enigmaticus samples. As reported for introduced plants and vertebrates, epigenetic variation could compensate for relatively lower genetic variation caused by founder effects. These phenomena were compared with epigenetic mechanisms involved in metastasis, as parallel processes of community (biological invasion) and organism (cancer) invasions.
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Deep Sequencing Reveals Highly Variable Gut Microbial Composition of Invasive Fish Mossambicus Tilapia ( Oreochromis mossambicus) Collected from Two Different Habitats. Indian J Microbiol 2017; 57:235-240. [PMID: 28611502 DOI: 10.1007/s12088-017-0641-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Accepted: 01/23/2017] [Indexed: 10/20/2022] Open
Abstract
Tilapia (Oreochromis mossambicus) is one of the most invasive fish found throughout the World and emerged as a major threat to the indigenous fishes in many countries. Investigating the gut microbial diversity of such fishes is one of the ways to understand its physiology. In the present study, we have explored the gut microbial community structure of tilapia using 16S rRNA gene sequencing on the Illumina Miseq platform. Our study showed significant differences in tilapia gut microbiota collected from different habitats (i.e. river and lakes) suggesting the influence of habitat on the gut microbial diversity of tilapia. This study gives a first insight into the mossambicus tilapia gut microbiota and provides a reference for future studies.
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Marathe NP, Gaikwad SS, Vaishampayan AA, Rasane MH, Shouche YS, Gade WN. Mossambicus tilapia (Oreochromis mossambicus) collected from water bodies impacted by urban waste carries extended-spectrum beta-lactamases and integron-bearing gut bacteria. J Biosci 2016; 41:341-6. [DOI: 10.1007/s12038-016-9620-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Schrieber K, Lachmuth S. The Genetic Paradox of Invasions revisited: the potential role of inbreeding × environment interactions in invasion success. Biol Rev Camb Philos Soc 2016; 92:939-952. [DOI: 10.1111/brv.12263] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 02/12/2016] [Accepted: 02/18/2016] [Indexed: 12/17/2022]
Affiliation(s)
- Karin Schrieber
- Geobotany and Botanical Garden, Institute of Biology; Martin Luther University of Halle; 06108 Halle (Saale) Germany
| | - Susanne Lachmuth
- Geobotany and Botanical Garden, Institute of Biology; Martin Luther University of Halle; 06108 Halle (Saale) Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig; 04103 Leipzig Germany
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Ahmed MZ, Ma J, Qiu BL, He RR, Wu MT, Liang F, Zhao JP, Lin L, Hu XN, Lv LH, Breinholt JW, Lu YY. Genetic Record for a Recent Invasion of Phenacoccus solenopsis (Hemiptera: Pseudococcidae) in Asia. ENVIRONMENTAL ENTOMOLOGY 2015; 44:907-918. [PMID: 26313998 DOI: 10.1093/ee/nvv034] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Accepted: 02/26/2015] [Indexed: 06/04/2023]
Abstract
The cotton mealybug Phenacoccus solenopsis Tinsley is an emerging invasive insect pest. Since its first report as a pest in the United States in 1991, it has invaded and colonized more than 23 countries over the past century. It was first recorded from Pakistan in 2006 and from China in 2008. In this study, we performed field surveys from 2010 to 2012 and obtained mtCOI sequences from specimens across China and Pakistan, then compared them with already available mtCOI sequences from additional Asian and North American countries. Our genetic analysis provides evidence that P. solenopsis should be classified into two groups, one of which is found only in the United States, and the other found only in Asia. The Asian group contains nine unique haplotypes, two of which have invaded and spread across China, Pakistan, India, and Vietnam over the last 4-6 yr. Our genetic analysis also indicates that P. solenopsis has a close relationship with the parasitoid wasp Aenasius bambawalei Hayat, providing preliminary evidence of a congruent spread of this mealybug and its parasitoids across China.
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Affiliation(s)
- Muhammad Z Ahmed
- Plant Quarantine Laboratory, Guangdong Inspection and Quarantine Technology Center, No. 66 Huacheng Ave., Guangzhou 510623, People's Republic of China Department of Entomology, South China Agricultural University, Guangzhou 510640, China Tropical Research and Education Center, University of Florida, 18905 SW 280th St., Homestead, FL 33031, USA *These two authors contributed equally to this work.
| | - Jun Ma
- Plant Quarantine Laboratory, Guangdong Inspection and Quarantine Technology Center, No. 66 Huacheng Ave., Guangzhou 510623, People's Republic of China *These two authors contributed equally to this work.
| | - Bao-Li Qiu
- Department of Entomology, South China Agricultural University, Guangzhou 510640, China
| | - Ri-Rong He
- Plant Quarantine Laboratory, Guangdong Inspection and Quarantine Technology Center, No. 66 Huacheng Ave., Guangzhou 510623, People's Republic of China
| | - Mu-Tao Wu
- Plant Quarantine Laboratory, Guangdong Inspection and Quarantine Technology Center, No. 66 Huacheng Ave., Guangzhou 510623, People's Republic of China
| | - Fan Liang
- Plant Quarantine Laboratory, Guangdong Inspection and Quarantine Technology Center, No. 66 Huacheng Ave., Guangzhou 510623, People's Republic of China
| | - Ju-Peng Zhao
- Plant Quarantine Laboratory, Guangdong Inspection and Quarantine Technology Center, No. 66 Huacheng Ave., Guangzhou 510623, People's Republic of China
| | - Li Lin
- Plant Quarantine Laboratory, Guangdong Inspection and Quarantine Technology Center, No. 66 Huacheng Ave., Guangzhou 510623, People's Republic of China
| | - Xue-Nan Hu
- Plant Quarantine Laboratory, Guangdong Inspection and Quarantine Technology Center, No. 66 Huacheng Ave., Guangzhou 510623, People's Republic of China
| | - Li-Hua Lv
- Institute of plant protection, Guangdong Academy of Agricultural Sciences, 510640 Guangzhou, China
| | - Jesse W Breinholt
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Yong-Yue Lu
- Department of Entomology, South China Agricultural University, Guangzhou 510640, China
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Successful Establishment of a Non-Native Species after an Apparent Single Introduction Event: Investigating ND4 Variability in Introduced Black Spiny-Tailed Iguanas ( Ctenosaura similis) in Southwestern Florida. J HERPETOL 2015. [DOI: 10.1670/13-060] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Rollins LA, Richardson MF, Shine R. A genetic perspective on rapid evolution in cane toads (Rhinella marina). Mol Ecol 2015; 24:2264-76. [PMID: 25894012 DOI: 10.1111/mec.13184] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Revised: 03/24/2015] [Accepted: 03/25/2015] [Indexed: 12/12/2022]
Abstract
The process of biological invasion exposes a species to novel pressures, in terms of both the environments it encounters and the evolutionary consequences of range expansion. Several invaders have been shown to exhibit rapid evolutionary changes in response to those pressures, thus providing robust opportunities to clarify the processes at work during rapid phenotypic transitions. The accelerating pace of invasion of cane toads (Rhinella marina) in tropical Australia during its 80-year history has been well characterized at the phenotypic level, including common-garden experiments that demonstrate heritability of several dispersal-relevant traits. Individuals from the invasion front (and their progeny) show distinctive changes in morphology, physiology and behaviour that, in combination, result in far more rapid dispersal than is true of conspecifics from long-colonized areas. The extensive body of work on cane toad ecology enables us to place into context studies of the genetic basis of these traits. Our analyses of differential gene expression from toads from both ends of this invasion-history transect reveal substantial upregulation of many genes, notably those involved in metabolism and cellular repair. Clearly, then, the dramatically rapid phenotypic evolution of cane toads in Australia has been accompanied by substantial shifts in gene expression, suggesting that this system is well suited to investigating the genetic underpinnings of invasiveness.
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Affiliation(s)
- Lee A Rollins
- Centre for Integrative Ecology, School of Life & Environmental Sciences, Deakin University, Pigdons Road, Geelong, Vic., 3217, Australia
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Mihalca AD. Ticks imported to Europe with exotic reptiles. Vet Parasitol 2015; 213:67-71. [PMID: 25913453 DOI: 10.1016/j.vetpar.2015.03.024] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Revised: 03/10/2015] [Accepted: 03/25/2015] [Indexed: 10/23/2022]
Abstract
It is known that traded exotic animals carry with them an immense number of associated symbionts, including parasites. Reptiles are no exception. Most of the imported reptiles originate from tropical countries and their possibility to carry potentially dangerous pathogens is high. According to CITES, Europe is currently the main reptile importer in the world. Despite this, there is no review or analysis available for the risk related to the importation of tick-borne diseases with traded reptile to the EU. The main aim of the manuscript is to provide a review on the available literature on ticks introduced to and exchanged between European countries via the live reptile trade. So far, the published reports of ticks imported on reptiles are limited to few European countries: Italy, Poland, Spain, Netherlands, Belgium, Slovenia and UK. The following species have been reported: Hyalomma aegyptium, Amblyomma dissimile, Amblyomma exornatum, Amblyomma flavomaculatum, Amblyomma fuscolineatum, Amblyomma latum, Amblyomma quadricavum, Amblyomma marmoreum, Amblyomma nuttalli, Amblyomma sparsum, Amblyomma sphenodonti, Amblyomma transversale and Amblyomma varanense. The majority of species are of African origin, followed by American and Asian species. All groups of reptiles (chelonians, snakes, lizards, crocodiles, tuataras) were involved. However, it seems that certain groups (i.e. tortoises of genus Testudo, monitor lizards of genus Varanus, snakes of genus Python) are more important as host for imported ticks, but this may be related to higher levels of international trade. Even fewer are the reports of tick-borne pathogens associated with imported reptile ticks. Despite the diversity of tick species reported on imported reptiles, the situations of truly invasive species are atypical and are limited in natural environments to maximum two cases where H. aegyptium was involved. Otherwise, the risk associated with reptile trade for introduction of invasive tick to Europe is low. Nevertheless, veterinary control is still to be reinforced for collecting more data.
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Affiliation(s)
- Andrei Daniel Mihalca
- University of Agricultural Sciences and Veterinary Medicine Cluj-Napoca, Calea Mănăştur 3-5, Cluj-Napoca 400372, Romania.
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Chown SL, Hodgins KA, Griffin PC, Oakeshott JG, Byrne M, Hoffmann AA. Biological invasions, climate change and genomics. Evol Appl 2015; 8:23-46. [PMID: 25667601 PMCID: PMC4310580 DOI: 10.1111/eva.12234] [Citation(s) in RCA: 126] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Accepted: 10/24/2014] [Indexed: 12/13/2022] Open
Abstract
The rate of biological invasions is expected to increase as the effects of climate change on biological communities become widespread. Climate change enhances habitat disturbance which facilitates the establishment of invasive species, which in turn provides opportunities for hybridization and introgression. These effects influence local biodiversity that can be tracked through genetic and genomic approaches. Metabarcoding and metagenomic approaches provide a way of monitoring some types of communities under climate change for the appearance of invasives. Introgression and hybridization can be followed by the analysis of entire genomes so that rapidly changing areas of the genome are identified and instances of genetic pollution monitored. Genomic markers enable accurate tracking of invasive species' geographic origin well beyond what was previously possible. New genomic tools are promoting fresh insights into classic questions about invading organisms under climate change, such as the role of genetic variation, local adaptation and climate pre-adaptation in successful invasions. These tools are providing managers with often more effective means to identify potential threats, improve surveillance and assess impacts on communities. We provide a framework for the application of genomic techniques within a management context and also indicate some important limitations in what can be achieved.
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Affiliation(s)
- Steven L Chown
- School of Biological Sciences, Monash UniversityClayton, Vic., Australia
| | - Kathryn A Hodgins
- School of Biological Sciences, Monash UniversityClayton, Vic., Australia
| | - Philippa C Griffin
- Department of Genetics, Bio21 Institute, The University of MelbourneParkville, Vic., Australia
| | - John G Oakeshott
- CSIRO Land and Water Flagship, Black Mountain LaboratoriesCanberra, ACT, Australia
| | - Margaret Byrne
- Science and Conservation Division, Department of Parks and Wildlife, Bentley Delivery CentreBentley, WA, Australia
| | - Ary A Hoffmann
- Departments of Zoology and Genetics, Bio21 Institute, The University of MelbourneParkville, Vic., Australia
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Caron V, Ede FJ, Sunnucks P. Unravelling the paradox of loss of genetic variation during invasion: superclones may explain the success of a clonal invader. PLoS One 2014; 9:e97744. [PMID: 24914550 PMCID: PMC4051638 DOI: 10.1371/journal.pone.0097744] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Accepted: 04/24/2014] [Indexed: 11/20/2022] Open
Abstract
Clonality is a common characteristic of successful invasive species, but general principles underpinning the success of clonal invaders are not established. A number of mechanisms could contribute to invasion success including clones with broad tolerances and preferences, specialist clones and adaptation in situ. The majority of studies to date have been of plants and some invertebrate parthenogens, particularly aphids, and have not necessarily caught invasion at very early stages. Here we describe the early stages of an invasion by a Northern Hemisphere Hymenopteran model in three different land masses in the Southern Hemisphere. Nematus oligospilus Förster (Hymenoptera: Tenthredinidae), a sawfly feeding on willows (Salix spp.), was recently introduced to the Southern Hemisphere where it has become invasive and is strictly parthenogenetic. In this study, the number of N. oligospilus clones, their distribution in the landscape and on different willow hosts in South Africa, New Zealand and Australia were assessed using 25 microsatellite markers. Evidence is presented for the presence of two very common and widespread multilocus genotypes (MLGs) or 'superclones' dominating in the three countries. Rarer MLGs were closely related to the most widespread superclone; it is plausible that all N. oligospilus individuals were derived from a single clone. A few initial introductions to Australia and New Zealand seemed to have occurred. Our results point towards a separate introduction in Western Australia, potentially from South Africa. Rarer clones that were dominant locally putatively arose in situ, and might be locally favoured, or simply have not yet had time to spread. Data presented represent rare baseline data early in the invasion process for insights into the mechanisms that underlie the success of a global invader, and develop Nematus oligospilus as a valuable model to understand invasion genetics of clonal pests.
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Affiliation(s)
- Valerie Caron
- School of Biological Sciences, Monash University, Clayton, Victoria, Australia
| | - Fiona J. Ede
- Biosciences Research Division, Department of Environment and Primary Industries, Bundoora, Victoria, Australia
| | - Paul Sunnucks
- School of Biological Sciences, Monash University, Clayton, Victoria, Australia
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Invasion genetics of Chromolaena odorata (Asteraceae): extremely low diversity across Asia. Biol Invasions 2014. [DOI: 10.1007/s10530-014-0669-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Kilvitis HJ, Alvarez M, Foust CM, Schrey AW, Robertson M, Richards CL. Ecological epigenetics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 781:191-210. [PMID: 24277301 DOI: 10.1007/978-94-007-7347-9_10] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Biologists have assumed that heritable variation due to DNA sequence differences (i.e., genetic variation) allows populations of organisms to be both robust and adaptable to extreme environmental conditions. Natural selection acts on the variation among different genotypes and ultimately changes the genetic composition of the population. While there is compelling evidence about the importance of genetic polymorphisms, evidence is accumulating that epigenetic mechanisms (e.g., chromatin modifications, DNA methylation) can affect ecologically important traits, even in the absence of genetic variation. In this chapter, we review this evidence and discuss the consequences of epigenetic variation in natural populations. We begin by defining the term epigenetics, providing a brief overview of various epigenetic mechanisms, and noting the potential importance of epigenetics in the study of ecology. We continue with a review of the ecological epigenetics literature to demonstrate what is currently known about the amount and distribution of epigenetic variation in natural populations. Then, we consider the various ecological contexts in which epigenetics has proven particularly insightful and discuss the potential evolutionary consequences of epigenetic variation. Finally, we conclude with suggestions for future directions of ecological epigenetics research.
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Affiliation(s)
- Holly J Kilvitis
- Department of Integrative Biology, University of South Florida, 4202 E Fowler Ave, Tampa, FL, 33620, USA,
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Hu ZM, Juan LB. Adaptation mechanisms and ecological consequences of seaweed invasions: a review case of agarophyte Gracilaria vermiculophylla. Biol Invasions 2013. [DOI: 10.1007/s10530-013-0558-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Liebl AL, Schrey AW, Richards CL, Martin LB. Patterns of DNA methylation throughout a range expansion of an introduced songbird. Integr Comp Biol 2013; 53:351-8. [PMID: 23535948 DOI: 10.1093/icb/ict007] [Citation(s) in RCA: 92] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The spread of invasive species presents a genetic paradox: how do individuals overcome the genetic barriers associated with introductions (e.g., bottlenecks and founder effects) to become adapted to the new environment? In addition to genetic diversity, epigenetic variation also contributes to phenotypic variation and could influence the spread of an introduced species in novel environments. This may occur through two different (non-mutually exclusive) mechanisms. Individuals may benefit from existing (and heritable) epigenetic diversity or de novo epigenetic marks may increase in response to the new environment; both mechanisms might increase flexibility in new environments. Although epigenetic changes in invasive plants have been described, no data yet exist on the epigenetic changes throughout a range expansion of a vertebrate. Here, we used methylation sensitive-amplified fragment length polymorphism to explore genome-wide patterns of methylation in an expanding population of house sparrows (Passer domesticus). House sparrows were introduced to Kenya in the 1950s and have significant phenotypic variation dependent on the time since colonization. We found that Kenyan house sparrows had high levels of variation in methylation across the genome. Interestingly, there was a significant, potentially compensatory relationship between epigenetic and genetic diversity: epigenetic diversity was negatively correlated with genetic diversity and positively correlated with inbreeding across the range expansion. Thus, methylation may increase phenotypic variation and/or plasticity in response to new environments and therefore be an important source of inter-individual variation for adaptation in these environments, particularly over the short timescales over which invasions occur.
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Affiliation(s)
- Andrea L Liebl
- Department of Integrative Biology, University of South Florida, Tampa, FL 33620, USA.
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Voss N, Eckstein RL, Durka W. Range expansion of a selfing polyploid plant despite widespread genetic uniformity. ANNALS OF BOTANY 2012; 110:585-593. [PMID: 22730022 PMCID: PMC3400446 DOI: 10.1093/aob/mcs117] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2012] [Accepted: 04/04/2012] [Indexed: 05/29/2023]
Abstract
BACKGROUND AND AIMS Ongoing and previous range expansions have a strong influence on population genetic structure of plants. In turn, genetic variation in the new range may affect the population dynamics and the expansion process. The annual Ceratocapnos claviculata (Papaveraceae) has expanded its Atlantic European range in recent decades towards the north and east. Patterns of genetic diversity were investigated across the native range to assess current population structure and phylogeographical patterns. A test was then made as to whether genetic diversity is reduced in the neophytic range and an attempt was made to identify source regions of the expansion. METHODS Samples were taken from 55 populations in the native and 34 populations in the neophytic range (Sweden, north-east Germany). Using amplified fragment length polymorphism markers an analysis was made of genetic variation and population structure (Bayesian statistical modelling) and population differentiation was quantified. Pollen/ovule ratio was analysed as a proxy for the breeding system. KEY RESULTS Genetic diversity at population level was very low (mean H(e) = 0·004) and two multilocus genotypes dominated large parts of the new range. Population differentiation was strong (F(ST) = 0·812). These results and a low pollen/ovule ratio are consistent with an autogamous breeding system. Genetic variation decreased from the native to the neophytic range. Within the native range, H(e) decreased towards the north-east, whereas population size increased. According to the Bayesian cluster analysis, the putative source regions of the neophytic range are situated in north-west Germany and adjacent regions. CONCLUSIONS Ceratocapnos claviculata shows a cline of genetic variation due to postglacial recolonization from putative Pleistocene refugia in south-west Europe. Nevertheless, the species has expanded successfully during the past 40 years to southern Sweden and north-east Germany where it occurs as an opportunistic neophyte. Recent expansion was mainly human-mediated by single long-distance diaspore transport and was facilitated by habitat modification.
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Affiliation(s)
- Nicole Voss
- Institute of Landscape Ecology and Resource Management, Research Centre for BioSystems, Land Use and Nutrition (IFZ), Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32, D-35392 Giessen, Germany.
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The role of epigenetics in evolution: the extended synthesis. GENETICS RESEARCH INTERNATIONAL 2012; 2012:286164. [PMID: 22567381 PMCID: PMC3335599 DOI: 10.1155/2012/286164] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/15/2011] [Accepted: 12/15/2011] [Indexed: 01/25/2023]
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Stefani F, Aquaro G, Azzurro E, Colorni A, Galli P. Patterns of genetic variation of a Lessepsian parasite. Biol Invasions 2012. [DOI: 10.1007/s10530-012-0183-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Epigenetic Variation May Compensate for Decreased Genetic Variation with Introductions: A Case Study Using House Sparrows (Passer domesticus) on Two Continents. GENETICS RESEARCH INTERNATIONAL 2012; 2012:979751. [PMID: 22567407 PMCID: PMC3335630 DOI: 10.1155/2012/979751] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2011] [Revised: 11/04/2011] [Accepted: 11/05/2011] [Indexed: 01/18/2023]
Abstract
Epigenetic mechanisms impact several phenotypic traits and may be important for ecology and evolution. The introduced house sparrow (Passer domesticus) exhibits extensive phenotypic variation among and within populations. We screened methylation in populations from Kenya and Florida to determine if methylation varied among populations, varied with introduction history (Kenyan invasion <50 years old, Florida invasion ~150 years old), and could potentially compensate for decrease genetic variation with introductions. While recent literature has speculated on the importance of epigenetic effects for biological invasions, this is the first such study among wild vertebrates. Methylation was more frequent in Nairobi, and outlier loci suggest that populations may be differentiated. Methylation diversity was similar between populations, in spite of known lower genetic diversity in Nairobi, which suggests that epigenetic variation may compensate for decreased genetic diversity as a source of phenotypic variation during introduction. Our results suggest that methylation differences may be common among house sparrows, but research is needed to discern whether methylation impacts phenotypic variation.
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FIRMAT CYRIL, SCHLIEWEN ULRICHK, LOSSEAU MICHÈLE, ALIBERT PAUL. Body shape differentiation at global and local geographic scales in the invasive cichlid Oreochromis mossambicus. Biol J Linn Soc Lond 2012. [DOI: 10.1111/j.1095-8312.2011.01802.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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46
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Patterns of spatial genetic structure and diversity at the onset of a rapid range expansion: colonisation of the UK by the small red-eyed damselfly Erythromma viridulum. Biol Invasions 2010. [DOI: 10.1007/s10530-010-9779-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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47
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The non-pest Australasian fungivore Cis bilamellatus Wood (Coleoptera: Ciidae) in northern Europe: spread dynamics, invasion success and ecological impact. Biol Invasions 2010. [DOI: 10.1007/s10530-009-9455-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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48
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Stürzenbaum SR, Andre J, Kille P, Morgan AJ. Earthworm genomes, genes and proteins: the (re)discovery of Darwin's worms. Proc Biol Sci 2009; 276:789-97. [PMID: 19129111 PMCID: PMC2664377 DOI: 10.1098/rspb.2008.1510] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Small incremental biological change, winnowed by natural selection over geological time scales to produce large consequences, was Darwin's singular insight that revolutionized the life sciences. His publications after 1859, including the ‘earthworm book’, were all written to amplify and support the evolutionary theory presented in the Origin. Darwin was unable to provide a physical basis for the inheritance of favoured traits because of the absence of genetic knowledge that much later led to the ‘modern synthesis’. Mistaken though he was in advocating systemic ‘gemmules’ as agents of inheritance, Darwin was perceptive in seeking to underpin his core vision with concrete factors that both determine the nature of a trait in one generation and convey it to subsequent generations. This brief review evaluates the molecular genetic literature on earthworms published during the last decade, and casts light on the specific aspects of earthworm evolutionary biology that more or less engaged Darwin: (i) biogeography, (ii) species diversity, (iii) local adaptations and (iv) sensitivity. We predict that the current understanding will deepen with the announcement of a draft earthworm genome in Darwin's bicentenary year, 2009. Subsequently, the earthworm may be elevated from the status of a soil sentinel to that elusive entity, an ecologically relevant genetic model organism.
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Affiliation(s)
- S R Stürzenbaum
- School of Biomedical & Health Sciences, King's College London, London SE1 9NH, UK.
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Justé A, Lievens B, Frans I, Marsh TL, Klingeberg M, Michiels CW, Willems KA. Genetic and physiological diversity of Tetragenococcus halophilus strains isolated from sugar- and salt-rich environments. Microbiology (Reading) 2008; 154:2600-2610. [DOI: 10.1099/mic.0.2008/018168-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Annelies Justé
- Research Group Process Microbial Ecology and Management and Leuven Food Science and Nutrition Research Centre (LFoRCe), Department Microbial and Molecular Systems, Katholieke Universiteit Leuven Association, De Nayer Institute, B-2860 Sint-Katelijne-Waver, Belgium
- Research Group Microbial Ecology and Biorational Control, Scientia Terrae Research Institute, B-2860 Sint-Katelijne-Waver, Belgium
- Laboratory of Food Microbiology and Leuven Food Science and Nutrition Research Centre (LFoRCe), Department Microbial and Molecular Systems, Katholieke Universiteit Leuven, B-3001 Leuven, Belgium
| | - Bart Lievens
- Research Group Process Microbial Ecology and Management and Leuven Food Science and Nutrition Research Centre (LFoRCe), Department Microbial and Molecular Systems, Katholieke Universiteit Leuven Association, De Nayer Institute, B-2860 Sint-Katelijne-Waver, Belgium
- Research Group Microbial Ecology and Biorational Control, Scientia Terrae Research Institute, B-2860 Sint-Katelijne-Waver, Belgium
| | - Ingeborg Frans
- Research Group Process Microbial Ecology and Management and Leuven Food Science and Nutrition Research Centre (LFoRCe), Department Microbial and Molecular Systems, Katholieke Universiteit Leuven Association, De Nayer Institute, B-2860 Sint-Katelijne-Waver, Belgium
- Research Group Microbial Ecology and Biorational Control, Scientia Terrae Research Institute, B-2860 Sint-Katelijne-Waver, Belgium
| | - Terence L. Marsh
- Center for Microbial Ecology, Michigan State University, East Lansing, Michigan 48824, USA
| | - Michael Klingeberg
- Department of Biotechnology, Südzucker AG, Mannheim/Ochsenfurt, ZAFES, Obrigheim/Pfalz, Germany
| | - Chris W. Michiels
- Laboratory of Food Microbiology and Leuven Food Science and Nutrition Research Centre (LFoRCe), Department Microbial and Molecular Systems, Katholieke Universiteit Leuven, B-3001 Leuven, Belgium
| | - Kris A. Willems
- Research Group Process Microbial Ecology and Management and Leuven Food Science and Nutrition Research Centre (LFoRCe), Department Microbial and Molecular Systems, Katholieke Universiteit Leuven Association, De Nayer Institute, B-2860 Sint-Katelijne-Waver, Belgium
- Research Group Microbial Ecology and Biorational Control, Scientia Terrae Research Institute, B-2860 Sint-Katelijne-Waver, Belgium
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Vizzini A, Zotti M, Mello A. Alien fungal species distribution: the study case of Favolaschia calocera. Biol Invasions 2008. [DOI: 10.1007/s10530-008-9259-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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