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Chang J, Nakamura K, Chao C, Luo M, Liao P. Ghost introgression facilitates genomic divergence of a sympatric cryptic lineage in Cycas revoluta. Ecol Evol 2023; 13:e10435. [PMID: 37600490 PMCID: PMC10439367 DOI: 10.1002/ece3.10435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 08/01/2023] [Accepted: 08/07/2023] [Indexed: 08/22/2023] Open
Abstract
A cryptic lineage is a genetically diverged but morphologically unrecognized variant of a known species. Clarifying cryptic lineage evolution is essential for quantifying species diversity. In sympatric cryptic lineage divergence compared with allopatric divergence, the forces of divergent selection and mating patterns override geographical isolation. Introgression, by supplying preadapted or neutral standing genetic variations, can promote sympatric cryptic lineage divergence via selection. However, most studies concentrated on extant species introgression, ignoring the genetic legacy of introgression from extinct or unsampled lineages ("ghost introgression"). Cycads are an ideal plant for studying the influence of ghost introgression because of their common interspecific gene flow and past high extinction rate. Here, we utilized reference-based ddRADseq to clarify the role of ghost introgression in the evolution of a previously identified sympatric cryptic lineage in Cycas revoluta. After re-evaluating the evolutionary independency of cryptic lineages, the group-wise diverged single-nucleotide polymorphisms among sympatric and allopatric lineages were compared and functionally annotated. Next, we employed an approximate Bayesian computation method for hypothesis testing to clarify the cryptic lineage evolution and ghost introgression effect. SNPs with the genomic signatures of ghost introgression were further annotated. Our results reconfirmed the evolutionary independency of cryptic lineage among C. revoluta and demonstrated that ghost introgression to the noncryptic lineage facilitated their divergence. Gene function related to heat stress and disease resistance implied ecological adaptation of the main extant populations of C. revoluta.
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Affiliation(s)
- Jui‐Tse Chang
- School of Life ScienceNational Taiwan Normal UniversityTaipeiTaiwan
| | - Koh Nakamura
- Botanic Garden, Field Science Center for Northern BiosphereHokkaido UniversitySapporoJapan
| | - Chien‐Ti Chao
- School of Life ScienceNational Taiwan Normal UniversityTaipeiTaiwan
| | - Min‐Xin Luo
- School of Life ScienceNational Taiwan Normal UniversityTaipeiTaiwan
| | - Pei‐Chun Liao
- School of Life ScienceNational Taiwan Normal UniversityTaipeiTaiwan
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Feng C, Zou S, Zhang J. Genetic architecture of microhabitat adaptation traits in a pair of sympatric Primulina species. BIOTECHNOL BIOTEC EQ 2023. [DOI: 10.1080/13102818.2023.2176169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023] Open
Affiliation(s)
- Chen Feng
- Jiangxi Provincial Key Laboratory of ex situ Plant Conservation and Utilization, Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, Jiangxi, PR China
| | - Shuaiyu Zou
- Jiangxi Provincial Key Laboratory of ex situ Plant Conservation and Utilization, Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, Jiangxi, PR China
| | - Jie Zhang
- Jiangxi Provincial Key Laboratory of ex situ Plant Conservation and Utilization, Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, Jiangxi, PR China
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Cornet C, Noret N, Van Rossum F. Pollinator sharing between reproductively isolated genetic lineages of Silene nutans. FRONTIERS IN PLANT SCIENCE 2022; 13:927498. [PMID: 36340351 PMCID: PMC9634645 DOI: 10.3389/fpls.2022.927498] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 09/22/2022] [Indexed: 06/16/2023]
Abstract
High reciprocal pollination specialization leading to pollinator isolation can prevent interspecific pollen transfer and competition for pollinators. Sharing pollinators may induce mating costs, but it may also increase pollination services and pollen dispersal and offer more resources to pollinators, which may be important in case of habitat fragmentation leading to pollination disruption. We estimated pollen dispersal and pollinator isolation or sharing between two reproductively isolated genetic lineages of Silene nutans (Caryophyllaceae), which are rare and occur in parapatry in southern Belgium, forming two edaphic ecotypes. As inter-ecotypic crosses may lead to pollen wastage and inviable progeny, pollinator isolation might have evolved between ecotypes. Silene nutans is mainly pollinated by nocturnal moths, including nursery pollinators, which pollinate and lay their eggs in flowers, and whose caterpillars feed on flowers and seeds. Pollinator assemblages of the two ecotypes are largely unknown and inter-ecotypic pollen flows have never been investigated. Fluorescent powdered dyes were used as pollen analogues to quantify intra- and inter-ecotypic pollen transfers and seeds were germinated to detect chlorotic seedlings resulting from inter-ecotypic pollination. Nocturnal pollinators were observed using infrared cameras on the field, and seed-eating caterpillars were collected and reared to identify nursery pollinator species. No pollinator isolation was found: we detected long-distance (up to 5 km) inter-ecotypic dye transfers and chlorotic seedlings, indicating inter-ecotypic fertilization events. The rare moth Hadena albimacula, a nursery pollinator specialized on S. nutans, was found on both ecotypes, as well as adults visiting flowers (cameras recordings) as seed-eating caterpillars. However, S. nutans populations harbor different abundance and diversity of seed predator communities, including other rare nursery pollinators, suggesting a need for distinct conservation strategies. Our findings demonstrate the efficiency of moths, especially of nursery pollinators, to disperse pollen over long distances in natural landscapes, so to ensure gene flow and population sustainability of the host plant. Seed-predator specificities between the two reproductively isolated genetic lineages of S. nutans, and pollinator sharing instead of pollinator isolation when plants occur in parapatry, suggest that conservation of the host plant is also essential for sustaining (rare) pollinator and seed predator communities.
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Affiliation(s)
- Camille Cornet
- Laboratoire d’Ecologie végétale et Biogéochimie, Université libre de Bruxelles, Brussels, Belgium
| | - Nausicaa Noret
- Laboratoire d’Ecologie végétale et Biogéochimie, Université libre de Bruxelles, Brussels, Belgium
| | - Fabienne Van Rossum
- Laboratoire d’Ecologie végétale et Biogéochimie, Université libre de Bruxelles, Brussels, Belgium
- Research Department, Meise Botanic Garden, Meise, Belgium
- Service général de l’Enseignement supérieur et de la Recherche scientifique, Fédération Wallonie-Bruxelles, Brussels, Belgium
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Bersweden L, Viruel J, Schatz B, Harland J, Gargiulo R, Cowan RS, Calevo J, Juan A, Clarkson JJ, Leitch AR, Fay MF. Microsatellites and petal morphology reveal new patterns of admixture in Orchis hybrid zones. AMERICAN JOURNAL OF BOTANY 2021; 108:1388-1404. [PMID: 34418070 DOI: 10.1002/ajb2.1710] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 02/20/2021] [Accepted: 02/23/2021] [Indexed: 05/23/2023]
Abstract
PREMISE The genetic structure of hybrid zones provides insight into the potential for gene flow to occur between plant taxa. Four closely related European orchid species (Orchis anthropophora, O. militaris, O. purpurea, and O. simia) hybridize when they co-occur. We aimed to characterize patterns of hybridization in O. militaris-O. purpurea, O. purpurea-O. simia, and O. anthropophora-O. simia hybrid zones using molecular and morphological data. METHODS We used 11 newly isolated nuclear microsatellites to genotype 695 individuals collected from seven hybrid zones and six allopatric parental populations in France. Geometric morphometric analysis was conducted using 15 labellum landmarks to capture the main aspects of petal shape. RESULTS Backcrossing was asymmetric toward O. militaris in multiple O. militaris-O. purpurea hybrid zones. Hybrids in O. purpurea-O. simia and O. anthropophora-O. simia hybrid zones were largely limited to F1 and F2 generations, but further admixture had occurred. These patterns were reflected in labellum geometric morphometric data, which correlated strongly with nuclear microsatellite data in all three species combinations. CONCLUSIONS The coexistence of parental and admixed individuals in these Orchis hybrid zones implies they are likely to be tension zones being maintained by a balance between gene flow into the hybrid zone and selection acting against admixed individuals. The pattern of admixture in the three species combinations suggests intrinsic selection acting on the hybrids is weaker in more closely related taxa.
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Affiliation(s)
- Leif Bersweden
- Jodrell Laboratory, Royal Botanic Gardens, Kew TW9 3DS, UK
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Juan Viruel
- Jodrell Laboratory, Royal Botanic Gardens, Kew TW9 3DS, UK
| | - Bertrand Schatz
- Centre for Ecology and Evolution, University of Montpellier, Montpellier 34090, France
| | - Joanna Harland
- Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | | | - Robyn S Cowan
- Jodrell Laboratory, Royal Botanic Gardens, Kew TW9 3DS, UK
| | - Jacopo Calevo
- Department of Life Sciences and Systems Biology, University of Turin, Turin 10125, Italy
| | - Ana Juan
- Department of Environmental Sciences & Natural Resources, University of Alicante, San Vicente, Alicante 03690, Spain
| | | | - Andrew R Leitch
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Michael F Fay
- Jodrell Laboratory, Royal Botanic Gardens, Kew TW9 3DS, UK
- School of Plant Biology, University of Western Australia, Crawley, WA 6009, Australia
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Binks RM, Steane DA, Byrne M. Genomic divergence in sympatry indicates strong reproductive barriers and cryptic species within Eucalyptus salubris. Ecol Evol 2021; 11:5096-5110. [PMID: 34025994 PMCID: PMC8131811 DOI: 10.1002/ece3.7403] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 02/05/2021] [Accepted: 02/09/2021] [Indexed: 12/26/2022] Open
Abstract
Genetic studies are increasingly detecting cryptic taxa that likely represent a significant component of global biodiversity. However, cryptic taxa are often criticized because they are typically detected serendipitously and may not receive the follow-up study required to verify their geographic or evolutionary limits. Here, we follow-up a study of Eucalyptus salubris that unexpectedly detected two divergent lineages but was not sampled sufficiently to make clear interpretations. We undertook comprehensive sampling for an independent genomic analysis (3,605 SNPs) to investigate whether the two purported lineages remain discrete genetic entities or if they intergrade throughout the species' range. We also assessed morphological and ecological traits, and sequenced chloroplast DNA. SNP results showed strong genome-wide divergence (F ST = 0.252) between two discrete lineages: one dominated the north and one the southern regions of the species' range. Within lineages, gene flow was high, with low differentiation (mean F ST = 0.056) spanning hundreds of kilometers. In the central region, the lineages were interspersed but maintained their genomic distinctiveness: an indirect demonstration of reproductive isolation. Populations of the southern lineage exhibited significantly lower specific leaf area and occurred on soils with lower phosphorus relative to the northern lineage. Finally, two major chloroplast haplotypes were associated with each lineage but were shared between lineages in the central distribution. Together, these results suggest that these lineages have non-contemporary origins and that ecotypic adaptive processes strengthened their divergence more recently. We conclude that these lineages warrant taxonomic recognition as separate species and provide fascinating insight into eucalypt speciation.
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Affiliation(s)
- Rachel M. Binks
- Biodiversity and Conservation ScienceDepartment of Biodiversity, Conservation and AttractionsBentley Delivery CentreBentleyWAAustralia
| | - Dorothy A. Steane
- School of Natural Sciences and ARC Training Centre for Forest ValueUniversity of TasmaniaHobartTasmaniaAustralia
- CSIRO Land and WaterSandy BayTasmaniaAustralia
| | - Margaret Byrne
- Biodiversity and Conservation ScienceDepartment of Biodiversity, Conservation and AttractionsBentley Delivery CentreBentleyWAAustralia
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Arslan M, Devisetty UK, Porsch M, Große I, Müller JA, Michalski SG. RNA-Seq analysis of soft rush (Juncus effusus): transcriptome sequencing, de novo assembly, annotation, and polymorphism identification. BMC Genomics 2019; 20:489. [PMID: 31195970 PMCID: PMC6567414 DOI: 10.1186/s12864-019-5886-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 06/05/2019] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Juncus effusus L. (family: Juncaceae; order: Poales) is a helophytic rush growing in temperate damp or wet terrestrial habitats and is of almost cosmopolitan distribution. The species has been studied intensively with respect to its interaction with co-occurring plants as well as microbes being involved in major biogeochemical cycles. J. effusus has biotechnological value as component of Constructed Wetlands where the plant has been employed in phytoremediation of contaminated water. Its genome has not been sequenced. RESULTS In this study we carried out functional annotation and polymorphism analysis of de novo assembled RNA-Seq data from 18 genotypes using 249 million paired-end Illumina HiSeq reads and 2.8 million 454 Titanium reads. The assembly comprised 158,591 contigs with a mean contig length of 780 bp. The assembly was annotated using the dammit! annotation pipeline, which queries the databases OrthoDB, Pfam-A, Rfam, and runs BUSCO (Benchmarking Single-Copy Ortholog genes). In total, 111,567 contigs (70.3%) were annotated with functional descriptions, assigned gene ontology terms, and conserved protein domains, which resulted in 30,932 non-redundant gene sequences. Results of BUSCO and KEGG pathway analyses were similar for J. effusus as for the well-studied members of the Poales, Oryza sativa and Sorghum bicolor. A total of 566,433 polymorphisms were identified in transcribed regions with an average frequency of 1 polymorphism in every 171 bases. CONCLUSIONS The transcriptome assembly was of high quality and genome coverage was sufficient for global analyses. This annotated knowledge resource can be utilized for future gene expression analysis, genomic feature comparisons, genotyping, primer design, and functional genomics in J. effusus.
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Affiliation(s)
- Muhammad Arslan
- Department Environmental Biotechnology, Helmholtz Centre for Environmental Research - UFZ, Permoserstr, 15, Leipzig, Germany.,Institute for Biology V (Environmental Research), RWTH Aachen University, Templergraben 55, 52062, Aachen, Germany
| | | | - Martin Porsch
- Institute of Computer Science, Martin-Luther-University Halle-Wittenberg, Von-Seckendorff-Platz 1, 06120, Halle (Saale), Germany.,Core Facility Deep Sequencing, Martin-Luther-University Halle-Wittenberg, Magdeburger Str. 2, 06112, Halle (Saale), Germany
| | - Ivo Große
- Institute of Computer Science, Martin-Luther-University Halle-Wittenberg, Von-Seckendorff-Platz 1, 06120, Halle (Saale), Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103, Leipzig, Germany
| | - Jochen A Müller
- Department Environmental Biotechnology, Helmholtz Centre for Environmental Research - UFZ, Permoserstr, 15, Leipzig, Germany.
| | - Stefan G Michalski
- Department of Community Ecology, Helmholtz Centre for Environmental Research - UFZ, Theodor-Lieser-Str. 4, 06120, Halle (Saale), Germany
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Born J, Michalski SG. Trait expression and signatures of adaptation in response to nitrogen addition in the common wetland plant Juncus effusus. PLoS One 2019; 14:e0209886. [PMID: 30608976 PMCID: PMC6319709 DOI: 10.1371/journal.pone.0209886] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 12/13/2018] [Indexed: 01/16/2023] Open
Abstract
Wetland ecosystems are known to mitigate high nutrient loadings and thus can improve water quality and prevent potential biodiversity loss caused by eutrophication. Plant traits affect wetland processes directly through effects on accumulation or metabolization of substances, and indirectly by affecting microbial transformation processes in the soil. Understanding the causes and consequences of intraspecific variation in plant functional traits and associated ecosystem processes can aid applied ecological approaches such as wetland restoration and construction. Here we investigated molecular variation and phenotypic variation in response to three levels of nitrogen availability for a regional set of populations of the common wetland plant Juncus effusus. We asked whether trait expression reveals signatures of adaptive differentiation by comparing genetic differentiation in quantitative traits and neutral molecular markers (QST—FST comparisons) and relating trait variation to soil conditions of the plant’s origin. Molecular analyses showed that samples clustered into three very distinct genetic lineages with strong population differentiation within and among lineages. Differentiation for quantitative traits was substantial but did not exceed neutral expectations when compared across treatments or for each treatment and lineage separately. However, variation in trait expression could be explained by local soil environmental conditions of sample origin, e.g. for aboveground carbon-to-nitrogen (C:N) ratios, suggesting adaptive differentiation to contribute to trait expression even at regional level.
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Affiliation(s)
- Jennifer Born
- Department of Community Ecology (BZF), Helmholtz Centre for Environmental Research – UFZ, Halle, Germany
- * E-mail:
| | - Stefan G. Michalski
- Department of Community Ecology (BZF), Helmholtz Centre for Environmental Research – UFZ, Halle, Germany
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8
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Stojanova B, Šurinová M, Klápště J, Koláříková V, Hadincová V, Münzbergová Z. Adaptive differentiation of Festuca rubra along a climate gradient revealed by molecular markers and quantitative traits. PLoS One 2018; 13:e0194670. [PMID: 29617461 PMCID: PMC5884518 DOI: 10.1371/journal.pone.0194670] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 03/07/2018] [Indexed: 12/02/2022] Open
Abstract
Species response to climate change is influenced by predictable (selective) and unpredictable (random) evolutionary processes. To understand how climate change will affect present-day species, it is necessary to assess their adaptive potential and distinguish it from the effects of random processes. This will allow predicting how different genotypes will respond to forecasted environmental change. Space for time substitution experiments are an elegant way to test the response of present day populations to climate variation in real time. Here we assess neutral and putatively adaptive variation in 11 populations of Festuca rubra situated along crossed gradients of temperature and moisture using molecular markers and phenotypic measurements, respectively. By comparing population differentiation in putatively neutral molecular markers and phenotypic traits (QST-FST comparisons), we show the existence of adaptive differentiation in phenotypic traits and their plasticity across the climatic gradient. The observed patterns of differentiation are due to the high genotypic and phenotypic differentiation of the populations from the coldest (and wettest) environment. Finally, we observe statistically significant covariation between markers and phenotypic traits, which is likely caused by isolation by adaptation. These results contribute to a better understanding of the current adaptation and evolutionary potential to face climate change of a widespread species. They can also be extrapolated to understand how the studied populations will adjust to upcoming climate change without going through the lengthy process of phenotyping.
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Affiliation(s)
- Bojana Stojanova
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic
| | - Mária Šurinová
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic
- Institute of Botany, Academy of Sciences of the Czech Republic, Průhonice, Czech Republic
| | - Jaroslav Klápště
- Scion (New Zealand Forest Research Institute Ltd.), Whakarewarewa, Rotorua, New Zealand
| | - Veronika Koláříková
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic
| | - Věroslava Hadincová
- Institute of Botany, Academy of Sciences of the Czech Republic, Průhonice, Czech Republic
| | - Zuzana Münzbergová
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic
- Institute of Botany, Academy of Sciences of the Czech Republic, Průhonice, Czech Republic
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Laphitz RML, Ezcurra C, Vidal-Russell R. Cryptic species in the Andean hemiparasite Quinchamalium chilense (Schoepfiaceae: Santalales). SYST BIODIVERS 2017. [DOI: 10.1080/14772000.2017.1404504] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Rita M Lopez Laphitz
- Departamento de Botánica, Instituto de Investigaciones en Biodiversidad y Medioambiente, CONICET-UNComahue, Quintral 1250, S. C. de Bariloche, 8400 Río Negro, Argentina
| | - Cecilia Ezcurra
- Departamento de Botánica, Instituto de Investigaciones en Biodiversidad y Medioambiente, CONICET-UNComahue, Quintral 1250, S. C. de Bariloche, 8400 Río Negro, Argentina
| | - Romina Vidal-Russell
- Departamento de Botánica, Instituto de Investigaciones en Biodiversidad y Medioambiente, CONICET-UNComahue, Quintral 1250, S. C. de Bariloche, 8400 Río Negro, Argentina
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