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Belton S, Cubry P, Roche JR, Kelleher CT. Molecular characterisation of Pinus sylvestris (L.) in Ireland at the western limit of the species distribution. BMC Ecol Evol 2024; 24:12. [PMID: 38262959 PMCID: PMC10807061 DOI: 10.1186/s12862-023-02181-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 11/26/2023] [Indexed: 01/25/2024] Open
Abstract
BACKGROUND Scots pine (Pinus sylvestris L.) underwent significant population declines across much of northwest Europe during the mid-to-late Holocene and was thought to have become extirpated in Ireland from about 400 AD. However, most extant populations are plantations reintroduced from Scotland. Others are naturalised therefrom and one in Western Ireland is a putative relict. In this paper, Scots pine in Ireland are genetically described for the first time. RESULTS Using two mitochondrial (mtDNA) loci, eight chloroplast (cpSSR) and 18 nuclear (nSSR) loci, the genetic composition and diversity of 19 Irish Scots pine populations is described and compared to other European populations. All trees sampled in Ireland were fixed for mitotype a, which is the most common across northwest Europe. By contrast, cpSSR (HCP = 0.967) and nSSR (He = 0.540) variation was high, and comparable with estimates for other regions across the species range. Differentiation at both sets of loci were similarly low (cpSSR FST = 0.019; nSSR FST = 0.018), but populations from continental Europe were significantly differentiated from all Irish populations based on nSSR variation. CONCLUSIONS All Irish Scots pine are likely part of a common Irish-Scottish gene pool which diverged from continental Scots pine following post-glacial recolonisation. A high genetic diversity and an absence of evidence of inbreeding suggests the regional decline of Scots pine did not critically reduce allelic variation. The post-glacial relationship between Irish and Scottish pine is discussed, and a suggestion from recent palaeoecological work that reintroduced Scots pine be managed as a native species is now further supported by genetic data.
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Affiliation(s)
- Samuel Belton
- DBN Plant Molecular Laboratory, National Botanic Gardens of Ireland, Glasnevin, Dublin, Ireland
| | - Philippe Cubry
- DBN Plant Molecular Laboratory, National Botanic Gardens of Ireland, Glasnevin, Dublin, Ireland
- DIADE, Univ de Montpellier, CIRAD, IRD, Montpellier, F-34090, France
| | - Jenni R Roche
- National Parks and Wildlife Service, Department of Housing, Local Government and Heritage, 90 King Street North, Smithfield, Dublin, Ireland
| | - Colin T Kelleher
- DBN Plant Molecular Laboratory, National Botanic Gardens of Ireland, Glasnevin, Dublin, Ireland.
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2
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New Insight into Genetic Structure and Diversity of Scots Pine (Pinus sylvestris L.) Populations in Lithuania Based on Nuclear, Chloroplast and Mitochondrial DNA Markers. FORESTS 2022. [DOI: 10.3390/f13081179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
We studied the genetic differentiation, structure, and diversity of Scots pine populations in Lithuania based on nuclear, chloroplast microsatellite, and mitochondrial DNA markers. We focused on revealing evolutionary history, country-wide geneflow patterns, and structuring among the Scots pine populations. We genotyped 439 Scots pine individuals of mature age from 23 natural Scots pine stands in Lithuania and used the AMOVA and a set of genetic-clustering methods. The among-population differentiation was weak for nuclear microsatellite loci (nSSRs) (FST = 0.005) but much stronger for cpSSRs (PhiST = 0.240). The populations were structured into highland and lowland populations based on cpSSRs and eastern highland versus the rest for nSSRs. We detected two mtDNA mitotypes—the universal type A and northeastern type B, and the latter occurred at a markedly higher frequency in eastern Lithuania. Within-population genetic diversity was higher in large pine-dominated forest tracts in the eastern highlands than in fragmented forests in the western highlands. We concluded that phenology-based genetic networks following the temperature climate gradients have a strong effect on shaping the genetic structure of otherwise rather homogeneous gene pools of Scots pine populations in Lithuania. The possible effects of human interference with forests on genetic diversity of Scots pine populations in Lithuania are discussed.
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Complete Chloroplast Genome Sequence of Sonchus brachyotus Helps to Elucidate Evolutionary Relationships with Related Species of Asteraceae. BIOMED RESEARCH INTERNATIONAL 2021; 2021:9410496. [PMID: 34901281 PMCID: PMC8654571 DOI: 10.1155/2021/9410496] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 11/07/2021] [Accepted: 11/08/2021] [Indexed: 11/18/2022]
Abstract
Sonchus brachyotus DC. possesses both edible and medicinal properties and is widely distributed throughout China. In this study, the complete cp genome of S. brachyotus was sequenced and assembled. The total length of the complete S. brachyotus cp genome was 151,977 bp, including an LSC region of 84,553 bp, SSC region of 18,138 bp, and IR region of 24,643 bp. Sequence analyses revealed that the cp genome encoded 132 genes, including 87 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The GC content was 37.6%. One hundred mononucleotide microsatellites, 4 dinucleotide microsatellites, 67 trinucleotide microsatellites, 4 tetranucleotide microsatellites, and 1 long repeat were identified. The SSR frequency of the LSC region was significantly greater than that of the IR and SSC regions. In total, 175 SSRs and highly variable regions were recognized as potential cp markers. By analyzing the IR/LSC and IR/SSC boundaries, structural differences between S. brachyotus and 6 other species were detected. According to phylogenetic analyses, S. brachyotus was most closely related to S. arvensis and S. oleraceus. Overall, this study provides complete cp genome resources for S. brachyotus that will be beneficial for identifying potential molecular markers and evolutionary patterns of S. brachyotus and its closely related species.
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Chloroplast DNA Diversity in Populations of P. sylvestris L. from Middle Siberia and the Romanian Carpathians. FORESTS 2021. [DOI: 10.3390/f12121757] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Scots pine is one of the dominant conifer species in forest ecosystems of the boreal zone in Eurasia. Knowledge of the genetic structure and the level of genetic variability of Scots pine populations is relevant for the development of measures aimed at conservation of species’ diversity. In this study, we used ten paternally inherited chloroplast microsatellite loci to investigate the genetic diversity of nineteen Scots pine populations from Middle Siberia and the Romanian Carpathians. The results of the study showed high genetic diversity (HCP = 0.91–1.00) in all of the investigated populations. The cpSSR analysis yielded a total of 158 haplotypes. The majority of the haplotypes (85%) were detected only once (unique haplotypes). Three common haplotypes were found between the Carpathian and the Siberian populations of Scots pine. Analysis of molecular variance (AMOVA) showed that only 3% of the variation occurred among populations from Middle Siberia and 6% of the variation existed among populations from the Carpathian Mountains. Overall, we found a weak geographic population structure in Scots pine from Middle Siberia and the Romanian Carpathians. The present study on genetic diversity in the Siberian and the Carpathian populations of Scots pine may contribute to the sustainable management and conservation of Scots pine genetic resources in Middle Siberia and the Romanian Carpathians.
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Yang J, Takayama K, Pak JH, Kim SC. Comparison of the Whole-Plastome Sequence between the Bonin Islands Endemic Rubus boninensis and Its Close Relative, Rubus trifidus (Rosaceae), in the Southern Korean Peninsula. Genes (Basel) 2019; 10:E774. [PMID: 31581648 PMCID: PMC6826710 DOI: 10.3390/genes10100774] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 09/19/2019] [Accepted: 09/27/2019] [Indexed: 12/03/2022] Open
Abstract
Rubus boninensis is a rare endemic species found on the Bonin Islands with a very restricted distribution. It is morphologically most closely related to Rubus trifidus, occurring widely in the southern Korean peninsula and Japan. This species pair provides a good example of anagenetic speciation on an oceanic island in the northwestern Pacific Ocean-R. trifidus as a continental progenitor and R. boninensis as an insular derivative species. In this study, we firstly characterized the complete plastome of R. boninensis and R. trifidus and compared this species pair to another anagenetically derived species pair (R. takesimensis-R. crataegifolius). The complete plastome of R. trifidus was 155,823 base pairs (bp) long, slightly longer (16 bp) than that of R. boninensis (155,807 bp). No structural or content rearrangements were found between the species pair. Eleven hotspot regions, including trnH/psbA, were identified between R. trifidus and R. boninensis. Phylogenetic analysis of 19 representative plastomes within the family Rosaceae suggested sister relationships between R. trifidus and R. boninensis, and between R. crataegifolius and R. takesimensis. The plastome resources generated by the present study will help elucidate plastome evolution and resolve phylogenetic relationships within highly complex and reticulated lineages of the genus Rubus.
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Affiliation(s)
- JiYoung Yang
- Department of Biology, Research Institute for Dok-do and Ulleung-do Island, School of Life Sciences, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu, Gyeongsangbuk-do 41566, Korea.
| | - Koji Takayama
- Department of Botany, Graduate School of Science, Kyoto University, Oiwake-cho, Kitashirakawa, Sakyo-ku, Kyoto 606-8502, Japan.
| | - Jae-Hong Pak
- Department of Biology, Research Institute for Dok-do and Ulleung-do Island, School of Life Sciences, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu, Gyeongsangbuk-do 41566, Korea.
| | - Seung-Chul Kim
- Department of Biological Sciences, Sungkyunkwan University, 2066 Seobu-ro, Suwon, Gyeonggi-do 16419, Korea.
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Genetic resources of relict populations of Pinus sylvestris (L.) in Western Carpathians assessed by chloroplast microsatellites. Biologia (Bratisl) 2019. [DOI: 10.2478/s11756-019-00255-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
AbstractThe relict character of the Scots pine populations from the Tatra Mts. (Western Carpathians) was formed on scarcely accessible, ecologically extreme habitats, in areas which were not under human activity. An exhaustive genetic analysis of the Scots pine populations from the refugial locations in the Tatra Mts. (Poland) had not yet been. In this study, we characterize the genetic variation and differentiation of the relict Scots pine populations from the Tatra Mts., to provide information on their genetic resources and the conservation implications. Eight paternally inherited chloroplast microsatellite loci were used to investigate the genetic structure of 4 relict populations, which were compared with the natural populations from the Baltic region (5 populations from Lithuania, Latvia and Estonia) and to a northern range from Russia (5 populations from the Kola Peninsula and Arkhangelsk Oblast). The four relict pine populations were characterized by a lower level of genetic variation when compared to the Baltic and northern populations, which was expressed in lower values of particular genetic parameters: numbers of alleles and haplotypes, haplotype genetic diversity, haplotype differentiation, and mean genetic distance between individuals in the population. Our results revealed a very high and significant genetic differentiation between all the analyzed populations, as well as between the three analyzed regions (PhiPT = 8%). Furthermore, the relict populations within a close geographic location showed higher differentiation (PhiPT = 5%) compared to the northern Russian and Baltic populations that were separated by tens and hundreds of kilometers. The relict populations of P. sylvestris from the Tatra Mts. deserve conservation efforts due to the fact that they are an important component if the species-poor Tatra forests.
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Evolutionary Comparison of the Chloroplast Genome in the Woody Sonchus Alliance (Asteraceae) on the Canary Islands. Genes (Basel) 2019; 10:genes10030217. [PMID: 30875850 PMCID: PMC6470973 DOI: 10.3390/genes10030217] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 03/04/2019] [Accepted: 03/11/2019] [Indexed: 11/16/2022] Open
Abstract
The woody Sonchus alliance consists primarily of woody species of the genus Sonchus (subgenus Dendrosonchus; family Asteraceae). Most members of the alliance are endemic to the oceanic archipelagos in the phytogeographic region of Macaronesia. They display extensive morphological, ecological, and anatomical diversity, likely caused by the diverse habitats on islands and rapid adaptive radiation. As a premier example of adaptive radiation and insular woodiness of species endemic to oceanic islands, the alliance has been the subject of intensive evolutionary studies. While phylogenetic studies suggested that it is monophyletic and its major lineages radiated rapidly early in the evolutionary history of this group, genetic mechanisms of speciation and genomic evolution within the alliance remain to be investigated. We first attempted to address chloroplast (cp) genome evolution by conducting comparative genomic analysis of three representative endemic species (Sonchus acaulis, Sonchus canariensis, and Sonchus webbii) from the Canary Islands. Despite extensive morphological, anatomical, and ecological differences among them, their cp genomes were highly conserved in gene order and content, ranging from 152,071 to 152,194 bp in total length. The number of repeat variations and six highly variable regions were identified as valuable molecular markers. Phylogenetic analysis of 32 species in the family Asteraceae revealed the phylogenetic position of the woody Sonchus alliance within the tribe Cichorieae and the sister relationship between the weedy Sonchus oleraceus and the alliance.
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Pawlaczyk EM, Bobowicz MA. Variability of silver fir (Abies alba Mill.) progeny from the Tisovik Reserve expressed in needle traits and chloroplast microsatellite DNA. BIODIVERSITY: RESEARCH AND CONSERVATION 2017. [DOI: 10.1515/biorc-2017-0001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Abstract
Progeny from nineteen family lines of silver fir (Abies alba Mill.) from the Tisovik Reserve growing in an experimental plot were analyzed based on 4 chloroplast microsatellite DNA loci and 12 morphological and anatomical needle traits. The Tisovik Reserve is located in Białowieża Primeval Forest, 120 km north of the natural range limit of this species, and embraces a small and isolated natural population of silver fir. The aim of this study was to determine genetic variation within and between progeny lines. Analysis of phenotypic variation showed that the traits which differed most among individuals were the needle width and the distance from resin canals to vascular bundle. Those traits, which differed most between the progeny lines, were the number of endodermic cells around the vascular bund and the weight of hypodermic cells. In Tisovik progeny, we detected 107 different haplotypes. In progeny lines, we detected more haplotypes than in maternal trees, and most haplotypes did not exist in maternal trees. This may be the result of pollen influx from other silver fir stands. Progeny from Tisovik showed a higher level of variability in comparison with maternal trees.
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Affiliation(s)
- Ewa M. Pawlaczyk
- Department of Genetics, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznań , Poland
| | - Maria A. Bobowicz
- Department of Genetics, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznań , Poland
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Whittet R, Cavers S, Cottrell J, Rosique‐Esplugas C, Ennos R. Substantial variation in the timing of pollen production reduces reproductive synchrony between distant populations of Pinus sylvestris L. in Scotland. Ecol Evol 2017; 7:5754-5765. [PMID: 28894569 PMCID: PMC5586338 DOI: 10.1002/ece3.3154] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 04/24/2017] [Accepted: 05/17/2017] [Indexed: 12/31/2022] Open
Abstract
The ability of a population to genetically adapt to a changing environment is contingent not only on the level of existing genetic variation within that population, but also on the gene flow received from differently adapted populations. Effective pollen-mediated gene flow among plant populations requires synchrony of flowering. Therefore differences in timing of flowering among genetically divergent populations may reduce their ability to adapt to environmental change. To determine whether gene flow among differently adapted populations of native Scots pine (Pinus sylvestris) in Scotland was restricted by differences in their flowering phenology, we measured timing of pollen release among populations spanning a steep environmental gradient over three consecutive seasons (2014-2016). Results showed that, over a distance of 137 km, there were as many as 15.8 days' difference among populations for the predicted timing of peak pollen shedding, with the earliest development in the warmer west of the country. There was much variation between years, with the earliest development and least synchrony in the warmest year (2014) and latest development and greatest synchrony in the coolest year (2015). Timing was negatively correlated with results from a common-garden experiment, indicative of a pattern of countergradient variation. We conclude that the observed differences in reproductive synchrony were sufficient to limit gene flow via pollen between populations of P. sylvestris at opposite ends of the environmental gradient across Scotland. We also hypothesize that continually warming, or asymmetrically warming spring temperatures will decrease reproductive synchrony among pine populations.
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Affiliation(s)
- Richard Whittet
- Institute of Evolutionary BiologyUniversity of EdinburghEdinburghUK
- NERC Centre for Ecology and HydrologyPenicuikUK
| | | | | | - Cristina Rosique‐Esplugas
- Institute of Evolutionary BiologyUniversity of EdinburghEdinburghUK
- Forest ResearchNorthern Research StationRoslinUK
| | - Richard Ennos
- Institute of Evolutionary BiologyUniversity of EdinburghEdinburghUK
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10
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Genetic Diversity among Age Classes of a Pinus sylvestris (L.) Population from the Białowieża Primeval Forest, Poland. FORESTS 2017. [DOI: 10.3390/f8070227] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The Białowieża Primeval Forest (BPF) is Europe’s last primeval forest and an irreplaceable area for biodiversity conservation due to its size, protection status, and substantially undisturbed nature. There is no other forest in Europe with such a large surface representing highly-advanced natural succession. This article reports on the first analysis of the genetic variability and demographic structure of a self-renewed Pinus sylvestris population located in BPF, using both chloroplast and mitochondrial DNA markers. The analysis of molecular variance (AMOVA) for chloroplast simple sequence repeats (cpSSRs) revealed a significant genetic differentiation among age classes that accounted for about 2% of the total variance, comparable to those reported among different populations of Scots pine. None of the 117 detected chloroplast haplotypes were common to all age classes. Haplotype diversity ranged from 0.370 to 0.415 for cpSSRs and from 0.320 to 0.455 for mitochondrial markers. The genetic variation of the studied age classes—represented by mitochondrial markers—strongly depicts the maternal genetic structure, indicating limited seed dispersal. Temporal genetic substructuring is maintained within a self-renewed population of Scots pine from the BPF.
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11
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Dering M, Kosiński P, Wyka TP, Pers-Kamczyc E, Boratyński A, Boratyńska K, Reich PB, Romo A, Zadworny M, Żytkowiak R, Oleksyn J. Tertiary remnants and Holocene colonizers: Genetic structure and phylogeography of Scots pine reveal higher genetic diversity in young boreal than in relict Mediterranean populations and a dual colonization of Fennoscandia. DIVERS DISTRIB 2017. [DOI: 10.1111/ddi.12546] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Affiliation(s)
- Monika Dering
- Laboratory of Systematics and Geography; Institute of Dendrology; Polish Academy of Sciences; Kórnik Poland
| | - Piotr Kosiński
- Laboratory of Systematics and Geography; Institute of Dendrology; Polish Academy of Sciences; Kórnik Poland
- Department of Botany; Poznań University of Life Sciences; Poznań Poland
| | - Tomasz P. Wyka
- General Botany Laboratory; Institute of Experimental Biology; Department of Biology; Adam Mickiewicz University; Poznań Poland
| | - Emilia Pers-Kamczyc
- Laboratory of Systematics and Geography; Institute of Dendrology; Polish Academy of Sciences; Kórnik Poland
| | - Adam Boratyński
- Laboratory of Systematics and Geography; Institute of Dendrology; Polish Academy of Sciences; Kórnik Poland
| | - Krystyna Boratyńska
- Laboratory of Systematics and Geography; Institute of Dendrology; Polish Academy of Sciences; Kórnik Poland
| | - Peter B. Reich
- Department of Forest Resources; University of Minnesota; St. Paul MN USA
- Hawkesbury Institute for the Environment; Western Sydney University; Penrith NSW Australia
| | - Angel Romo
- Institute of Botany; Consejo Superior de Investigaciones Científicas; IBB-CSIC-ICUB; Barcelona Spain
| | - Marcin Zadworny
- Laboratory of Systematics and Geography; Institute of Dendrology; Polish Academy of Sciences; Kórnik Poland
| | - Roma Żytkowiak
- Laboratory of Systematics and Geography; Institute of Dendrology; Polish Academy of Sciences; Kórnik Poland
| | - Jacek Oleksyn
- Laboratory of Systematics and Geography; Institute of Dendrology; Polish Academy of Sciences; Kórnik Poland
- Department of Forest Resources; University of Minnesota; St. Paul MN USA
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Donnelly K, Cottrell J, Ennos RA, Vendramin GG, A'Hara S, King S, Perry A, Wachowiak W, Cavers S. Reconstructing the plant mitochondrial genome for marker discovery: a case study using Pinus. Mol Ecol Resour 2017; 17:943-954. [DOI: 10.1111/1755-0998.12646] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Revised: 11/25/2016] [Accepted: 12/14/2016] [Indexed: 11/29/2022]
Affiliation(s)
- Kevin Donnelly
- NERC Centre for Ecology and Hydrology, Edinburgh; Bush Estate Penicuik Midlothian EH26 0QB UK
- Institute of Evolutionary Biology; School of Biological Sciences; Ashworth Laboratories; University of Edinburgh; Edinburgh EH9 3JT UK
| | - Joan Cottrell
- Forest Research, Northern Research Station; Roslin Midlothian EH25 9SY UK
| | - Richard A. Ennos
- Institute of Evolutionary Biology; School of Biological Sciences; Ashworth Laboratories; University of Edinburgh; Edinburgh EH9 3JT UK
| | - Giovanni Giuseppe Vendramin
- Institute of Biosciences and BioResources; Division of Florence; National Research Council; Via Madonna del Piano, 10 50019 Sesto Fiorentino (Firenze) Italy
| | - Stuart A'Hara
- Forest Research, Northern Research Station; Roslin Midlothian EH25 9SY UK
| | - Sarah King
- NERC Centre for Ecology and Hydrology, Edinburgh; Bush Estate Penicuik Midlothian EH26 0QB UK
| | - Annika Perry
- NERC Centre for Ecology and Hydrology, Edinburgh; Bush Estate Penicuik Midlothian EH26 0QB UK
| | - Witold Wachowiak
- NERC Centre for Ecology and Hydrology, Edinburgh; Bush Estate Penicuik Midlothian EH26 0QB UK
- Institute of Dendrology; Polish Academy of Sciences; Parkowa 5 62-035 Kórnik Poland
| | - Stephen Cavers
- NERC Centre for Ecology and Hydrology, Edinburgh; Bush Estate Penicuik Midlothian EH26 0QB UK
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13
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Dzialuk A, Boratyńska K, Romo A, Boratyński A. Taxonomic and geographic variation of the Pinus mugo complex on chloroplast microsatellite markers. SYST BIODIVERS 2016. [DOI: 10.1080/14772000.2016.1257518] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Artur Dzialuk
- Kazimierz Wielki University, Department of Genetics, Powstańców Wielkopolskich 10, 85-090 Bydgoszcz, Poland
| | - Krystyna Boratyńska
- Institute of Dendrology, Polish Academy of Sciences, Parkowa 5, 63-036 Kórnik, Poland
| | - Angel Romo
- Institute of Botany, Consejo Superior de Investigaciones Cientificas, Passeig del Migdia, s/n 08038 Barcelona, Spain
| | - Adam Boratyński
- Institute of Dendrology, Polish Academy of Sciences, Parkowa 5, 63-036 Kórnik, Poland
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14
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Semerikov VL, Semerikova SA, Dymshakova OS, Zatsepina KG, Tarakanov VV, Tikhonova IV, Ekart AK, Vidyakin AI, Jamiyansuren S, Rogovtsev RV, Kalchenko LI. Microsatellite loci polymorphism of chloroplast DNA of scots pine (Pinus sylvestris L.) in Asia and eastern Europe. RUSS J GENET+ 2014. [DOI: 10.1134/s1022795414040127] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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15
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Wang B, Mao JF, Zhao W, Wang XR. Impact of Geography and Climate on the Genetic Differentiation of the Subtropical Pine Pinus yunnanensis. PLoS One 2013; 8:e67345. [PMID: 23840668 PMCID: PMC3693954 DOI: 10.1371/journal.pone.0067345] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Accepted: 05/16/2013] [Indexed: 12/22/2022] Open
Abstract
Southwest China is a biodiversity hotspot characterized by complex topography, heterogeneous regional climates and rich flora. The processes and driving factors underlying this hotspot remain to be explicitly tested across taxa to gain a general understanding of the evolution of biodiversity and speciation in the region. In this study, we examined the role played by historically neutral processes, geography and environment in producing the current genetic diversity of the subtropical pine Pinus yunnanensis. We used genetic and ecological methods to investigate the patterns of genetic differentiation and ecological niche divergence across the distribution range of this species. We found both continuous genetic differentiation over the majority of its range, and discrete isolated local clusters. The discrete differentiation between two genetic groups in the west and east peripheries is consistent with niche divergence and geographical isolation of these groups. In the central area of the species' range, population structure was shaped mainly by neutral processes and geography rather than by ecological selection. These results show that geographical and environmental factors together created stronger and more discrete genetic differentiation than isolation by distance alone, and illustrate the importance of ecological factors in forming or maintaining genetic divergence across a complex landscape. Our findings differ from other phylogenetic studies that identified the historical drainage system in the region as the primary factor shaping population structure, and highlight the heterogeneous contributions that geography and environment have made to genetic diversity among taxa in southwest China.
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Affiliation(s)
- Baosheng Wang
- Department of Ecology and Environmental Science, Umeå University, Umeå, Sweden
| | - Jian-Feng Mao
- National Engineering Laboratory for Forest Tree Breeding, Key Laboratory for Genetics and Breeding of Forest Trees and Ornamental Plants of Ministry of Education, Beijing Forestry University, Beijing, People’s Republic of China
| | - Wei Zhao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Xiao-Ru Wang
- Department of Ecology and Environmental Science, Umeå University, Umeå, Sweden
- * E-mail:
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16
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Gulsen O, Ceylan A. Elucidating polyploidization of bermudagrasses as assessed by organelle and nuclear DNA markers. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2011; 15:903-12. [PMID: 22106951 DOI: 10.1089/omi.2011.0100] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Clarification of relationships among ploidy series of Cynodon accessions could be beneficial to bermudagrass breeding programs, and would enhance our understanding of the evolutionary biology of this warm season grass species. This study was initiated to elucidate polyploidization among Cynodon accessions with different ploidy series collected from Turkey based on chloroplast and nuclear DNA. Forty Cynodon accessions including 7 diploids, 3 triploids, 10 tetraploids, 11 pentaploids, and 9 hexaploids were analyzed using chloroplast DNA restriction fragment-length polymorphism (cpDNA RFLP), chloroplast DNA simple sequence repeat (cpDNA SSR), and nuclear DNA markers based on neighbor-joining (NJ) and principle component analyses (PCA). All three-marker systems with two statistical algorithms clustered the diploids apart from the other ploidy levels. Assuming autopolyploidy, spontaneous polyploidization followed by rapid diversification among the higher ploidy levels than the diploids is likely in Cynodon's evolution. Few tetraploid and hexaploid accessions were clustered with or closely to the group of diploids, supporting the hypothesis above. Eleven haplotypes as estimated by cpDNA RFLP and SSR markers were detected. This study indicated that the diploids had different organelle genome from the rest of the ploidy series and provided valuable insight into relationships among ploidy series of Cynodon accessions based on cp and nuclear DNAs.
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Affiliation(s)
- Osman Gulsen
- Department of Horticulture, Erciyes University, Melikgazi, Kayseri, Turkey.
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Wang B, Mao JF, Gao J, Zhao W, Wang XR. Colonization of the Tibetan Plateau by the homoploid hybrid pine Pinus densata. Mol Ecol 2011; 20:3796-811. [PMID: 21689188 DOI: 10.1111/j.1365-294x.2011.05157.x] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Pinus densata is an intriguingly successful homoploid hybrid species that occupies vast areas of the southeastern Tibetan Plateau in which neither of its parental species are present, but the colonization processes involved are poorly understood. To shed light on how this species colonized and became established on the plateau, we surveyed paternally inherited chloroplast (cp) and maternally inherited mitochondrial (mt) DNA variation within and among 54 populations of P. densata and its putative parental species throughout their respective ranges. Strong spatial genetic structure of both cp and mtDNA were detected in P. densata populations. Mitotypes specific to P. densata were likely generated by complex recombination events. A putative ancestral hybrid zone in the northeastern periphery of P. densata was identified, and we propose that the species then colonized the plateau by migrating westwards. Along the colonization route, consecutive bottlenecks and surfing of rare alleles caused a significant reduction in genetic diversity and strong population differentiation. The direction and intensity of introgression from parental species varied among geographic regions. In western parts of its range, the species seems to have been isolated from seed and pollen flow from its parent species for a long time. The observed spatial distribution of genetic diversity in P. densata also appears to reflect the persistence of this species on the plateau during the last glaciation. Our results indicate that both ancient and contemporary population dynamics have contributed to the spatial distribution of genetic diversity in P. densata, which accordingly reflects its evolutionary history.
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Affiliation(s)
- Baosheng Wang
- Department of Ecology and Environmental Science, Umeå University, SE-901 87 Umeå, Sweden
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Wachowiak W, Salmela MJ, Ennos RA, Iason G, Cavers S. High genetic diversity at the extreme range edge: nucleotide variation at nuclear loci in Scots pine (Pinus sylvestris L.) in Scotland. Heredity (Edinb) 2011; 106:775-87. [PMID: 20823905 PMCID: PMC3186241 DOI: 10.1038/hdy.2010.118] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2009] [Revised: 07/02/2010] [Accepted: 07/30/2010] [Indexed: 02/01/2023] Open
Abstract
Nucleotide polymorphism at 12 nuclear loci was studied in Scots pine populations across an environmental gradient in Scotland, to evaluate the impacts of demographic history and selection on genetic diversity. At eight loci, diversity patterns were compared between Scottish and continental European populations. At these loci, a similar level of diversity (θ(sil)= ~0.01) was found in Scottish vs mainland European populations, contrary to expectations for recent colonization, however, less rapid decay of linkage disequilibrium was observed in the former (ρ=0.0086±0.0009, ρ=0.0245±0.0022, respectively). Scottish populations also showed a deficit of rare nucleotide variants (multi-locus Tajima's D=0.316 vs D=-0.379) and differed significantly from mainland populations in allelic frequency and/or haplotype structure at several loci. Within Scotland, western populations showed slightly reduced nucleotide diversity (π(tot)=0.0068) compared with those from the south and east (0.0079 and 0.0083, respectively) and about three times higher recombination to diversity ratio (ρ/θ=0.71 vs 0.15 and 0.18, respectively). By comparison with results from coalescent simulations, the observed allelic frequency spectrum in the western populations was compatible with a relatively recent bottleneck (0.00175 × 4N(e) generations) that reduced the population to about 2% of the present size. However, heterogeneity in the allelic frequency distribution among geographical regions in Scotland suggests that subsequent admixture of populations with different demographic histories may also have played a role.
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Affiliation(s)
- W Wachowiak
- Centre for Ecology and Hydrology Edinburgh, Bush Estate, Penicuik, Midlothian, UK
- Institute of Dendrology, Polish Academy of Sciences, Kórnik, Poland
| | - M J Salmela
- Centre for Ecology and Hydrology Edinburgh, Bush Estate, Penicuik, Midlothian, UK
- Institute of Evolutionary Biology, School of Biological Sciences, Ashworth Laboratories, University of Edinburgh, Edinburgh, UK
| | - R A Ennos
- Institute of Evolutionary Biology, School of Biological Sciences, Ashworth Laboratories, University of Edinburgh, Edinburgh, UK
| | - G Iason
- Macaulay Land Use Research Institute, Craigiebuckler, Aberdeen, UK
| | - S Cavers
- Centre for Ecology and Hydrology Edinburgh, Bush Estate, Penicuik, Midlothian, UK
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GÉRARDI SÉBASTIEN, JARAMILLO-CORREA JUANP, BEAULIEU JEAN, BOUSQUET JEAN. From glacial refugia to modern populations: new assemblages of organelle genomes generated by differential cytoplasmic gene flow in transcontinental black spruce. Mol Ecol 2010; 19:5265-80. [DOI: 10.1111/j.1365-294x.2010.04881.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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Artyukova EV, Kozyrenko MM, Gorovoy PG, Zhuravlev YN. Plastid DNA variation in highly fragmented populations of Microbiota decussata Kom. (Cupressaceae), an endemic to Sikhote Alin Mountains. Genetica 2009; 137:201-12. [PMID: 19629720 DOI: 10.1007/s10709-009-9386-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2009] [Accepted: 07/07/2009] [Indexed: 11/30/2022]
Abstract
Microbiota decussata Kom. (Cupressaceae) is a subalpine species endemic to the Sikhote Alin Mountains with populations scattered throughout the range. We used sequence data for four noncoding regions of chloroplast DNA to characterize the genetic diversity in populations sampled from different parts of M. decussata natural range. No variation was observed in the trnT-trnF region, whereas the trnH-psbA, trnS-trnfM, and trnS-trnG regions showed polymorphisms. At the species level, we found a low nucleotide diversity (pi = 0.0009) and high haplotype diversity (h = 0.981) as well as high differentiation (Phi(ST) = 0.420). N(ST) and G(ST) values suggested the existence of a phylogeographic structure in M. decussata. The observed patterns of diversity could be explained in part by ecological features of the species and its long-term persistence throughout the range with population expansion, successive fragmentation and isolation.
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Affiliation(s)
- Elena V Artyukova
- Institute of Biology and Soil Science, Far East Branch of Russian Academy of Sciences, 690022 Vladivostok, Russia.
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Estimating gametic introgression rates in a risk assessment context: a case study with Scots pine relicts. Heredity (Edinb) 2009; 103:385-93. [DOI: 10.1038/hdy.2009.78] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
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Ebert D, Peakall R. Chloroplast simple sequence repeats (cpSSRs): technical resources and recommendations for expanding cpSSR discovery and applications to a wide array of plant species. Mol Ecol Resour 2009; 9:673-90. [PMID: 21564725 DOI: 10.1111/j.1755-0998.2008.02319.x] [Citation(s) in RCA: 136] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Chloroplast microsatellites, or simple sequence repeats (cpSSRs), are typically mononucleotide tandem repeats. When located in the noncoding regions of the chloroplast genome (cpDNA), they commonly show intraspecific variation in repeat number. Despite the growing number of studies applying cpSSRs, studies of economically important plants and their relatives remain over-represented. Thus, the potential of cpSSRs to offer unique insights into ecological and evolutionary processes in wild plant species has yet to be fully realized. This review provides an overview of the technical resources available to aid cpSSR discovery including a list of cpSSR primer sets available and cpDNA sequencing resources. Our updated analysis of 99 whole chloroplast genomes downloaded from GenBank confirms that potentially variable cpSSRs are abundant in the noncoding cpDNA of plants. Overall variation in the frequency of cpSSRs was extreme, ranging from one to 700 per genome (median = 93), while in 81 vascular plants, between 35 and 160 cpSSRs were detected per genome (median = 86). We offer five recommendations to aid wider development and application of cpSSRs: (i) When genus-specific cpSSR primers are available, cross-species amplification can often be fruitful. (ii) While potentially useful, universal cpSSR primers at best provide access to only a small number of variable markers. (iii) De novo sequencing of noncoding cpDNA is the most effective and efficient way to develop cpSSR markers in wild species. (iv) DNA sequencing of cpSSR alleles is essential, given the complex nature of the genetic variation associated with hypervariable cpDNA regions. (v) The reliability of cpSSR length based genetic assays need to be validated in all studies.
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Affiliation(s)
- Daniel Ebert
- School of Botany and Zoology, The Australian National University, Canberra ACT 0200, Australia
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Provan J, Beatty GE, Hunter AM, McDonald RA, McLaughlin E, Preston SJ, Wilson S. Restricted gene flow in fragmented populations of a wind-pollinated tree. CONSERV GENET 2007. [DOI: 10.1007/s10592-007-9484-y] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Semerikova SA, Semerikov VL. The diversity of chloroplast microsatellite loci in Siberian fir (Abies sibirica Ledeb.) and two Far East fir species A. nephrolepis (Trautv.) Maxim. and A. sachalinensis Fr. Schmidt. RUSS J GENET+ 2007. [DOI: 10.1134/s102279540712006x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Jakobsson M, Säll T, Lind-Halldén C, Halldén C. Evolution of chloroplast mononucleotide microsatellites in Arabidopsis thaliana. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2007; 114:223-35. [PMID: 17123063 DOI: 10.1007/s00122-006-0425-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2005] [Accepted: 09/30/2006] [Indexed: 05/09/2023]
Abstract
The level of variation and the mutation rate were investigated in an empirical study of 244 chloroplast microsatellites in 15 accessions of Arabidopsis thaliana. In contrast to SNP variation, microsatellite variation in the chloroplast was found to be common, although less common than microsatellite variation in the nucleus. No microsatellite variation was found in coding regions of the chloroplast. To evaluate different models of microsatellite evolution as possible explanations for the observed pattern of variation, the length distribution of microsatellites in the published DNA sequence of the A. thaliana chloroplast was subsequently used. By combining information from these two analyses we found that the mode of evolution of the chloroplast mononucleotide microsatellites was best described by a linear relation between repeat length and mutation rate, when the repeat lengths exceeded about 7 bp. This model can readily predict the variation observed in non-coding chloroplast DNA. It was found that the number of uninterrupted repeat units had a large impact on the level of chloroplast microsatellite variation. No other factors investigated--such as the position of a locus within the chromosome, or imperfect repeats--appeared to affect the variability of chloroplast microsatellites. By fitting the slippage models to the Genbank sequence of chromosome 1, we show that the difference between microsatellite variation in the nucleus and the chloroplast is largely due to differences in slippage rate.
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Affiliation(s)
- Mattias Jakobsson
- Department of Cell and Organism Biology, Genetics, Lund University, Lund, Sweden
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Naydenov KD, Tremblay FM, Alexandrov A, Fenton NJ. Structure of Pinus sylvestris L. populations in Bulgaria revealed by chloroplast microsatellites and terpenes analysis: Provenance tests. BIOCHEM SYST ECOL 2005. [DOI: 10.1016/j.bse.2005.07.011] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Muir G, Lowe AJ, Fleming CC, Vogl C. High nuclear genetic diversity, high levels of outcrossing and low differentiation among remnant populations of Quercus petraea at the margin of its range in Ireland. ANNALS OF BOTANY 2004; 93:691-7. [PMID: 15087303 PMCID: PMC4242301 DOI: 10.1093/aob/mch096] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
BACKGROUND AND AIMS Quercus petraea colonized Ireland after the last glaciation from refugia on mainland Europe. Deforestation, however, beginning in Neolithic times, has resulted in small, scattered forest fragments, now covering less than 12,000 ha. METHODS Plastid (three fragments) and microsatellite variation (13 loci) were characterized in seven Irish populations sampled along a north-south gradient. Using Bayesian approaches and Wright's F-statistics, the effects of colonization and fragmentation on the genetic structure and mating patterns of extant oak populations were investigated. KEY RESULTS All populations possessed cytotypes common to the Iberian Peninsula. Despite the distance from the refugial core and the extensive deforestation in Ireland, nuclear genetic variation was high and comparable to mainland Europe. Low population differentiation was observed within Ireland and populations showed no evidence for isolation by distance. As expected of a marker with an effective population size of one-quarter relative to the nuclear genome, plastid variation indicated higher differentiation. Individual inbreeding coefficients indicated high levels of outcrossing. CONCLUSIONS Consistent with a large effective population size in the historical migrant gene pool and/or with high gene flow among populations, high within-population diversity and low population differentiation was observed within Ireland. It is proposed that native Q. petraea populations in Ireland share a common phylogeographic history and that the present genetic structure does not reflect founder effects.
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Affiliation(s)
- Graham Muir
- Institut für Tierzucht und Genetik, Veterinärmedizinische Universität Wien, Josef Baumann Gasse 1, 1210, Vienna, Austria.
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Mengoni A, Gonnelli C, Brocchini E, Galardi F, Pucci S, Gabbrielli R, Bazzicalupo M. Chloroplast genetic diversity and biogeography in the serpentine endemic Ni-hyperaccumulator Alyssum bertolonii. THE NEW PHYTOLOGIST 2003; 157:349-356. [PMID: 33873638 DOI: 10.1046/j.1469-8137.2003.00664.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
• Chloroplast microsatellites (cpSSR) were used to analyze the patterns of genetic variation within and among populations of the serpentine endemic, Alyssum bertolonii . • Thirty-five different chloroplast haplotypes were identified in 90 plants sampled from nine populations originating from the four disjunct northern-Italian serpentine regions where the species is found. • High levels of genetic diversity were found within each of the populations sampled. Analysis of Molecular Variance (AMOVA) showed high degrees of differentiation among both different populations of the same serpentine region and different regions (Φ ST = 0.622, Φ CT = 0.252, respectively). • The results indicated that: each population was established by few founders and then subsequently differentiated the existing chloroplast haplotypes; each population is a distinct genetic entity; and populations within the same serpentine region are more related than populations from different regions.
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Affiliation(s)
- A Mengoni
- Dipartimento di Biologia Animale e Genetica, Università di Firenze, via Romana 17-19, I-50125 Firenze, Italy
| | - C Gonnelli
- Dipartimento di Biologia Vegetale, Laboratorio di Fisiologia Vegetale, Università di Firenze, via Micheli 1, I-50121 Firenze, Italy
| | - E Brocchini
- Dipartimento di Biologia Animale e Genetica, Università di Firenze, via Romana 17-19, I-50125 Firenze, Italy
- Dipartimento di Biologia Vegetale, Laboratorio di Fisiologia Vegetale, Università di Firenze, via Micheli 1, I-50121 Firenze, Italy
| | - F Galardi
- Dipartimento di Biologia Vegetale, Laboratorio di Fisiologia Vegetale, Università di Firenze, via Micheli 1, I-50121 Firenze, Italy
| | - S Pucci
- Dipartimento di Biologia Vegetale, Laboratorio di Fisiologia Vegetale, Università di Firenze, via Micheli 1, I-50121 Firenze, Italy
| | - R Gabbrielli
- Dipartimento di Biologia Vegetale, Laboratorio di Fisiologia Vegetale, Università di Firenze, via Micheli 1, I-50121 Firenze, Italy
| | - M Bazzicalupo
- Dipartimento di Biologia Animale e Genetica, Università di Firenze, via Romana 17-19, I-50125 Firenze, Italy
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Deguilloux MF, Dumolin-Lapègue S, Gielly L, Grivet D, Petit RJ. A set of primers for the amplification of chloroplast microsatellites inQuercus. ACTA ACUST UNITED AC 2002. [DOI: 10.1046/j.1471-8286.2003.00339.x] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Abstract
Previous morphological, allozyme and chloroplast DNA data have suggested that Pinus densata originated through hybridization between P. tabuliformis and P. yunnanensis. In the present study, sequence and restriction site analyses of maternally inherited mitochondrial nad1 intron were used to detect variation patterns in 19 populations of P. tabuliformis, P. yunnanensis and P. densata. A total of three mitotypes (A, B, C) were detected. All but one of the populations of P. yunnanensis possessed mitotype B while all populations of P. tabuliformis had mitotype A. Pinus densata populations, on the other hand, harboured both mitotypes A and B, which are characteristic of P. tabuliformis and P. yunnanensis, respectively. This result gives strong additional evidence supporting the hybrid origin of this diploid pine. The distribution of mitotypes indicated very different mating compositions and evolutionary history among P. densata populations. It seems that local founder populations and backcrosses may have played important roles in the early establishment of P. densata populations. The uplift of the Tibetan Plateau had a significant impact on the distribution of maternal lineages of P. densata populations.
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Affiliation(s)
- Bao-Hua Song
- Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
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Abstract
Variation in the chloroplast genome of Calluna vulgaris (heather), the dominant species of northwest European heath communities, was analysed using polymerase chain reaction-restriction fragment length polymorphisms (PCR-RFLPs) and microsatellites. No length polymorphisms were detected in the 100-200 base pair (bp) fragments amplified by the conserved microsatellite primers, and sequencing revealed that the repeat regions were interrupted relative to the corresponding sequence in Nicotiana tabacum. In contrast, PCR-RFLP analysis revealed high levels of haplotype diversity within populations (hS = 0.443, hT = 0.842), as well as substantial differentiation between populations (GST = 0.473). Diversity and differentiation were higher in southern Europe than in northern Europe. Interpreted in the light of data from allozyme studies and pollen core records, the results suggest that the main glacial refugia for C. vulgaris were located in southwest Europe, including northern Spain, the Pyrenees and the Massif Central region of France. There is also evidence for diffuse survival of the species at more northerly latitudes.
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Affiliation(s)
- S Rendell
- Institute of Ecology and Resource Management, University of Edinburgh, Darwin Building, King's Buildings, Mayfield Road, Edinburgh EH9 3JU, UK
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Mengoni A, Barabesi C, Gonnelli C, Galardi F, Gabbrielli R, Bazzicalupo M. Genetic diversity of heavy metal-tolerant populations in Silene paradoxa L. (Caryophyllaceae): a chloroplast microsatellite analysis. Mol Ecol 2001; 10:1909-16. [PMID: 11555235 DOI: 10.1046/j.0962-1083.2001.01336.x] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Eight populations of Silene paradoxa L. (Caryophyllaceae) growing in copper mine deposits, in serpentine outcrops or in uncontaminated soil in central Italy were studied. Genetic diversity was estimated using five polymorphic chloroplast microsatellite loci (cpSSR), identifying 27 different chloroplast haplotypes. The effective number of alleles, the haplotypic diversity and a stepwise mutational model-based parameter (DSH2) were computed. The effective number of alleles observed within populations from copper mine deposits was 20% that of the serpentine neighbouring populations, suggesting the occurrence of a founder effect. Moreover, 13 of the 27 different haplotypes scored were exclusive to only one population, indicating genetic isolation for all tolerant populations. Even the copper-tolerant populations appeared to have evolved independently. Finally, analysis of molecular variance (AMOVA) of the cpSSR markers gave statistical significance to the grouping of populations according to their geographical location. This study demonstrates that cpSSR markers could be a useful complementary tool to isoenzymes or random amplified polymorphic DNA markers for elucidating the pattern of genetic differentiation in heavy metal-tolerant populations.
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Affiliation(s)
- A Mengoni
- Dipartimento di Biologia Animale e Genetica, Università di Firenze, via Romana 17, I-50125 Firenze, Italy
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Gugerli F, Senn J, Anzidei M, Madaghiele A, Büchler U, Sperisen C, Vendramin GG. Chloroplast microsatellites and mitochondrial nad1 intron 2 sequences indicate congruent phylogenetic relationships among Swiss stone pine (Pinus cembra), Siberian stone pine (Pinus sibirica), and Siberian dwarf pine (Pinus pumila). Mol Ecol 2001; 10:1489-97. [PMID: 11412370 DOI: 10.1046/j.1365-294x.2001.01285.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We studied the phylogenetic relationships among the three stone pine species, Pinus cembra, P. sibirica, and P. pumila, using chloroplast microsatellites and mitochondrial nad1 intron 2 sequences. The three chloroplast microsatellite loci combined into a total of 18 haplotypes. Fourteen haplotypes were detected in 15 populations of P. cembra and one population of P. sibirica, five of which were shared between the two species, and the two populations of P. pumila comprised four species-specific haplotypes. Mitochondrial intron sequences confirmed this grouping of species. Sequences of P. cembra and P. sibirica were identical, but P. pumila differed by several nucleotide substitutions and insertions/deletions. A repeat region found in the former two species showed no intraspecific variation. These results indicate a relatively recent evolutionary separation of P. cembra and P. sibirica, despite their currently disjunct distributions. The species-specific chloroplast and mitochondrial markers of P. sibirica and P. pumila should help to trace the hybridization in their overlapping distribution area and to identify fossil remains with respect to the still unresolved postglacial re-colonization history of these two species.
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Affiliation(s)
- F Gugerli
- Eidgenössische Forschungsanstalt WSL, Zürcherstrasse 111, CH-8903 Birmensdorf, Switzerland.
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Viard F, El-Kassaby YA, Ritland K. Diversity and genetic structure in populations of Pseudotsuga menziesii (Pinaceae) at chloroplast microsatellite loci. Genome 2001; 44:336-44. [PMID: 11444691 DOI: 10.1139/g01-010] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Genetic variation was compared between uniparentally-inherited (chloroplast simple sequence repeats, cpSSRs) vs. biparentally-inherited (isozyme and random amplified polymorphic DNA, RAPD) genetic markers in Douglas-fir (Pseudotsuga mensiezii) from British Columbia. Three-hundred twenty-three individuals from 11 populations were assayed. In Douglas-fir, the cpSSR primer sites were well-conserved relative to Pinus thunbergii (11 of 17 loci clearly amplified), but only 3 loci were appreciably polymorphic. At these cpSSR loci, we found an unexpectedly low level of polymorphism within populations, and no genetic differentiation among populations. By contrast, the nuclear markers showed variation typical of conifers, with significant among-population differentiation. This difference is likely the outcome of both historical factors and high pollen dispersal.
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Affiliation(s)
- F Viard
- Laboratoire Génétique et Evolution des Populations Vegetales, Centre National de la Recherche Scientifique (UPRESA-CNRS) 8016, Fédération de Recherche, Univ Lille 1, Villeneuve d'Ascq, France.
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Provan J, Powell W, Hollingsworth PM. Chloroplast microsatellites: new tools for studies in plant ecology and evolution. Trends Ecol Evol 2001; 16:142-147. [PMID: 11179578 DOI: 10.1016/s0169-5347(00)02097-8] [Citation(s) in RCA: 333] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The nonrecombinant, uniparentally inherited nature of organelle genomes makes them useful tools for evolutionary studies. However, in plants, detecting useful polymorphism at the population level is often difficult because of the low level of substitutions in the chloroplast genome, and because of the slow substitution rates and intramolecular recombination of mtDNA. Chloroplast microsatellites represent potentially useful markers to circumvent this problem and, to date, studies have demonstrated high levels of intraspecific variability. Here, we discuss the use of these markers in ecological and evolutionary studies of plants, as well as highlighting some of the potential problems associated with such use.
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Soranzo N, Alia R, Provan J, Powell W. Patterns of variation at a mitochondrial sequence-tagged-site locus provides new insights into the postglacial history of European Pinus sylvestris populations. Mol Ecol 2000; 9:1205-11. [PMID: 10972760 DOI: 10.1046/j.1365-294x.2000.00994.x] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Due to their maternal mode of inheritance, mitochondrial markers can be regarded as almost 'ideal' tools in evolutionary studies of conifer populations. In the present study, polymorphism was analysed at one mitochondrial intron (nad 1, exon B/C) in 23 native European Pinus sylvestris populations. In a preliminary screening for variation using a polymerase chain reaction-restriction fragment length polymorphism approach, two length variants were identified. By fully sequencing the 2.5 kb region, the observed length polymorphism was found to result from the insertion of a 31 bp sequence, with no other mutations observed within the intron. A set of primers was designed flanking the observed mutation, which identified a novel sequence-tagged-site mitochondrial marker for P. sylvestris. Analysis of 747 trees from the 23 populations using these primers revealed the occurrence of two distinct haplotypes in Europe. Within the Iberian Peninsula, the two haplotypes exhibited extensive population differentiation (PhiST = 0.59; P < or = 0.001) and a marked geographical structuring. In the populations of central and northern Europe, one haplotype largely predominated, with the second being found in only one individual of one population.
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Affiliation(s)
- N Soranzo
- Department of Cell and Molecular Genetics, Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, Scotland,Depto Sistemas Forestales, CIT-INIA, Madrid, Spain
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Scotti I, Magni F, Fink R, Powell W, Binelli G, Hedley PE. Microsatellite repeats are not randomly distributed within Norway spruce (Picea abies K.) expressed sequences. Genome 2000. [DOI: 10.1139/g99-095] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A Norway spruce (Picea abies K.) cDNA library obtained from vegetative bud tissue was screened for the presence of (AG)n and (AC)n microsatellite repeats. Ten (AG)n and six (AC)n microsatellites were found, with an average length of 25.5 repeat units. Most of the microsatellites are simple perfect repeats. The microsatellite distribution within the clones is clearly non-random, with different classes of repeats lying in different positions relative to the coding region and in a highly conserved orientation. An estimate of the frequency of dinucleotide microsatellites in expressed regions was obtained, showing that SSRs (simple sequence repeats) are found in genes about 20 times less frequently than in random genomic clones, with (AG)n repeats more frequent than (AC)n repeats. Potential applications of these sequences as expressed region-based molecular markers are shown by developing six SSR markers for the detection of natural variation in Norway spruce populations and testing two of them for the identification of illegitimate progenies from a mapping population. Key words: Picea abies, microsatellites, SSRs, ESTs, population genetics, trees.
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Vendramin GG, Anzidei M, Madaghiele A, Sperisen C, Bucci G. Chloroplast microsatellite analysis reveals the presence of population subdivision in Norway spruce (Picea abies K.). Genome 2000. [DOI: 10.1139/g99-093] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Three chloroplast microsatellites (cpSSRs), previously sequence characterized and for which paternal inheritance was tested and confirmed, were used to assess their usefulness as informative markers for phylogeographic studies in Norway spruce (Picea abies K.) and to detect spatial genetic differentiation related to the possible recolonization processes in the postglacial period. Ninety-seven populations were included in the survey. Some 8, 7, and 6 different size variants for the three cpSSRs, respectively, were scored by analysing 1105 individuals. The above 21 variants combined into 41 different haplotypes. The distribution of some haplotypes showed a clear geographic structure and seems to be related to the existence of different refugia during the last glacial period. The analysis of chloroplast SSR variation detected the presence of two main gene pools (Sarmathic-Baltic and Alpine - Centre European) and a relatively low degree of differentiation (RST of about 10%), characteristic of tree species with large distribution and probably influenced by an intensive human impact on this species. Based on our data, we were not able to detect any evidence concerning the existence of additional gene pools (e.g., from Balkan and Carpathian glacial refugia), though we cannot exclude the existence of genetic discontinuity within the species' European range. A large proportion of population-specific haplotypes were scored in this species, thus indicating a possible usefulness of these markers for the identification of provenances, seed-lots, and autochthonous stands. Key words: haplotypic diversity, phylogeography, chloroplast microsatellites, recolonization.
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Desplanque B, Viard F, Bernard J, Forcioli D, Saumitou-Laprade P, Cuguen J, Van Dijk H. The linkage disequilibrium between chloroplast DNA and mitochondrial DNA haplotypes in Beta vulgaris ssp. maritima (L.): the usefulness of both genomes for population genetic studies. Mol Ecol 2000; 9:141-54. [PMID: 10672158 DOI: 10.1046/j.1365-294x.2000.00843.x] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The structure and evolution of the plant mitochondrial genome may allow recurrent appearance of the same mitochondrial variants in different populations. Whether the same mitochondrial variant is distributed by migration or appears recurrently by mutation (creating homoplasy) in different populations is an important question with regard to the use of these markers for population genetic analyses. The genetic association observed between chloroplasts and mitochondria (i.e. two maternally inherited cytoplasmic genomes) may indicate whether or not homoplasy occurs in the mitochondrial genome. Four-hundred and fourteen individuals sampled in wild populations of beets from France and Spain were screened for their mitochondrial and chloroplast polymorphisms. Mitochondrial DNA (mtDNA) polymorphism was investigated with restriction fragment length polymorphism (RFLP) and chloroplast DNA (cpDNA) polymorphism was investigated with polymerase chain reaction PCR-RFLP, using universal primers for the amplification. Twenty and 13 variants for mtDNA and cpDNA were observed, respectively. Most exhibited a widespread geographical distribution. As a very strong linkage disequilibrium was estimated between mtDNA and cpDNA haplotypes, a high rate of recurrent mutation was excluded for the mitochondrial genome of beets. Identical mitochondrial variants found in populations of different regions probably occurred as a result of migration. We concluded from this study that mtDNA is a tool as valuable as cpDNA when a maternal marker is needed for population genetics analyses in beet on a large regional scale.
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Affiliation(s)
- B Desplanque
- Laboratoire de Génétique et Evolution des Populations Végétales, UPRESA CNRS 8016 FR CNRS 1818, Bât. SN2, Université de Lille 1, F-59655 Villeneuve d'Ascq cedex, France
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Provan J, Russell JR, Booth A, Powell W. Polymorphic chloroplast simple sequence repeat primers for systematic and population studies in the genus Hordeum. Mol Ecol 1999; 8:505-11. [PMID: 10199011 DOI: 10.1046/j.1365-294x.1999.00545.x] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
In this study we report the development of primers to amplify polymorphic chloroplast simple sequence repeats in the genus Hordeum, which includes cultivated barley (H. vulgare ssp. vulgare) and its wild progenitor H. vulgare ssp. spontaneum. Polymorphic products were amplified in a wide range of Hordeum spp. and intraspecific variation was detected in both cultivated and wild barley. A decrease in cytoplasmic diversity was observed between sspp. spontaneum and vulgare as well as between ssp. vulgare landraces and cultivars, which is characteristic of domestication processes in many corp species. We also observed possible evidence for reticulate evolution of H. brachyantherum polyploids, with apparent multiple cytoplasmic introgressions during successive polyploidization events.
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Affiliation(s)
- J Provan
- Department of Cell and Molecular Genetics, Scottish Crop Research Institute, Invergowrie, Dundee, UK.
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