scholarly journals Highly Clonal Structure and Abundance of One Haplotype Characterise the Diplodia sapinea Populations in Europe and Western Asia

2021 ◽  
Vol 7 (8) ◽  
pp. 634
Author(s):  
Kalev Adamson ◽  
Marili Laas ◽  
Kathrin Blumenstein ◽  
Johanna Busskamp ◽  
Gitta J. Langer ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
North America ◽  
Opportunistic Pathogen ◽  
Pcr Primers ◽  
High Genetic Diversity ◽  
Multiple Introductions ◽  
Single Tree ◽  
Western Asia ◽  
Species Specific ◽  
Pinus Spp

Diplodia sapinea is a cosmopolitan endophyte and opportunistic pathogen having occurred on several conifer species in Europe for at least 200 years. In Europe, disease outbreaks have increased on several Pinus spp. in the last few decades. In this study, the genetic structure of the European and western Asian D. sapinea population were investigated using 13 microsatellite markers. In total, 425 isolates from 15 countries were analysed. A high clonal fraction and low genetic distance between most subpopulations was found. One single haplotype dominates the European population, being represented by 45.3% of all isolates and found in nearly all investigated countries. Three genetically distinct subpopulations were found: Central/North European, Italian and Georgian. The recently detected subpopulations of D. sapinea in northern Europe (Estonia) share several haplotypes with the German subpopulation. The northern European subpopulations (Latvia, Estonia and Finland) show relatively high genetic diversity compared to those in central Europe suggesting either that the fungus has existed in the North in an asymptomatic/endophytic mode for a long time or that it has spread recently by multiple introductions. Considerable genetic diversity was found even among isolates of a single tree as 16 isolates from a single tree resulted in lower clonal fraction index than most subpopulations in Europe, which might reflect cryptic sexual proliferation. According to currently published allelic patterns, D. sapinea most likely originates from North America or from some unsampled population in Asia or central America. In order to enable the detection of endophytic or latent infections of planting stock by D. sapinea, new species-specific PCR primers (DiSapi-F and Diplo-R) were designed. During the search for Diplodia isolates across the world for species specific primer development, we identified D. africana in California, USA, and in the Canary Islands, which are the first records of this species in North America and in Spain.

scholarly journals Highly clonal structure and abundance of one haplotype characterize the Diplodia sapinea populations in Europe and western Asia

2021 ◽  
Author(s):  
Kalev Adamson ◽  
Marili Laas ◽  
Kathrin Blumenstein ◽  
Johanna Busskamp ◽  
Gitta Langer ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
North America ◽  
Central Europe ◽  
Opportunistic Pathogen ◽  
Pcr Primers ◽  
First Record ◽  
German Population ◽  
Multiple Introductions ◽  
Western Asia ◽  
Pinus Spp

Diplodia sapinea is a cosmopolitan endophyte and opportunistic pathogen occurring on several conifer species in Europe for at least 200 years. In Europe, disease outbreaks have increased on several Pinus spp. in the last few decades. In this study, the genetic structure of the European D. sapinea population was investigated using thirteen microsatellite markers. In total, 425 isolates from 15 countries were analysed. A high clonal fraction and low genetic distance between most populations was found. One single haplotype dominates the European population, being represented by 44% of all isolates and found in nearly all investigated countries. Three genetically distinct subpopulations were found: Central/North European, Italian and Georgian. The recently detected populations of D. sapinea in northern Europe (Latvia, Estonia and Finland) share several haplotypes with the German population, suggesting introduction from Central Europe. The northern European populations show similar genetic diversity to those in Central Europe suggesting either that the fungus has existed in the North in an asymptomatic mode for a long time or that it has spread recently by multiple introductions. Although this fungus reproduces predominantly asexually, considerable genetic diversity was found even among isolates of a single tree. According to currently published allelic patterns, D. sapinea most likely originates from North America. In order to enable the detection of endophytic or latent infections of planting stock by D. sapinea, new species-specific PCR primers were designed. During the search for Diplodia isolates, we identified D. africana in California, USA, which is the first record of this species in North America.

scholarly journals Haplotype variation in the Physa acuta group (Basommatophora): genetic diversity and distribution in Serbia

2016 ◽  
Vol 17 (1) ◽  
pp. 292 ◽  
Author(s):  
M. J. RAKOVIĆ ◽  
M. B. RAKOVIĆ ◽  
A. M. PETROVIĆ ◽  
N. Z. POPOVIĆ ◽  
J. A. ĐUKNIĆ ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
North America ◽  
Abundant Species ◽  
Separate Species ◽  
High Genetic Diversity ◽  
Freshwater Gastropods ◽  
Multiple Introductions ◽  
Physa Acuta ◽  
Haplotype Variation ◽  
Migrating Birds

The genus Physa (= Physella) includes the most abundant and diverse freshwater gastropods native to North America. Due to their invasive nature many species occur throughout the world. The most abundant species, Physa acuta, has been introduced to Europe, Africa, Asia and Australia by human commerce and migrating birds. This species is widely distributed throughout Serbia. The aim of this study was to explore the genetic diversity of P. acuta from Serbia, and to determine the evolutionary relationships among native Physidae populations from North America, Mexico and Cuba and populations from Europe using sequences of the mitochondrial 16S rDNA gene. The ML (Maximum Likelihood) tree revealed two clades within Physidae, and two clades that correspond to the families Planorbidae and Lymnaeidae. In the Physidae clade there are two separate clades: one includes the species Physa spelunca, and the second includes samples of P. acuta. We determined three different haplotypes within specimens from Serbia. One haplotype is genetically closest to species Physa heterostrofa (synonym of P. acuta) from Philadelphia, while the other two are very close to P. acuta specimens from New Mexico. Together with other samples our findings corroborate the notion that we are dealing with one panmictic population of P. acuta and not with several separate species, despite the high genetic diversity between and among the populations. Our results indicate that in the same population in Serbia, there is high genetic distance between samples. Despite the small number of analyzed samples, our findings point to multiple introductions of P. acuta from different locations in America.

scholarly journals Patterns of Genetic Diversity in the Globally Invasive Species Wild Parsnip (Pastinaca sativa)

2015 ◽  
Vol 8 (4) ◽  
pp. 415-429 ◽  
Author(s):  
Tania Jogesh ◽  
Rhiannon Peery ◽  
Stephen R. Downie ◽  
May R. Berenbaum
Keyword(s):  
Genetic Diversity ◽  
Invasive Species ◽  
North America ◽  
Nuclear Ribosomal Dna ◽  
High Genetic Diversity ◽  
Wild Parsnip ◽  
Multiple Introductions ◽  
Cpdna Markers ◽  
Global Invasion ◽  
Accidental Introduction

AbstractWild parsnip is an invasive species with a global distribution in temperate climates. Parsnips are native to Eurasia and have been cultivated for more than five centuries. It is unclear whether the global invasion of this species is a consequence of escape from cultivation or the accidental introduction of a Eurasian wild subspecies. In this study, we used nuclear ribosomal DNA internal transcribed spacer (ITS) and chloroplast DNA (cpDNA) markers to evaluate the genetic structure of wild parsnip in its native range (Europe) and in three distinct geographic regions where it is considered invasive: eastern North America, western North America, and New Zealand. We also compared wild and cultivated parsnips to determine whether they are genetically distinct. From 112 individuals, we recovered 14 ITS and 27 cpDNA haplotypes. One ITS haplotype was widespread; few haplotypes were rare singletons. In contrast, at least two lineages of cpDNA haplotypes were recovered, with several novel haplotypes restricted to Europe. Cultivated parsnips were not genetically distinct from wild parsnips, and numerous wild parsnip populations shared haplotypes with cultivars. High genetic diversity was recovered in all three regions, suggesting multiple introductions.

scholarly journals Population genetics of the freshwater fish Prochilodus magdalenae (Characiformes: Prochilodontidae), using species-specific microsatellite loci

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e10327
Author(s):  
Ricardo M. Landínez-García ◽  
Juan Carlos Narváez ◽  
Edna J. Márquez
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Freshwater Fish ◽  
Microsatellite Loci ◽  
Natural Populations ◽  
Genetic Stock ◽  
High Genetic Diversity ◽  
Genetic Diversity And Structure ◽  
Genetic Stocks ◽  
Species Specific

Prochilodus magdalenae is a freshwater fish endemic to the Colombian Magdalena-Cauca and Caribbean hydrographic basins. The genetic structure patterns of populations of different members of Prochilodus and the historic restocking of its depleted natural populations suggest that P. magdalenae exhibits genetic stocks that coexist and co-migrate throughout the rivers Magdalena, Cauca, Cesar, Sinú and Atrato. To test this hypothesis and explore the levels of genetic diversity and population demography of 725 samples of P. magdalenae from the studied rivers, we developed a set of 11 species-specific microsatellite loci using next-generation sequencing, bioinformatics, and experimental tests of the levels of diversity of the microsatellite loci. The results evidenced that P. magdalenae exhibits high genetic diversity, significant inbreeding coefficient ranging from 0.162 to 0.202, and signs of erosion of the genetic pool. Additionally, the population genetic structure constitutes a mixture of genetic stocks heterogeneously distributed along the studied rivers, and moreover, a highly divergent genetic stock was detected in Chucurí, Puerto Berrío and Palagua that may result from restocking practices. This study provides molecular tools and a wide framework regarding the genetic diversity and structure of P. magdalenae, which is crucial to complement its baseline information, diagnosis and monitoring of populations, and to support the implementation of adequate regulation, management, and conservation policies.

scholarly journals Long live the alien: is high genetic diversity a pivotal aspect of crested porcupine (Hystrix cristata) long-lasting and successful invasion?

2015 ◽  
Author(s):  
Emiliano Trucchi ◽  
Benoit Facon ◽  
Paolo Gratton ◽  
Emiliano Mori ◽  
Nils Chr. Stenseth ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Evolutionary Dynamics ◽  
Leading Edge ◽  
High Genetic Diversity ◽  
Hystrix Cristata ◽  
The North ◽  
Fundamental Information ◽  
Genome Wide ◽  
Crested Porcupine ◽  
Species Specific

AbstractStudying the evolutionary dynamics of an alien species surviving and continuing to expand after several generations can provide fundamental information on the relevant features of clearly successful invasions. Here, we tackle this task by investigating the dynamics of the genetic diversity in invasive crested porcupine (Hystrix cristata) populations, introduced to Italy about 1500 years ago, which are still growing in size, distribution range and ecological niche. Using genome-wide RAD markers, we describe the structure of the genetic diversity and the demographic dynamics of the H. cristata invasive populations and compare their genetic diversity with that of native African populations of both H. cristata and its sister species, H. africaeaustralis. First, we demonstrate that genetic diversity is lower in both the invasive Italian and the North Africa source range relative to other native populations from Sub-Saharan and South Africa. Second, we find evidence of multiple introduction events in the invasive range followed by very limited gene flow. Through coalescence-based demographic reconstructions, we also show that the bottleneck at introduction was mild and did not affect the introduced genetic diversity. Finally, we reveal that the current spatial expansion at the northern boundary of the range is following a leading-edge model characterized by a general reduction of genetic diversity towards the edge of the expanding range. We conclude that the level of genome-wide diversity of H. cristata invasive populations is less important in explaining its successful invasion than species-specific life-history traits or the phylogeographic history in the native source range.

scholarly journals An identification tool for the Australian weedy Sporobolus species based on random amplified polymorphic DNA (RAPD) profiles

2005 ◽  
Vol 56 (2) ◽  
pp. 157 ◽  
Author(s):  
Sangita Shrestha ◽  
Stephen W. Adkins ◽  
Glenn C. Graham ◽  
Donald S. Loch
Keyword(s):  
Genetic Diversity ◽  
Genetic Markers ◽  
Native Species ◽  
Random Amplified Polymorphic Dna ◽  
Data Matrix ◽  
High Genetic Diversity ◽  
Considerable Difficulty ◽  
Major Cluster ◽  
Weedy Species ◽  
Species Specific

Based on morphological features alone, there is considerable difficulty in identifying the 5 most economically damaging weed species of Sporobolus [viz. S. pyramidalis P. Beauv., S. natalensis (Steud.) Dur and Schinz, S. fertilis (Steud.) Clayton, S. africanus (Poir.) Robyns and Tourney, and S. jacquemontii Kunth.] found in Australia. A polymerase chain reaction (PCR)-based random amplified of polymorphic DNA (RAPD) technique was used to create a series of genetic markers that could positively identify the 5 major weeds from the other less damaging weedy and native Sporobolus species. In the initial RAPD profiling experiment, using arbitrarily selected primers and involving 12 species of Sporobolus, 12 genetic markers were found that, when used in combination, could consistently identify the 5 weedy species from all others. Of these 12 markers, the most diagnostic were UBC51490 for S. pyramidalis and S. natalensis; UBC43310, 2000, 2100 for S. fertilis and S. africanus; and OPA20850 and UBC43470 for S. jacquemontii. Species-specific markers could be found only for S. jacquemontii. In an effort to understand why there was difficulty in obtaining species-specific markers for some of the weedy species, a RAPD data matrix was created using 40 RAPD products. These 40 products amplified by 6 random primers from 45 individuals belonging to 12 species, were then subjected to numerical taxonomy and multivariate system (NTSYS pc version 1.70) analysis. The RAPD similarity matrix generated from the analysis indicated that S. pyramidalis was genetically more similar to S. natalensis than to other species of the ‘S. indicus complex’. Similarly, S. jacquemontii was more similar to S. pyramidalis, and S. fertilis was more similar to S. africanus than to other species of the complex. Sporobolus pyramidalis, S. jacquemontii, S. africanus, and S. creber exhibited a low within-species genetic diversity, whereas high genetic diversity was observed within S. natalensis, S. fertilis, S. sessilis, S. elongates, and S. laxus. Cluster analysis placed all of the introduced species (major and minor weedy species) into one major cluster, with S. pyramidalis and S. natalensis in one distinct subcluster and S. fertilis and S. africanus in another. The native species formed separate clusters in the phenograms. The close genetic similarity of S. pyramidalis to S. natalensis, and S. fertilis to S. africanus may explain the difficulty in obtaining RAPD species-specific markers. The importance of these results will be within the Australian dairy and beef industries and will aid in the development of integrated management strategy for these weeds.

scholarly journals Looks can be deceiving: the deceptive milkcaps (Lactifluus, Russulaceae) exhibit low morphological variance but harbour high genetic diversity

IMA Fungus ◽  
2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Lynn Delgat ◽  
Glen Dierickx ◽  
Serge De Wilde ◽  
Claudio Angelini ◽  
Eske De Crop ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
North America ◽  
Species Complex ◽  
Molecular Study ◽  
Similar Species ◽  
High Genetic Diversity ◽  
Its1 Sequence ◽  
Neotropical Species ◽  
Species Complexes ◽  
Thin Walled

Abstract The ectomycorrhizal genus Lactifluus is known to contain many species complexes, consisting of morphologically very similar species, which can be considered cryptic or pseudocryptic. In this paper, a thorough molecular study is performed of the clade around Lactifluus deceptivus (originally described by Peck from North America) or the deceptive milkcaps. Even though most collections were identified as L. deceptivus, the clade is shown to contain at least 15 species, distributed across Asia and America, indicating that the L. deceptivus clade represents a species complex. These species are morphologically very similar and are characterized by a tomentose pileus with thin-walled hyphae and a velvety stipe with thick-walled hyphae. An ITS1 sequence was obtained through Illumina sequencing for the lectotype of L. deceptivus, dating from 1885, revealing which clade represents the true L. deceptivus. In addition, it is shown that three other described species also belong to the L. deceptivus clade: L. arcuatus, L. caeruleitinctus and L. mordax, and molecularly confirmed that L. tomentoso-marginatus represents a synonym of L. deceptivus. Furthermore, two new Neotropical species are described: Lactifluus hallingii and L. domingensis.

scholarly journals High Genetic Diversity among Breeding Red-Backed Shrikes Lanius collurio in the Western Palearctic

Diversity ◽  
2019 ◽  
Vol 11 (3) ◽  
pp. 31 ◽  
Author(s):  
Liviu Pârâu ◽  
Roberto Frias-Soler ◽  
Michael Wink
Keyword(s):  
Genetic Diversity ◽  
Direct Consequence ◽  
Migration Routes ◽  
Genetic Population ◽  
High Genetic Diversity ◽  
Lanius Collurio ◽  
Breeding Populations ◽  
Western Palearctic ◽  
Western Asia ◽  
Mitochondrial Cytochrome B

Revealing the genetic population structure in abundant avian species is crucial for understanding speciation, conservation, and evolutionary history. The Red-backed Shrike Lanius collurio, an iconic songbird renowned for impaling its prey, is widely distributed as a breeder across much of Europe, Asia Minor and western Asia. However, in recent decades, many populations have declined significantly, as a result of habitat loss, hunting along migration routes, decrease of arthropod food, and climate change e.g., severe droughts in Africa. Within this context, gene flow among different breeding populations becomes critical to ensure the survival of the species, but we still lack an overview on the genetic diversity of the species. In this paper, we analyzed the mitochondrial cytochrome b gene (mtDNA) and the cytochrome c oxidase subunit 1 gene (mtDNA) of 132 breeding Red-backed Shrikes from across the entire breeding range to address this knowledge gap. Our results revealed consistent genetic diversity and 76 haplotypes among the Eurasian populations. Birds are clustered in two major groups, with no clear geographical separation, as a direct consequence of Pleistocene glaciations and apparent lineage mixing in refugia. This has led to genetic panmixia.

Sign in / Sign up

Export Citation Format

Share Document