Dynamics of genetic variation in Taxus baccata: local versus regional perspectives

2004 ◽  
Vol 82 (2) ◽  
pp. 219-227 ◽  
Author(s):  
Karin Hilfiker ◽  
Rolf Holderegger ◽  
Peter Rotach ◽  
Felix Gugerli
Keyword(s):  
Genetic Variation ◽  
Gene Flow ◽  
Isolation By Distance ◽  
Random Amplified Polymorphic Dna ◽  
Alpine Region ◽  
Population Variation ◽  
Regional Differentiation ◽  
Taxus Baccata ◽  
Long Distance ◽  
Significant Differentiation

Increasing loss of habitat tends to reduce biodiversity at the inter- and intra-specific levels. Within species, the remaining diversity is often partitioned so that a great amount of neutral genetic variation is assigned to among-population variation. This implies reduced gene flow as a consequence of population isolation. We tested whether random amplified polymorphic DNA (RAPD) markers indicate population and (or) regional differentiation in Swiss populations of English yew (Taxus baccata L.), a dioecious forest tree species with scattered distribution. Our sampling included three northern Swiss regions, each containing four populations, and a central-Alpine region with two populations. Four RAPD primers, giving rise to 41 scorable marker bands, identified all but two sampled individuals as unique genotypes. Analyses of molecular variance (AMOVA) detected no significant differentiation among the three northern Swiss regions yet a marginally significant differentiation of these regions versus the central-Alpine region. Concordantly, Mantel tests revealed isolation by distance only when considering all 14 populations. We postulate that the inferred level of gene flow, through wind-borne pollen and occasional long-distance seed dispersal, prevents isolation by distance in northern Switzerland, where stands of T. baccata are relatively abundant. This perpetuates a coherent regional network of occurrences of T. baccata, as might be expected in a metapopulation.Key words: genetic variation, isolation by distance, metapopulation, population differentiation, RAPD-PCR, Taxus baccata.

scholarly journals Spatial population genomics of a recent mosquito invasion

2020 ◽  
Author(s):  
Thomas L Schmidt ◽  
T. Swan ◽  
Jessica Chung ◽  
Stephan Karl ◽  
Samuel Demok ◽  
...  
Keyword(s):  
Gene Flow ◽  
Population Genomics ◽  
Isolation By Distance ◽  
Spatial Genetic Structure ◽  
Nucleotide Polymorphisms ◽  
Discrete Events ◽  
Long Distance ◽  
Population Genomic ◽  
Asian Tiger ◽  
Study Designs

AbstractPopulation genomic approaches can characterise dispersal across a single generation through to many generations in the past, bridging the gap between individual movement and intergenerational gene flow. These approaches are particularly useful when investigating dispersal in recently altered systems, where they provide a way of inferring long-distance dispersal between newly established populations and their interactions with existing populations. Human-mediated biological invasions represent such altered systems which can be investigated with appropriate study designs and analyses. Here we apply temporally-restricted sampling and a range of population genomic approaches to investigate dispersal in a 2004 invasion of Aedes albopictus (the Asian tiger mosquito) in the Torres Strait Islands (TSI) of Australia. We sampled mosquitoes from 13 TSI villages simultaneously and genotyped 373 mosquitoes at genome-wide single nucleotide polymorphisms (SNPs): 331 from the TSI, 36 from Papua New Guinea (PNG), and 4 incursive mosquitoes detected in uninvaded regions. Within villages, spatial genetic structure varied substantially but overall displayed isolation by distance and a neighbourhood size of 232–577. Close kin dyads revealed recent movement between islands 31–203 km apart, and deep learning inferences showed incursive Ae. albopictus had travelled to uninvaded regions from both adjacent and non-adjacent islands. Private alleles and a coancestry matrix indicated direct gene flow from PNG into nearby islands. Outlier analyses also detected four linked alleles introgressed from PNG, with the alleles surrounding 12 resistance-associated cytochrome P450 genes. By treating dispersal as both an intergenerational process and a set of discrete events, we describe a highly interconnected invasive system.

scholarly journals Elucidating the drivers of genetic differentiation in Malaysian torrent frogs (Anura: Ranidae: Amolops): a landscape genomics approach

2019 ◽  
Vol 190 (1) ◽  
pp. 65-78 ◽  
Author(s):  
Kin Onn Chan ◽  
Rafe M Brown
Keyword(s):  
Genetic Variation ◽  
Gene Flow ◽  
Genetic Differentiation ◽  
Isolation By Distance ◽  
Variance Partitioning ◽  
Nucleotide Polymorphisms ◽  
Landscape Genomics ◽  
Mountain Ranges ◽  
Historical Factors ◽  
Environmental Attributes

Abstract The interplay between environmental attributes and evolutionary processes can provide valuable insights into how biodiversity is generated, partitioned and distributed. This study investigates the role of spatial, environmental and historical factors that could potentially drive diversification and shape genetic variation in Malaysian torrent frogs. Torrent frogs are ecologically conserved, and we hypothesize that this could impose tight constraints on dispersal routes, gene flow and consequently genetic structure. Moreover, levels of gene flow were shown to vary among populations from separate mountain ranges, indicating that genetic differentiation could be influenced by landscape features. Using genome-wide single nucleotide polymorphisms, in conjunction with landscape variables derived from Geographic Information Systems, we performed distance-based redundancy analyses and variance partitioning to disentangle the effects of isolation-by-distance (IBD), isolation-by-resistance (IBR) and isolation-by-colonization (IBC). Our results demonstrated that IBR contributed minimally to genetic variation. Intraspecific population structure can be largely attributed to IBD, whereas interspecific diversification was primarily driven by IBC. We also detected two distinct population bottlenecks, indicating that speciation events were likely driven by vicariance or founder events.

scholarly journals Genetic Structure of Cronartium ribicola Populations in Eastern Canada

1999 ◽  
Vol 89 (10) ◽  
pp. 915-919 ◽  
Author(s):  
K. Et-touil ◽  
L. Bernier ◽  
J. Beaulieu ◽  
J. A. Bérubé ◽  
A. Hopkin ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Genetic Differentiation ◽  
Distribution Systems ◽  
Gene Diversity ◽  
Isolation By Distance ◽  
Random Amplified Polymorphic Dna ◽  
Cronartium Ribicola ◽  
Eastern Canada ◽  
Long Distance ◽  
Evolutionary Forces

The genetic structure of populations of Cronartium ribicola was studied by sampling nine populations from five provinces in eastern Canada and generating DNA profiles using nine random amplified polymorphic DNA markers. Most of the total gene diversity (Ht = 0.386) was present within populations (Hw = 0.370), resulting in a low level of genetic differentiation among populations in northeastern North America (Fst = 0.062). A hierarchical analysis of genetic structure using an analysis of molecular variance (AMOVA) revealed no statistically significant genetic differentiation among provinces or among regions. Yet, genetic differentiation among populations within regions or provinces was small (AMOVA φst = 0.078) but statistically significant (P < 0.001) and was several orders of magnitude larger than differentiation among provinces. This is consistent with a scenario of subpopulations within a metapopulation, in which random drift following migration and new colonization are major evolutionary forces. A phenetic analysis using genetic distances revealed no apparent correlation between genetic distance and the province of origin of the populations. The hypothesis of isolation-by-distance in the eastern populations of C. ribicola was rejected by computing Mantel correlation coefficients between genetic and geographic distance matrices (P > 0.05). These results show that eastern Canadian provinces are part of the same white pine blister rust epidemiological unit. Nursery distribution systems are controlled provincially, with virtually no seedling movement among provinces; therefore, infected nursery material may not play an important role in the dissemination of this disease. Long-distance spore dispersal across provincial boundaries appears to be an epidemiologically important factor for this pathogen.

scholarly journals Genetic variation in the emblematic Puya raimondii (Bromeliaceae) from Huascarán National Park, Peru

2013 ◽  
Vol 13 (1) ◽  
pp. 67-74 ◽  
Author(s):  
Claudia Teresa Hornung-Leoni ◽  
Victoria Sosa ◽  
June Simpson ◽  
Katia Gil
Keyword(s):  
Genetic Diversity ◽  
Cluster Analysis ◽  
Genetic Variation ◽  
Gene Flow ◽  
Genetic Variability ◽  
National Park ◽  
Conservation Strategies ◽  
Long Distance Dispersal ◽  
Long Distance ◽  
Mountain Systems

Puya raimondii, the giant Peruvian and Bolivian terrestrial bromeliad, is an emblematic endemic Andean species well represented in Huascarán National Park in Peru. This park is the largest reserve of puna (high altitude plateau) vegetation. The objective of this study is to report on genetic variation in populations of P. raimondii from Huascarán and neighboring areas. AFLP profiles with four selective primer combinations were retrieved for 60 individuals from different zones. Genetic variability was estimated and a total of 172 bands were detected, of which 79.1% were polymorphic loci. The results showed genetic differentiation among populations, and gene flow. A cluster analysis showed that individuals of P. raimondii populations located in different mountain systems could be grouped together, suggesting long distance dispersal. Thus, conservation strategies for P. raimondii have to take into account exchange between populations located far apart in distance in order to preserve the genetic diversity of this showy species.

Life-history characteristics and landscape attributes as drivers of genetic variation, gene flow, and fine-scale population structure in northern Dolly Varden (Salvelinus malma malma) in Canada

2015 ◽  
Vol 72 (10) ◽  
pp. 1477-1493 ◽  
Author(s):  
Les N. Harris ◽  
Robert Bajno ◽  
Colin P. Gallagher ◽  
Itsuro Koizumi ◽  
Lucy K. Johnson ◽  
...  
Keyword(s):  
Population Structure ◽  
Genetic Variation ◽  
Life History ◽  
Gene Flow ◽  
Isolation By Distance ◽  
Dolly Varden ◽  
Salvelinus Malma ◽  
Dolly Varden Salvelinus Malma ◽  
Northern Dolly Varden ◽  
Population Demographic

The northern Dolly Varden (Salvelinus malma malma) displays variable life-history types and occupies freshwater habitats with varying levels of connectivity. Here, we assayed microsatellite DNA variation in northern Dolly Varden from the western Canadian Arctic to resolve landscape and life-history variables driving variation in genetic diversity and population structure. Overall, genetic variation was highest in anadromous populations and lowest in those isolated above waterfalls, with stream-resident forms intermediate between the two. Anadromous and isolated populations were genetically divergent from each other, while no genetic differentiation was detectable between sympatric anadromous and stream-resident forms. Population structure was stable over 25 years, hierarchically organized, and conformed to an isolation-by-distance pattern, but stream-isolated forms often deviated from these patterns. Gene flow occurred primarily among Yukon North Slope populations and between sympatric anadromous and resident forms. These results were sex-dependent to some extent, but were influenced more by reproductive status and life history. Our study provides novel insights into the life history, population demographic, and habitat variables that shape the distribution of genetic variation and population structure in Arctic fluvial habitats while providing a spatial context for management and conservation.

scholarly journals Genetic Structure of Populations of the Rice-Infecting Pathogen Rhizoctonia solani AG-1 IA from China

2009 ◽  
Vol 99 (9) ◽  
pp. 1090-1099 ◽  
Author(s):  
Joana Bernardes-de-Assis ◽  
Michelangelo Storari ◽  
Marcello Zala ◽  
Wenxiang Wang ◽  
Daohong Jiang ◽  
...  
Keyword(s):  
Gene Flow ◽  
Rhizoctonia Solani ◽  
Sexual Reproduction ◽  
Isolation By Distance ◽  
Reproductive Mode ◽  
Population Subdivision ◽  
Long Distance ◽  
Sheath Blight Disease ◽  
Genetic Structure Of Populations ◽  
Contemporary Gene Flow

Sheath blight disease (SBD) on rice, caused by Rhizoctonia solani AG-1 IA, is one of the most devastating rice diseases on a global basis, including China (in Eastern Asia), the world's largest rice-growing country. We analyzed the population genetics of nine rice-infecting populations from China using nine microsatellite loci. One allopatric population from India (Southern Asia) was included in the analyses. In total, 300 different multilocus genotypes were found among 572 fungal isolates. Clonal fractions within rice fields were 16 to 95%, suggesting that sclerotia were a major source of primary inoculum in some fields. Global ΦST statistics (ΦST = 42.49; P ≤ 0.001) were consistent with a relatively high level of differentiation among populations overall; however, pairwise comparisons gave nonsignificant RST values, consistent with contemporary gene flow among five of the populations. Four of these populations were located along the Yangtze River tributary network. Gene flow followed an isolation-by-distance model consistent with restricted long-distance migration. Historical migration rates were reconstructed and yielded values that explained the current levels of population subdivision. Except for one population which appeared to be strictly clonal, all populations showed evidence of a mixed reproductive mode, including both asexual and sexual reproduction. One population had a strictly recombining structure (all loci were in Hardy-Weinberg equilibrium) but the remaining populations from China and the one from India exhibited varying degrees of sexual reproduction. Six populations showed significant FIS values consistent with inbreeding.

scholarly journals Gene-flow between populations of cotton bollworm Helicoverpa armigera (Lepidoptera: Noctuidae) is highly variable between years

2005 ◽  
Vol 95 (4) ◽  
pp. 381-392 ◽  
Author(s):  
K.D. Scott ◽  
K.S. Wilkinson ◽  
N. Lawrence ◽  
C.L. Lange ◽  
L.J. Scott ◽  
...  
Keyword(s):  
Gene Flow ◽  
Helicoverpa Armigera ◽  
Isolation By Distance ◽  
Resistance Management ◽  
Small Scale ◽  
Genetic Structuring ◽  
Long Distance ◽  
Helicoverpa Armígera ◽  
To Come ◽  
Average Gene

AbstractBoth large and small scale migrations of Helicoverpa armigera Hübner in Australia were investigated using AMOVA analysis and genetic assignment tests. Five microsatellite loci were screened across 3142 individuals from 16 localities in eight major cotton and grain growing regions within Australia, over a 38-month period (November 1999 to January 2003). From November 1999 to March 2001 relatively low levels of migration were characterized between growing regions. Substantially higher than average gene-flow rates and limited differentiation between cropping regions characterized the period from April 2001 to March 2002. A reduced migration rate in the year from April 2002 to March 2003 resulted in significant genetic structuring between cropping regions. This differentiation was established within two or three generations. Genetic drift alone is unlikely to drive genetic differentiation over such a small number of generations, unless it is accompanied by extreme bottlenecks and/or selection. Helicoverpa armigera in Australia demonstrated isolation by distance, so immigration into cropping regions is more likely to come from nearby regions than from afar. This effect was most pronounced in years with limited migration. However, there is evidence of long distance dispersal events in periods of high migration (April 2001–March 2002). The implications of highly variable migration patterns for resistance management are considered.

scholarly journals Applied phylogeography of Cyclopia intermedia (Fabaceae) highlights the need for ‘duty of care’ when cultivating honeybush

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9818 ◽  
Author(s):  
Nicholas C. Galuszynski ◽  
Alastair J. Potts
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Gene Flow ◽  
Isolation By Distance ◽  
Cultivated Plants ◽  
Duty Of Care ◽  
Mountain Range ◽  
Wild Populations ◽  
Genetic Structuring ◽  
Mountain Ranges

Background The current cultivation and plant breeding of Honeybush tea (produced from members of CyclopiaVent.) do not consider the genetic diversity nor structuring of wild populations. Thus, wild populations may be at risk of genetic contamination if cultivated plants are grown in the same landscape. Here, we investigate the spatial distribution of genetic diversity within Cyclopia intermedia E. Mey.—this species is widespread and endemic in the Cape Floristic Region (CFR) and used in the production of Honeybush tea. Methods We applied High Resolution Melt analysis (HRM), with confirmation Sanger sequencing, to screen two non-coding chloroplast DNA regions (two fragments from the atpI-aptH intergenic spacer and one from the ndhA intron) in wild C. intermedia populations. A total of 156 individuals from 17 populations were analyzed for phylogeographic structuring. Statistical tests included analyses of molecular variance and isolation-by-distance, while relationships among haplotypes were ascertained using a statistical parsimony network. Results Populations were found to exhibit high levels of genetic structuring, with 62.8% of genetic variation partitioned within mountain ranges. An additional 9% of genetic variation was located amongst populations within mountains, suggesting limited seed exchange among neighboring populations. Despite this phylogeographic structuring, no isolation-by-distance was detected (p > 0.05) as nucleotide variation among haplotypes did not increase linearly with geographic distance; this is not surprising given that the configuration of mountain ranges dictates available habitats and, we assume, seed dispersal kernels. Conclusions Our findings support concerns that the unmonitored redistribution of Cyclopia genetic material may pose a threat to the genetic diversity of wild populations, and ultimately the genetic resources within the species. We argue that ‘duty of care’ principles be used when cultivating Honeybush and that seed should not be translocated outside of the mountain range of origin. Secondarily, given the genetic uniqueness of wild populations, cultivated populations should occur at distance from wild populations that is sufficient to prevent unintended gene flow; however, further research is needed to assess gene flow within mountain ranges.

scholarly journals Comparison of Genetic and Virulence Diversity of Melampsora larici-populina Populations on Wild and Cultivated Poplar and Influence of the Alternate Host

2006 ◽  
Vol 96 (9) ◽  
pp. 1027-1036 ◽  
Author(s):  
Pierre R. Gérard ◽  
Claude Husson ◽  
Jean Pinon ◽  
Pascal Frey
Keyword(s):  
Rapd Markers ◽  
Isolation By Distance ◽  
Random Amplified Polymorphic Dna ◽  
Rust Fungus ◽  
Alternate Host ◽  
Long Distance ◽  
High Genetic Diversity ◽  
Linkage Disequilibria ◽  
Poplar Trees ◽  
Virulence Diversity

The aims of this study were, first, to compare the genetic and virulence diversity between populations of the rust fungus Melampsora larici-populina on wild and cultivated poplar stands and, second, to investigate the influence of the presence of the alternate host of the pathogen, larch, on which its sexual reproduction occurs, on these diversities. Nine French M. larici-populina populations collected from poplar trees in autumn and four populations collected from larch trees during the following spring were analyzed using both virulence factors and neutral markers. In all, 30 pathotypes were identified within the 13 populations studied. The pathotypic structure clearly distinguished the cultivated stands with high richness and complexity from the wild stands with low richness and complexity. High linkage disequilibria between virulences indicated preferential virulence associations, probably due to selection by the host. In all, 19 random amplified polymorphic DNA (RAPD) markers were used, which revealed a very high genetic diversity in the 743 isolates analyzed. The nine populations from poplar appeared moderately differentiated, indicating long-distance gene flow, and no isolation by distance was found. Linkage disequilibria between RAPD markers generally were low, indicating frequent recombination, but they were not lower in populations located near larch, probably due to long-distance dispersal.

scholarly journals Limited long-distance dispersal success in a Western European fairy shrimp evidenced by nuclear and mitochondrial lineage structuring

2019 ◽  
Vol 66 (3) ◽  
pp. 227-237
Author(s):  
Paula C Rodríguez-Flores ◽  
Ernesto Recuero ◽  
Yolanda Jiménez-Ruiz ◽  
Mario García-París
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Iberian Peninsula ◽  
Isolation By Distance ◽  
Local Scale ◽  
Long Distance Dispersal ◽  
Evolutionary Potential ◽  
Long Distance ◽  
Widespread Species ◽  
Spatio Temporal

Abstract Anostraca are known by their ability for long-distance dispersal, but the existence in several species of deep, geographically structured mtDNA lineages suggests their populations are subjected to allopatric differentiation, isolation, and prevalence of local scale dispersion. Tanymastix stagnalis is one of the most widespread species of Anostraca and previous studies revealed an unclear geographical pattern of mtDNA genetic diversity. Here, we analyze populations from the Iberian and Italian Peninsulas, Central Europe, and Scandinavia, with the aim to characterize the patterns of genetic diversity in a spatio-temporal framework using mtDNA and nuclear markers to test gene flow among close populations. For these aims we built a time-calibrated phylogeny and carried out Bayesian phylogeographic analyses using a continuous diffusion model. Our results indicated that T. stagnalis presents a deeply structured genetic diversity, including 7 ancient lineages, some of them even predating the Pleistocene. The Iberian Peninsula harbors high diversity of lineages, with strong isolation and recent absence of gene flow between populations. Dispersal at local scale seems to be the prevailing dispersal mode of T. stagnalis, which exhibits a pattern of isolation-by-distance in the Iberian Peninsula. We remark the vulnerability of most of these lineages, given the limited known geographic distribution of some of them, and the high risk of losing important evolutionary potential for the species.

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