scholarly journals Intense Browsing by Sika Deer (Cervus Nippon) Drives the Genectic Differentiation of Hairy Nettle (Urtica Thunbergiana) Populations

2021 ◽  
Author(s):  
Tetsuo I. Kohyama ◽  
Mei Yoshida ◽  
Masahito T. Kimura ◽  
Hiroaki Sato
Keyword(s):  
Gene Flow ◽  
Natural Selection ◽  
Genetic Differentiation ◽  
Genetic Drift ◽  
Sika Deer ◽  
Cervus Nippon ◽  
Deer Browsing ◽  
Principal Coordinates ◽  
Outlier Loci ◽  
Two Populations

Abstract Many studies have inferred the way in which natural selection, genetic drift and gene flow shape the population genetic structures, but very few have quantified the population differentiation under spatially and temporally varying levels of selection pressure, population fluctuation and gene flow. In Nara Park (6.6 km2; NP), central Japan, where several hundred sika deer (Cervus nippon) have been protected for more than 1,200 years, heavily- or moderately-haired nettle (Uritica thunbergiana) populations have evolved probably in response to intense deer browsing. Here, we analysed the genetic structure of two populations from NP and five from surrounding areas using amplified fragment length polymorphism markers. A total of 546 marker loci were genotyped from 210 individuals. A Bayesian method estimated 5.5% of these loci to be outliers, which are putatively under natural selection. Neighbour-joining, Bayesian clustering and principal coordinates analyses using all-loci, non-outlier loci and outlier loci datasets showed that the two populations from NP formed a cluster distinct from the surroundings. These results indicate the genome-wide differentiation of the populations from NP and the surroundings. Moreover, these imply that: (1) gene flow is limited between these populations and thus genetic drift is a major factor causing the differentiation; and (2) natural selection imposed by intense deer browsing has contributed to some extent to the differentiation. In conclusion, sika deer seems to have counteracted genetic drift to drive the genetic differentiation of hairy nettles in NP. This study suggests that a single herbivore species could lead genetic differentiation among plant populations.

scholarly journals Adaptive divergence in resistance to herbivores inDatura stramonium

PeerJ ◽  
2015 ◽  
Vol 3 ◽  
pp. e1411 ◽  
Author(s):  
Guillermo Castillo ◽  
Pedro L. Valverde ◽  
Laura L. Cruz ◽  
Johnattan Hernández-Cumplido ◽  
Guadalupe Andraca-Gómez ◽  
...  
Keyword(s):  
Gene Flow ◽  
Genetic Differentiation ◽  
Genetic Drift ◽  
Datura Stramonium ◽  
Adaptive Divergence ◽  
Restricted Gene Flow ◽  
Trichome Density ◽  
Phenotypic Differentiation ◽  
Phenotypic Resistance ◽  
Resistance Traits

Defensive traits exhibited by plants vary widely across populations. Heritable phenotypic differentiation is likely to be produced by genetic drift and spatially restricted gene flow between populations. However, spatially variable selection exerted by herbivores may also give rise to differences among populations. To explore to what extent these factors promote the among-population differentiation of plant resistance of 13 populations ofDatura stramonium, we compared the degree of phenotypic differentiation (PST) of leaf resistance traits (trichome density, atropine and scopolamine concentration) against neutral genetic differentiation (FST) at microsatellite loci. Results showed that phenotypic differentiation in defensive traits among-population is not consistent with divergence promoted by genetic drift and restricted gene flow alone. Phenotypic differentiation in scopolamine concentration was significantly higher thanFSTacross the range of trait heritability values. In contrast, genetic differentiation in trichome density was different fromFSTonly when heritability was very low. On the other hand, differentiation in atropine concentration differed from the neutral expectation when heritability was less than or equal to 0.3. In addition, we did not find a significant correlation between pair-wise neutral genetic distances and distances of phenotypic resistance traits. Our findings reinforce previous evidence that divergent natural selection exerted by herbivores has promoted the among-population phenotypic differentiation of defensive traits inD. stramonium.

scholarly journals Microsatellite Characterization of Malaysian Mahseer (Tor spp.) for Improvement of Broodstock Management and Utilization

Animals ◽  
2021 ◽  
Vol 11 (9) ◽  
pp. 2633
Author(s):  
Poh Chiang Chew ◽  
Annie Christianus ◽  
Jaapar M. Zudaidy ◽  
Md Yasin Ina-Salwany ◽  
Chou Min Chong ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Gene Flow ◽  
Genetic Differentiation ◽  
Genetic Relatedness ◽  
Genetic Distances ◽  
Group Method ◽  
Genetic Management ◽  
Principal Coordinates Analysis ◽  
Principal Coordinates ◽  
Geographical Regions

In this study, a mixture of Tor tambra and T. tambroides with unknown genetic background were collected from 11 localities in Malaysia for broodstock development and sperm cryo-banking. This study aims to assess the microsatellite (simple sequence repeat, SSR) variation, genetic diversity, genetic differentiation, level of gene flow, population structure, genetic relatedness and their demographic aspects among these Tor populations, in addition to establishing their SSR profile by employing 22 SSR markers via fragment analysis. Total genomic DNA was extracted from 181 samples (91 cryopreserved milt samples and 90 scale samples of live broodfish). Results showed the Tor spp. collection retained their genetic variation but exhibited excessive homozygosity among individuals within population. Moderate genetic differentiation was shown among the populations, with highly significant (p < 0.001) fixation indices (FST, FIS and FIT). A low gene flow over all loci (Nm 1.548) indicates little genetic variation transfer between populations. The genetic structures of all the populations were successfully resolved into four main clusters by an unweighted pair group method with arithmetic mean (UPGMA) dendrogram generated based on Nei’s genetic distances. The population structures based on principal coordinates analysis (PCoA) and the Bayesian model also suggested four distinct clusters following geographical regions and eight closely related populations. This study provided a useful baseline reference for better genetic management and utilization of the Tor spp. stocks in their breeding and conservation programmes.

scholarly journals Population Structure, Pathogenicity, and Mating Type Distribution of Magnaporthe oryzae Isolates from East Africa

2015 ◽  
Vol 105 (8) ◽  
pp. 1137-1145 ◽  
Author(s):  
Geoffrey Onaga ◽  
Kerstin Wydra ◽  
Birger Koopmann ◽  
Yakouba Séré ◽  
Andreas von Tiedemann
Keyword(s):  
Population Structure ◽  
Gene Flow ◽  
Genetic Differentiation ◽  
East Africa ◽  
Mating Type ◽  
Magnaporthe Oryzae ◽  
Geographic Origin ◽  
The Philippines ◽  
Genetic Population ◽  
Principal Coordinates

Rice blast, caused by Magnaporthe oryzae, is one of the emergent threats to rice production in East Africa (EA), where little is known about the population genetics and pathogenicity of this pathogen. We investigated the genetic diversity and mating type (MAT) distribution of 88 isolates of M. oryzae from EA and representative isolates from West Africa (WA) and the Philippines (Asia) using amplified fragment length polymorphism markers and mating-type-specific primer sets. In addition, the aggressiveness of each isolate was evaluated by inoculating on the susceptible Oryza sativa indica ‘Co39’, scoring the disease severity and calculating the disease progress. Hierarchical analysis of molecular variance revealed a low level of genetic differentiation at two levels (FST 0.12 and FCT 0.11). No evidence of population structure was found among the 65 isolates from EA, and gene flow among EA populations was high. Moreover, pairwise population differentiation (GST) in EA populations ranged from 0.03 to 0.04, suggesting that >96% of genetic variation is derived from within populations. However, the populations from Asia and WA were moderately differentiated from EA ones. The spatial analysis of principal coordinates and STRUCTURE revealed overlapping between individual M. oryzae isolates from EA, with limited distinctness according to the geographic origin. All the populations were clonal, given the positive and significant index of association (IA) and standardized index of association (rd), which indicates a significant (P < 0.001) departure from panmixia (IA and rd = 0). Both MAT1-1 and MAT1-2 were detected. However, MAT1-1 was more prevalent than MAT1-2. Pathogenicity analysis revealed variability in aggressiveness, suggesting a potential existence of different races. Our data suggest that either M. oryzae populations from EA could be distributed as a single genetic population or gene flow is exerting a significant influence, effectively swamping the action of selection. This is the first study of genetic differentiation of rice-infecting M. oryzae strains from EA, and may guide further studies on the pathogen as well as resistance breeding efforts.

Habitat type promotes rapid and extremely localised genetic differentiation in dolphins

2007 ◽  
Vol 58 (7) ◽  
pp. 640 ◽  
Author(s):  
Luciana M. Möller ◽  
Joanna Wiszniewski ◽  
Simon J. Allen ◽  
Luciano B. Beheregaray
Keyword(s):  
Gene Flow ◽  
Genetic Differentiation ◽  
Habitat Type ◽  
Local Area ◽  
Fixation Index ◽  
Geographic Proximity ◽  
Mitochondrial Dna Control Region ◽  
Open Coast ◽  
Clustering Approach ◽  
Two Populations

The high potential for dispersal of many marine organisms often results in low population differentiation over large distances. Here, we report that dolphin communities living in very close geographic proximity (<16 km) but in two different environments – open coast and enclosed embayment – exhibit unexpected genetic differentiation at nine microsatellite loci. Results based on a fixation index and a Bayesian clustering approach suggested that gene flow between communities within an embayment is high, as is gene flow between coastal communities. However, lower gene flow between embayment and open coast communities translated into substantial genetic differentiation between dolphin communities from the two environments, and assignment of individuals into two populations. Along with patterns observed in 403 bp of the mitochondrial DNA control region, the results suggest that restriction of gene flow likely occurred in the last 6000 years, after coastal dolphins colonised the embayment. We hypothesise that factors such as fidelity to the local area and resource and behavioural specialisations may have played a major role in promoting and maintaining genetic subdivision between dolphins of the two environments. Importantly, our study shows that habitat type can rapidly promote extremely fine-scale genetic structure in a long-lived, highly mobile marine mammal.

scholarly journals Prevalence of disruptive selection predicts extent of species differentiation in Lake Victoria cichlids

2018 ◽  
Vol 285 (1871) ◽  
pp. 20172630 ◽  
Author(s):  
Jacco C. van Rijssel ◽  
Florian N. Moser ◽  
David Frei ◽  
Ole Seehausen
Keyword(s):  
Gene Flow ◽  
Natural Selection ◽  
Genetic Differentiation ◽  
Lake Victoria ◽  
Sister Species ◽  
Disruptive Selection ◽  
Nuptial Coloration ◽  
Ecological Selection ◽  
Evolutionary Response ◽  
Species Pairs

Theory suggests that speciation with gene flow is most likely when both sexual and ecological selection are divergent or disruptive. Divergent sexual and natural selection on the visual system have been demonstrated before in sympatric, morphologically similar sister species of Lake Victoria cichlids, but this does not explain the subtle morphological differences between them. To investigate the significance of natural selection on morphology during speciation, we here ask whether the prevalence of disruptive ecological selection differs between sympatric sister species that are at different stages of speciation. Some of our species pairs do ( Pundamilia ) and others do not ( Neochromis ) differ distinctively in sexually selected male nuptial coloration. We find that (i) evidence for disruptive selection, and for evolutionary response to it, is prevalent in traits that are differentiated between sister species; (ii) prevalence of both predicts the extent of genetic differentiation; and (iii) genetic differentiation is weaker in species pairs with conserved male nuptial coloration. Our results speak to the existence of two different mechanisms of speciation with gene flow: speciation mainly by sexual selection tightly followed by ecological character displacement in some cases and speciation mainly by divergent ecological selection in others.

scholarly journals The genetic structure of populations of orchids and its evolutionary importance: understanding processes from patterns

Lankesteriana ◽  
2016 ◽  
Vol 3 (2) ◽  
Author(s):  
Raymond L. Tremblay
Keyword(s):  
Gene Flow ◽  
Natural Selection ◽  
Genetic Structure ◽  
Population Size ◽  
Effective Population Size ◽  
Genetic Drift ◽  
Mating Systems ◽  
Mutation Rates ◽  
Effective Population ◽  
Genetic Structure Of Populations

<div class="page" title="Page 1"><div class="layoutArea"><div class="column"><p><span>Evolution through either natural selection or genetic drift is dependent on variation at the genetic and mor- phological levels. Processes that influence the genetic structure of populations include mating systems, effective population size, mutation rates and gene flow among populations. </span></p></div></div></div>

scholarly journals Contrasting the effects of natural selection, genetic drift and gene flow on urban evolution in white clover ( Trifolium repens )

2018 ◽  
Vol 285 (1883) ◽  
pp. 20181019 ◽  
Author(s):  
Marc T. J. Johnson ◽  
Cindy M. Prashad ◽  
Mélanie Lavoignat ◽  
Hargurdeep S. Saini
Keyword(s):  
Gene Flow ◽  
Natural Selection ◽  
Genetic Drift ◽  
White Clover ◽  
Trifolium Repens ◽  
Rural Areas ◽  
Isolation By Distance ◽  
Urban Centre ◽  
Production Of Hydrogen ◽  
Urban Rural

Urbanization is a global phenomenon with profound effects on the ecology and evolution of organisms. We examined the relative roles of natural selection, genetic drift and gene flow in influencing the evolution of white clover ( Trifolium repens ), which thrives in urban and rural areas. Trifolium repens exhibits a Mendelian polymorphism for the production of hydrogen cyanide (HCN), a potent antiherbivore defence. We quantified the relative frequency of HCN in 490 populations sampled along urban–rural transects in 20 cities. We also characterized genetic variation within 120 populations in eight cities using 16 microsatellite loci. HCN frequency increased by 0.6% for every kilometre from an urban centre, and the strength of this relationship did not significantly vary between cities. Populations did not exhibit changes in genetic diversity with increasing urbanization, indicating that genetic drift is unlikely to explain urban–rural clines in HCN frequency. Populations frequently exhibited isolation-by-distance and extensive gene flow along most urban–rural transects, with the exception of a single city that exhibited genetic differentiation between urban and rural populations. Our results show that urbanization repeatedly drives parallel evolution of an ecologically important trait across many cities that vary in size, and this evolution is best explained by urban–rural gradients in natural selection.

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