Strong genetic differentiation among populations of Fosterella rusbyi (Bromeliaceae) in Bolivia

2019 ◽  
Vol 192 (4) ◽  
pp. 744-759 ◽  
Author(s):  
Tina Wöhrmann ◽  
Ingo Michalak ◽  
Georg Zizka ◽  
Kurt Weising
Keyword(s):  
Genetic Differentiation ◽  
Microsatellite Markers ◽  
Haplotype Diversity ◽  
Natural Populations ◽  
Population Expansion ◽  
Genetic Distances ◽  
Allopatric Speciation ◽  
Seasonally Dry ◽  
Nuclear Microsatellite ◽  
Suitable Habitats

Abstract The terrestrial bromeliad Fosterella rusbyi is endemic to the Bolivian Andes, where it mainly grows on steep, exposed slopes along roadsides and riverbeds in the seasonally dry tropical forest (SDTF) and the mesic montane forest (Yungas) biomes. We hypothesize that allopatric speciation may have been a main driver of diversification in Fosterella since the Miocene and that the scattered distribution of suitable habitats fostered the evolution of the high degree of endemism observed today. To provide further information relating to this hypothesis, we analysed the partition of genetic diversity and the extent of gene flow among natural populations of F. rusbyi using plastid and nuclear microsatellite markers. Nineteen plastid haplotypes were found, but the mean haplotype diversity per population was low. Nuclear microsatellite markers revealed 177 different multilocus genotypes (MLGs), of which 31 occurred in more than one plant. Recurrent MLGs were found in 76 plants that were therefore identified as clones. A considerable deficit of heterozygotes was detected at all nuclear loci. Geographical and genetic distances between populations were only weakly correlated with each other. Genetic divergence between populations was extremely high for both marker classes, suggesting that seed and pollen flow are low, even over short distances. The observed patterns are consistent with our hypothesis that newly available sites are sporadically colonized by one or a few founders, followed by in situ population expansion via vegetative propagation, self-pollination and/or biparental inbreeding, genetic differentiation among persistent populations and, ultimately, allopatric speciation.

scholarly journals Genetic diversity and differentiation in reef-buildingMilleporaspecies, as revealed by cross-species amplification of fifteen novel microsatellite loci

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e2936 ◽  
Author(s):  
Caroline E. Dubé ◽  
Serge Planes ◽  
Yuxiang Zhou ◽  
Véronique Berteaux-Lecellier ◽  
Emilie Boissin
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Microsatellite Loci ◽  
Natural Populations ◽  
454 Sequencing ◽  
Genetic Distances ◽  
Null Alleles ◽  
Future Research ◽  
Significant Linkage ◽  
Pacific Species

Quantifying the genetic diversity in natural populations is crucial to address ecological and evolutionary questions. Despite recent advances in whole-genome sequencing, microsatellite markers have remained one of the most powerful tools for a myriad of population genetic approaches. Here, we used the 454 sequencing technique to develop microsatellite loci in the fire coralMillepora platyphylla, an important reef-builder of Indo-Pacific reefs.We tested the cross-species amplification of these loci in five other species of the genusMilleporaand analysed its success in correlation with the genetic distances between species using mitochondrial 16S sequences. We succeeded in discovering fifteen microsatellite loci in our target speciesM. platyphylla,among which twelve were polymorphic with 2–13 alleles and a mean observed heterozygosity of 0.411. Cross-species amplification in the five otherMilleporaspecies revealed a high probability of amplification success (71%) and polymorphism (59%) of the loci. Our results show no evidence of decreased heterozygosity with increasing genetic distance. However, only one locus enabled measures of genetic diversity in the Caribbean speciesM. complanatadue to high proportions of null alleles for most of the microsatellites. This result indicates that our novel markers may only be useful for the Indo-Pacific species ofMillepora.Measures of genetic diversity revealed significant linkage disequilibrium, moderate levels of observed heterozygosity (0.323–0.496) and heterozygote deficiencies for the Indo-Pacific species. The accessibility to new polymorphic microsatellite markers for hydrozoanMilleporaspecies creates new opportunities for future research on processes driving the complexity of their colonisation success on many Indo-Pacific reefs.

scholarly journals Development of microsatellite markers for horse-chestnut (Aesculus hippocastanum), their polymorphism in natural Greek populations, and cross-amplification in related species

Dendrobiology ◽  
2021 ◽  
pp. 105-116
Author(s):  
Łukasz Walas ◽  
Grzegorz Iszkuło ◽  
Zoltan Barina ◽  
Monika Dering
Keyword(s):  
Microsatellite Markers ◽  
Gene Diversity ◽  
Natural Populations ◽  
Illumina Miseq ◽  
Balkan Peninsula ◽  
Mean Value ◽  
Aesculus Hippocastanum ◽  
Horse Chestnut ◽  
Nuclear Microsatellite ◽  
Species Specific

New nuclear microsatellite markers (SSRs) were developed for Aesculus hippocastanum, a relict tree species from the Balkan Peninsula. The development of microsatellites was done using the Illumina MiSeq PE300 platform. Out of a set of 500 SSRs designed, a subset of 13 loci was tested using 290 individ­uals from seven natural populations. Twelve species-specific loci were polymorphic. The number of alleles per locus ranged from 2 to 17 and expected heterozygosity from 0.089 to 0.800 with a mean value of 0.484. The population of Kalampaka had the lowest value of allelic richness (2.63) and gene diversity in compari­son to the remaining populations. STRUCTURE analysis confirmed isolation of population Mariolata from the southern edge of the species range and genetic similarity among populations from the Pindos Mts. Ad­ditionally, the utility of new SSRs in 29 individuals from nine other Aesculus taxa was tested. Eleven markers gave polymorphic products for all tested species. For 24 individuals, a high-quality product was obtained for each marker. Results confirmed the utility of specific markers for future population genetics studies.

scholarly journals Genetic Differentiation Studies among Natural Populations of Tilapia zillii

2015 ◽  
Vol 7 (4) ◽  
pp. 423-429
Author(s):  
Tofunmi E. OLADIMEJI ◽  
Michael O. AWODIRAN ◽  
Olaniyi O. KOMOLAFE
Keyword(s):  
Genetic Differentiation ◽  
Random Amplified Polymorphic Dna ◽  
Natural Populations ◽  
Principal Component ◽  
Genetic Distances ◽  
Morphological Studies ◽  
Tilapia Zillii ◽  
Meristic Counts ◽  
Ctab Method ◽  
Group Relationships

The population structure of Tilapia zillii (Gervais 1848) from three reservoirs in Nigeria, Osun State (Opa, Osu and Igun) was determined by employing morphological and molecular (Random Amplified Polymorphic DNA) methods. For morphological studies, 25 morphometric measurements and six meristic counts were recorded on 40 individuals within each population. Principal Component Analysis (PCA) was performed on the morphometric and meristic data using the PAST software. For RAPD studies, genomic DNA was extracted from caudal fin tissue using CTAB method and five primers were used to initiate PCR amplifications. All the clusters produced by the Principal components analysis (PCA) of the morphometric and meristic parameters overlapped indicating a low level of genetic differentiation between the three populations of T. zillii studied. The UPGMA cluster diagram from RAPD analysis identified two major genotypic groups with inter and intra group relationships. All individuals in the first cluster were from the Osu reservoir, while individuals from Opa and Igun reservoirs constituted the second cluster. Nei’s unbiased measure of genetic distances was 0.8532, 0.7321 and 0.7111 for Osu, Igun and Opa populations respectively. This revealed that Opa and Igun populations were genetically closer, while Osu populations is distant from them. The results suggest that the RAPD technique could be used to differentiate populations of T. zillii. However, additional methods such as microsatellite and sequence analysis can be used to maximize the efficiency of genetic differentiation studies.

scholarly journals GENETIC CHANGE AND RATES OF CLADOGENESIS

Genetics ◽  
1975 ◽  
Vol 81 (4) ◽  
pp. 757-773
Author(s):  
John C Avise ◽  
Francisco J Ayala
Keyword(s):  
Genetic Differentiation ◽  
Genetic Distance ◽  
Genetic Divergence ◽  
Natural Populations ◽  
Genetic Distances ◽  
Genetic Change ◽  
The Other ◽  
Limited Information ◽  
History Of ◽  
The Relationship

ABSTRACT Models are introduced which predict ratios of mean levels of genetic divergence in species-rich versus species-poor phylads under two competing assumptions: (1) genetic differentiation is a function of time, unrelated to the number of cladogenetic events and (2) genetic differentiation is proportional to the number of speciation events in the group. The models are simple, general, and biologically real, but not precise. They lead to qualitatively distinct predictions about levels of genetic divergence depending upon the relationship between rates of speciation and amount of genetic change. When genetic distance between species is a function of time, mean genetic distances in speciose and depauperate phylads of equal evolutionary age are very similar. On the contrary, when genetic distance is a function of the number of speciations in the history of a phylad, the ratio of mean genetic distances separating species in speciose versus depauperate phylads is greater than one, and increases rapidly as the frequency of speciations in one group relative to the other increases. The models may be tested with data from natural populations to assess (1) possible correlations between rates of anagenesis and cladogenesis and (2) the amount of genetic differentiation accompanying the speciation process. The data collected in electrophoretic surveys and other kinds of studies can be used to test the predictions of the models. For this purpose genetic distances need to be measured in speciose and depauperate phylads of equal evolutionary age. The limited information presently available agrees better with the model predicting that genetic change is primarily a function of time, and is not correlated with rates of speciation. Further testing of the models is, however, required before firm conclusions can be drawn.

scholarly journals Novel microsatellite DNA markers indicate strict parthenogenesis and few genotypes in the invasive willow sawfly Nematus oligospilus

2012 ◽  
Vol 103 (1) ◽  
pp. 74-88 ◽  
Author(s):  
V. Caron ◽  
M. Norgate ◽  
F.J. Ede ◽  
T. Nyman ◽  
P. Sunnucks
Keyword(s):  
Microsatellite Markers ◽  
Southern Hemisphere ◽  
Genetic Recombination ◽  
Phenotypic Diversity ◽  
Natural Populations ◽  
Population Expansion ◽  
Evolutionary Genetics ◽  
Reproductive Mode ◽  
Invasive Range ◽  
Invasive Organisms

AbstractInvasive organisms can have major impacts on the environment. Some invasive organisms are parthenogenetic in their invasive range and, therefore, exist as a number of asexual lineages (=clones). Determining the reproductive mode of invasive species has important implications for understanding the evolutionary genetics of such species, more especially, for management-relevant traits. The willow sawfly Nematus oligospilus Förster (Hymenoptera: Tenthredinidae) has been introduced unintentionally into several countries in the Southern Hemisphere where it has subsequently become invasive. To assess the population expansion, reproductive mode and host-plant relationships of this insect, microsatellite markers were developed and applied to natural populations sampled from the native and expanded range, along with sequencing of the cytochrome-oxidase I mitochondrial DNA (mtDNA) region. Other tenthredinids across a spectrum of taxonomic similarity to N. oligospilus and having a range of life strategies were also tested. Strict parthenogenesis was apparent within invasive N. oligospilus populations throughout the Southern Hemisphere, which comprised only a small number of genotypes. Sequences of mtDNA were identical for all individuals tested in the invasive range. The microsatellite markers were used successfully in several sawfly species, especially Nematus spp. and other genera of the Nematini tribe, with the degree of success inversely related to genetic divergence as estimated from COI sequences. The confirmation of parthenogenetic reproduction in N. oligospilus and the fact that it has a very limited pool of genotypes have important implications for understanding and managing this species and its biology, including in terms of phenotypic diversity, host relationships, implications for spread and future adaptive change. It would appear to be an excellent model study system for understanding evolution of invasive parthenogens that diverge without sexual reproduction and genetic recombination.

Analysis of genetic diversity of Lactarius hatsudake in South China

2011 ◽  
Vol 57 (8) ◽  
pp. 661-666 ◽  
Author(s):  
Li He ◽  
Guo Liang ◽  
Zhou Guoying ◽  
Liu Jun-ang
Keyword(s):  
Genetic Analysis ◽  
Genetic Differentiation ◽  
Linear Relationship ◽  
South China ◽  
Genetic Difference ◽  
Haplotype Diversity ◽  
Natural Populations ◽  
Ectomycorrhizal Fungus ◽  
Its Sequences ◽  
Geographical Distance

Lactarius hatsudake is a type of ectomycorrhizal fungus that significantly influences the growth of pine trees. It is widely prevalent in Asian countries and has a high economic value. Artificial cultivation of this fungus has not been achieved as yet; therefore, excessive manual harvesting may cause serious damages to the site of its production. In this study, we analyzed 41 samples of L. hatsudake from south China using internal transcribed spacer (ITS) sequences. By comparing the differences among ITS sequences to identify the haplotype diversity within each population, the relationships among local populations, the relationship between the level of genetic differentiation and geographical separation, and the contributions of local and regional geographical separations to the overall ITS haplotype variation were analyzed. Genetic analysis indicates that ITS sequences obtained from these 41 L. hatsudake samples could be identified as 18 haplotypes, of which 13 haplotypes were contained in only a single sample, whereas the remaining sequence types all were contained in two or more samples. The most common sequence type, haplotype 6, was found in 16 samples and was distributed across nearly every region. The Mantel test demonstrated that there is no significant linear relationship between geographical distance and the FST value of genetic difference. Results of this research illustrates that there exists a certain degree of genetic intermixing among natural populations of L. hatsudake. From the group genetic analysis, it appears that there exists genetic differentiation of lower frequencies in natural populations of L. hatsudake; however, the linear relationship between the degree of genetic differentiation and geographical distance is not distinctly apparent.

scholarly journals Genetic Differentiation between Quercus frainetto Ten. and Q. pubescens Willd. in Romania

2011 ◽  
Vol 39 (1) ◽  
pp. 275 ◽  
Author(s):  
Alexandru Lucian CURTU ◽  
Ioan Calin MOLDOVAN ◽  
Mihai Cristian ENESCU ◽  
Iacob CRACIUNESC ◽  
Nicolae SOFLETEA
Keyword(s):  
Genetic Differentiation ◽  
Natural Populations ◽  
Introgressive Hybridization ◽  
Genetic Distances ◽  
Assignment Test ◽  
Quercus Frainetto ◽  
Marker Loci ◽  
Genetic Clusters ◽  
Individual Trees ◽  
Expressed Sequence

Little is known about genetic differences among Quercus frainetto and Q. pubescens, two species of section Dascia Kotschy (subgenus Lepidobalanus, white oaks) that reach in Romania the margins of their natural distribution range. A set of genomic SSRs (simple sequence repeats) and EST (expressed sequence tags)-SSRs was used to estimate the genetic differentiation among four natural populations of the two species. Q. pubescens had higher values of genetic diversity than Q. frainetto, although the differences were not significant. Two out of seven marker-loci, QrZAG112 and QpZAG110, displayed very high FST values. Averaged across loci, the genetic differentiation was high and significant (FST = 0.067). Genetic distances were much higher among species than among populations within species. A Bayesian analysis indicated that two is the most appropriate number of genetic clusters. Using a blind procedure (i.e. based on multilocus genotypes only) the vast majority of sampled individuals (90%) could be assigned to the cluster corresponding to their phenotypes. When information about sampling localities was introduced in the assignment test, all individual trees were correctly classified. The higher degree of admixture in Q. frainetto as compared to Q. pubescens may be explained by different rates of introgressive hybridization.

scholarly journals Short Note: Cross-Species Amplification and Characterization of Pinus Chloroplast Microsatellite Markers in Cedrus deodara Roxb.

2011 ◽  
Vol 60 (1-6) ◽  
pp. 65-69 ◽  
Author(s):  
H. S. Ginwal ◽  
P. Chauhan ◽  
S. Barthwal ◽  
A. Sharma ◽  
R. Sharma
Keyword(s):  
Microsatellite Markers ◽  
Short Note ◽  
Haplotype Diversity ◽  
Natural Populations ◽  
Chloroplast Microsatellite ◽  
Cedrus Deodara ◽  
Genetic Studies ◽  
Adult Trees ◽  
Two Populations

AbstractThe study reports the transferability of chloroplast microsatellite markers developed forPinusspecies toCedrus deodara. A total of 49 primer pairs (both nuclear and chloroplast) of Pinus species were tested inC. deodaraout of which 21 chloroplast primers showed positive amplification and 20 were found polymorphic. The primers were screened on 100 adult trees of two natural populations ofC. deodara. Using twenty cpSSR primers, a total of 64 variants were found which combined in 70 different haplotypes. The total haplotype diversity in two populations was 0.860 and 0.876 with a mean of 0.868. These sets of markers can further be used for population genetic studies and characterization inC. deodarafor which no cpSSR markers have been reported till date.

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