scholarly journals Tracing back the origin of pumpkins ( Cucurbita pepo ssp. pepo L.) in Mexico

2019 ◽  
Vol 286 (1908) ◽  
pp. 20191440 ◽  
Author(s):  
Gabriela Castellanos-Morales ◽  
Karen Y. Ruiz-Mondragón ◽  
Helena S. Hernández-Rosales ◽  
Guillermo Sánchez-de la Vega ◽  
Niza Gámez ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Genetic Differentiation ◽  
Microsatellite Loci ◽  
Approximate Bayesian Computation ◽  
Cucurbita Pepo ◽  
Improved Varieties ◽  
Nuclear Microsatellite ◽  
Well Differentiated ◽  
Approximate Bayesian ◽  
Chloroplast Haplotypes

Cucurbita pepo is an economically important crop, which consists of cultivated C. pepo ssp. pepo , and two wild taxa ( C. pepo ssp. fraterna and C. pepo ssp. ovifera ) . We aimed at understanding the domestication and the diversity of C. pepo in Mexico. We used two chloroplast regions and nine nuclear microsatellite loci to assess the levels of genetic variation and structure for C. pepo ssp. pepo 's landraces sampled in 13 locations in Mexico, five improved varieties, one C. pepo ssp. fraterna population and ornamental C. pepo ssp. ovifera . We tested four hypotheses regarding the origin of C. pepo ssp. pepo 's ancestor through approximate Bayesian computation: C. pepo ssp. ovifera as the ancestor; C. pepo ssp. fraterna as the ancestor; an unknown extinct lineage as the ancestor; and C. pepo ssp. pepo as hybrid from C. pepo ssp. ovifera and C. pepo ssp. fraterna ancestors. Cucurbita pepo ssp. pepo showed high genetic variation and low genetic differentiation. Cucurbita pepo ssp. fraterna and C. pepo ssp. pepo shared two chloroplast haplotypes. The three subspecies were well differentiated for microsatellite loci. Cucurbita pepo ssp. fraterna was probably C. pepo ssp. pepo 's wild ancestor, but subsequent hybridization between taxa complicate defining C. pepo ssp. pepo 's ancestor.

Genetic Differentiation of Rhododendron aureum Georgi at Nuclear Microsatellite Loci

2019 ◽  
Vol 55 (6) ◽  
pp. 762-766
Author(s):  
M. A. Polezhaeva ◽  
N. A. Tikhonova ◽  
M. V. Modorov ◽  
M. N. Ranyuk ◽  
O. S. Korchagina
Keyword(s):  
Genetic Differentiation ◽  
Microsatellite Loci ◽  
Nuclear Microsatellite ◽  
Rhododendron Aureum ◽  
Rhododendron Aureum Georgi

Genetic variation within and relationships among five subpopulations of Slovak Thoroughbred

2004 ◽  
Vol 52 (3) ◽  
pp. 259-265
Author(s):  
Daniela Šátková-Jakabová ◽  
J. Trandžík ◽  
Ľudmila Hudecová-Kvasňáková ◽  
Erika Hegedüšová-Zetochová ◽  
A. Bugarský ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Genetic Differentiation ◽  
International Society ◽  
Microsatellite Loci ◽  
Genetic Relationships ◽  
Allele Frequencies ◽  
Weinberg Equilibrium ◽  
Hardy Weinberg Equilibrium

Genetic variation at six microsatellite loci was analysed for five Thoroughbred subpopulations to determine the magnitude of genetic differentiation and the genetic relationships among the subpopulations. Significant deviations from Hardy-Weinberg equilibrium were shown for a number of locus-population combinations, with all subpopulations. The genetic diversities and relationships of five Thoroughbred subpopulations were evaluated using six microsatellites recommended by the International Society of Animal Genetics (ISAG). The allele frequencies, the effective numbers of alleles, and the observed and expected heterozygosities were calculated. POPGENE v. 1.31 (Yeh et al., 1997) was used to test for deviations from the Hardy-Weinberg (H-W) equilibrium and to assign FIS estimates (Weir, 1990). The utility of microsatellites for evaluating genetic diversity of horses is discussed.

scholarly journals Phylogeographic evidence that the distribution of cryptic euryhaline species in the Gambusia punctata species group in Cuba was shaped by the archipelago geological history

2019 ◽  
Author(s):  
Erik García-Machado ◽  
José L. Ponce de Léon ◽  
María A. Gutiérrez-Costa ◽  
Alice Michel-Salzat ◽  
Isabelle Germon ◽  
...  
Keyword(s):  
Microsatellite Loci ◽  
Strong Association ◽  
Species Group ◽  
Hybrid Zones ◽  
Long Distance ◽  
Putative Species ◽  
Salinity Levels ◽  
Nuclear Microsatellite ◽  
Well Differentiated ◽  
Main Factor

AbstractThe main drivers of diversification of freshwater fishes in Cuba are not yet well understood. For example, salt tolerance was thought as the main factor involved in the diversification of Gambusia punctata species group in this archipelago. However, evidence from a recent DNA barcoding survey suggested the presence of cryptic species and no correlation between species delimitation and level of salinity. In this study, we analyzed the cryptic diversification of G. punctata species group in Cuba, based on a comprehensive sampling of its distribution and including habitats with different salinity levels. We evaluated the patterns of molecular divergence of the samples by sequencing a set of mitochondrial DNA (mtDNA) regions and genotyping nine nuclear microsatellite loci. We also used cytochrome b gene (cytb) partial sequences and these microsatellite loci to analyze population structure inside putative species. Five mtDNA well-differentiated haplogroups were found, four of them also identified by the analysis of the microsatellite polymorphism which corresponds to two already recognized species, G. punctata, and G. rhizophorae, and three putative new species. The extent of hybrid zones between these groups is also described. In each group, populations inhabiting environments with contrasting salinity levels were identified, indicating a generalized trait not specific to G. rhizophorae. The geographic distribution of the groups suggested a strong association with major relict territories of the Cuban Archipelago that was periodically joined or split-up by changes in seawater levels and land uplifts. Salinity tolerance might have facilitated sporadic and long-distance oversea dispersal but did not prevent speciation in the Cuban archipelago.

scholarly journals Spring-spawning herring (Clupea harengus L.) in the southwestern Baltic Sea: do they form genetically distinct spawning waves?

2005 ◽  
Vol 62 (6) ◽  
pp. 1065-1075 ◽  
Author(s):  
Hanne B. Hede Jørgensen ◽  
Michael Møller Hansen ◽  
Volker Loeschcke
Keyword(s):  
Genetic Variation ◽  
Genetic Differentiation ◽  
Baltic Sea ◽  
Microsatellite Loci ◽  
Temporal Patterns ◽  
Clupea Harengus ◽  
Spawning Season ◽  
Otolith Microstructure ◽  
Individual Assignment ◽  
Temporal Sampling

Abstract Temporal sampling within the spring-spawning season has revealed differentiation in length-at-age in herring at Rügen and differentiation in, e.g., Anisakis infestation rate, otolith microstructure, and gillraker counts in Gdańsk Bay, leading to the expectation that spawning waves consist of distinct herring populations. We tested this expectation by analysing genetic variation at nine microsatellite loci in samples collected at different times during the March to May spawning season in 2 consecutive years, 2002 and 2003. Length-at-age, mean length, and age distributions were compared among samples within locations but did not show consistent temporal patterns. Pairwise genetic differentiation among temporal samples within season was low and non-significant in the Gdańsk Bay (0 < FST < 0.0025) but higher among Rügen samples (0.0008 < FST < 0.0113). Samples from Rügen collected in 2002 differed significantly from each other, and individual assignment tests showed increased divergence with time. Differentiation was not confounded by effects of age class or sex. We conclude that spawning waves are not genetically differentiated among Gdańsk samples based on factors analysed in this study, whereas genetically distinct but sympatric spawning populations may be found at Rügen.

Genetic differentiation of Sorbus torminalis in Eastern Europe as determined by microsatellite markers

Biologia ◽  
2010 ◽  
Vol 65 (5) ◽  
Author(s):  
Veronika Kučerová ◽  
Martin Honec ◽  
Ladislav Paule ◽  
Petar Zhelev ◽  
Dušan Gömöry
Keyword(s):  
Genetic Variation ◽  
Gene Flow ◽  
Genetic Differentiation ◽  
Bayesian Methods ◽  
Isolation By Distance ◽  
General Pattern ◽  
The Other ◽  
Hand Model ◽  
Sorbus Torminalis ◽  
Nuclear Microsatellite

AbstractThe genetic variation in fourteen Sorbus torminalis (L.) Crantz. populations distributed over the eastern and south-eastern part of its range was studied using seven nuclear microsatellite loci. The differentiation level was relatively high (F ST = 0.228), as expected for a species with a fragmented range. The distance-based approach to the analysis of differentiation patterns (neighbour-joining tree based on pairwise coefficients of differentiation) did not reveal a clear geographical structure. On the other hand, model-based Bayesian methods (BAPS and STRUCTURE) gave geographically continuous clusters of populations. The occurrence of populations deviating strongly from the general pattern is attributed to founder effect. In spite of a generally high differentiation, a significant isolation-by-distance pattern was found, which might be a consequence of postglacial migration and gene flow among descendants of different refugia.

scholarly journals Assessing the relationship between height growth and molecular genetic variation in Douglas-fir (Pseudotsuga menziesii) provenances

2016 ◽  
Author(s):  
Charalambos Neophytou ◽  
Anna-Maria Weisser ◽  
Daniel Landwehr ◽  
Muhidin Šeho ◽  
Ulrich Kohnle ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Genetic Differentiation ◽  
Growth Performance ◽  
Pseudotsuga Menziesii ◽  
Phenotypic Variation ◽  
Microsatellite Loci ◽  
Variety Versus ◽  
Height Growth ◽  
Douglas Fir

Douglas-fir (Pseudotsuga menziesii) is a conifer tree native to western North America. In central Europe, it shows superior growth performance and is considered a suitable substitute for tree species impaired in vitality due to climate change. Maintenance and improvement of growth performance in a changing environment is a main challenge for forest tree breeders. In this context, genetic variation as a factor underlying phenotypic variation, but also as the basis for future adaptation, is of particular interest. The aims of this study were to analyse (i) genetic diversity of selected Douglas-fir provenances, (ii) variation in height growth among provenances, and (iii) to assess the link between genetic and phenotypic variation height growth. Genotyping was done on microsatellite loci. Effects of provenance, genotype, and site on height growth were assessed by fitting mixed linear models. The most significant genetic differentiation was observed between provenances of the coastal variety, versus a provenance of the interior variety originating from British Columbia. Although genetic differentiation among provenances of the coastal variety was lower, genetic structures within this variety were identified. Moreover, genetic diversity showed a latitudinal gradient with the southernmost provenances being more diverse, probably reflecting the species' evolutionary history. The modelling approach revealed that height growth differed significantly by provenance, site, and the interaction between site and provenance, demonstrating that height growth is under strong genetic control. Additionally, this analysis showed that genetic variation captured by the genotyped microsatellite loci was significantly related to variation in height growth, providing statistical evidence for a genetic component in the observed phenotypic variation.

scholarly journals Genetic diversity in Tunisian horse breeds

2017 ◽  
Vol 60 (2) ◽  
pp. 153-160 ◽  
Author(s):  
Bayrem Jemmali ◽  
Mohamed Mezir Haddad ◽  
Nawel Barhoumi ◽  
Syrine Tounsi ◽  
Faten Lasfer ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Genetic Structure ◽  
Genetic Differentiation ◽  
Microsatellite Loci ◽  
Genomic Dna ◽  
Genetic Distances ◽  
Jugular Veins ◽  
Blood Samples ◽  
Important Amount

Abstract. This study aimed at screening genetic diversity and differentiation in four horse breeds raised in Tunisia, the Barb, Arab-Barb, Arabian, and English Thoroughbred breeds. A total of 200 blood samples (50 for each breed) were collected from the jugular veins of animals, and genomic DNA was extracted. The analysis of the genetic structure was carried out using a panel of 16 microsatellite loci. Results showed that all studied microsatellite markers were highly polymorphic in all breeds. Overall, a total of 147 alleles were detected using the 16 microsatellite loci. The average number of alleles per locus was 7.52 (0.49), 7.35 (0.54), 6.3 (0.44), and 6 (0.38) for the Arab-Barb, Barb, Arabian, and English Thoroughbred breeds, respectively. The observed heterozygosities ranged from 0.63 (0.03) in the English Thoroughbred to 0.72 in the Arab-Barb breeds, whereas the expected heterozygosities were between 0.68 (0.02) in the English Thoroughbred and 0.73 in the Barb breeds. All FST values calculated by pairwise breed combinations were significantly different from zero (p  <  0.05) and an important genetic differentiation among breeds was revealed. Genetic distances, the factorial correspondence, and principal coordinate analyses showed that the important amount of genetic variation was within population. These results may facilitate conservation programs for the studied breeds and enhance preserve their genetic diversity.

Population Genetics ofCaenorhabditis elegans: The Paradox of Low Polymorphism in a Widespread Species

Genetics ◽  
2003 ◽  
Vol 163 (1) ◽  
pp. 147-157 ◽  
Author(s):  
Arjun Sivasundar ◽  
Jody Hey
Keyword(s):  
Genetic Variation ◽  
Microsatellite Loci ◽  
Population Expansion ◽  
Widespread Species ◽  
C Elegans ◽  
Model Research ◽  
The World ◽  
Natural Isolates ◽  
History Of ◽  
Low Levels

AbstractCaenorhabditis elegans has become one of the most widely used model research organisms, yet we have little information on evolutionary processes and recent evolutionary history of this widespread species. We examined patterns of variation at 20 microsatellite loci in a sample of 23 natural isolates of C. elegans from various parts of the world. One-half of the loci were monomorphic among all strains, and overall genetic variation at microsatellite loci was low, relative to most other species. Some population structure was detected, but there was no association between the genetic and geographic distances among different natural isolates. Thus, despite the nearly worldwide occurrence of C. elegans, little evidence was found for local adaptation in strains derived from different parts of the world. The low levels of genetic variation within and among populations suggest that recent colonization and population expansion might have occurred. However, the patterns of variation are not consistent with population expansion. A possible explanation for the observed patterns is the action of background selection to reduce polymorphism, coupled with ongoing gene flow among populations worldwide.

scholarly journals Weighted approximate Bayesian computation via Sanov’s theorem

2021 ◽  
Author(s):  
Cecilia Viscardi ◽  
Michele Boreale ◽  
Fabio Corradi
Keyword(s):  
Large Deviations ◽  
Posterior Distribution ◽  
Approximate Bayesian Computation ◽  
Bayesian Computation ◽  
Information Theoretic ◽  
Discrete Random Variables ◽  
Positive Weights ◽  
Approximate Bayesian ◽  
Information Theoretic Method ◽  
Computational Resources

AbstractWe consider the problem of sample degeneracy in Approximate Bayesian Computation. It arises when proposed values of the parameters, once given as input to the generative model, rarely lead to simulations resembling the observed data and are hence discarded. Such “poor” parameter proposals do not contribute at all to the representation of the parameter’s posterior distribution. This leads to a very large number of required simulations and/or a waste of computational resources, as well as to distortions in the computed posterior distribution. To mitigate this problem, we propose an algorithm, referred to as the Large Deviations Weighted Approximate Bayesian Computation algorithm, where, via Sanov’s Theorem, strictly positive weights are computed for all proposed parameters, thus avoiding the rejection step altogether. In order to derive a computable asymptotic approximation from Sanov’s result, we adopt the information theoretic “method of types” formulation of the method of Large Deviations, thus restricting our attention to models for i.i.d. discrete random variables. Finally, we experimentally evaluate our method through a proof-of-concept implementation.

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