mantel test
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Author(s):  
H. Bougrine ◽  
A. Mebarkia ◽  
S. Bechkri

Background: In the present study, we have set a goal, to study the genetic variability and phylogenetic affinities of 26 spontaneous Vicia sativa L. accessions collected in Algeria, as part of the recovery and enhancement of the local genetic heritage and its integration into the breeding and varietal creation programs. Methods: Morphological traits, performance parameters and phenological stages of each accession were tracked during an experimental test in pots under greenhouse conditions from December 29, 2019 to June 1, 2020. An eco-geographical characterization of samples was also carried out through geographical coordinates. On the other side and for the first time in Algeria, soil analyses of each site were undertaken. Result: The phylogenetic study of accessions confirm the taxonomic complexity of the group V. sativa L. According to the principal component analyses and kruskal-Wallis test, the most segregating variables with the highest values and the largest K variance ratios are most of the attributes associated with the flower, pod and seed. The association of the two dissimilarity matrix carried out by a Mantel test between the morphological and eco-geographic parameters showed a significant effect with a p value = 0.004 at the threshold of alpha=0.05 and a correlation coefficient r (AB) = 0.156.


Forests ◽  
2022 ◽  
Vol 13 (1) ◽  
pp. 78
Author(s):  
Katarina Tumpa ◽  
Zlatko Liber ◽  
Zlatko Šatović ◽  
Jasnica Medak ◽  
Marilena Idžojtić ◽  
...  

Common or English yew (Taxus baccata L., Taxaceae) is a conifer species, native to Europe, northern Africa, Asia Minor and Caucasus. It is a dioecious, wind-pollinated and animal-dispersed tree, known for its high-quality wood and medicinal properties, albeit poisonous. The species is rare and has been legally protected at the European and national levels. In addition, its low population density and disjunct character of distribution have reinforced the need for its protection as regeneration is mostly lacking. The aim of this study was to phenotypically characterise the north-western Balkan yew populations. Phenotypic diversity was examined for seven populations, using morphometric analysis of nine phenotypic traits of needles. Descriptive and multivariate statistical analyses were conducted to evaluate the inter- and intrapopulation variability. In addition, to test correlations between geographic, climatic and phenotypic data, Mantel test was used. We identified a geographic structure across studied populations that exhibited high levels of variability on intra- and interpopulation levels. Two groups of populations have been defined and are consistent with previously described genetic divergent lineages from separate refugia. In addition, a significant correlation between phenotypic and geographic data were revealed, i.e., isolation by distance (IBD). However, the Mantel test revealed no significant correlation between morphometric and environmental data. In conclusion, our data reveal that the historical events and persistent IBD acted in combination to produce the morphological patterns observed in common yew populations in the north-western part of the Balkan Peninsula. Finally, we suggested conservation measures to be implemented on a stand level, with habitat preservation as the main goal. In addition, ex situ conservation should be considered, both in the form of collections and urban planting, as both provide additional gene pool reserves.


2022 ◽  
Vol 12 ◽  
Author(s):  
Elmira Khussainova ◽  
Ilya Kisselev ◽  
Olzhas Iksan ◽  
Bakhytzhan Bekmanov ◽  
Liliya Skvortsova ◽  
...  

Ethnogenesis of Kazakhs took place in Central Asia, a region of high genetic and cultural diversity. Even though archaeological and historical studies have shed some light on the formation of modern Kazakhs, the process of establishment of hierarchical socioeconomic structure in the Steppe remains contentious. In this study, we analyzed haplotype variation at 15 Y-chromosomal short-tandem-repeats obtained from 1171 individuals from 24 tribes representing the three socio-territorial subdivisions (Senior, Middle and Junior zhuz) in Kazakhstan to comprehensively characterize the patrilineal genetic architecture of the Kazakh Steppe. In total, 577 distinct haplotypes were identified belonging to one of 20 haplogroups; 16 predominant haplogroups were confirmed by SNP-genotyping. The haplogroup distribution was skewed towards C2-M217, present in all tribes at a global frequency of 51.9%. Despite signatures of spatial differences in haplotype frequencies, a Mantel test failed to detect a statistically significant correlation between genetic and geographic distance between individuals. An analysis of molecular variance found that ∼8.9% of the genetic variance among individuals was attributable to differences among zhuzes and ∼20% to differences among tribes within zhuzes. The STRUCTURE analysis of the 1164 individuals indicated the presence of 20 ancestral groups and a complex three-subclade organization of the C2-M217 haplogroup in Kazakhs, a result supported by the multidimensional scaling analysis. Additionally, while the majority of the haplotypes and tribes overlapped, a distinct cluster of the O2 haplogroup, mostly of the Naiman tribe, was observed. Thus, firstly, our analysis indicated that the majority of Kazakh tribes share deep heterogeneous patrilineal ancestries, while a smaller fraction of them are descendants of a founder paternal ancestor. Secondly, we observed a high frequency of the C2-M217 haplogroups along the southern border of Kazakhstan, broadly corresponding to both the path of the Mongolian invasion and the ancient Silk Road. Interestingly, we detected three subclades of the C2-M217 haplogroup that broadly exhibits zhuz-specific clustering. Further study of Kazakh haplotypes variation within a Central Asian context is required to untwist this complex process of ethnogenesis.


2022 ◽  
Author(s):  
Yu Zhang ◽  
Qiaoqiao He ◽  
Xixi Zhou ◽  
Yewen Wang ◽  
Peijiang Li ◽  
...  

Abstract Background: The Qinba region is the transition region between Indica and Japonica varieties in China. It has a long history of Indica rice planting of more than 7000 years and is also a planting area for fine-quality Indica rice. The aims of this study are to explore different genetic markers applied to the analysis population structure, genetic diversity, selection and optimization of molecular markers of Indica rice, thus providing more information for the protection and utilization on germplasm resources of Indica rice. Methods: 15 phenotypic traits, a core set of 48 SSR markers as well as SNPs data obtained by genotyping-by-sequencing (GBS, NlaIII and MseI digestion, referred to as SNPs-NlaIII and SNPs-MseI, respectively) for this panel of 93 samples using the Illumina HiSeq2000 sequencing platform, were employed to explore the genetic diversity and population structure of 93 samples.Results: The average of coefficient of variation (CV) and diversity index (He) were 29.72% and 1.83 ranging from 3.07% to 137.43%, and from 1.45 to 2.03, respectively. The correlation coefficient between 15 phenotypic traits ranged from 0.984 to -0.604. The first four PCs accounted for 70.693% phenotypic variation based on phenotypic analysis. A total of 379 alleles were obtained using SSR markers, encompassing an average of 8.0 alleles per primer. Polymorphic bands (PPB) and polymorphism information content (PIC) was 88.65% and 0.77, respectively. The Mantel test showed that the correlation between the genetic distance matrix based on SNPs-NlaIII and SNPs-MseI was the largest (R2=0.88), and that based on 15 phenotypic traits and SSR was the smallest (R2=0.09). The 93 samples could be clustered into two subgroups by 3 types of genetic markers. Molecular variance analysis revealed that the genetic variation was 2% among populations and 98% within populations (the Nm was 0.16), Tajima’s D value was 1.66, the FST between the two populations was 0.61 based on 72,824 SNPs. Conclusions: The population genetic variation explained by SNPs was larger than that explained by SSRs. The gene flow of 93 samples used in this study was larger than that of naturally self-pollinated crops, which may be caused by long-term breeding selection of Indica rice in the Qinba region. The genetic structure of the 93 samples was simple and lacked rare alleles.


PLoS ONE ◽  
2021 ◽  
Vol 16 (12) ◽  
pp. e0261813
Author(s):  
Alfredo Cortell-Nicolau ◽  
Oreto García-Puchol ◽  
María Barrera-Cruz ◽  
Daniel García-Rivero

In the present article we use geometric microliths (a specific type of arrowhead) and Approximate Bayesian Computation (ABC) in order to evaluate possible origin points and expansion routes for the Neolithic in the Iberian Peninsula. In order to do so, we divide the Iberian Peninsula in four areas (Ebro river, Catalan shores, Xúquer river and Guadalquivir river) and we sample the geometric microliths existing in the sites with the oldest radiocarbon dates for each zone. On this data, we perform a partial Mantel test with three matrices: geographic distance matrix, cultural distance matrix and chronological distance matrix. After this is done, we simulate a series of partial Mantel tests where we alter the chronological matrix by using an expansion model with randomised origin points, and using the distribution of the observed partial Mantel test’s results as a summary statistic within an Approximate Bayesian Computation-Sequential Monte-Carlo (ABC-SMC) algorithm framework. Our results point clearly to a Neolithic expansion route following the Northern Mediterranean, whilst the Southern Mediterranean route could also find support and should be further discussed. The most probable origin points focus on the Xúquer river area.


Caryologia ◽  
2021 ◽  
Vol 74 (3) ◽  
pp. 141-150
Author(s):  
Bo Shi ◽  
Majid Khayatnezhad ◽  
Abdul Shakoor

One of the most crucial aspects of biological diversity for conservation strategies is genetic diversity, particularly in rare and narrow endemic species. Our study is the first attempt to utilize SCoT markers to check the genetic diversity in Iran. We used 115 plant samples. Our objectives were 1) to check genetic diversity among Geranium species 2) Genetic structure of the Geranium 3) Do the Geranium species exchange genes? 4) To detect isolation by distance among the Geranium species. We used traditional morphological and molecular methods to assess genetic diversity and genetic structure in the Geranium species. A total of 129 amplified polymorphic bands were generated across 13 Geranium species. The size of the amplified fragments ranged from 150 to 3000 bp. G. stepporum showed the highest values for the effective number of alleles (Ne = 1.30) and Shannon information index (I =0.35). Significant ANOVA results (P <0.01) showed differences in quantitative morphological characters in plant species. G. sylvaticum showed high genetic diversity. Mantel test showed a significant correlation (r = 0.17, p=0.0002) between genetic distance and geographical distance, so isolation by distance (IBD) occurred among the Geranium species. According to the SCoT markers analysis, G. kotschyi and G. dissectum had the lowest similarity, and the species of G. sylvaticum and G. pratense had the highest similarity. The present study revealed that a combination of morphological and SCoT methods could distinguish the species of Geranium.


2021 ◽  
pp. 1-16
Author(s):  
Célia Kamel ◽  
Bérengère Saliba-Serre ◽  
Marie-Hélène Lizee ◽  
Michel Signoli ◽  
Caroline Costedoat

Abstract An analysis of the distribution of surnames through time and space allows us to understand the structure of human groups, their exchanges or even their possible isolation. The French population has already been studied through surnames and it has been shown that the Sud-Provence-Alpes-Côte d’Azur region differed from the rest of France in both the 20th and 21st centuries (Mourrieras et al., 1995; Scapoli et al., 2005). The objective of this study was to understand the population evolution and particularities of the Sud-Provence-Alpes-Côte d’Azur region through an analysis of the distribution of surnames over an earlier period: the 19th century. For this work, 806,069 birth records from 521 communes between 1810 and 1890 were recorded and a total of 23,340 surnames were collected. The estimation of various isonymic parameters has allowed a description of this corpus never exploited before. In order to appreciate the population evolution, the data set was divided into three periods of 25 years. The canton was the geographical unit of this study, and similarities and differences between each of them were evaluated using Lasker distances, which allow the construction of dendrograms. A positive and significant correlation (p<0.0001) was found between Lasker distances and geographical distances using the Mantel test. The lowest inbreeding estimates were found in the Durance Valley. Migration, estimated from the v-index of Karlin and McGregor (1967), showed higher values in the south-western quarter of the region. The decrease in Rst values across the three periods is consistent with a homogenization of the patronymic between the cantons. This three-period approach showed a population evolution influenced by linguistic, cultural, historical and migratory phenomena since the Middle Ages, disrupted by the socioeconomic changes of the 19th century.


2021 ◽  
Author(s):  
Clara Inés Saldamando-Benjumea ◽  
Gloria Patricia Cañas-Gutiérrez ◽  
Jorge Muñoz ◽  
Rafael Arango Isaza

Avocado (Persea americana) Mill represents one of the most consumed fruits around the world. This species has been differentiated into three main races Guatemalan, Mexican and West Indian according to several molecular markers. However, the interaction between genotypic and phenotypic traits of this crop is still unknown. For this reason, a landscape genetics analysis was made in 90 criollo trees from Northeast Colombia (Antioquia) with 14 microsatellites, sequencing of 3 nuclear loci, endo-1-4-D-glucanase (Cell), Chalcone synthase (CHS) and serine-threonine-kinase (STK) and 28 morphological traits. High genetic diversity was found suggesting a hybrid origin of criollo trees. Morphological variation showed intermixed racial features. FST = 0.03, p =0.001 (measured with microsatellites) suggested low genetic differentiation. According to STRUCTURE, K = 2 for both microsatellites and concatenated nuclear sequences. Criollo trees were assigned together with the Guatemalan and Mexican races. Pearson correlation was significant between expected heterozygocities and elevation. Mantel test was low (r2 = 0.0097, p = 0.015) but significant demonstrating isolation by distance. Grafting is suitable between criollo trees and Hass variety is possible since both avocados are produced within the same altitudes.


Author(s):  
Abdul Shakoor ◽  
Gul Zaib ◽  
Fang Zhao ◽  
Wuyang Li ◽  
Xincan Lan ◽  
...  

Hedera helix L. is an invasive, but medicinally important plant. In Iran, there is no available study on the H. helix population to reveal the genetic diversity and population structure. Fifty-six individual plants belonging to nine geographical populations were collected in four provinces of Iran. High genetic diversity, polymorphisms, and a Shannon diversity index of 0.269 were detected in Mazandaran, Kandovan (Population 3). Analysis of the molecular variance indicated 40% of total genetic variation of the whole population was present in the subpopulation. A high genetic similarity (0.922) between plant Populations 5 (Kermanshah; Islamabad) and 6 (Kermanshah; Paveh) was noted. On the other hand, a low genetic similarity was observed between plant Populations 1 (Tehran; Darband) and 8 (Ardabil; Hur). The Mantel test revealed a correlation between the genetic and geographical distances. Furthermore, it demonstrated the isolation mechanism responsible for the population structure in the H. helix plant populations. The principal component analysis explained the majority of the variation in the morphological characteristics. Three components explained 87% of the variation, and the first component explained 60% of the variation. For instance, the leaf morphology showed a correlation of &gt; 0.7 between leaf morphological and floral characters. The plant leaves and quantitative flower characteristics separated the plant populations according to the differences in length. The current results have implications for plant conservation and management.


2021 ◽  
Vol 63 (4) ◽  
pp. 308-316
Author(s):  
Sergiy Boiko

Abstract Changes that occur on the local level can explain the processes on the population level and, at the same time, are the driving force of species adaptation. This manuscript reports data about genetic diversities of the fungus Schizophyllum commune on the level of a local population. Objects of the study were dicarious cultures of S. commune collected from 38 basidiocarps grown on the territory of Holosiivskyi National Nature Park, Lysa Hora Regional Landscape Park and Feofaniya forest parcel (Ukraine). Results showed similarity of genetic variability of S. commune in different local populations. The heterozygote deficiency of some loci that was discovered might have resulted from new forms of allozymes that have not become widespread or due to small population sizes. The degree of differentiation of genes between local studied populations was moderate due to the high flow of genes. The absence of spatial structuration of genotypes is established, and the Mantel test showed a lack of interconnection between the genetic component and the geographical coordinates of the samples. It has been suggested that wind direction and terrain are the factors that influence the genetic structure of local populations.


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