Genetic Differentiation And Relationships Of Populations In The Cycas Balansae Complex Pdf
File Name: genetic differentiation and relationships of populations in the cycas balansae complex .zip
- Genetic diversity through life history of Dioon edule Lindley (Zamiaceae, Cycadales
- DDC Clustering Results
Genetic diversity through life history of Dioon edule Lindley (Zamiaceae, Cycadales
Garcinia kola Heckel is a versatile tree indigenous to West and Central Africa. All parts of the tree have value in traditional medicine. Natural populations of the species have declined over the years due to overexploitation. Assessment of genetic diversity and population structure of G.
The present study investigates the genetic diversity and population structure of G. From the accessions sampled, two were excluded from the final dataset owing to poor genotyping coverage.
Analysis revealed low genetic diversity with expected heterozygosity per population ranging from 0. Population structure analysis through clustering and discriminant analysis on principal component revealed two admixed clusters, implying little genetic structure. However, the model-based maximum likelihood in Admixture indicated only one genetic cluster.
The present study indicated low genetic diversity of G. This is an open access article distributed under the terms of the Creative Commons Attribution License , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Data Availability: All relevant data are within the manuscript and its Supporting Information files. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing interests: The authors have declared that no competing interests exist. Garcinia kola Heckel is endemic in coastal areas, lowland plains and humid lowland rainforest of West and Central Africa [ 1 ]. The tree can naturally grow up to 30 m in height with a maximum of cm in trunk diameter.
The species is dioecious and flowering usually occurs once per year [ 1 ]. Garcinia kola is an indigenous tree with cultural and medicinal importance to local populations [ 2 ]. In folkloric medicine, it has important uses in the treatment of various ailments such as cough, chest pain, tooth ache, rheumatism, hernia, dysentery and malaria [ 3 , 4 ]. It is also used to induce labor for easy delivery and during socio-cultural engagement like naming and wedding ceremonies [ 3 , 4 ].
However, the species is only found in the Southern areas [ 1 ] where the highest destructive anthropogenic activities are recorded. It is potentially threatened by indiscriminate bark sampling used in the preparation of different infusions [ 2 ].
These anthropogenic activities may have led to the drastic decline in natural populations of the G. In spite of the socio-economic importance of G.
Genetic diversity is important in species conservation and is correlated to population size [ 5 ]. Therefore, a reduction of population size is likely to lead to a reduction in genetic diversity over time [ 6 ]. SNP markers are the most widely used genotyping markers due to their abundance in the genome [ 13 ]. Diversity array technology DArT along with other high throughput sequencing techniques have been increasingly adopted as a rapid and low-cost molecular techniques for SNP discovery, genotyping, and genetic variability analysis for various plant species as they allow for the study of the genetic diversity of a large number of entities and complex genomes [ 14 — 17 ].
The present study investigates the current level of genetic diversity and population structure of G. The specific questions addressed in this study were:.
The study was carried out on private lands between June and August Leaders of the communities as well as agriculture extension workers were made aware of our presence and the purpose of the study. Samples were collected upon owners' permission. Eight populations of G. A population was defined as a group of trees separated from their nearest conspecifics by at least 1 km [ 18 ].
The minimum distance between two sites was 5 km. The number of trees sampled within each locality was proportional to the number of trees within each locality. Tender and apparently healthy leaf tissues were collected randomly from sampled adult trees.
The samples were placed in labelled envelopes and dried in silica gel until transport to the laboratory for DNA extraction. The forward adapter PstI -compatible included an Illumina flow cell attachment sequence, sequencing primer sequence and, varying length barcode region [ 20 , 22 ] and the reverse adapter contained a flow cell attachment region and a SphI -compatible overhang sequence. Samples were processed in batches of For each sample, amplification of the fragments containing both PstI and SphI mixed fragments [ 22 ] was performed using specially designed primers.
A pool of all the amplified products was then assembled. Samples were normalized and pooled using an automated liquid handler, at equimolar ratios and sequencing was performed using an Illumina HiSeq platform.
After cluster generation and amplification, 77 bp single-end sequencing was performed. The sequence data was analyzed using DArT analytical pipelines. In the primary pipeline, the FASTQ files were processed to filter out poor-quality sequences, applying more stringent selection criteria to the barcode region than the rest of the sequence.
Two technical replicates of each DNA sample were genotyped to calculate the reproducibility of the marker data. Using the KDCompute 1. Two accessions from the Adjarra population were excluded from the final dataset due to poor genotyping coverage. This was because of severe allelic dropout during the genotyping by sequencing process, which led to considerable missing genetic information. To assess hierarchical levels of population structuring, an analysis of molecular variance AMOVA was computed among populations and between regions based on 10, permutations using Arlequin 3.
To avoid bias and for the purpose of software requirements, the population of one individual Ketou was merged to the closest population Adjohoun. A hierarchical clustering analysis was performed based on the dissimilarity matrix, and a dendogram was generated in DARwin software 6.
Finally, a maximum likelihood estimation of individual ancestries with no prior population assumptions was performed to assess population structure using Admixture software 1. The raw dataset contained a total of 43, SNPs genotyped across accessions. A total of 6, The PIC values of the markers varied from 0. About 2. Informative markers with the highest PIC values 0. The proportion of heterozygosity ranged from 0 1 SNP to 0. However, more than half of the markers Analysis of diversity revealed low diversity with He values per population ranging from 0.
The highest He value was observed in the Adjarra population and the lowest in the Kpomasse-Tori population Table 2. The F IS , which measures the inbreeding of an individual within a sub-population was significantly high ranging from 0. The results of the AMOVA Table 3 indicated significant but weak genetic structure between regions and among populations. Only 0. Most of the variations Cluster I was composed of 94 accessions from all sampled populations while cluster II was composed of 6 accessions.
The result showed no clustering based on geographical locations Fig 4. This genetic structure is similar to the high admixture observed through the UPGMA tree, indicating high genetic relatedness among the accessions. Indeed, the best value of k clusters is the value with the lowest cross-validation error. This study provides the first-ever molecular assessment of G. The PIC values were useful in studying the level of polymorphisms among the accessions.
The average PIC of 0. A previous study on G. Low to moderate levels of observed heterozygosity 0. In contrast, very high heterozygosity was observed in G. The low heterozygosity may be due to a severe bottleneck event that occurred during domestication and selection [ 33 ].
In Benin, G. The results of this study are consistent with other studies reporting a reduction in genetic diversity in domesticated crops as compared to their wild progenitors [ 29 , 34 ]. Heterozygote deficit has been observed in many threatened species such as Cycad balansae [ 35 ], Glyptostrobus pensilis [ 36 ], Pulsatilla patens [ 18 ].
This could be attributed to self-pollination in G. Indeed, G. Low genetic diversity and inbreeding depression have been observed in many studies on threatened species as a consequence of a decrease in population size. This is likely the case in the studied populations of G. Population differentiation is important for understanding the relative effect of evolutionary gene flow, mating system, selection, adaptation, and genetic drift on populations [ 38 ]. The F ST values below 0.
It was also observed that genetic variation was mainly found within populations This could be due to the small distribution range of G. In addition, G. Hierarchical clustering analysis performed on G. However, in the present study, an admixture of almost all the populations was noted within the two clusters.
The presence of admixture within the two genetic clusters implied the lack of any discernable population structure [ 41 ], thus further indicating that interbreeding or sharing of alleles has occurred between the populations. An admixture analysis was performed with the program admixture, which reduces the false-positive rates, corrects for bias toward spurious admixture, and allows identification of different mating systems in structured as well as unstructured populations [ 42 ].
The present study provides insights into the molecular diversity of G. Results indicate low genetic variation among the studied populations and high variation among individuals within populations.
Finally, population structure analysis indicates the studied populations of G. However, it is not possible to ascertain if these results and observations can be extrapolated to the larger distribution range of G.
DDC Clustering Results
E Corresponding author: Email: terry biology. Bailey, we surveyed this central Queensland cycad for its population abundance and health and its pollinator type and pollination syndrome thermogenesis and volatile emissions. Plants are highly restricted to a small area of occupancy, seed dispersal is nearly non-existent and extreme fires appear to have destroyed almost all seeds and seedlings and decimated the pollinators. Of known Macrozamia pollinators, only the thrips, Cycadothrips chadwicki Mound, were found on cones, and these were found in very low numbers. The pollination syndrome for this cycad appears to be unique, based on two cone traits.
Garcinia kola Heckel is a versatile tree indigenous to West and Central Africa. All parts of the tree have value in traditional medicine. Natural populations of the species have declined over the years due to overexploitation. Assessment of genetic diversity and population structure of G. The present study investigates the genetic diversity and population structure of G.
Cinnamomum , contains —, or more, species worldwide and is a species-rich genus of evergreen aromatic tree and shrub belonging to the Lauraceae family. As the representative species of Cinanamomum , the camphor tree Cinnamomum camphora is a broad-leaved evergreen characterized by aromatic oils in all of the plant parts. This species originated in the southern parts of China and Japan, and has a widespread naturalized distribution in many other countries. Camphor trees can reach up to 40 m in height and live to be over 1, years old. They have oval or elliptical leaves with wavy margins that give off a distinctive aromatic smell when crushed.
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Я д-думал, - заикаясь выговорил Бринкерхофф. - Я думал, что вы в Южной Америке. Лиланд Фонтейн окинул своего помощника убийственным взглядом. - Я был. Но сейчас я. ГЛАВА 69 - Эй, мистер.
Хейл влез в ее компьютер, когда она выходила. Именно он и подал ручную команду на отзыв Следопыта. Вопрос насколько. уступил место другому - с какой целью?. У Хейла не было мотивов для вторжения в ее компьютер.
Через несколько секунд на экране показалась надпись: ОБЪЕКТ НЕ НАЙДЕН Не зная, что искать дальше, она ненадолго задумалась и решила зайти с другой стороны. НАЙТИ: ЗАМОК ЭКРАНА Монитор показал десяток невинных находок - и ни одного намека на копию ее персонального кода в компьютере Хейла. Сьюзан шумно вздохнула. Какими же программами он пользовался. Открыв меню последних программ, она обнаружила, что это был сервер электронной почты. Сьюзан обшарила весь жесткий диск и в конце концов нашла папку электронной почты, тщательно запрятанную среди других директорий.
Как ты могла догадаться, - продолжал он, - вскоре я собираюсь выйти в отставку. Но я хотел уйти с высоко поднятой головой. Я хотел уйти с сознанием, что добился своей цели. - Но вы добились своей цели, - словно со стороны услышала Сьюзан собственный голос, - Вы создали ТРАНСТЕКСТ.
- Стремительная. Все люди на подиуме потянулись к терминалу в одно и то же мгновение, образовав единое сплетение вытянутых рук. Но Сьюзан, опередив всех, прикоснулась к клавиатуре и нажала цифру 3. Все повернулись к экрану, где над всем этим хаосом появилась надпись: ВВЕСТИ ПАРОЛЬ.
Без воска. - Он улыбнулся в ответ. Она поцеловала. - Скажи, что это .