Recent distribution changes affect geographic clines in genetic diversity and structure of Pinus densiflora natural populations in Japan

The objective of this study was to assess the genetic variability in two natural populations ofCalophyllum brasilienselocated along two different rivers in the state of Minas Gerais, Brazil, using RAPD molecular markers. Eighty-two polymorphic fragments were amplified using 27 primers. The values obtained for Shannon index (I) were 0.513 and 0.530 for the populations located on the margins of the Rio Grande and Rio das Mortes, respectively, demonstrating the high genetic diversity in the studied populations. Nei’s genetic diversity (He) was 0.341 for the Rio Grande population and 0.357 for the Rio das Mortes population. These results were not significantly different between populations and suggest a large proportion of heterozygote individuals within both populations. AMOVA showed that 70.42% of the genetic variability is found within populations and 29.58% is found among populations (ФST=0.2958). The analysis of kinship coefficients detected the existence of family structures in both populations. Average kinship coefficients between neighboring individuals were 0.053 (P<0.001) in Rio das Mortes and 0.040 (P<0.001) in Rio Grande. This could be due to restricted pollen and seed dispersal and the history of anthropogenic disturbance in the area. These factors are likely to contribute to the relatedness observed among these genotypes.

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Population genetics of the freshwater fish Prochilodus magdalenae (Characiformes: Prochilodontidae), using species-specific microsatellite loci

PeerJ ◽

10.7717/peerj.10327 ◽

2020 ◽

Vol 8 ◽

pp. e10327

Author(s):

Ricardo M. Landínez-García ◽

Juan Carlos Narváez ◽

Edna J. Márquez

Keyword(s):

Genetic Diversity ◽

Genetic Structure ◽

Freshwater Fish ◽

Microsatellite Loci ◽

Natural Populations ◽

Genetic Stock ◽

High Genetic Diversity ◽

Genetic Diversity And Structure ◽

Genetic Stocks ◽

Species Specific

Prochilodus magdalenae is a freshwater fish endemic to the Colombian Magdalena-Cauca and Caribbean hydrographic basins. The genetic structure patterns of populations of different members of Prochilodus and the historic restocking of its depleted natural populations suggest that P. magdalenae exhibits genetic stocks that coexist and co-migrate throughout the rivers Magdalena, Cauca, Cesar, Sinú and Atrato. To test this hypothesis and explore the levels of genetic diversity and population demography of 725 samples of P. magdalenae from the studied rivers, we developed a set of 11 species-specific microsatellite loci using next-generation sequencing, bioinformatics, and experimental tests of the levels of diversity of the microsatellite loci. The results evidenced that P. magdalenae exhibits high genetic diversity, significant inbreeding coefficient ranging from 0.162 to 0.202, and signs of erosion of the genetic pool. Additionally, the population genetic structure constitutes a mixture of genetic stocks heterogeneously distributed along the studied rivers, and moreover, a highly divergent genetic stock was detected in Chucurí, Puerto Berrío and Palagua that may result from restocking practices. This study provides molecular tools and a wide framework regarding the genetic diversity and structure of P. magdalenae, which is crucial to complement its baseline information, diagnosis and monitoring of populations, and to support the implementation of adequate regulation, management, and conservation policies.

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Genetic diversity and structure of the narrow endemic Seseli farrenyi (Apiaceae): implications for translocation

PeerJ ◽

10.7717/peerj.10521 ◽

2021 ◽

Vol 9 ◽

pp. e10521

Author(s):

Núria Garcia-Jacas ◽

Jèssica Requena ◽

Sergi Massó ◽

Roser Vilatersana ◽

Cèsar Blanché ◽

...

Keyword(s):

Genetic Diversity ◽

Population Decline ◽

Natural Populations ◽

Ex Situ ◽

Endemic Plant ◽

Genetic Lineages ◽

Narrow Endemic ◽

Management Measures ◽

Genetic Diversity And Structure ◽

Nw Mediterranean

Seseli farrenyi (Apiaceae) is an extremely narrow endemic plant, which is considered as one of the species of most conservation concern in Catalonia (NW Mediterranean Basin). Given the accelerated fragmentation and reduction of population size (of over 90%), the environmental agency of Catalonia is currently preparing a recovery plan that includes reinforcements of the extant populations. The present study is aimed at providing the necessary knowledge to carry out genetically-informed translocations, by using microsatellites as genetic markers. Fourteen microsatellites have been specifically developed for S. farrenyi, of which nine have been used. Besides the extant natural populations, the three ex situ collections that are known to exist of this species have also been studied, as they would be the donor sources for translocation activities. Our main finding is that levels of genetic diversity in the natural populations of S. farrenyi are still high (He = 0.605), most likely as a result of a predominantly outcrossing mating system in combination with the limited time elapsed since the population decline. However, population fragmentation is showing the first genetic signs, as the values of genetic differentiation are relatively high, and two well-differentiated genetic lineages have been found even in such a narrow geographic range. These genetic results provide important information when designing conservation management measures.

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Genetic diversity and structure analyses on the natural populations of diploids and triploids of tiger lily, Lilium lancifolium Thunb., from Korea, China, and Japan

Genes & Genomics ◽

10.1007/s13258-016-0398-2 ◽

2016 ◽

Vol 38 (5) ◽

pp. 467-477 ◽

Cited By ~ 8

Author(s):

Sung-Il Lee ◽

Xuan Truong Nguyen ◽

Jong-Hwa Kim ◽

Nam-Soo Kim

Keyword(s):

Genetic Diversity ◽

Natural Populations ◽

Genetic Diversity And Structure ◽

Lilium Lancifolium ◽

China And Japan

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Genetic diversity and structure of natural populations of Gossypium mustelinum, a wild relative of cotton, in the basin of the De Contas River in Bahia, Brazil

Genetica ◽

10.1007/s10709-014-9757-6 ◽

2014 ◽

Vol 142 (1) ◽

pp. 99-108 ◽

Cited By ~ 9

Author(s):

Ivandilson Pessoa Pinto de Menezes ◽

Fernanda Amato Gaiotto ◽

Lucia Vieira Hoffmann ◽

Ana Yamaguishi Ciampi ◽

Paulo Augusto Vianna Barroso

Keyword(s):

Genetic Diversity ◽

Natural Populations ◽

Wild Relative ◽

Genetic Diversity And Structure ◽

Gossypium Mustelinum

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Genetic Diversity and Structure of Pinus densiflora Siebold & Zucc. Populations in Republic of Korea Based on Microsatellite Markers

Forests ◽

10.3390/f12060750 ◽

2021 ◽

Vol 12 (6) ◽

pp. 750

Author(s):

Ji-Young Ahn ◽

Jei-Wan Lee ◽

Kyung-Nak Hong

Keyword(s):

Genetic Diversity ◽

Genetic Differentiation ◽

Microsatellite Markers ◽

Environmental Changes ◽

Pinus Densiflora ◽

Republic Of Korea ◽

Conifer Species ◽

Principal Coordinates ◽

Genetic Diversity And Structure ◽

The Republic

Pinus densiflora Siebold & Zucc. is a widely distributed conifer species in the Republic of Korea with economic and ecologic importance. However, P. densiflora is negatively influenced by various factors, such as forest fires, clearing of large numbers of trees infected with Pinus disease, and dieback. We aimed to use microsatellite markers to estimate the genetic diversity, differentiation, and structure of P. densiflora populations in the Republic of Korea. A total of 1844 samples from 60 populations were evaluated using 11 polymorphic microsatellite markers. The observed heterozygosity and expected heterozygosity were 0.652 and 0.673, respectively. The mean genetic differentiation among the populations was 0.013. Moreover, P. densiflora showed high genetic diversity and low genetic differentiation compared with conifer species, including Pinus species with similar life histories. Principal coordinates analysis and Bayesian clustering showed that P. densiflora has a weak geographical structure. The P. densiflora population at Mt. Halla, Jeju Island, showed the lowest genetic diversity and significant genetic differentiation compared with other mainland populations due to genetic drift and restricted gene flow. These findings can be useful for designing new conservation, management, and breeding strategies for P. densiflora populations in response to future environmental changes.

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Population Genetic Diversity and Structure of an Endangered Salicaceae Species in Northeast China: Chosenia arbutifolia (Pall.) A. Skv.

Forests ◽

10.3390/f12091282 ◽

2021 ◽

Vol 12 (9) ◽

pp. 1282

Author(s):

Yu Wang ◽

Zhongyi Jiao ◽

Jiwei Zheng ◽

Jie Zhou ◽

Baosong Wang ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Management Strategies ◽

Natural Populations ◽

Snp Markers ◽

Fixation Index ◽

Landscape Genomics ◽

Population Structure Analysis ◽

Genetic Diversity And Structure ◽

Chosenia Arbutifolia

Chosenia arbutifolia (Pall.) A. Skv. is a unique and endangered species belonging to the Salicaceae family. It has great potential for ornamental and industrial use. However, human interference has led to a decrease in and fragmentation of its natural populations in the past two decades. To effectively evaluate, utilize, and conserve available resources, the genetic diversity and population structure of C. arbutifolia were analyzed in this study. A total of 142 individuals from ten provenances were sampled and sequenced. Moderate diversity was detected among these, with a mean expected heterozygosity and Shannon’s Wiener index of 0.3505 and 0.5258, respectively. The inbreeding coefficient was negative, indicating a significant excess of heterozygotes. The fixation index varied from 0.0068 to 0.3063, showing a varied genetic differentiation between populations. Analysis of molecular variance demonstrated that differentiation accounted for 82.23% of the total variation among individuals, while the remaining 17.77% variation was between populations. Furthermore, the results of population structure analysis indicated that the 142 individuals originated from three primitive groups. To provide genetic information and help design conservation and management strategies, landscape genomics analysis was performed by investigating loci associated with environmental variables. Eighteen SNP markers were associated with altitude and annual average temperature, of which five were ascribed with specific functions. In conclusion, the current study furthers the understanding of C. arbutifolia genetic architecture and provides insights for germplasm protection.

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Inter simple sequence repeat markers to assess genetic diversity of the desert date (Balanites aegyptiaca Del.) for Sahelian ecosystem restoration

Scientific Reports ◽

10.1038/s41598-020-71835-9 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Selouka Mint Abdelaziz ◽

Leila Medraoui ◽

Mohammed Alami ◽

Ouafae Pakhrou ◽

Meryem Makkaoui ◽

...

Keyword(s):

Genetic Diversity ◽

Natural Populations ◽

Inter Simple Sequence Repeat ◽

Resolving Power ◽

Balanites Aegyptiaca ◽

Marker Index ◽

Information Index ◽

Genetic Diversity And Structure ◽

Two Populations ◽

Amova Analysis

Abstract Drought and desertification are the major environmental constraints facing the Sahelian agro-ecosystems for decades. Assessing genetic diversity of native tree species is critical to assist ecosystems restoration efforts. Here we describe genetic diversity and structure of seven Balanites aegyptiaca L. natural populations distributed across the Sahelian-Saharan zone of Mauritania using 16 polymorphic ISSR primers. These generated 505 polymorphic bands. Polymorphism information content (PIC) varied from (0.13–0.29) with an average 0.23, marker index (MI) averaged 7.3 (range 3.3–10.3) and resolving power (RP) ranged from (4.53–14.6) with an average 9.9. The number of observed alleles (Na) ranged from (0.62–1.39), Effective number of alleles (Ne) varied from (1.26–1.37), Shannon’s information index (I) ranged from (0.25–0.36). AMOVA analysis showed that 80% of the genetic variation was fined within populations, which is supported by a low level of genetic differentiation between population (GST = 0.21) and an overall estimate of gene flow among populations (Nm = 1.9). The dendrogram based on Jaccard's similarity coefficient and the structure analysis divided the seven populations into two main clusters in which two populations from the Saharan zone were grouped. Our results provide baseline data for genetic conservation programs of this Sahelian neglected crop and with an important econ-ecological role.

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