scholarly journals “Jumping Jack”: Genomic Microsatellites Underscore the Distinctiveness of Closely Related Pseudoperonospora cubensis and Pseudoperonospora humuli and Provide New Insights Into Their Evolutionary Past

2021 ◽  
Vol 12 ◽  
Author(s):  
Marcin Nowicki ◽  
Denita Hadziabdic ◽  
Robert N. Trigiano ◽  
Sarah L. Boggess ◽  
Loukas Kanetis ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Genetics ◽  
Distinct Species ◽  
Pseudoperonospora Cubensis ◽  
Herbarium Specimens ◽  
High Genetic Diversity ◽  
Genetics Research ◽  
Downy Mildews ◽  
History Of ◽  
Genomic Microsatellites

Downy mildews caused by obligate biotrophic oomycetes result in severe crop losses worldwide. Among these pathogens, Pseudoperonospora cubensis and P. humuli, two closely related oomycetes, adversely affect cucurbits and hop, respectively. Discordant hypotheses concerning their taxonomic relationships have been proposed based on host–pathogen interactions and specificity evidence and gene sequences of a few individuals, but population genetics evidence supporting these scenarios is missing. Furthermore, nuclear and mitochondrial regions of both pathogens have been analyzed using microsatellites and phylogenetically informative molecular markers, but extensive comparative population genetics research has not been done. Here, we genotyped 138 current and historical herbarium specimens of those two taxa using microsatellites (SSRs). Our goals were to assess genetic diversity and spatial distribution, to infer the evolutionary history of P. cubensis and P. humuli, and to visualize genome-scale organizational relationship between both pathogens. High genetic diversity, modest gene flow, and presence of population structure, particularly in P. cubensis, were observed. When tested for cross-amplification, 20 out of 27 P. cubensis-derived gSSRs cross-amplified DNA of P. humuli individuals, but few amplified DNA of downy mildew pathogens from related genera. Collectively, our analyses provided a definite argument for the hypothesis that both pathogens are distinct species, and suggested further speciation in the P. cubensis complex.

Season of birth interacts with measures of inbreeding in multiplex schizophrenia pedigrees: evidence from genetic isolates in Daghestan

Open Medicine ◽  
2006 ◽  
Vol 1 (4) ◽  
pp. 392-398
Author(s):  
Kazima Bulayeva ◽  
John McGrath
Keyword(s):  
Genetic Diversity ◽  
Family History ◽  
Age Of Onset ◽  
Population Genetic Study ◽  
Season Of Birth ◽  
High Genetic Diversity ◽  
Low Genetic Diversity ◽  
High Prevalence ◽  
History Of ◽  
Genetic Isolates

AbstractWhile the season-of-birth effect is one of the most consistent epidemiological features of schizophrenia, there is a lack of consistency with respect to the interaction between season of birth and family history of schizophrenia. Apart from family history, measures related to consanguinity can be used as proxy markers of genomic heterogeneity. Thus, these measures may provide an alternate, indirect index of genetic susceptibility. We had the opportunity to explore the interaction between season of birth and measure of consanguinity in well-described genetic isolates in Daghestan, some of which are known for their relatively high prevalence of schizophrenia. Our previous population-genetic study showed Daghestan has an extremely high genetic diversity between the ethnic populations and a low genetic diversity within them. The isolates selected for this study include some with more than 200 and some with less than 100 generations of demographical history since their founding. Based on pedigrees of multiply-affected families, we found that among individuals with schizophrenia, the measure of consanguinity was significantly higher in the parents of those born in winter/spring compared to those born in summer/autumn. Furthermore, compared to summer/autumn born, winter/spring born individuals with schizophrenia had an earlier age-of-onset, and more prominent auditory hallucinations. Our results suggest that the offspring of consanguineous marriages, and thus those with reduced allelic heterogeneity, may be more susceptible to the environmental factor(s) underpinning the season-of-the effect in schizophrenia.

Gene flow from multiple sources maintains high genetic diversity and stable population history of Common MoorhenGallinula chloropusin China

Ibis ◽  
2018 ◽  
Vol 160 (4) ◽  
pp. 855-869 ◽  
Author(s):  
Luzhang Ruan ◽  
Wei Xu ◽  
Yuqing Han ◽  
Chaoying Zhu ◽  
Bicai Guan ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Population History ◽  
Stable Population ◽  
Multiple Sources ◽  
High Genetic Diversity ◽  
History Of

scholarly journals High genetic diversity and demographic history of captive Siamese and Saltwater crocodiles suggest the first step toward the establishment of a breeding and reintroduction program in Thailand

PLoS ONE ◽  
2017 ◽  
Vol 12 (9) ◽  
pp. e0184526 ◽  
Author(s):  
Sorravis Lapbenjakul ◽  
Watcharaporn Thapana ◽  
Panupon Twilprawat ◽  
Narongrit Muangmai ◽  
Thiti Kanchanaketu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Demographic History ◽  
High Genetic Diversity ◽  
History Of

scholarly journals Population Genetic Structure and Genetic Diversity in Twisted-Jaw Fish, Belodontichthys truncatus Kottelat & Ng, 1999 (Siluriformes: Siluridae), from Mekong Basin

2017 ◽  
Vol 2017 ◽  
pp. 1-7 ◽  
Author(s):  
Surapon Yodsiri ◽  
Komgrit Wongpakam ◽  
Adisak Ardharn ◽  
Chadaporn Senakun ◽  
Sutthira Khumkratok
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Demographic History ◽  
Hydropower Plant ◽  
Mekong River ◽  
Demographic Expansion ◽  
High Genetic Diversity ◽  
History Analysis ◽  
History Of ◽  
Important Food Source

The Mekong River and its tributaries possess the second highest diversity in fish species in the world. However, the fish biodiversity in this river is threatened by several human activities, such as hydropower plant construction. Understanding the genetic diversity and genetic structure of the species is important for natural resource management. Belodontichthys truncatus Kottelat & Ng is endemic to the Mekong River basin and is an important food source for people in this area. In this study, the genetic diversity, genetic structure, and demographic history of the twisted-jaw fish, B. truncatus, were investigated using mitochondrial cytochrome b gene sequences. A total of 124 fish specimens were collected from 10 locations in the Mekong and its tributaries. Relatively high genetic diversity was found in populations of B. truncatus compared to other catfish species in the Mekong River. The genetic structure analysis revealed that a population from the Chi River in Thailand was genetically significantly different from other populations, which is possibly due to the effect of genetic drift. Demographic history analysis indicated that B. truncatus has undergone recent demographic expansion dating back to the end of the Pleistocene glaciation.

scholarly journals The effect of population bottleneck size and selective regime on genetic diversity and evolvability in bacteria

2019 ◽  
Author(s):  
Tanita Wein ◽  
Tal Dagan
Keyword(s):  
Genetic Diversity ◽  
Genetic Drift ◽  
Evolutionary Dynamics ◽  
Natural Populations ◽  
Population Bottleneck ◽  
Population Bottlenecks ◽  
High Genetic Diversity ◽  
Temperature Regimes ◽  
Consequent Reduction ◽  
History Of

AbstractPopulation bottlenecks leading to a drastic reduction of the population size are common in the evolutionary dynamics of natural populations; their occurrence is known to have implications for genome evolution due to genetic drift, the consequent reduction in genetic diversity and the rate of adaptation. Nevertheless, an empirical characterization of the effect of population bottleneck size on evolutionary dynamics of bacteria is currently lacking. Here we show that selective conditions have a stronger effect on the evolutionary history of bacteria in comparison to genetic drift following population bottlenecks. We evolved Escherichia coli populations under three different population bottlenecks (small, medium, large) in two temperature regimes (37°C and 20°C). We find a high genetic diversity in the large in comparison to the small bottleneck size. Nonetheless, the cold temperature led to reduced genetic diversity in all bottleneck sizes, hence, the temperature has a stronger effect on the genetic diversity in comparison to the bottleneck size. A comparison of the fitness gain among the evolved populations reveals a similar pattern where the temperature has a significant effect on the fitness. Our study demonstrates that population bottlenecks are an important determinant of the evolvability in bacteria; their consequences depend on the selective conditions and are best understood via their effect on the standing genetic variation.

scholarly journals Multilocus approach reveals a complex evolutionary history of the invasive mile-a-minute plant, Mikania micrantha (Asteraceae), in its natural habitat

2019 ◽  
Vol 191 (2) ◽  
pp. 188-215
Author(s):  
Sara Mataroli De Godoy ◽  
João Fernando Marques Da Silva ◽  
Paulo Maurício Ruas ◽  
Mara Rejane Ritter ◽  
Gabriela Barbosa Navarro De Paula ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Difference ◽  
Natural Habitat ◽  
High Genetic Diversity ◽  
Mikania Micrantha ◽  
Conservation Actions ◽  
History Of ◽  
Genetic Clusters ◽  
Multilocus Approach ◽  
Evolutionary Lineages

Abstract Mikania micrantha is native to Central and South America and exhibits morphological and cytological polymorphism, and evidence of a non-monophyletic origin. In Brazil, the species is widely distributed in the Atlantic Forest, one of the most threatened biomes in the world. AFLP, ITS, ETS and rps16 markers were employed to estimate the genetic diversity and the existence of independent evolutionary lineages in the species, and chromosomes were counted to determine ploidy of 11 populations of M. micrantha. Molecular markers showed relatively high genetic diversity and absence of genetic structure, and chromosome counts revealed pure diploid and tetraploid populations and mixed-cytotype populations in M. micrantha. There was no significant genetic difference between cytotypes, suggesting an autopolyploid origin for tetraploids. However, analyses of species delimitation showed that two highly divergent genetic clusters, constituted of samples from different populations, consisted of two independent evolutionary lineages, demonstrating putative cryptic species in M. micrantha. Our data highlight the need for more genetic studies in M. micrantha to ensure effective conservation actions in its natural area of occurrence and the correct management of the species in introduced areas, where it causes severe damage to forests and plantations.

scholarly journals Phylogeographic patterns and demographic history of Pomacea canaliculata and Pomacea maculata from different countries (Ampullariidae, Gastropoda, Mollusca)

2019 ◽  
Vol 36 ◽  
pp. 71-92
Author(s):  
Xiongjun Liu ◽  
Yu Zhou ◽  
Shan Ouyang ◽  
Xiaoping Wu
Keyword(s):  
Genetic Diversity ◽  
Invasive Species ◽  
Demographic History ◽  
Pomacea Canaliculata ◽  
High Genetic Diversity ◽  
Effective Prevention ◽  
Pomacea Maculata ◽  
History Of ◽  
Coi Sequences ◽  
And Control

Invasive species of Pomacea snails are of growing concern when it comes to the conservation of global biodiversity. Pomacea canaliculata has been listed among the world’s 100 worst invasive species. In this work, phylogeographic patterns and the demographic history of P. canaliculata and P. maculata from different countries were analyzed using mtDNA cytochrome c oxidase subunit-I (COI) sequences. The results showed that P. canaliculata and P. maculata had high genetic diversity, significant genetic differentiation, limited gene flow and stable population dynamics among different countries. Genetic diversity of P. canaliculata was higher than P. maculata. Our study will also provide important information for the effective prevention and control of the spread of Pomacea snails.

scholarly journals New insights on spatial genetic structure and diversity of Coffea canephora (Rubiaceae) in Upper Guinea based on old herbaria

2020 ◽  
Vol 153 (1) ◽  
pp. 82-100
Author(s):  
Jean-Pierre Labouisse ◽  
Philippe Cubry ◽  
Frédéric Austerlitz ◽  
Ronan Rivallan ◽  
Hong Anh Nguyen
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Spatial Genetic Structure ◽  
Coffea Canephora ◽  
Ex Situ ◽  
Herbarium Specimens ◽  
Robusta Coffee ◽  
Forest Remnants ◽  
History Of ◽  
Genetic Structure And Diversity

Backgrounds and aims – Previous studies showed that robusta coffee (Coffea canephora Pierre ex A.Froehner), one of the two cultivated coffee species worldwide, can be classified in two genetic groups: the Guinean group originating in Upper Guinea and the Congolese group in Lower Guinea and Congolia. Although C. canephora of the Guinean group is an important resource for genetic improvement of robusta coffee, its germplasm is under-represented in ex situ gene banks and its genetic diversity and population structure have not yet been investigated. Methods – To overcome the limitations of living collections, we explored old herbarium specimens collected in Guinea and Côte d’Ivoire and conserved at the Muséum National d’Histoire Naturelle, Paris. First, we reviewed the history of collection missions in both countries and how the C. canephora herbaria from the Muséum were assembled. Then, using 23 nuclear microsatellite markers, factorial and model-based Bayesian analyses, we investigated the genetic diversity of 126 specimens and 36 controls, analysed their distribution among the Congolese and Guinean groups, and estimated admixture proportions for each individual.Key results – For the first time, we detected population genetic structure within the Guinean group of C. canephora. The Guinean genotypes can be assigned to five sub-groups with distinct geographic distribution, especially in Guinea where two sub-groups (Maclaudii and Gamé) are characterized by a low level of admixture due to geographical isolation.Conclusions – We showed how combining a literature review and genetic data from old herbarium specimens can shed light on previous observations made by botanists and guide further actions to better preserve native coffee plants in forest remnants of West Africa.

scholarly journals Macro- and microevolutionary perspectives on Seynesiella juniperi, a fungus in the Venturiales (Dothideomycetes, Ascomycota)

2021 ◽  
Vol 45 ◽  
pp. e73217
Author(s):  
Isaac Garrido Benavent
Keyword(s):  
Type Species ◽  
Distinct Species ◽  
Species Boundaries ◽  
Phylogenetic Study ◽  
Cryptic Speciation ◽  
Plant Association ◽  
High Genetic Diversity ◽  
Biogeographic History ◽  
The Family ◽  
History Of

The present work represents the first comprehensive phylogenetic study of the dothideomycete genus Seynesiella. The genus belongs into the family Cylindrosympodiaceae within the order Venturiales, based on a phylogeny reconstructed with five loci. The high genetic diversity found within the type species, S. juniperi, points towards cryptic speciation, with up to five distinct species that might be associated to different Juniperus hosts. Combining phylogenetics and multi-locus delimitation analyses, together with more detailed measurements of ascospores, will be fundamental for a better understanding of species boundaries and the biogeographic history of the delimited species, as well as for revealing more specific fungal-plant association patterns.

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