Secondary origin, hybridization and sexual reproduction in a diploid- tetraploid contact zone of the facultative apomictic orchid Zygopetalum mackayi

ABSTRACT>Mixed-cytotype populations are ideal to understand polyploid establishment and diversification. We used the orchid Zygopetalum mackayi to understand how facultative apomictic reproduction relates to polyploidy. Sexual diploids and facultative apomictic tetraploids occur under distinct niches, with a contact zone where triploids occur. We hypothesized that facultative apomictic reproduction increases the fitness of tetraploids through reproductive interference between cytotypes. We predict patterns of genetic diversity of allopatric tetraploid populations to be significantly different from contact zone populations as a result of dominant apomictic reproduction in the later. We also describe the contact nature of diploids and tetraploids and the role of the intermediate triploids based on patterns of genetic structure within and among pure and mixed-cytotype populations.>We designed eight microsatellite markers and genotyped 155 individuals from six populations resulting in 237 alleles. We described patterns of genetic diversity and structure within and among populations and cytotypes.>Genotypic diversity is similarly high among all populations and cytotypes. Each cytotype emerged as a genetically cluster, combining individuals from different populations. Triploids clustered in an intermediate position between diploids andtetraploids.>We rejected the hypothesis of reproductive interference between cytotypes of Z. mackayi. Patterns of genetic diversity are incongruent with the occurrence of apomict reproduction in tetraploids. Mixed-cytotype populations originate from secondary contact and triploids are hybrids between diploids and tetraploids and act as a reproductive barrier. We suggest polyploidy rather than facultative apomixis explains higher fitness of tetraploids in this species and, therefore, eco-geographical patterns of distribution.

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Population genetics reveals cryptic lineages and ongoing hybridization in a declining migratory fish species complex

10.1101/2021.12.04.471201 ◽

2021 ◽

Author(s):

Quentin Rougemont ◽

Charles Perrier ◽

Anne-Laure Besnard ◽

Isabelle Lebel ◽

Yann Abdallah ◽

...

Keyword(s):

Genetic Diversity ◽

Life History ◽

Demographic History ◽

Life History Strategies ◽

Secondary Contact ◽

Allis Shad ◽

Twaite Shad ◽

Genetic Diversity And Structure ◽

Demographic Processes ◽

Hybridization And Introgression

AbstractDeciphering the effects of historical and recent demographic processes responsible for the spatial patterns of genetic diversity and structure is a key objective in evolutionary and conservation biology. Using genetic analyses, we investigated the demographic history, the contemporary genetic diversity and structure, and the occurrence of hybridization and introgression, of two species of anadromous fish with contrasted life history strategies and which have undergone recent demographic declines, the allis shad (Alosa alosa) and the twaite shad (Alosa fallax). We genotyped 706 individuals from 20 rivers and 5 sites at sea in Southern Europe at microsatellite markers. Genetic structure between populations was lower for the nearly semelparous species allis shad that disperse stronger distance compared to the iteroparous species, twaite shad. Individuals caught at sea were assigned at the river level for twaite shad and at the region level for allis shad. Using an approximate Bayesian computation framework, we inferred that the most likely long term historical divergence scenario between both species implicated historical separation followed by secondary contact accompanied by strong population size decline. Accordingly, we found evidence of contemporary hybridization and introgression between both species. Besides, our results support the existence of cryptic species in the Mediterranean sea. Overall, our results shed light on the interplay between historical and recent demographic processes and life history strategies in shaping population genetic diversity and structure of closely related species. The recent demographic decline of these species’ populations and their hybridization should be carefully considered while implementing conservation programs.

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Genetic Diversity and Structure in RegionalCercospora beticolaPopulations fromBeta vulgarissubsp.vulgarisSuggest Two Clusters of Separate Origin

Phytopathology ◽

10.1094/phyto-07-18-0264-r ◽

2019 ◽

Vol 109 (7) ◽

pp. 1280-1292 ◽

Cited By ~ 4

Author(s):

Noel L. Knight ◽

Niloofar Vaghefi ◽

Julie R. Kikkert ◽

Melvin D. Bolton ◽

Gary A. Secor ◽

...

Keyword(s):

Genetic Diversity ◽

New York ◽

Genotypic Diversity ◽

Population Divergence ◽

Cercospora Leaf Spot ◽

High Genetic Diversity ◽

Genetic Diversity And Structure ◽

The World ◽

Population Origin ◽

Geographic Regions

Cercospora leaf spot, caused by Cercospora beticola, is a highly destructive disease of Beta vulgaris subsp. vulgaris worldwide. C. beticola populations are usually characterized by high genetic diversity, but little is known of the relationships among populations from different production regions around the world. This information would be informative of population origin and potential pathways for pathogen movement. For the current study, the genetic diversity, differentiation, and relationships among 948 C. beticola isolates in 28 populations across eight geographic regions were investigated using 12 microsatellite markers. Genotypic diversity, as measured by Simpson’s complement index, ranged from 0.18 to 1.00, while pairwise index of differentiation values ranged from 0.02 to 0.42, with the greatest differentiation detected between two New York populations. In these populations, evidence for recent expansion was detected. Assessment of population structure identified two major clusters: the first associated with New York, and the second with Canada, Chile, Eurasia, Hawaii, Michigan, North Dakota, and one population from New York. Inferences of gene flow among these regions suggested that the source for one cluster likely is Eurasia, whereas the source for the other cluster is not known. These results suggest a shared origin of C. beticola populations across regions, except for part of New York, where population divergence has occurred. These findings support the hypothesis that dispersal of C. beticola occurs over long distances.

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Genetic diversity and structure in fragmented populations of the endangered species Ranunculus cabrerensis (Ranunculaceae): implications for conservation

Biologia ◽

10.2478/s11756-012-0126-6 ◽

2013 ◽

Vol 68 (1) ◽

Cited By ~ 6

Author(s):

Eduardo Cires ◽

Candela Cuesta ◽

José Fernández Prieto

Keyword(s):

Genetic Diversity ◽

Endangered Species ◽

Conservation Strategies ◽

Aflp Analysis ◽

Issr Primer ◽

Bayesian Analyses ◽

Principal Coordinates ◽

Genetic Diversity And Structure ◽

Different Populations ◽

Genetic Structures

AbstractRanunculus cabrerensis is an endemic and endangered species of the Northwestern Iberian Peninsula. The molecular markers AFLP and ISSR were used to investigate the genetic diversity and population structure of four populations across its known distribution. Fifteen selective primer combinations of AFLP and seventeen ISSR primer combinations produced a total of 2830 and 103 unambiguously repeatable fragments respectively, of which 97.57 and 81.38% were polymorphic for both markers. The genetic diversity of R. cabrerensis at species level was high (H E = 0.294 by ISSR and H E = 0.191 by AFLP) and differentiation between sampled locations was also relatively high (G ST = 0.316 and 0.158 by ISSR and AFLP analysis respectively) compared to other studies of endangered and rare species using the same techniques. The analysis of molecular variance (AMOVA) indicated that the main genetic variation was within sampled locations (73% by AFLP; 52% by ISSR), even though the variation among locations was also significant. Principal Coordinates, NeighborNet and Bayesian analyses revealed a weak but significant relationship between the genetic structures of different populations in R. cabrerensis, with gene flow acting as a homogenizing force that prevents stronger differentiation of populations. Finally, suggestions for conservation strategies to preserve the genetic resources of this species are outlined.

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Esterase Polymorphism for Analysis of Genetic Diversity and Structure of Wild Poinsettia (Euphorbia heterophylla) Populations

Weed Science ◽

10.1614/ws-08-096.1 ◽

2009 ◽

Vol 57 (1) ◽

pp. 54-60 ◽

Cited By ~ 10

Author(s):

Mariléia J. Frigo ◽

Claudete A. Mangolin ◽

Rubem S. Oliveira ◽

Maria de Fátima P. S. Machado

Keyword(s):

Genetic Diversity ◽

Polyacrylamide Gel Electrophoresis ◽

Herbicide Application ◽

Genetic Diversity And Structure ◽

Esterase Polymorphism ◽

Native Polyacrylamide Gel Electrophoresis ◽

Esterase Loci ◽

Leaf Tissues ◽

Different Populations ◽

And Control

Native polyacrylamide gel electrophoresis was used in the current study to identify polymorphism in α- and β-esterase loci in leaf tissues of wild poinsettia plants for the analysis of genetic diversity and structure of populations. Seeds were collected from different plants in 12 different populations. Two to three allelic variants were at Est-1, Est-2, Est-3, Est-4, Est-5, Est-6, and Est-7 loci. The estimated proportion of polymorphic loci in populations is 87.5%. High and low values of observed and expected proportion of heterozygous loci in 12 populations confirm our suspicion that the populations are genetically structured (FST = 0.1663). The heterozygous deficiencies are evidenced by the positive value of FIS (0.1248). The positive FIS value indicates a deficit of heterozygous (12.48%) or an excess of homozygous plants, which could be the result of frequent herbicide application in areas where seeds were collected and/or the result of self-pollination. Overall inbreeding or nonrandom breeding, according to the significant FIT value (0.2703), did play a major role in shaping the genetic structure of these populations. Identity values represented in the dendrogram should play a more central role in developing policies to manage and control this species.

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Genetic diversity and population structure of Plasmodium falciparum in Nigeria: insights from microsatellite loci analysis

Malaria Journal ◽

10.1186/s12936-021-03734-x ◽

2021 ◽

Vol 20 (1) ◽

Author(s):

Fehintola V. Ajogbasile ◽

Adeyemi T. Kayode ◽

Paul E. Oluniyi ◽

Kazeem O. Akano ◽

Jessica N. Uwanibe ◽

...

Keyword(s):

Genetic Diversity ◽

Plasmodium Falciparum ◽

Population Structure ◽

Microsatellite Loci ◽

Control Strategies ◽

Population Diversity ◽

Parasite Population ◽

Nested Polymerase Chain Reaction ◽

Public Health Burden ◽

Genetic Diversity And Structure

Abstract Background Malaria remains a public health burden especially in Nigeria. To develop new malaria control and elimination strategies or refine existing ones, understanding parasite population diversity and transmission patterns is crucial. Methods In this study, characterization of the parasite diversity and structure of Plasmodium falciparum isolates from 633 dried blood spot samples in Nigeria was carried out using 12 microsatellite loci of P. falciparum. These microsatellite loci were amplified via semi-nested polymerase chain reaction (PCR) and fragments were analysed using population genetic tools. Results Estimates of parasite genetic diversity, such as mean number of different alleles (13.52), effective alleles (7.13), allelic richness (11.15) and expected heterozygosity (0.804), were high. Overall linkage disequilibrium was weak (0.006, P < 0.001). Parasite population structure was low (Fst: 0.008–0.105, AMOVA: 0.039). Conclusion The high level of parasite genetic diversity and low population structuring in this study suggests that parasite populations circulating in Nigeria are homogenous. However, higher resolution methods, such as the 24 SNP barcode and whole genome sequencing, may capture more specific parasite genetic signatures circulating in the country. The results obtained can be used as a baseline for parasite genetic diversity and structure, aiding in the formulation of appropriate therapeutic and control strategies in Nigeria.

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Genetic diversity and structure of the endemic and endangered species Aristolochia delavayi growing along the Jinsha River

Plant Diversity ◽

10.1016/j.pld.2020.12.007 ◽

2021 ◽

Author(s):

Yu-Long Yu ◽

Hui-Chun Wang ◽

Zhi-Xiang Yu ◽

Johann Schinnerl ◽

Rong Tang ◽

...

Keyword(s):

Genetic Diversity ◽

Endangered Species ◽

Jinsha River ◽

Genetic Diversity And Structure

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Genetic and Epigenetic Changes during the Upward Expansion of Deyeuxia angustifolia Kom. in the Alpine Tundra of the Changbai Mountains, China

Plants ◽

10.3390/plants10020291 ◽

2021 ◽

Vol 10 (2) ◽

pp. 291

Author(s):

Biao Ni ◽

Jian You ◽

Jiangnan Li ◽

Yingda Du ◽

Wei Zhao ◽

...

Keyword(s):

Genetic Diversity ◽

Dna Methylation ◽

Genetic Variation ◽

Soil Properties ◽

Changbai Mountains ◽

Epigenetic Variation ◽

Geographical Distance ◽

Mantel Tests ◽

Epigenetic Diversity ◽

Different Populations

Ecological adaptation plays an important role in the process of plant expansion, and genetics and epigenetics are important in the process of plant adaptation. In this study, genetic and epigenetic analyses and soil properties were performed on D. angustifolia of 17 populations, which were selected in the tundra zone on the western slope of the Changbai Mountains. Our results showed that the levels of genetic and epigenetic diversity of D. angustifolia were relatively low, and the main variation occurred among different populations (amplified fragment length polymorphism (AFLP): 95%, methylation sensitive amplification polymorphism (MSAP): 87%). In addition, DNA methylation levels varied from 23.36% to 35.70%. Principal component analysis (PCA) results showed that soil properties of different populations were heterogeneous. Correlation analyses showed that soil moisture, pH and total nitrogen were significantly correlated with genetic diversity of D. angustifolia, and soil temperature and pH were closely related to epigenetic diversity. Simple Mantel tests and partial Mantel tests showed that genetic variation significantly correlated with habitat or geographical distance. However, the correlation between epigenetic variation and habitat or geographical distance was not significant. Our results showed that, in the case of low genetic variation and genetic diversity, epigenetic variation and DNA methylation may provide a basis for the adaptation of D. angustifolia.

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