scholarly journals Genome diversity of tuber-bearing Solanum uncovers complex evolutionary history and targets of domestication in the cultivated potato

2017 ◽  
Vol 114 (46) ◽  
pp. E9999-E10008 ◽  
Author(s):  
Michael A. Hardigan ◽  
F. Parker E. Laimbeer ◽  
Linsey Newton ◽  
Emily Crisovan ◽  
John P. Hamilton ◽  
...  

Cultivated potatoes (Solanum tuberosum L.), domesticated from wild Solanum species native to the Andes of southern Peru, possess a diverse gene pool representing more than 100 tuber-bearing relatives (Solanum section Petota). A diversity panel of wild species, landraces, and cultivars was sequenced to assess genetic variation within tuber-bearing Solanum and the impact of domestication on genome diversity and identify key loci selected for cultivation in North and South America. Sequence diversity of diploid and tetraploid S. tuberosum exceeded any crop resequencing study to date, in part due to expanded wild introgressions following polyploidy that captured alleles outside of their geographic origin. We identified 2,622 genes as under selection, with only 14–16% shared by North American and Andean cultivars, showing that a limited gene set drove early improvement of cultivated potato, while adaptation of upland (S. tuberosum group Andigena) and lowland (S. tuberosum groups Chilotanum and Tuberosum) populations targeted distinct loci. Signatures of selection were uncovered in genes controlling carbohydrate metabolism, glycoalkaloid biosynthesis, the shikimate pathway, the cell cycle, and circadian rhythm. Reduced sexual fertility that accompanied the shift to asexual reproduction in cultivars was reflected by signatures of selection in genes regulating pollen development/gametogenesis. Exploration of haplotype diversity at potato’s maturity locus (StCDF1) revealed introgression of truncated alleles from wild species, particularly S. microdontum in long-day–adapted cultivars. This study uncovers a historic role of wild Solanum species in the diversification of long-day–adapted tetraploid potatoes, showing that extant natural populations represent an essential source of untapped adaptive potential.

2015 ◽  
Vol 26 (3-4) ◽  
pp. 116-123
Author(s):  
A. P. Korzh ◽  
T. V. Zahovalko

Recently, the number of published works devoted to the processes of synanthropization of fauna, is growing like an avalanche, which indicates the extreme urgency of this theme. In our view, the process of forming devices to coexist with human and the results of his life reflects the general tandency of the modern nature evolution. Urbanization is characteristic for such a specific group of animals like amphibians, the evidence of which are numerous literature data. Many researchers use this group to assess the bioindicative quality of the environment. For this aim a variety of indicators are used: from the cellular level of life of organization up to the species composition of the group in different territories. At the same time, the interpretation of the results is not always comparable for different areas and often have significantly different interpretations by experts. Urban environment, primarily due to the contamination is extremely aggressive to amphibians. As a consequence, the urban populations of amphibians may be a change in the demographic structure, affecting the reproductive ability of the population, the disappearance of the most sensitive species or individuals, resizing animals, the appearance of abnormalities in the development, etc. At the same time play an important amphibians in the ecosystems of cities, and some species in these conditions even feel relatively comfortable. Therefore, it is interesting to understand the mechanisms of self-sustaining populations of amphibians in urban environments. To assess the impact of natural and anthropogenic factors on the development of amphibian populations were used cognitive modeling using the program Vensim PLE. Cognitive map of the model for urban and suburban habitat conditions were the same. The differences concerned the strength of connections between individual factors (migration, fertility, pollution) and their orientation. In general, factors like pollution, parasites, predators had negative impact on the population, reducing its number. The birth rate, food and migration contributed to raising number of individuals. Some of the factors affected on the strength to of each other as well: the majority of the factors affected the structure of the population, had an influence on the fertility. Thanks to it the model reflects the additive effect of complex of factors on the subsequent status of the population. Proposed and analyzed four scenarios differing strength and duration of exposure. In the first scenario, a one-time contamination occurs and not subsequently repeated. The second and third scenario assumes half board contamination, 1 year (2 scenario) and two years (scenario 3). In the fourth scenario, the pollution affected the population of amphibians constantly. In accordance with the results of simulation, much weaker than the natural populations respond to pollution - have them as an intensive population growth and its disappearance at constant pollution is slow. Changes to other parameters of the model showed that this pollution is the decisive factor -only the constant action leads to a lethal outcome for the populations. All other components of the model have a corrective effect on the population dynamics, without changing its underlying trand. In urban areas due to the heavy impact of pollution maintaining the population is only possible thanks to the migration process – the constant replenishment of diminishing micropopulations of natural reserves. This confirms the assumption that the form of existence metapopulations lake frog in the city. In order to maintain the number of amphibians in urban areas at a high level it is necessary to maintain existing migration routes and the creation of new ones. Insular nature of the placement of suitable habitats in urban areas causes the metapopulation structure of the types of urbanists. Therefore, the process of urbanization is much easier for those species whicht are capable of migration in conditions of city. In the initial stages of settling the city micropopulationis formed by selective mortality of the most susceptible individuals to adverse effects. In future, maintaining the categories of individuals is provided mainly due to migration processes metapopulisation form of the species of existence is supported). It should be noted that the changes in the previous levels are always saved in future. In the case of reorganizations of individuals we of morphology can assume the existence of extremely adverse environmental conditions that threaten the extinction of the micropopulations. 


Biology ◽  
2021 ◽  
Vol 10 (6) ◽  
pp. 471
Author(s):  
Camino Gutiérrez-Corbo ◽  
Bárbara Domínguez-Asenjo ◽  
María Martínez-Valladares ◽  
Yolanda Pérez-Pertejo ◽  
Carlos García-Estrada ◽  
...  

Diseases caused by trypanosomatids (Sleeping sickness, Chagas disease, and leishmaniasis) are a serious public health concern in low-income endemic countries. These diseases are produced by single-celled parasites with a diploid genome (although aneuploidy is frequent) organized in pairs of non-condensable chromosomes. To explain the way they reproduce through the analysis of natural populations, the theory of strict clonal propagation of these microorganisms was taken as a rule at the beginning of the studies, since it partially justified their genomic stability. However, numerous experimental works provide evidence of sexual reproduction, thus explaining certain naturally occurring events that link the number of meiosis per mitosis and the frequency of mating. Recent techniques have demonstrated genetic exchange between individuals of the same species under laboratory conditions, as well as the expression of meiosis specific genes. The current debate focuses on the frequency of genomic recombination events and its impact on the natural parasite population structure. This paper reviews the results and techniques used to demonstrate the existence of sex in trypanosomatids, the inheritance of kinetoplast DNA (maxi- and minicircles), the impact of genetic exchange in these parasites, and how it can contribute to the phenotypic diversity of natural populations.


2021 ◽  
Vol 11 (1) ◽  
pp. 32
Author(s):  
Helen Adam

The importance of recognising, valuing and respecting a child’s family, culture, language and values is central to socially just education and is increasingly articulated in educational policy worldwide. Inclusive children’s literature can support children’s human rights and contribute to equitable and socially just outcomes for all children. However, evidence suggests many educational settings provide monocultural book collections which are counterproductive to principles of diversity and social justice. Further, that educators’ understandings and beliefs about diversity can contribute to inequitable provision and use of diverse books and to inequitable outcomes of book sharing for many children. This paper reports on a larger study investigating factors and relationships influencing the use of children’s literature to support principles of cultural diversity in the kindergarten rooms of long day care centres. The study was conducted within an ontological perspective of constructivism and an epistemological perspective of interpretivism informed by sociocultural theory. A mixed methods approach was adopted, and convergent design was employed interpret significant relationships and their meanings. Twenty-four educators and 110 children from four long day care centres in Western Australia participated. Data were collected through semi-structured interviews, video-based observations, field notes, document analysis and a book audit. This study firstly identified that current book collections in kindergarten rooms of long day care centres promote mono-cultural viewpoints and ‘othering’ of minority groups through limited access to books portraying inclusive and authentic cultural diversity. Secondly, that educators had limited understandings of the role of literature in acknowledging and valuing diversity and rarely used it to promote principles of diversity, resulting in a practice of “othering” those from minority group backgrounds. The key challenges which emerged from the study concerned beliefs, understanding and confidence of educators about diversity and inclusion, and the impact of these on their approaches to promoting principles of diversity through the use of children’s books. This research contributes to discussion on the value of children’s literature in achieving international principles of diversity. These findings have important social justice implications. The outcomes of this study have implications for educators, policy makers, early childhood organisations and those providing higher education and training for early childhood educators.


Genetics ◽  
1997 ◽  
Vol 147 (3) ◽  
pp. 1169-1180 ◽  
Author(s):  
Daven C Presgraves ◽  
Emily Severance ◽  
Gerald S Willrinson

Meiotically driven sex chromosomes can quickly spread to fixation and cause population extinction unless balanced by selection or suppressed by genetic modifiers. We report results of genetic analyses that demonstrate that extreme female-biased sex ratios in two sister species of stalk-eyed flies, Cyrtodiopsis dalmanni and C. whitei, are due to a meiotic drive element on the X chromosome (Xd). Relatively high frequencies of Xd in C. dalmanni and C. whitei (13–17% and 29%, respectively) cause female-biased sex ratios in natural populations of both species. Sex ratio distortion is associated with spermatid degeneration in male carriers of Xd. Variation in sex ratios is caused by Y-linked and autosomal factors that decrease the intensity of meiotic drive. Y-linked polymorphism for resistance to drive exists in C. dalmanni in which a resistant Y chromosome reduces the intensity and reverses the direction of meiotic drive. When paired with Xd, modifying Y chromosomes (Ym) cause the transmission of predominantly Y-bearing sperm, and on average, production of 63% male progeny. The absence of sex ratio distortion in closely related monomorphic outgroup species suggests that this meiotic drive system may predate the origin of C. whitei and C. dalmanni. We discuss factors likely to be involved in the persistence of these sex-linked polymorphisms and consider the impact of Xd on the operational sex ratio and the intensity of sexual selection in these extremely sexually dimorphic flies.


Author(s):  
Luis E. Rodríguez de Francisco ◽  
Rosanna Carreras-De León ◽  
Rafael M. Navarro Cerrillo ◽  
Liz A. Paulino-Gervacio ◽  
María-Dolores Rey ◽  
...  

<i>Pinus occidentalis</i> is the dominant species of forest ecosystems in the Dominican Republic, located between 200 and 3000 meters above sea level, with extensive and overexploited natural populations. However, over the years, various restoration plans have been performed, which could affect the genetic structure of <i>P. occidentalis</i>. Despite being the species with the highest occurrence in the Dominican forests, there is no existing information on genetic structure and molecular characterization among natural populations with limited information on both phenological and productive characterization. In this study, the genetic structure, diversity, and gene flow of the five <i>P. occidentalis</i> natural populations of the Dominican Republic were determined using microsatellite markers. A total of 145 individuals were genotyped with eight polymorphic chloroplastic microsatellites, producing an average of 41 haplotypes with high genetic diversity across populations (H<sub>E</sub> = 0.90). Significant population genetic structure was found between populations (F<sub>ST</sub> = 0.123). These results reflect the impact of reforestation programs on natural populations and diluting the natural genetic signature. Analysis of population genetic data is, therefore, crucial for the breeding and conservation programs of <i>P. occidentalis</i> in the country.


2008 ◽  
Vol 9 (1) ◽  
pp. 30 ◽  
Author(s):  
Mrittunjai Srivastava ◽  
Lara Bosco ◽  
Joe Funderburk ◽  
Anthony Weiss

Feeding by the western flower thrips, Frankliniella occidentalis, causes damage to the fruits of pepper, and the species is the key vector of Tomato spotted wilt virus. Effective management integrates conservation of populations of the natural predator, Orius insidiosus, with the use of reduced-risk insecticides, namely spinosad. We conducted field experiments in northern Florida in 2005 and 2006 and in central Florida in 2006 to evaluate the new reduced-risk insecticide spinetoram for control of thrips and to determine the impact on natural populations of O. insidiosus. Spinetoram at 61 g ai/ha was as effective as spinosad at 140 g ai/ha against the western flower thrips and the other common thrips in Florida, Frankliniella tritici and Frankliniella bispinosa. The mean numbers of the predator were very high in all treatments in each experiment, and their numbers relative to the numbers of thrips indicated that predation was sufficient to suppress thrips populations in all treatments. Broad-spectrum insecticides when included in the experiments provided little or no control; sometimes, they flared thrips numbers compared to untreated pepper. Accepted for publication 25 October 2007. Published 18 January 2008.


2016 ◽  
Vol 75 (1) ◽  
pp. 53-59 ◽  
Author(s):  
Marko Zebec ◽  
Marilena Idžojtić ◽  
Zlatko Šatović ◽  
Igor Poljak ◽  
Zlatko Liber

AbstractThe main objective of this research was to assess the genetic diversity of 5 natural field elm populations in Croatia. The study results suggest that the observed populations are characterized by a satisfactory amount of heterozygosity, and that the impact of the Dutch elm disease on the amount of genetic diversity in the sampled populations is currently negligible. However, one population displayed a significant excess of heterozygosity, implying a genetic bottleneck. The existence of a very clear genetic differentiation between the continental and the Mediterranean populations of Ulmus minor in Croatia was noticed.


2019 ◽  
Vol 36 (10) ◽  
pp. 2358-2374
Author(s):  
Nicolas Alcala ◽  
Amy Goldberg ◽  
Uma Ramakrishnan ◽  
Noah A Rosenberg

Abstract Natural populations display a variety of spatial arrangements, each potentially with a distinctive impact on genetic diversity and genetic differentiation among subpopulations. Although the spatial arrangement of populations can lead to intricate migration networks, theoretical developments have focused mainly on a small subset of such networks, emphasizing the island-migration and stepping-stone models. In this study, we investigate all small network motifs: the set of all possible migration networks among populations subdivided into at most four subpopulations. For each motif, we use coalescent theory to derive expectations for three quantities that describe genetic variation: nucleotide diversity, FST, and half-time to equilibrium diversity. We describe the impact of network properties on these quantities, finding that motifs with a high mean node degree have the largest nucleotide diversity and the longest time to equilibrium, whereas motifs with low density have the largest FST. In addition, we show that the motifs whose pattern of variation is most strongly influenced by loss of a connection or a subpopulation are those that can be split easily into disconnected components. We illustrate our results using two example data sets—sky island birds of genus Sholicola and Indian tigers—identifying disturbance scenarios that produce the greatest reduction in genetic diversity; for tigers, we also compare the benefits of two assisted gene flow scenarios. Our results have consequences for understanding the effect of geography on genetic diversity, and they can assist in designing strategies to alter population migration networks toward maximizing genetic variation in the context of conservation of endangered species.


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