Strategies for genetic conservation of trees in the Peruvian Amazon

Forestry practices and high rates of land clearance for agriculture are causing genetic erosion of valuable tree species in the Peruvian Amazon, thereby endangering the economic sustainability of rural communities and limiting Peru's opportunities for the development of new timber and non-timber forest products. The potential utility and limitations of six low-input interventions to help forestall further genetic erosion in the region are discussed, with a focus on local community involvement. Improved agroforestry systems may help reduce deforestation by increasing farm productivity, although methods to increase the currently low adoption rate of these technologies need to be developed. Use of strategic tree domestication techniques can also improve farm productivity and prevent inadvertent genetic drift and inbreeding associated with traditional domestication practices, although to have a major impact, current programs need to be extended across the region. Woodlot forestry could supplant selective extraction of timber and offers an attractive opportunity for poverty alleviation if appropriate credit and land tenure policies can be developed. However, it may also result in increased deforestation if activities on public land cannot be controlled. The implementation of improved seed collection systems and simple seed transfer guidelines would help to reduce the collection of seed of poor quality and low genetic diversity, and avoid maladapted plantings, although such programs are difficult to monitor and seed costs may increase. Strategic identification and design of in situ conservation areas would help to ensure the viability of conserved populations, but requires the forfeiture of significant revenue from timber concessions.     

A stochastic context free grammar based framework for analysis of protein sequences

Background  

In the last decade, there have been many applications of formal language theory in bioinformatics such as RNA structure prediction and detection of patterns in DNA. However, in the field of proteomics, the size of the protein alphabet and the complexity of relationship between amino acids have mainly limited the application of formal language theory to the production of grammars whose expressive power is not higher than stochastic regular grammars. However, these grammars, like other state of the art methods, cannot cover any higher-order dependencies such as nested and crossing relationships that are common in proteins. In order to overcome some of these limitations, we propose a Stochastic Context Free Grammar based framework for the analysis of protein sequences where grammars are induced using a genetic algorithm.     

Growth units construction in trees: A stochastic approach

Trees architectural study shows gradients in the meristematic activity. This activity is described by the number of internodes per growth unit, which is considered as the output of a dynamic random process. Several species were observed, which led us to propose and then estimate some mathematical models. Computing the functioning of a tree in a given environment therefore involves finding the probability function of the meristems and following the evolution of the parameters of this law along the botanical gradients (order, trend, acrotony) within its architecture.     

Standardized genetic diversity‐life history correlates for improved genetic resource management of Neotropical trees

Aim

Life history traits and range size are key correlates of genetic diversity in trees. We used a standardized sampling protocol to explore how life history traits and range size relate to the magnitude, variance and structuring (both between‐ and within‐population) of genetic diversity in Neotropical tree species.

Location

The Neotropics

Methods

We present a meta‐analysis of new population genetic data generated for 23 Neotropical tree species (=2,966 trees, 86 populations) across a shared and broad geographic area. We compared established population genetic metrics across these species (e.g., genetic diversity, population structure, fine‐scale genetic structure), plus we estimated the rarely used variance in genetic diversity among populations. We used a multivariate, maximum likelihood, multimodel inference approach to explore the relative influence of life history traits and range size on patterns of neutral genetic diversity.

Results

We found that pioneer and narrow range species had lower levels but greater variance in genetic diversity—signs of founder effects and stronger genetic drift. Animal‐dispersed species had lower population differentiation, indicating extensive gene flow. Abiotically dispersed and pioneer species had stronger fine‐scale genetic structure, suggesting restricted seed dispersal and family cohort establishment.

Main conclusions

Our multivariable and multispecies approach allows ecologically relevant conclusions, since knowing whether one parameter has an effect, or one species shows a response in isolation, is dependent on the combination of traits expressed by a species. Our study demonstrates the influence of ecological processes on the distribution of genetic variation in tropical trees, and will help guide genetic resource management, and contribute to predicting the impacts of land use change.

     

Recent advances in the genetic transformation of trees

As the commercial production of transgenic annual crops becomes a reality in many parts of the world, many people wonder if the genetic engineering of perennial trees will allow their eventual commercialization. Not long ago, trees were considered to be recalcitrant material for most molecular biology techniques, including genetic transformation. However, transgenes for shortening the juvenile phase or for phytoremediation purposes have now been incorporated, and the alteration of lignin biosynthesis and increased cellulose accumulation in forest trees have also been accomplished. For long-lived tree species, new questions arise regarding the stability of integration and expression of foreign genes. Biosafety considerations, including transgene dispersion through the pollen and advances in strategies to avoid this, are also important.     

Components of genetic variance for plant survival and vigor of apple trees

Summary The additive and non-additive variance components were estimated from progenies derived from two samples of parents (representing a northern continental type climate) for five factors relating to plant survival and two composites of the factors. It was found that additive variance made up 90 and 100%, 91 and 100%, 91 and 100%, 100 and 100%, 82 and 59%, 91 and 100%, and 90 and 100% of the total genetic variance for leafing-out date, leafingout percent, tip injury, stem damage, root damage, a shoot composite, and a shoot-root composite for the two samples respectively. A third sample had 100% additive variance for plant height while, in contrast, a sample of rootstocks, differing from each other in their ability to dwarf grafted scions, had approximately 50–70% additive variance for plant height. It was shown that breeding progress for both winter survival and plant height could be achieved by exploiting the additive variance, the total genetic variance, or (where progenies were the selection unit rather than individuals) by progeny selection. By exploiting the additive variance, it should be possible to improve plant survival and change plant height in each of several successive generations. It is predicted that (with the exception of selection for vigor in a population having a range of dwarfing abilities) potential parents could be efficiently screened phenotypically and so obviate the need for genotypic evaluation. A total of 9180 progeny trees were involved in the analyses considered in this paper.

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Zusammenfassung Für Symptome, die Frostschäden bei zwei Stichproben eines nördlich-kontinentalen Klimatyps des Apfels anzeigen, wurden die additiven und nicht additiven Varianzkomponenten von fünf einfachen und zwei zusammengesetzten Faktoren geschätzt. Die Werte der additiven Varianz betrugen für beide Stichproben 90 und 100%, 91 und 100%, 91 und 100%, 100 und 100%, 82 und 59%, 91 und 100% sowie 90 und 100% der Gesamtvarianz für Zeitpunkt der Knospenentfaltung, Prozentsatz der Knospenentfaltung, Schäden an Triebspitzen, Stammschäden, Wurzelschäden sowie für das komplexe Schadbild Sproßschäden und Wurzelschäden insgesamt. In einer dritten Stichprobe betrug die additive Varianz für das Merkmal Pflanzenhöhe 100%, im Gegensatz zu einer Stichprobe von Unterlagen, die Zwergwüchsigkeit bei aufgepfropften Reisern hervorruft, bei der die additive Varianz 51–70% betrug. Es konnte gezeigt werden, daß Fortschritte in der Züchtung auf Frostwiderstandsfähigkeit und Wuchsstärke durch Ausnutzung der additiven Varianz, der Gesamtvarianz oder, wo Nachkommenschaften und nicht Individuen selektiert worden sind, durch Nachkommenschaftsselektion erreicht werden können. Durch Ausnutzung der additiven Varianz sollte es möglich sein, Frostwiderstandsfähigkeit und Wuchsstärke in den folgenden Generationen zu verbessern. Mit Ausnahme auf Starkwüchsigkeit in einer Population mit der Tendenz zur Zwergwüchsigkeit können Elternpflanzen wirksam auf Grund ihres Phänotyps selektiert werden, so daß eine genotypische Analyse entbehrlich ist. Insgesamt wurden für die in der vorliegenden Veröffentlichung mitgeteilten Schätzungen 9180 Sämlinge bonitiert.

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Contribution No. 243 from the Research Station, Central Experimental Farm, Ottawa, Ontario.     

Robust filtering for stochastic genetic regulatory networks with time-varying delay

This paper addresses the robust filtering problem for a class of linear genetic regulatory networks (GRNs) with stochastic disturbances, parameter uncertainties and time delays. The parameter uncertainties are assumed to reside in a polytopic region, the stochastic disturbance is state-dependent described by a scalar Brownian motion, and the time-varying delays enter into both the translation process and the feedback regulation process. We aim to estimate the true concentrations of mRNA and protein by designing a linear filter such that, for all admissible time delays, stochastic disturbances as well as polytopic uncertainties, the augmented state estimation dynamics is exponentially mean square stable with an expected decay rate. A delay-dependent linear matrix inequality (LMI) approach is first developed to derive sufficient conditions that guarantee the exponential stability of the augmented dynamics, and then the filter gains are parameterized in terms of the solution to a set of LMIs. Note that LMIs can be easily solved by using standard software packages. A simulation example is exploited in order to illustrate the effectiveness of the proposed design procedures.     

A stochastic flowering model describing an asynchronically flowering set of trees

A general stochastic model is presented that simulates the time course of flowering of individual trees and populations, integrating the synchronization of flowering both between and within trees. Making some hypotheses, a simplified expression of the model, called the 'shoot' model, is proposed, in which the synchronization of flowering both between and within trees is characterized by specific parameters. Two derived models, the 'tree' model and the 'population' model, are presented. They neglect the asynchrony of flowering, respectively, within trees, and between and within trees. Models were fitted and tested using data on flowering of Psidium cattleianum observed at study sites at elevations of 200, 520 and 890 m in Reunion Island. The 'shoot' model fitted the data best and reproduced the strong irregularities in flowering shown by empirical data. The asynchrony of flowering in P. cattleianum was more pronounced within than between trees. Simulations showed that various flowering patterns can be reproduced by the 'shoot' model. The use of different levels of organization of the general model is discussed.     

Robust stability of stochastic delayed genetic regulatory networks

Gene regulation is an intrinsically noisy process, which is subject to intracellular and extracellular noise perturbations and environment fluctuations. In this paper, we consider the robust stability analysis problem of genetic regulatory networks with time-varying delays and stochastic perturbation. Different from other papers, the genetic regulate system considers not only stochastic perturbation but also parameter disturbances, it is in close proximity to the real gene regulation process than determinate model. Based on the Lyapunov functional theory, sufficient conditions are given to ensure the stability of the genetic regulatory networks. All the stability conditions are given in terms of LMIs which are easy to be verified. Illustrative examples are presented to show the effectiveness of the obtained results.     

The value of scattered trees for wildlife: Contrasting effects of landscape context and tree size

Aim

The biodiversity value of scattered trees in modified landscapes is often overlooked in planning and conservation decisions. We conducted a multitaxa study to determine how wildlife abundance, species richness and community composition at individual trees are affected by (1) the landscape context in which trees are located; and (2) the size of trees.

Location

Canberra, south‐eastern Australia.

Methods

Trunk arthropod, bat and bird surveys were undertaken over 3 years (2012–2014) at 72 trees of three sizes (small (20–50 cm DBH), medium (51–80 cm), large (≥80 cm)) located in four landscape contexts (reserves, pasture, urban parklands, urban built‐up areas).

Results

Landscape context affected all taxa surveyed. Trunk arthropod communities differed between trees in urban built‐up areas and reserves. Bat activity and richness were significantly reduced at trees in urban built‐up areas suggesting that echolocating bats may be disturbed by high levels of urbanization. Bird abundance and richness were highest at trees located in modified landscapes, highlighting the value of scattered trees for birds. Bird communities also differed between non‐urban and urban trees. Tree size had a significant effect on birds but did not affect trunk arthropods and bats. Large trees supported higher bird abundance, richness and more unique species compared to medium and small trees.

Main conclusions

Scattered trees support a diversity of wildlife. However, landscape context and tree size affected wildlife in contrasting ways. Land management strategies are needed to collectively account for responses exhibited by multiple taxa at varying spatial scales. We recommend that the retention and perpetuation of scattered trees in modified landscapes should be prioritized, hereby providing crucial habitat benefits to a multitude of taxa.     

A method for estimating stochastic noise in large genetic regulatory networks

MOTIVATION: Genetic regulatory networks are often affected by stochastic noise, due to the low number of molecules taking part in certain reactions. The networks can be simulated using stochastic techniques that model each reaction as a stochastic event. As models become increasingly large and sophisticated, however, the solution time can become excessive; particularly if one wishes to determine the effect on noise of changes to a series of parameters, or the model structure. Methods are therefore required to rapidly estimate stochastic noise. RESULTS: This paper presents an algorithm, based on error growth techniques from non-linear dynamics, to rapidly estimate the noise characteristics of genetic networks of arbitrary size. The method can also be used to determine analytical solutions for simple sub-systems. It is demonstrated on a number of cases, including a prototype model of the galactose regulatory pathway in yeast. AVAILABILITY: A software tool which incorporates the algorithm is available for use as part of the stochastic simulation package Dizzy. It is available for download at http://labs.systemsbiology.net/bolouri/software/Dizzy/ CONTACT: dorrell@systemsbiology.org SUPPLEMENTARY INFORMATION: A conceptual model of the regulatory part of the galactose utilization pathway in yeast, used as an example in the paper, is available at http://labs.systemsbiology.net/bolouri/models/galconcept.dizzy     

Centennial olive trees as a reservoir of genetic diversity

Background and Aims

Genetic characterization and phylogenetic analysis of the oldest trees could be a powerful tool both for germplasm collection and for understanding the earliest origins of clonally propagated fruit crops. The olive tree (Olea europaea L.) is a suitable model to study the origin of cultivars due to its long lifespan, resulting in the existence of both centennial and millennial trees across the Mediterranean Basin.

Methods

The genetic identity and diversity as well as the phylogenetic relationships among the oldest wild and cultivated olives of southern Spain were evaluated by analysing simple sequence repeat markers. Samples from both the canopy and the roots of each tree were analysed to distinguish which trees were self-rooted and which were grafted. The ancient olives were also put into chronological order to infer the antiquity of traditional olive cultivars.

Key Results

Only 9·6 % out of 104 a priori cultivated ancient genotypes matched current olive cultivars. The percentage of unidentified genotypes was higher among the oldest olives, which could be because they belong to ancient unknown cultivars or because of possible intra-cultivar variability. Comparing the observed patterns of genetic variation made it possible to distinguish which trees were grafted onto putative wild olives.

Conclusions

This study of ancient olives has been fruitful both for germplasm collection and for enlarging our knowledge about olive domestication. The findings suggest that grafting pre-existing wild olives with olive cultivars was linked to the beginnings of olive growing. Additionally, the low number of genotypes identified in current cultivars points out that the ancient olives from southern Spain constitute a priceless reservoir of genetic diversity.     

Dizzy: stochastic simulation of large-scale genetic regulatory networks

We describe Dizzy, a software tool for stochastically and deterministically modeling the spatially homogeneous kinetics of integrated large-scale genetic, metabolic, and signaling networks. Notable features include a modular simulation framework, reusable modeling elements, complex kinetic rate laws, multi-step reaction processes, steady-state noise estimation, and spatial compartmentalization.     

Connectedness among test series in mixed linear models of genetic evaluation for forest trees

In forest tree species with large natural ranges, there are usually several to many separate breeding populations, each designed to capture elite material suited to a particular geographic region. Separate test series are often dedicated to each population. Because the aim is to optimise gain in the meta-population, it is important to ensure that test series are linked so that individuals can be compared across test series as well as within. Computer simulation was used to determine the most efficient strategy for obtaining linkage. The average accuracy of a genetic value contrast between individuals in the same and in different test series was used as the criterion for assessing the optimal level of linkage. Accuracy is a function of the elements of the inverse coefficient matrix for a mixed linear model within a best linear unbiased prediction framework (BLUP). Material used to link test series was either common test families, common check-lots such as seed orchard bulks, or families generated by inter-crossing parents from different test series. Use of common test families was the most efficient strategy for the scenarios tested, which included having 50 parents crossed to produce 50 test families in each of three populations. For a low-heritability scenario, the amount of linkage material, relative to test material, needed to be 8 and 12 %, for progeny and parents, respectively, in order for a contrast between individuals in different test series to have equivalent accuracy as a contrast between individuals in the same test series. Other strategies were less efficient in terms of the amount of linkage material needed to obtain this equivalency.     

Mass propagation and genetic improvement of forest trees for biomass production by tissue culture

Wood derived from forest trees can serve as a major alternative source of energy and fuel because of the current energy shortage and increase in price of oil and natural gas. Normally, trees take several years to grow and produce seeds. But, in recent years, ‘test tube trees’ have been produced in large numbers (as many as 3000 plants per year) from one seedling using tissue culture by treating a few cells of a tree with specific chemical substances. Tissue culture is a promising technique for mass production of large numbers of superior trees, derived through genetic improvement, and may prove widely applicable to trees which show promise as energy sources.Three selected tree genera, viz. Sapium sebiferum (Chinese Tallow), Leucaena leucocephala (giant ipil-ipil, a tropical legume) and Copaifera multijuga (Copaiba tree from Brazil) have been studied because of their potential usefulness for biomass production. Regeneration of vegetatively produced plantlets has been achieved from embryos and callus cells grown in specific culture medium for two of the above genera. High yields of protoplasts have been obtained isolated from cells of different plant parts and grown as calli. Conditions which will enable callus derived from protoplasts to undergo in vitro regeneration, plantlet formation and eventually growth into plants are being investigated.