1,721,070 research outputs found
Impact of asymmetric male and female gamete dispersal on allelic diversity and spatial genetic structure in valley oak (Quercus lobata Née)
No full textThe distribution and abundance of genetic diversity in plant populations is initiated by sexually asymmetric propagule dispersal through pollen and seeds. Because these processes occur serially, it is not transparent how each contributes to subsequent patterns of genetic diversity. Using combined seedling/seed coat assay for naturally distributed seedlings of Quercus lobata Née, we extracted male and female gametic genotypes, and then assessed (wind-vectored) paternal and (gravity- and animal-vectored) maternal contributions to spatially distributed allelic diversity. We evaluated 200 naturally recruited seedlings from 4 open patches away from any adult canopies (denoted ‘open’), and 174 seedlings from 14 patches immediately beneath adult canopies (denoted ‘canopy’). The open patches included 19 % long distant dispersal events of >1 km while the canopy patches contained seedlings from one tree overhead. For each patch type, we partitioned average allelic diversity for six microsatellite loci for the whole study site (γ) into separate within-patch (α) and among-patch (β) components, translated into among-patch divergence (δ). We found that α-diversity resulting from seed dispersal was much less than that from pollen dispersal in both patch types, while total γ-diversity across the site was similar. Divergence (δ) among canopy patches was significantly greater than δ among open patches. We then evaluated spatial genetic autocorrelation (kinship) patterns for both open and canopy strata, separately for male and female gametes. Female gametes showed sharply declining kinship with increasing distance for canopy patches and modestly for open patches. In sharp contrast, male gametes from both patches showed only subtle decline of kinship, but seedlings still showed significant structure across patch types. On balance, sexual asymmetry in propagule dispersal shapes both the abundance and distribution of allelic diversity, with pollen dispersal promoting overall diversity but reducing spatial structure, but seed-dispersal reduces overall diversity and markedly increases spatial genetic structure. © 2015, Springer International Publishing Switzerland
Measuring recent effective gene flow among large populations in Pinus sylvestris: Local pollen shedding does not preclude substantial long-distance pollen immigration
No full text17 Pág.
Instituto de Ciencias Forestales (ICIFOR)The estimation of recent gene flow rates among vast and often weakly genetically differentiated tree populations remains a great challenge. Yet, empirical information would help understanding the interaction between gene flow and local adaptation in present-day non-equilibrium forests. We investigate here recent gene flow rates between two large native Scots pine (Pinus sylvestris L.) populations in central Iberian Peninsula (Spain), which grow on contrasting edaphic conditions six kilometers apart from each other and show substantial quantitative trait divergence in common garden experiments. Using a sample of 1,200 adult and offspring chloroplast-microsatellite haplotypes and a Bayesian inference model, we estimated substantial male gametic gene flow rates (8 and 21%) between the two natural populations, and even greater estimated immigration rates (42 and 64%) from nearby plantations into the two natural populations. Our results suggest that local pollen shedding within large tree populations does not preclude long-distance pollen immigration from large external sources, supporting the role of gene flow as a homogenizing evolutionary force contributing to low molecular genetic differentiation among populations of widely distributed wind-pollinated species. Our results also indicate the high potential for reproductive connectivity in large fragmented populations of wind-pollinated trees, and draw attention to a potential scenario of adaptive genetic divergence in quantitative traits under high gene flow.This work was supported by CGL2015-64164-R project grant to JJRA and DG and by BES-2016-078969 PhD grant to AJR, both co-financed by MINECO (https://www.mineco.gob.es) and ERDF (https://ec.europa.eu/regional_policy/en/funding/erdf/). Research was also supported by AEG 17-048 project grant from MAPAMA (https://www.mapama.gob.es), established in the frame of the measure 15.2 “support to the conservation and use of forest genetic resources” and under Regulation (EU) No 1305/2013 of the European Parliament and of the Council of 17 December 2013 on support for rural development by the European Agricultural Fund for Rural Development (EAFRD; https://ec.europa.eu/info/food-farmingfisheries/key-policies/common-agricultural-policy/ rural-development_en) with 75% co-financing. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. No additional external funding was secured for this study.Peer reviewe
Species-diagnostic markers in the genus Pinus: evaluation of the chloroplast regions matK and ycf1
Full text linkAim of study: The identification of material of forest tree species using genetic markers was carried out. Two promising chloroplast barcode markers, matK and ycf1, were tested for species identification and reconstruction of phylogenetic relationships in pines.
Area of study: The present study included worldwide Pinus species, with a wide representation of European taxa.
Material and methods: All matK sequences longer than 1600 base pairs and ycf1 sequences for the same species were downloaded from GenBank, aligned and subsequently analyzed to estimate alignment statistics, phylogenetic trees and substitution saturation signals.
Main results: We confirm the usefulness of the ycf1 marker for barcoding purposes and phylogenetic studies in pines, especially in studies focusing at the within-genus level relationships, but caution in the use of the matK marker is recommended.
Research highlights: Incongruent phylogenetic signals between these two chloroplast markers are demonstrated in pines for the first time.
Keywords: barcoding, conifers, phylogeny.
Abbreviations: posterior probabilities (PP), bootstrap (BS)
Née): a multivariate genetic approach to conservation planning
No full textCalifornia valley oak (Quercus lobata Née) is a seriously threatened endemic oak species in California and a keystone species for foothill oak ecosystems. Urban and agricultural development affects a significant fraction of the species' range and predicted climate change is likely to dislocate many current populations. Here, we explore spatial patterns of multivariate genotypes and genetic diversity throughout the range of valley oak to determine whether ongoing and future patterns of habitat loss could threaten the evolutionary potential of the species by eradicating populations of distinctive genetic composition. This manuscript will address three specific questions (i) What is the spatial genetic structure of the chloroplast and nuclear genetic markers? (ii) What are the geographical trends in the distribution of chloroplast and nuclear genotypes? (iii) Is there any part of the species' range where allelic diversity in either the chloroplast or nuclear genomes is particularly high? We analysed six chloroplast and seven nuclear microsatellite genetic markers of individuals widespread across the valley oak range. We then used a multivariate approach correlating genetic markers and geographical variables through a canonical trend surface analysis, followed by GIS mapping of the significant axes. We visualized population allelic richness spatially with GIS tools to identify regions of high diversity. Our findings, based on the distribution of multivariate genotypes and allelic richness, identify areas with distinctive histories and genetic composition that should be given priority in reserve network design, especially because these areas also overlap with landscape change and little degree of protection. Thus, without a careful preservation plan, valuable evolutionary information will be lost for valley oak. © 2007 The Authors
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Gene movement and genetic association with regional climate gradients in California valley oak (Quercus lobata Née) in the face of climate change
No full textRapid climate change jeopardizes tree populations by shifting current climate zones. To avoid extinction, tree populations must tolerate, adapt, or migrate. Here we investigate geographic patterns of genetic variation in valley oak, Quercus lobata Née, to assess how underlying genetic structure of populations might influence this species' ability to survive climate change. First, to understand how genetic lineages shape spatial genetic patterns, we examine historical patterns of colonization. Second, we examine the correlation between multivariate nuclear genetic variation and climatic variation. Third, to illustrate how geographic genetic variation could interact with regional patterns of 21st Century climate change, we produce region-specific bioclimatic distributions of valley oak using Maximum Entropy (MAXENT) models based on downscaled historical (1971-2000) and future (2070-2100) climate grids. Future climatologies are based on a moderate-high (A2) carbon emission scenario and two different global climate models. Chloroplast markers indicate historical range-wide connectivity via colonization, especially in the north. Multivariate nuclear genotypes show a strong association with climate variation that provides opportunity for local adaptation to the conditions within their climatic envelope. Comparison of regional current and projected patterns of climate suitability indicates that valley oaks grow in distinctly different climate conditions in different parts of their range. Our models predict widely different regional outcomes from local displacement of a few kilometres to hundreds of kilometres. We conclude that the relative importance of migration, adaptation, and tolerance are likely to vary widely for populations among regions, and that late 21st Century conditions could lead to regional extinctions. © 2010 Blackwell Publishing Ltd
Assessing vulnerability of two Mediterranean conifers to support genetic conservation management in the face of climate change
No full textAim:To integrate two major components of vulnerability to climate change: adaptive capacity (approached by genetic groups) and exposure (approached by risk of habitat loss) illustrated with the maritime (Pinus pinaster Ait.) and Aleppo (Pinus halepensis Mill.) pines. To integrate such information in the selection of conservation strategies (ex situ vs. in situ) and to evaluate current European efforts in the conservation of forest genetic resources. Location: Mediterranean Basin and European Atlantic coast. Methods: With the objective of preserving the overall genetic diversity of our two target species, we individually assess each of their genetic groups. We fit a species distribution model and project it to current climate and 42 different future climatic predictions. We create future suitability maps to assess risk of habitat loss based on the number of future climate projections that predict suitability. According to this assessment on the risk of habitat loss, we propose suitable conservation strategies. Results: We found areas suitable for in situ conservation for most of the genetic groups, the exception being the central-eastern-southern Iberian genetic groups of maritime pine and the Moroccan genetic group of Aleppo pine which required ex situ conservation. In the current European conservation network, three genetic groups for maritime pine and two for Aleppo pine remain unrepresented, and the representation of the rest is unbalanced. Main conclusions: We provide a tool to support conservation management of forest trees, an increasingly important task given the negative impact of climate change on forest ecosystems. We also provide a framework to increase the efficiency of the European conservation network: (i) exposure assessment should be considered as a requirement for a population to become a dynamic conservation unit (DCU); and (ii) as illustrated with our two target species, the selection of DCUs should represent all existing genetic groups.Peer reviewe
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