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Scotti, I.; Burelli, A.; Cattonaro, F.; Chagne, D.; Fuller, J.; Hedley, P.E.; Jansson, G.; Lalanne, C.; Madur, D.; Neale, D.; Plomion, C.; Powell, W.; Troggio, M.; Morgante, M. |
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Title |
Analysis of the distribution of marker classes in a genetic linkage map: a case study in Norway spruce (Picea abies karst) |
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Journal Article |
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Year |
2005 |
Publication |
Tree Genetics & Genomes |
Abbreviated Journal |
Tree Genet. Genomes |
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Volume |
1 |
Issue |
3 |
Pages |
93-102 |
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Keywords |
Picea abies; conifers; linkage map; genome structure; molecular markers; autocorrelation |
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Abstract |
In order to analyze the large-scale structure of the genome of Norway spruce (Picea abies Karst.), a pseudo-testcross genetic linkage map was built using markers of six different types, belonging to the low (amplified fragment length polymorphisms, simple sequence repeats) or high (sequence-specific amplified polymorphisms, inter-retrotransposon amplified polymorphisms) copy-number fraction of the genome, and including expressed region-derived markers (expressed sequence tag polymorphisms). Twenty seven and 23 linkage groups of at least four markers were obtained for the female and the male parent maps, respectively. A subset of these linkage groups coalesced into 13 bi-parental linkage groups through markers shared between the two maps. This map was used to investigate the frequency of each marker type over chromosomes and the distribution of marker types relative to each other, using autocorrelation techniques. Our results show that, while the composition of chromosomes is homogeneous, low- and high-copy-number markers tend to occupy separate regions of the linkage groups, and that expressed sequences are preferentially associated with microsatellites and separated from retrotranspo sons. These results indicate that the spatial structure of Norway spruce chromosomes is not homogeneous. |
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INRA, UMR ECOFOG, Kourou 97387, French Guiana, Email: ivan.scotti@kourou.cirad.fr |
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SPRINGER HEIDELBERG |
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1614-2942 |
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ISI:000244896200002 |
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EcoFoG @ eric.marcon @ |
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167 |
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Scotti, I.; Paglia, G.; Magni, F.; Morgante, M. |
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Title |
Population genetics of Norway spruce (Picea abies Karst.) at regional scale: sensitivity of different microsatellite motif classes in detecting differentiation |
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Journal Article |
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Year |
2006 |
Publication |
Annals of Forest Science |
Abbreviated Journal |
Ann. For. Sci. |
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Volume |
63 |
Issue |
5 |
Pages |
485-491 |
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Keywords |
conifers; SSR; divergence; statistical testing; genetic distance |
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Abstract |
Four populations of Norway spruce (Picea abies Karst.) were screened using nine nuclear microsatellite markers (three trinucleotides and six dinucleotides) and four chloroplast markers (all mononucleotides). Marker classes were compared for their variability, mutation rate and ability to detect differentiation between stands. Dinucleotide markers proved to be the most variable group and chloroplast stretches the least variable, with differences in mutation rate between the former and the latter spanning over two orders of magnitude. Variability correlated to the number of repeats but not to the absolute length of the microsatellite region. The different marker classes were combined with two different measures of genetic distance in order to investigate the performance of markers and evolutionary models for the study of genetic variation in natural populations of Norway spruce. Weir and Cockeram's F-ST generally performed better in this clear-cut, four-population model study. Chloroplast haplotypes turned out to be the most sensitive marker system, being able to differentiate populations and to detect differences in genetic variability between sub-regions. |
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INRA, UMR ECOFOG, Kourou 97387, French Guiana, Email: ivan.scotti@kourou.cirad.fr |
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EDP SCIENCES S A |
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1286-4560 |
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ISI:000240514800005 |
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EcoFoG @ eric.marcon @ |
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177 |
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Zalamea, P.-C.; Sarmiento, C.; Stevenson, P.R.; Rodríguez, M.; Nicolini, E.; Heuret, P. |
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Title |
Effect of rainfall seasonality on the growth of Cecropia sciadophylla: Intra-annual variation in leaf production and node length |
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Journal Article |
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Year |
2013 |
Publication |
Journal of Tropical Ecology |
Abbreviated Journal |
J. Trop. Ecol. |
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29 |
Issue |
4 |
Pages |
361-365 |
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Keywords |
leaf phenology; Neotropics; pioneer plants; plant growth; plant morphology; rainfall seasonality; Urticaceae |
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Abstract |
Patterns of leaf production and leaf fall directly influence leaf area index and forest productivity. Here, we focused on Cecropia sciadophylla individuals inhabiting the extremes of the gradient in seasonality in rainfall at which C. sciadophylla occurs. In Colombia and French Guiana we compared the intra-annual variation in leaf production as well as the intra-annual fluctuation in internode length on a total of 69 saplings ranging in size from 1 to 2 m. The mean rate of leaf production was ~2 leaves mo -1 in both populations, and the rate of leaf production was constant throughout the year. Our results showed monthly variation in internode length and the number of live leaves per sapling in the seasonal habitat and variation only in internode length in the everwet habitat. Because the rate of leaf production is constant at both localities, the difference in number of live leaves per sapling at the seasonal site must reflect seasonal variation in leaf life span. We show that in Cecropia, internode length can serve as an indicator of precipitation seasonality. Finally an open question is whether leaf production in other pioneer species is also independent of climatic seasonal cues. This information could allow us to link growth and climate of secondary forest species and better understand how past and future climate can affect plant growth trajectories. © Cambridge University Press 2013. |
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INRA, UMR ECOFOG, Kourou F-97310, French Guiana |
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Export Date: 14 July 2013; Source: Scopus |
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EcoFoG @ webmaster @ |
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496 |
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Latouche-Halle, C.; Ramboer, A.; Bandou, E.; Caron, H.; Kremer, A. |
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Title |
Long-distance pollen flow and tolerance to selfing in a neotropical tree species |
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Journal Article |
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Year |
2004 |
Publication |
Molecular Ecology |
Abbreviated Journal |
Mol. Ecol. |
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13 |
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5 |
Pages |
1055-1064 |
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Dicorynia guianensis; microsatellites; outcrossing rate; pollen flow; reproductive success; tropical tree |
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Outcrossing rates, pollen dispersal and male mating success were assessed in Dicorynia guianensis Amshoff, a neotropical tree endemic to the Guiana shield. All adult trees within a continuous area of 40 ha (n = 157) were mapped, and were genotyped with six microsatellite loci. In addition, progenies were genotyped from 22 mature trees. At the population level, the species was mostly outcrossing (t(m) = 0.89) but there was marked variation among individuals. One tree exhibited mixed mating, confirming earlier results obtained with isozymes that D. guianensis can tolerate selfing. A Bayesian extension of the fractional paternity method was used for paternity analysis, and was compared with the neighbourhood method used widely for forest trees. Both methods indicated that pollen dispersal was only weakly related to distance between trees within the study area, and that the majority (62%) of pollen came from outside the study stand. Using maximum likelihood, male potential population size was estimated to be 1119, corresponding to a neighbourhood size of 560 hectares. Male mating success was, however, related to the diameter of the stem and to flowering intensity assessed visually. The mating behaviour of D. guianensis is a combination of long-distance pollen flow and occasional selfing. The species can still reproduce when it is extremely rare, either by selfing or by dispersing pollen at long distances. These results, together with the observation that male mating success was correlated with the size of the trees, could be implemented in management procedures aiming at regenerating the species. |
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INRA, UMR Ecol Forets Guyane, F-97387 Kourou, France, Email: caron@pierroton.mra.fr |
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BLACKWELL PUBLISHING LTD |
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0962-1083 |
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ISI:000221016300007 |
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no |
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EcoFoG @ eric.marcon @ |
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237 |
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Jaouen, G.; Almeras, T.; Coutand, C.; Fournier, M. |
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Title |
How to determine sapling buckling risk with only a few measurements |
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Journal Article |
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2007 |
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American Journal of Botany |
Abbreviated Journal |
Am. J. Bot. |
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94 |
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10 |
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1583-1593 |
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biomechanics; critical buckling height; French Guiana; risk factor; sapling; stem form; tropical rain forest; trunk volume |
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Tree buckling risk (actual height/critical buckling height) is an important biomechanical trait of plant growth strategies, and one that contributes to species coexistence. To estimate the diversity of this trait among wide samples, a method that minimizes damage to the plants is necessary. On the basis of the rarely used, complete version of Greenhill's model (1881, Proceedings of the Cambridge Philosophical Society 4(2): 65-73), we precisely measured all the necessary parameters on a sample of 236 saplings of 16 species. Then, using sensitivity (variance) analysis, regressions between successive models for risk factors and species ranks and the use of these models on samples of self- and nonself-supporting saplings, we tested different degrees of simplification up to the most simple and widely used formula that assumes that the tree is a cylindrical homogeneous pole. The size factor had the greatest effect on buckling risk, followed by the form factor and the modulus of elasticity of the wood. Therefore, estimates of buckling risk must consider not only the wood properties but especially the form factor. Finally, we proposed a simple but accurate method of assessing tree buckling risk that is applicable to a wide range of samples and that requires mostly nondestructive measurements. |
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INRA, UMR Ecol Forets Guyane, Kourou 97379, French Guiana, Email: jaouen-g@kourou.cirad.fr |
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BOTANICAL SOC AMER INC |
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0002-9122 |
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ISI:000251466600001 |
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EcoFoG @ eric.marcon @ |
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148 |
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Baraloto, C.; Morneau, F.; Bonal, D.; Blanc, L.; Ferry, B. |
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Title |
Seasonal water stress tolerance and habitat associations within four neotropical tree genera |
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Journal Article |
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2007 |
Publication |
Ecology |
Abbreviated Journal |
Ecology |
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88 |
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2 |
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478-489 |
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drought tolerance; French Guiana; photosynthetic capacity; phylogenetically independent contrast; relative growth rate; seasonally flooded forest; specific leaf area; torus translation method; tropical forest |
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Abstract |
We investigated the relationship between habitat association and physiological performance in four congeneric species pairs exhibiting contrasting distributions between seasonally flooded and terra firme habitats in lowland tropical rain forests of French Guiana, including Virola and Iryanthera ( Myristicaceae), Symphonia ( Clusiaceae), and Eperua (Caesalpiniaceae). We analyzed 10-year data sets of mapped and measured saplings ( stems >= 150 cm in height and < 10 cm diameter at breast height [dbh]) and trees ( stems >= 10 cm dbh) across 37.5 ha of permanent plots covering a 300-ha zone, within which seasonally flooded areas ( where the water table never descends below 1 m) have been mapped. Additionally, we tested the response of growth, survival, and leaf functional traits of these species to drought and flood stress in a controlled experiment. We tested for habitat preference using a modi. cation of the torus translation method. Strong contrasting associations of the species pairs of Iryanthera, Virola, and Symphonia were observed at the sapling stage, and these associations strengthened for the tree stage. Neither species of Eperua was significantly associated with flooded habitats at the sapling stage, but E. falcata was significantly and positively associated with flooded forests at the tree stage, and trees of E. grandiflora were found almost exclusively in nonflooded habitats. Differential performance provided limited explanatory support for the observed habitat associations, with only congeners of Iryanthera exhibiting divergent sapling survival and tree growth. Seedlings of species associated with flooded forest tended to have higher photosynthetic capacity than their congeners at field capacity. In addition, they tended to have the largest reductions in leaf gas exchange and growth rate in response to experimental drought stress and the least reductions in response to experimental inundation. The corroboration of habitat association with differences in functional traits and, to a lesser extent, measures of performance provides an explanation for the regional coexistence of these species pairs. We suggest that specialization to seasonally flooded habitats may explain patterns of adaptive radiation in many tropical tree genera and thereby provide a substantial contribution to regional tree diversity. |
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INRA, UMR Ecol Forets Guyane, Kourou, French Guiana, Email: baraloto@botany.ufl.edu |
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ECOLOGICAL SOC AMER |
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0012-9658 |
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ISI:000245668400021 |
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EcoFoG @ eric.marcon @ |
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165 |
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Leroy, C.; Maes, A.Q.; Louisanna, E.; Séjalon-Delmas, N. |
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How significant are endophytic fungi in bromeliad seeds and seedlings? Effects on germination, survival and performance of two epiphytic plant species |
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Journal Article |
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2019 |
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Fungal Ecology |
Abbreviated Journal |
Fungal Ecol. |
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39 |
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296-306 |
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Aechmea; Bromeliads; Endophytic fungi; Fusarium spp.; Germination; Survival; Trichoderma spp.; Vertical transmission |
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In bromeliads, nothing is known about the associations fungi form with seeds and seedling roots. We investigated whether fungal associations occur in the seeds and seedling roots of two epiphytic Aechmea species, and we explored whether substrate and fungal associations contribute to seed germination, and seedling survival and performance after the first month of growth. We found a total of 21 genera and 77 species of endophytic fungi in the seeds and seedlings for both Aechmea species by Illumina MiSeq sequencing. The fungal associations in seeds were found in the majority of corresponding seedlings, suggesting that fungi are transmitted vertically. Substrate quality modulated the germination and growth of seedlings, and beneficial endophytic fungi were not particularly crucial for germination but contributed positively to survival and growth. Overall, this study provides the first evidence of an endophytic fungal community in both the seeds and seedlings of two epiphytic bromeliads species that subsequently benefit plant growth. © 2019 Elsevier Ltd and British Mycological Society |
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INRA, UMR Ecologie des Forêts de Guyane (AgroParisTech, CIRAD, CNRS, INRA, Université de Guyane, Université des Antilles), Campus Agronomique, BP 316, Kourou cedex, F-97379, France |
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Elsevier Ltd |
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17545048 (Issn) |
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EcoFoG @ webmaster @ |
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867 |
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Ferry, B.; Bontemps, J.-D.; Blanc, L.; Baraloto, C. |
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Is climate a stronger driver of tree growth than disturbance? A comment on Toledo et al. (2011) |
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Journal Article |
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2012 |
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Journal of Ecology |
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J. Ecol. |
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100 |
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5 |
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1065-1068 |
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Basal area change; Bolivia; Climate; Disturbance; Logging; Plant-climate interactions; Tree growth; Tropical forest |
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1.A recent article published by Toledo (2011b) investigates the effects of spatial variations in climate and soil, and of logging disturbance, on tree and forest growth in Bolivia. It concludes that climate is the strongest driver of tree and forest growth and that climate change may therefore have large consequences for forest productivity and carbon sequestration. However, serious methodological and conceptual discrepancies have been found that challenge these conclusions. 2.Because of an errant coding of 'time after logging' in the regression analysis, and because floristic changes induced by logging could not be incorporated into the analysis, the effect of logging on the average diameter growth is likely to have been strongly underestimated. 3.Basal area growth was improperly calculated as basal area change, and it displayed surprisingly high values, even among unlogged plots. We hypothesize that either these plots may be actually located in secondary forests recovering from past logging, or measurement biases may have hampered the data set. 4.Regardless of climate-growth relationships established across these plots, any inference concerning the potential effects of climate change on forest growth would require a specific quantitative assessment. 5.Synthesis. It is critical to re-assess the relative weight of climate and logging disturbance as driving factors of tree and forest growth, and to find an explanation for the very high basal area increment reported among the unlogged plots. We provide specific recommendations for further analyses of this and similar data sets. © 2012 British Ecological Society. |
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INRA, UMR Ecologie des Forêts de Guyane, 97379 Kourou, French Guiana |
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00220477 (Issn) |
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Cited By (since 1996): 1; Export Date: 4 September 2012; Source: Scopus; Coden: Jecoa; doi: 10.1111/j.1365-2745.2011.01895.x; Language of Original Document: English; Correspondence Address: Ferry, B.; AgroParisTech, ENGREF-Nancy, UMR 1092, F-54000 Nancy, France; email: bruno.ferry@engref.agroparistech.fr |
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EcoFoG @ webmaster @ |
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426 |
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Rockwell, C.A.; Kainer, K.A.; d'Oliveira, M.V.N.; Staudhammer, C.L.; Baraloto, C. |
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Title |
Logging in bamboo-dominated forests in southwestern Amazonia: Caveats and opportunities for smallholder forest management |
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Journal Article |
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2014 |
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Forest Ecology and Management |
Abbreviated Journal |
For. Ecol. Manage. |
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315 |
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202-210 |
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Bamboo; Community forest management; Guadua; Logging; Timber management; Tropical forest |
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Guadua sarcocarpa and Guadua weberbaueri (Poaceae: Bambuseae) have a negative influence on tree regeneration and recruitment in bamboo-dominated forests of southwestern Amazonia. The lack of advanced regeneration and sparse canopy in this forest type present a considerable challenge for developing sustainable timber management plans. We conducted field studies in the Porto Dias Agroextractive Settlement Project in Acre, Brazil to assess influences of logging in bamboo-dominated forest sites. Taxonomic composition, stand structure, aboveground biomass, commercial timber volume, and commercial tree seedling and bamboo culm density were compared between five logged vs. unlogged sites in different landholdings, using modified 0.5. ha Gentry plots. No differences in taxonomic composition, aboveground biomass, adult and juvenile stem density, or woody seedling and bamboo culm density were detected between paired logged and unlogged sites. Commercial timber volume, however, was reduced by almost two-thirds in logged plots, suggesting that long-term timber management goals in this forest type are compromised since so few future crop trees remained onsite. Our findings indicate that in order to maximize local management objectives, community forest managers must approach logging in bamboo-dominated forests with caution. We suggest an integration of non-timber forest product extraction with low harvest intensity and low-impact logging, tending of natural regeneration, and diversification of commercial species. © 2014 Elsevier B.V. |
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INRA, UMR Ecologie des Forêts de Guyane, 97387 Kourou Cedex, French Guiana |
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03781127 (Issn) |
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Export Date: 15 February 2014; Source: Scopus; Coden: Fecmd; Language of Original Document: English; Correspondence Address: Rockwell, C.A.; School of Forest Resources and Conservation, University of Florida, Gainesville, FL 32611, United States; email: rockwell_cara@yahoo.com; Funding Details: DGE-0221599, NSF, National Science Foundation |
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EcoFoG @ webmaster @ |
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528 |
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Soong, J.L.; Marañon-Jimenez, S.; Cotrufo, M.F.; Boeckx, P.; Bodé, S.; Guenet, B.; Peñuelas, J.; Richter, A.; Stahl, C.; Verbruggen, E.; Janssens, I.A. |
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Title |
Soil microbial CNP and respiration responses to organic matter and nutrient additions: Evidence from a tropical soil incubation |
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Journal Article |
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2018 |
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Soil Biology and Biochemistry |
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122 |
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141-149 |
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13c; Cnp; Microbial stoichiometry; Priming; Soil respiration; Tropics |
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Abstract |
Soil nutrient availability has a strong influence on the fate of soil carbon (C) during microbial decomposition, contributing to Earth's C balance. While nutrient availability itself can impact microbial physiology and C partitioning between biomass and respiration during soil organic matter decomposition, the availability of labile C inputs may mediate the response of microorganisms to nutrient additions. As soil organic matter is decomposed, microorganisms retain or release C, nitrogen (N) or phosphorus (P) to maintain a stoichiometric balance. Although the concept of a microbial stoichiometric homeostasis has previously been proposed, microbial biomass CNP ratios are not static, and this may have very relevant implications for microbial physiological activities. Here, we tested the hypothesis that N, P and potassium (K) nutrient additions impact C cycling in a tropical soil due to microbial stoichiometric constraints to growth and respiration, and that the availability of energy-rich labile organic matter in the soil (i.e. leaf litter) mediates the response to nutrient addition. We incubated tropical soil from French Guiana with a 13C labeled leaf litter addition and with mineral nutrient additions of +K, +N, +NK, +PK and +NPK for 30 days. We found that litter additions led to a ten-fold increase in microbial respiration and a doubling of microbial biomass C, along with greater microbial N and P content. We found some evidence that P additions increased soil CO2 fluxes. Additionally, we found microbial biomass CP and NP ratios varied more widely than CN in response to nutrient and organic matter additions, with important implications for the role of microorganisms in C cycling. The addition of litter did not prime soil organic matter decomposition, except in combination with +NK fertilization, indicating possible P-mining of soil organic matter in this P-poor tropical soil. Together, these results point toward an ultimate labile organic substrate limitation of soil microorganisms in this tropical soil, but also indicate a complex interaction between C, N, P and K availability. This highlights the difference between microbial C cycling responses to N, P, or K additions in the tropics and explains why coupled C, N and P cycle modeling efforts cannot rely on strict microbial stoichiometric homeostasis as an underlying assumption. |
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INRA, UMR Ecology of Guiana Forests (Ecofog), AgroParisTech, Cirad, CNRS, Université de Guyane, Université des Antilles, Kourou, France |
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Export Date: 16 May 2018 |
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EcoFoG @ webmaster @ |
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804 |
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