paleofire 1.1.9 !

A new version of the R package paleofire 1.1.9 is available on CRAN ( and GitHub ( The release includes few bug fixes and improvements of existing functions, including more flexibility in pfAddData function and new options in kdffreq, see examples below:

# Control the type and format of user defined charcoal files
# here for examples csv files with three columns 
#(depth, age and char) separated with semicolon and with "." 
# character used in the file for decimal points:

mydata=pfAddData(files=files, sep=";", dec=".")
# Transform and compositing:
TR=pfTransform(add=mydata, method=c("MinMax","Box-Cox","Z-Score"),
COMP=pfComposite(TR1, bins=seq(0,8000,500))


# Estimate the frequency of armed conflicts from 1946 to 2014 
 # using kernel density estimation from kdffreq
 # Data from the The Uppsala Conflict Data Program (UCDP) available at:

 res=kdffreq(dat$Year,bandwidth = "bw.ucv", nbboot=1000, up = 1946, lo = 2014, interval=1, pseudo=T)
 plot(res, ylab="# armed conflict/year")


New paper: Land-use change outweighs projected effects of changing rainfall on tree cover in sub-Saharan Africa

I am pleased to share this new article with Julie Aleman and Carla Staver: DOI: 10.1111/gcb.13299 (preprint) about modelling of future tree cover in sub-Saharan Africa.

Global change will likely affect savanna and forest structure and distributions, with implications for diversity within both biomes. Few studies have examined the impacts of both expected precipitation and land-use changes on vegetation structure in the future, despite their likely severity. Here we modeled tree cover in Sub-Saharan Africa, as a proxy for vegetation structure and land cover change, using climatic, edaphic and anthropic data (R2 = 0.97).
Projected tree cover for the year 2070, simulated using scenarios that include climate and land-use projections, generally decreased, both in forest and savanna, although the directionality of changes varied locally. The main driver of tree cover changes was land-use change; the effects of precipitation change were minor by comparison. Interestingly, carbon emissions mitigation via increasing biofuels production resulted in decreases in tree cover, more severe than scenarios with more intense precipitation change, especially within savannas.
Evaluation of tree cover change against protected area extent at the WWF Ecoregion scale suggested areas of high biodiversity and ecosystem services concern. Those forests most vulnerable to large decreases in tree cover were also highly protected, potentially buffering the effects of global change. Meanwhile, savannas, especially where they immediately bordered forests (e.g. West and Central Africa), were characterized by a dearth of protected areas, making them highly vulnerable. Savanna must become an explicit policy priority in the face of climate and land use change if conservation and livelihoods are to remain viable into the next century.

Screen Shot 2016-03-31 at 10.48.03 PM

Figure 3 | Tree cover change projections from 2000-2070 – RCP 2.6 (left maps), biome distribution shifts based on tree cover changes (middle), and WWF Ecoregion conservation risk based on tree cover change and protected area coverage (right). Projections are based on climate and anthropogenic change together (a), anthropogenic change only (b) and climate change only (c).

New paper: Biomass offsets little or none of permafrost carbon release from soils, streams, and wildfire: an expert assessment

I am pleased to share this new article based on an expert assessment approach leaded by Ben Abbott. The paper is available via;

Abstract: As the permafrost region warms, its large organic carbon pool will be increasingly vulnerable to decomposition, combustion, and hydrologic export. Models predict that some portion of this release will be offset by increased production of Arctic and boreal biomass; however, the lack of robust estimates of net carbon balance increases the risk of further overshooting international emissions targets. Precise empirical or model-based assessments of the critical factors driving carbon balance are unlikely in the near future, so to address this gap, we present estimates from 98 permafrost-region experts of the response of biomass, wildfire, and hydrologic carbon flux to climate change. Results suggest that contrary to model projections, total permafrost-region biomass could decrease due to water stress and disturbance, factors that are not adequately incorporated in current models. Assessments indicate that end-of-the-century organic carbon release from Arctic rivers and collapsing coastlines could increase by 75% while carbon loss via burning could increase four-fold. Experts identified water balance, shifts in vegetation community, and permafrost degradation as the key sources of uncertainty in predicting future system response. In combination with previous findings, results suggest the permafrost region will become a carbon source to the atmosphere by 2100 regardless of warming scenario but that 65%–85% of permafrost carbon release can still be avoided if human emissions are actively reduced.

Figure 2. Estimates of change in non-soil biomass, wildfire emissions, and hydrologic carbon flux from the permafrost region for four warming scenarios at three time points. All values represent change from current pools or fluxes reported in table 2. Biomass includes above and belowground living biomass, standing deadwood, and litter. Dissolved and particulate organic carbon (DOC and POC respectively) fluxes represent transfer of carbon from terrestrial to aquatic ecosystems. ‘Coast’ represents POC released by coastal erosion. Representative concentration pathway (RCP) scenarios range from aggressive emissions reductions (RCP2.6) to sustained human emissions (RCP8.5). Box plots represent median, quartiles, and minimum and maximum within 1.5 times the interquartile range. Relative change (percent change from current state) is presented in figure S1 and full distributions are presented in figures S2–S4.

Citation: Abbott, B. W., Jones, J. B., Schuur, E. A. G., III, F. S. C., Bowden, W. B., Bret-Harte, M. S., Epstein, H. E., Flannigan, M. D., Harms, T. K., Hollingsworth, T. N., Mack, M. C., McGuire, A. D., Natali, S. M., Rocha, A. V., Tank, S. E., Turetsky, M. R., Vonk, J. E., Wickland, K. P., Aiken, G. R., Alexander, H. D., Amon, R. M. W., Benscoter, B. W., Bergeron, Y., Bishop, K., Blarquez, O., Bond-Lamberty, B., Breen, A. L., Buffam, I., Cai, Y., Carcaillet, C., Carey, S. K., Chen, J. M., Chen, H. Y. H., Christensen, T. R., Cooper, L. W., Cornelissen, J. H. C., de Groot, W. J., DeLuca, T. H., Dorrepaal, E., Fetcher, N., Finlay, J. C., Forbes, B. C., French, N. H. F., Gauthier, S., Girardin, M. P., Goetz, S. J., Goldammer, J. G., Gough, L., Grogan, P., Guo, L., Higuera, P. E., Hinzman, L., Hu, F. S., Hugelius, G., Jafarov, E. E., Jandt, R., Johnstone, J. F., Karlsson, J., Kasischke, E. S., Kattner, G., Kelly, R., Keuper, F., Kling, G. W., Kortelainen, P., Kouki, J., Kuhry, P., Laudon, H., Laurion, I., Macdonald, R. W., Mann, P. J., Martikainen, P. J., McClelland, J. W., Molau, U., Oberbauer, S. F., Olefeldt, D., Par ́e, D., Parisien, M.-A., Payette, S., Peng, C., Pokrovsky, O. S., Rastetter, E. B., Raymond, P. A., Raynolds, M. K., Rein, G., Reynolds, J. F., Robard, M., Rogers, B. M., Sch ̈adel, C., Schaefer, K., Schmidt, I. K., Shvidenko, A., Sky, J., Spencer, R. G. M., Starr, G., Striegl, R. G., Teisserenc, R., Tranvik, L. J., Virtanen, T., Welker, J. M., and Zimov, S. (2016). Biomass offsets little or none of permafrost carbon release from soils, streams, and wildfire: an expert assessment. Environmental Research Letters, 11(3):034014.

PhD: Dynamique plurimillénaire des écosystèmes de l’est du Québec et du Labrador: influence des feux et du climat

Description : Deux principaux types de pessières noires caractérisent aujourd’hui les forêts boréales de la portion est de l’Amérique du Nord (Québec méridional) : la pessière noire à mousses et la pessière noire à lichens. Plusieurs auteurs ont démontré que le régime des feux des derniers millénaires a conduit à une ouverture des paysages forestiers par la transformation de la pessière à mousses (forêt fermée) en pessière à lichens (forêt ouverte) (Richard et al. 1982, Asselin et Payette 2005). La présente étude s’inscrit dans la poursuite de ces travaux. Elle est également en relation avec le développement de stratégies d’aménagement visant à assurer la résilience des forêts d’épinette noire (régénération, densité et croissance) dans un contexte de changements climatiques. La reconstruction des paléoincendies en lien avec les changements climatiques est une information indispensable afin de mieux comprendre la dynamique plurimillénaire de la végétation (Ali et al. 2012, Blarquez et al. 2015). Les objectifs spécifiques de ce projet sont :

  • D’utiliser les outils de la paléoécologie (pollen, charbons de bois, macro-restes contenus dans les sédiments lacustres) afin de déterminer les mécanismes responsables de la transition de la pessière à mousses vers la pessière à lichens.
  • De reconstruire, pour l’Holocène, la réponse des pessières à mousses aux modifications de la fréquence des incendies et du climat le long d’un gradient écologique longitudinal et d’un gradient latitudinal. Le long du gradient longitudinal (ouest vers est), les forêts sont de plus en plus influencées par des conditions océaniques (Atlantique). Le long du gradient latitudinal (sud vers nord), le climat se refroidit, le relief s’adoucit et les feux sont de plus en plus fréquents.
  • De combler un manque important de connaissances paléoécologiques dans l’est du Québec et au Labrador.
  • D’établir des liens avec les autres composantes d’un programme d’étude visant à mieux comprendre les facteurs qui affectent la densité et la croissance des peuplements situés aux limites de la forêt boréale fermée suite à des perturbations naturelles ou anthropiques (coupe forestière), dans un contexte de changements climatiques.
  • À bonifier les états de référence (ex. proportion de vieilles forêts à maintenir dans les paysages aménagés) par de meilleures connaissances sur la variabilité naturelle des forêts au cours de l’Holocène (Boucher et al. 2009).

Afin de caractériser les deux gradients à l’étude, trois transects d’une longueur moyenne de 100km seront définis. Le premier sera localisé au nord de Sept-Îles, le second le long de la rivière Romaine et le troisième au nord de Blanc-Sablon. Les travaux de terrain seront réalisés à l’été 2016. Au total, 6 lacs seront échantillonnés. Tous seront analysés en regard des charbons de bois alors que trois (1 par transect) seront étudiés pour le pollen et les macrorestes. Les charbons de bois seront utilisés afin de reconstruire l’incidence passée des incendies, les assemblages polliniques et les macrorestes permettront de reconstruire la végétation alors que les données climatiques seront obtenues par simulation (GCM) (Ali et al. 2009). Ces résultats seront mis en relation avec ceux provenant de l’analyse de sédiments organiques (étude connexe) dans un but de comparaison de l’histoire Holocène provenant de deux types d’archives (lacs et tourbières).

Supervision : Olivier Blarquez (Université de Montréal); Adam Ali (Université de Montpellier)

Qualifications requises :     Maîtrise en biologie, en écologie, en géographie ou en foresterie. Bilinguisme (français-anglais).

Soutien financier : Bourse annuelle de 18 000 $ (CDN) pour trois ans (compléments disponibles).

Les personnes intéressées sont priées de faire parvenir leur curriculum vitae, une lettre de motivation ainsi que les coordonnées de deux référents par email à Olivier Blarquez ( et Adam Ali (

Image credits

Data: Tree biomass reconstruction shows no lag in post-glacial afforestation of eastern Canada

Data from: Blarquez O. and J. Aleman. Tree biomass reconstruction shows no lag in post-glacial afforestation of eastern Canada. Canadian Journal of Forest Research. DOI: 10.1139/cjfr-2015-0201

You can use the application below for viewing and downloading specific time slice data. The shiny application is also available here, all data are zipped here. Simply decompress the archive, then in R use for example:

# plot the raster object
# view data
# check projection
# gr is an object of the class "pfGridding" 
# from the paleofire package and can be manipulated 
# and modified using the plot function: 
       cpal = "Purples", anomalies=FALSE, points=TRUE,
       empty_space = 5)


New paper: Tree biomass reconstruction shows no lag in post-glacial afforestation of eastern Canada

Notre nouveau papier avec Julie Aleman est publié sur le site du Canadian Journal of Forest Research: Just-IN articles

Les données sont disponibles via une application web ici.

Citation: Blarquez O. and J. Aleman. Tree biomass reconstruction shows no lag in post-glacial afforestation of eastern Canada. Canadian Journal of Forest Research. DOI: 10.1139/cjfr-2015-0201

Abstract: Forest ecosystems in eastern Canada are particularly sensitive to climate change and may shift from carbon sinks to carbon sources in the coming decades. Understanding how forest biomass responded to past climate change is thus of crucial interest. But past biomass reconstruction still represents a challenge. Here we used transfer functions based on modern pollen assemblages and remote sensed biomass estimation to reconstruct and quantify, for the last 14 000 years, tree biomass dynamics for the six main tree genera of the boreal and mixed-wood forests (Abies, Acer, Betula, Picea, Pinus, Populus). We compared the mean genera and total biomass to climatic (summer temperatures and annual precipitation), physical (CO2, insolation, ice area) and disturbance (burned biomass) variables, to identify the potential drivers influencing the long-term trends in tree biomass. Tree biomass was for most genera related with summer temperature, insolation and CO2 levels; Picea was the exception and its biomass also correlated with annual precipitation. At the onset of the Holocene and during the Holocene Thermal Maximum c. 10000-6000 BP), tree biomass tracked the melting of the Laurentide Ice sheet with high values (>50 t.ha-1 and a total of 12 Pg). These values, in the range of modern forest ecosystems biomass, indicate that trees were probably able to survive in a periglacial environment and to colonize the region without any discernible lag by tracking the ice retreat. High biomass at the beginning of the Holocene was likely favoured by higher than present insolation, CO2 levels higher than during the Last Glacial Maximum, and temperature and precipitation close to present day levels. Past tree biomass reconstruction thus brings novel insights about the drivers of postglacial tree biomass and the overall biogeography of the region since the deglaciation.


Legend: Temporal trend of mean genera biomass compared to climatic and physical variables. (a) Mean tree genera biomass temporal trends obtained by fitting a LOWESS (with a 200 years half window width) on reconstructed biomass from all sites. (b) Total biomass in 1000 years windows obtained by calculating the total biomass for each genera in each 50 $*$ 50 km pixel and then summing all pixel values within the studied territory. Total biomass values were expressed as petagrams (Pg) for convenience. (c) Biomass burning trend obtained by the analysis of charcoal series contained in the Global Charcoal Database. (d) Laurentide ice sheet area trend from (Dyke 2004). (e) NGRIP d18O record (grey line) and trend evaluated using 1000 years windows averages (plain red line). (f) Epica Dome C CO2 from (Monnin et al. 2004). Summer (june, july, august) temperatures (g) and annual precipitation (h) anomalies from the HadCM3 and CCSM3 GCM experiments. (i) Summer (JJA) insolation anomalies at 45° N.