RAPTOR: Row and position tracheid organizer in R Peters, Richard L.; Balanzategui, Daniel; Hurley, Alexander G. ...
Dendrochronologia (Verona),
February 2018, 2018-02-00, Letnik:
47
Journal Article
Recenzirano
Odprti dostop
Mechanistic understanding of tree-ring formation and its modelling requires a cellular-based and spatially organized characterization of a tree ring, moving from whole rings, to intra-annual growth ...zones and individual cells. A tracheidogram is a radial profile of conifer anatomical features, such as lumen area and cell wall thickness, of sequentially- and positionally-ranked tracheids. However, its construction is tedious and time-consuming since image-analysis-based measurements do not recognize the position of cells within a radial file, and present-day tracheidograms must be constructed manually.
Here we present the R-package RAPTOR that complements tracheid anatomical data obtained from quantitative wood anatomy software (e.g., ROXAS, WinCELL, ImageJ), with the specific positional information necessary for the automated construction of tracheidograms. The package includes functions to read and visualize tracheid anatomical data, and uses local search algorithms to ascribe a ranked position to each tracheid in identified radial files. The package also provides functions to ensure that tracheids are adequately aligned for identifying the first tracheid in each radial file, and obtaining the correct ranking of tracheids along each radial file. Additional functions allow automating the analyses for multiple samples and rings (batch mode) and exporting data and plots for quality control.
RAPTOR allows tracheidogram users to take advantage of the latest generation of cell anatomical measuring systems. With this R-package we aim to facilitate the construction of more robust and versatile tracheidograms for the benefit of the research community.
Fennoscandia is one of the most prominent regions in the world for dendroclimatological research. Yet, millennium-long tree-ring chronologies in this region have mainly been developed from Scots pine ...(Pinus sylvestris L.). To explore the possibility of building long-term chronologies using other dominating tree species in the region, this paper presents the first two millennia-long Norway spruce (Picea abies (L.) Karst.) ring-width chronology from Northern Europe. The chronology is composed of living trees and subfossil wood and covers the period from BCE 115 to 2012 CE. A sufficiently replicated and robust chronology is built for the past 360 years back to 1649 CE. Further back in time, the common growth signal is reduced, and hence the reliability of the earlier section of the chronology is lower. The climate calibration results show that the spruce ring-width correlation with June-July mean temperatures over the period 1901–2012 is positive and significant (r = 0.6, p < 0.01) and representing the temperature variability of a spatial domain covering west-central Scandinavia. These results show the ability of Norway spruce to serve as a proxy for paleoclimatic research and the possibility of extending the chronology far back in time in the region, and therefore present an opportunity for carrying out new inter-and intraregional proxy analyses.
The recent warming trend, and associated shifts in growing season length, challenge the principle of uniformitarianism, i.e., that current relations are persistent over time, and complicates the ...uncritical inferences of past climate from tree-ring data. Here we conduct a comparison between tree-ring width chronologies of Pinus sylvestris L. (Scots pine), Picea abies (L.) Karst. (Norway spruce) and Betula pubescens Ehrh. (Downy birch) and phenological observations (budburst and leaf senescence) of Fagus sylvatica L. (European beech), Quercus robur L. (European oak), Betula sp. (Birch), Norway spruce and Scots pine) in Sweden to assess to what extent the tree-ring width–temperature relationship and the timing of phenological phases are affected by increased temperature. Daily meteorological observations confirm a prolongation of the thermal growing season, most consistently observed as an earlier onset of around 1–2 weeks since the beginning of the 20th century. Observations of budburst closely mimic this pattern, with budburst of the deciduous trees occurring 1–2.5 weeks earlier. In contrast to the changes seen in phenology and observational temperature data, the tree-ring width–temperature relationships remain surprisingly stable throughout the 20th century. Norway spruce, Scots pine and Downy birch all show consistently significant correlations with at least one 30 day-long window of temperature starting in late June–early July season. Norway spruce displays the largest degree of stability, with a consistent 60 day-long temperature window with significant correlation starting around Julian calendar day 150. Thus, our results suggest that the principle of uniformitarianism is not violated during the period covered by modern meteorological observations. Further research is needed to determine at what thresholds the temperature sensitivity of these species may alter or deteriorate as a consequence of the ongoing climate change.
Reproducible climate reconstructions of the Common Era (1 CE to present) are key to placing industrial-era warming into the context of natural climatic variability. Here we present a ...community-sourced database of temperature-sensitive proxy records from the PAGES2k initiative. The database gathers 692 records from 648 locations, including all continental regions and major ocean basins. The records are from trees, ice, sediment, corals, speleothems, documentary evidence, and other archives. They range in length from 50 to 2000 years, with a median of 547 years, while temporal resolution ranges from biweekly to centennial. Nearly half of the proxy time series are significantly correlated with HadCRUT4.2 surface temperature over the period 1850-2014. Global temperature composites show a remarkable degree of coherence between high- and low-resolution archives, with broadly similar patterns across archive types, terrestrial versus marine locations, and screening criteria. The database is suited to investigations of global and regional temperature variability over the Common Era, and is shared in the Linked Paleo Data (LiPD) format, including serializations in Matlab, R and Python.
Key message
We found that indiscriminately using tree-ring MXD data with inhomogeneous temporal distribution from different elevations might cause biased chronologies. A mean-adjusting method was ...developed to overcome this bias.
Here we analyse maximum latewood density (MXD) of
Pinus sylvestris
L. (Scots pine), from deadwood (dry) and subfossil wood (from lakes) collected along an elevation gradient in and close to the central Scandinavian Mountains, in the province of Jämtland, Sweden. Focusing on two common time periods (900–1150 CE and 1300–1550 CE), the mean absolute MXD of deadwood samples showed an inverse relationship with elevation, i.e. the absolute MXD decreases with elevation. However, the MXD values of the subfossil samples did not show such a consistent relationship with elevation. It was also noted that the differences in mean absolute MXD values among sites of different elevations in a given period were larger than among sites of similar elevation between the two time periods, where the former was assumed to be warmer than the latter. Using a theoretical model and a real example, it was shown that indiscriminately using MXD data with inhomogeneous temporal distribution from different elevations may cause biased chronologies, which can have significant effects on subsequent interpretations of past climate variability. A mean-adjusting method was developed to overcome this bias, and its usefulness was demonstrated by comparing two chronologies built on mean-adjusted and unadjusted MXD samples. It was concluded that unadjusted samples from different elevations with inhomogeneous temporal distribution can distort the long-term trend in a final chronology, while this bias can be alleviated if mean-adjusted samples are used.
Moisture availability has been identified as one of the most important factors in the context of future climate change. This paper explores the potential of applying a multiproxy approach to ...dendroclimatology to infer the twentieth-century moisture variability over Fennoscandia. Fields of the warm-season (June-August) standardized precipitation evapotranspiration index (SPEI) were developed from a dense network of precipitation-sensitive annually resolved tree-ring width (TRW), maximum density (MXD), and stable carbon (δ^sup 13^C) and oxygen (δ^sup 18^O) isotope chronologies using a point-by-point local regression technique (PPR). Two different approaches were tested for selecting candidate tree-ring predictors of SPEI for each gridpoint reconstruction: a search radiusmethod and a search spatial correlation contourmethod. As confirmed by a range of metrics of reconstruction fidelity, both methods produced reconstructions showing a remarkably high accuracy in a temporal sense, but with some minor regional differences. As a whole, the spatial skill of the reconstructed fields was generally quite good, showing the greatest performance in the central and southern parts of the target region. Lower reconstruction skills were observed in northern part of the study domain. Regional-scale moisture anomalies were best captured by the reconstructions, while local-scale features were not as well represented. The authors speculate that a spatially and temporally varying tree-ring proxy response to temperature and precipitation in the region may cause some uncertainties in a Fennoscandian hydroclimatic reconstruction; this needs further investigation. Overall, this study shows a great potential for making long-term spatiotemporal reconstructions of moisture variability for the Fennoscandian region using tree-ring data.
X-ray microdensitometry on annually resolved tree-ring samples has gained an exceptional position in last-millennium paleoclimatology through the maximum latewood density (MXD) parameter, but also ...increasingly through other density parameters. For 50 years, X-ray based measurement techniques have been the de facto standard. However, studies report offsets in the mean levels for MXD measurements derived from different laboratories, indicating challenges of accuracy and precision. Moreover, reflected visible light-based techniques are becoming increasingly popular, and wood anatomical techniques are emerging as a potentially powerful pathway to extract density information at the highest resolution. Here we review the current understanding and merits of wood density for tree-ring research, associated microdensitometric techniques, and analytical measurement challenges. The review is further complemented with a careful comparison of new measurements derived at 17 laboratories, using several different techniques. The new experiment allowed us to corroborate and refresh "long-standing wisdom" but also provide new insights. Key outcomes include (i) a demonstration of the need for mass/volume-based recalibration to accurately estimate average ring density; (ii) a substantiation of systematic differences in MXD measurements that cautions for great care when combining density data sets for climate reconstructions; and (iii) insights into the relevance of analytical measurement resolution in signals derived from tree-ring density data. Finally, we provide recommendations expected to facilitate futureinter-comparability and interpretations for global change research.
Reproducible climate reconstructions of the Common Era (1 CE to present) are key to placing industrial-era warming into the context of natural climatic variability. Here we present a ...community-sourced database of temperature-sensitive proxy records from the PAGES2k initiative. The database gathers 692 records from 648 locations, including all continental regions and major ocean basins. The records are from trees, ice, sediment, corals, speleothems, documentary evidence, and other archives. They range in length from 50 to 2000 years, with a median of 547 years, while temporal resolution ranges from biweekly to centennial. Nearly half of the proxy time series are significantly correlated with HadCRUT4.2 surface temperature over the period 1850-2014. Global temperature composites show a remarkable degree of coherence between high-and low-resolution archives, with broadly similar patterns across archive types, terrestrial versus marine locations, and screening criteria. The database is suited to investigations of global and regional temperature variability over the Common Era, and is shared in the Linked Paleo Data (LiPD) format, including serializations in Matlab, R and Python. Since the pioneering work of D'Arrigo and Jacoby1-3, as well as Mann et al. 4,5, temperature reconstructions of the Common Era have become a key component of climate assessments6-9. Such reconstructions depend strongly on the composition of the underlying network of climate proxies10, and it is therefore critical for the climate community to have access to a community-vetted, quality-controlled database of temperature-sensitive records stored in a self-describing format. The Past Global Changes (PAGES) 2k consortium, a self-organized, international group of experts, recently assembled such a database, and used it to reconstruct surface temperature over continental-scale regions11 (hereafter, ` PAGES2k-2013'). This data descriptor presents version 2.0.0 of the PAGES2k proxy temperature database (Data Citation 1). It augments the PAGES2k-2013 collection of terrestrial records with marine records assembled by the Ocean2k working group at centennial12 and annual13 time scales. In addition to these previously published data compilations, this version includes substantially more records, extensive new metadata, and validation. Furthermore, the selection criteria for records included in this version are applied more uniformly and transparently across regions, resulting in a more cohesive data product. This data descriptor describes the contents of the database, the criteria for inclusion, and quantifies the relation of each record with instrumental temperature. In addition, the paleotemperature time series are summarized as composites to highlight the most salient decadal-to centennial-scale behaviour of the dataset and check mutual consistency between paleoclimate archives. We provide extensive Matlab code to probe the database-processing, filtering and aggregating it in various ways to investigate temperature variability over the Common Era. The unique approach to data stewardship and code-sharing employed here is designed to enable an unprecedented scale of investigation of the temperature history of the Common Era, by the scientific community and citizen-scientists alike.
Moisture availability has been identified as one of the most important factors in the context of future climate change. This paper explores the potential of applying a multiproxy approach to ...dendroclimatology to infer the twentieth-century moisture variability over Fennoscandia. Fields of the warm-season (June-August) standardized precipitation evapotranspiration index (SPEI) were developed from a dense network of precipitation-sensitive annually resolved tree-ring width (TRW), maximum density (MXD), and stable carbon ( delta super(13)C) and oxygen ( delta super(18)O) isotope chronologies using a point-by-point local regression technique (PPR). Two different approaches were tested for selecting candidate tree-ring predictors of SPEI for each gridpoint reconstruction: a search radius method and a search spatial correlation contour method. As confirmed by a range of metrics of reconstruction fidelity, both methods produced reconstructions showing a remarkably high accuracy in a temporal sense, but with some minor regional differences. As a whole, the spatial skill of the reconstructed fields was generally quite good, showing the greatest performance in the central and southern parts of the target region. Lower reconstruction skills were observed in northern part of the study domain. Regional-scale moisture anomalies were best captured by the reconstructions, while local-scale features were not as well represented. The authors speculate that a spatially and temporally varying tree-ring proxy response to temperature and precipitation in the region may cause some uncertainties in a Fennoscandian hydroclimatic reconstruction; this needs further investigation. Overall, this study shows a great potential for making long-term spatiotemporal reconstructions of moisture variability for the Fennoscandian region using tree-ring data.
På grund av kalhuggning har förutsättningen förändrats förhålboende fåglar. Bohålsbristen går att åtgärda med placering av nya fågelholkar. Genom att använda GIS går det att strategiskt välja de ...bästa områdena att sätta ut nya fågelholkar. Med hjälp av crowdsourcing och mobiltelefoner går det kartlägga holkarna som kan användas som underlag för nyplacering eller som hjälp för analys som t.ex. arters spridning. Studien visar hur man kan erhålla ett system för multikriterieanalys i realtid online för mobiltelefoner som utnyttjar crowdsourcing och öppna standarder. PostGIS, Leaflet, Geoserver, PyWPS, GRASS GIS har använts för att uppfylla kraven på prototypen. Tidsåtgången av detta system utvärderades genom att mäta tiden för utförande av algoritmen och tiden för förfrågan till utritningen av resultatet. Resultatet visar att det är möjligt att utföra multikriterieanalyser på kort tid som är acceptabel för användare av smarta mobiltelefoner på fält och att det går att urskilja närliggande fågelholkar. Denna metod skulle kunna anpassas för liknande scenarion.
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