Macro EWVA - an effective tool for analysis of earlywood conduits of ring porous species

V članku je predstavljena uporabnost programa ImageJ v lesni anatomiji. Njegova glavna prednost sta prosta dostopnost ter možnost vključevanja dodatnih vtičnikov in makrov. Program ImageJ smo uporabili kot platformo za razvoj makra EWVA za avtomatizirano prepoznavanje ranega lesa ter hitro in učinkovito analizo trahej venčastoporoznih listavcev. Uporabnost makra EWVA predstavljamo na primeru dveh dobov iz sestoja v Mlačah. V zaključku razpravljamo o prednostih in slabostih uporabljene metode.In this paper, program ImageJ and its application in tree-ring anatomy is presented. The main advantage of the program is its availability and possibility to add additional tools and macros. Platform of ImageJ programme was used to develop macro EWVA for automatized recognition of earlywood and effective analysis of vessels of ring porous species. Use of EWVA macro is presented in a case study of two pedunculate oaks from the Mlače stand. Advantages and disadvantages of the presented method are discussed

Pedunculate oak\u27s (Quercus robur L.) conductive elements size dependence on temperature at two Querco-Carpinetum sites in Slovenia

Namen študije je analizirati odnos med povprečnimi mesečnimi temperaturami in dimenzijami trahej dveh zdravih in ene propadajoče skupine dobov z dveh rastišč Querco-Carpinetum v Sloveniji. Kronologije povprečnih površin trahej in vsot površin trahej smo izdelali po predhodni skrbni pripravi površin vzorcev in analizi slik z makrom EWVA v programu ImageJ. Skupina propadajočih dreves s Cigonce je imela največje povprečne površine trahej in največjo površino prevodnega tkiva, kar povezujemo s propadanjem te skupine. Analiza časovne stabilnosti korelacijskih koeficientov je za propadajoča drevesa pojasnila negativne korelacijske koeficiente, ki niso bili stabilni v času. Vse skupine so se najbolj značilno odzivale na povprečne aprilske temperature. Pri vseh skupinah je bil klimatski signal najmočnejši v parametru povprečna površina trahej. Pri zdravih drevesih iz Mlač v primeru nadaljevanja trenda dvigovanja povprečnih temperatur pričakujemo večje povprečne površine trahej v prihodnjih desetletjih, ki so bolj izpostavljene problemu kavitacije. Padec podtalnice leta 1982 na Cigonci se časovno ujema s pričetkom padanja klimatskega signala v trahejah ranega lesa.The aim of our study is to fully investigate the relationship between mean monthly temperatures and vessel features. Two vital and one declining groups of pedunculate oak from two Querco-Carpinetum sites in Slovenia are analyzed. Chronologies of mean vessel area and sum of vessel area were developed after previous high quality surface preparation and image analysis with macro EWVA in the ImageJ program. Declining group from Cigonca had the biggest average vessel and the largest amount of conductive tissue, which was linked to the dieback of this group. The analysis of temporal stability of correlation coefficients for declining group explained negative correlations, which were not stable in time. All groups were most responsive to the April temperatures. For all groups, climate signal was the strongest in the mean vessel area parameter. For vital group from Mlače we can expect, in the event of continuous rising of mean temperatures, bigger mean vessels that are more likely to be affected by cavitation. Lower ground water table in 1982 at Cigonca coincides with the reduced climate signal in the vessels

Dendrochronologycal analysis of the radial growth of Norway spruce (Picea abies (L.) Karst.) In its natural and secondary stands in Slovenia

Z dendrokronološkimi metodami smo analizirali debelinsko priraščanje smreke na osmih lokacijah v Sloveniji. Med njimi je bilo pet naravnih smrekovih združb, v druge je bila smreka umetno vnesena v preteklosti, oziroma je bil povečan njen naravni delež. Na vsaki ploskvi smo s prirastoslovnim svedrom odvzeli izvrtke najmanj 20 dreves. V dendrokronološkem laboratoriju smo jih posušili in zbrusili do visokega sijaja, nato pa skenirali s pomočjo sistema ATRICS ter izmerili širine branik v programih CooRecorder in CDendro. Ugotovili smo, da med naravnimi in antropogenimi rastišči ni značilnih razlik v debelinskem priraščanju. Na lokacijah Sorško polje, Ravnik in Mašun smo opazili spremembe v debelinskem priraščanju, ki kažejo, da se vpliv temperature zraka (toplejša poletja) in padavin (pogostejši pojav suše) na rast povečuje. Analiza značilnih let je pokazala, da so le-ta v zadnjih 30 letih pogostejša in da se pojavljajo na več lokacijah hkrati, predvsem pa se je povečalo število negativnih značilnih let, t.j. nadpovprečno toplih in suhih let.A dendrochronological analysis of the spruce\u27s radial increment at eight different plots was conducted throughout Slovenia. The plots selected were diverse: five of them were natural spruce standsin others, the spruce was introduced anthropogenically in the past for economic reasons, or its natural share in stands was increased. We took samples of at least 20 trees per plot and examined them in the dendrochronological laboratory using Advanced Tree-Ring Image Capturing System (ATRICS) and specialized dendrochronological software. We compared the growth in natural spruce stands with the secondary (anthropogenic) ones and found no statistical differences in growth patterns between these two groups. However, we found some evidence for climate change effect on radial increment at locations Sorško polje, Ravnik and Mašun, which indicates that air temperature and precipitation now have stronger effect on spruce growth than in the past. Analysis of pointer years suggests that extreme events (exceptionally warm and dry years) are more common and widespread in the last 30 years

Climate–Growth Relationships in Laurus azorica—A Dominant Tree in the Azorean Laurel Forest

Forests on oceanic islands, such as the Azores archipelago, enable interesting dendroclimatic research, given their pronounced climatic gradients over short geographical distances, despite the less pronounced seasonality. The Lauraceae play an essential ecological role in Macaronesian natural forests. An example is Laurus azorica (Seub.) Franco, a relevant species given its high frequency and physiognomic dominance in Azorean laurel forests. This study aims to quantify climate–growth relationships in L. azorica using a dendroecological approach. We sampled four stands at São Miguel and two stands at Terceira islands, for a total of 206 trees. Following standard dendrochronological methods and rigorous sample selection procedures, we obtained relatively low rbar values and high temporal autocorrelation. Using a stepwise Random Forest analysis followed by Generalized Linear Models calculation, we found prominent effects of present and previous year temperature, but a low precipitation signal on growth rings, with some model variation between stands. Our results agreed with previous observations for broad-leaved species with diffuse porous wood, contributing to increase the baseline dendroecological knowledge about Azorean forests. Due to the high levels of within- and between-stand variation, and to refine the climatic signal analysis, complementary approaches should be explored in the future.FUNDING: D.C.P. is currently supported by a PhD studentship grant (SFRH/BD/136336/2018) from the Foundation for Science and Technology (FCT) of the Ministry of Science, Technology, and Higher Education. This research was also supported by national funds through the FCT under (FCT) UIDB/50027/2020 (CIBIO). J.J. was supported by the Alexander von Humboldt postdoctoral fellowship and the Slovenian Research Agency (“Forest Biology, Ecology and Technology—P4-0107”).info:eu-repo/semantics/publishedVersio

Macro EWVA - an effective tool for analysis of earlywood conduits of ring porous species

In this paper, program ImageJ and its application in tree-ring anatomy is presented. The main advantage of the program is its availability and possibility to add additional tools and macros. Platform of ImageJ programme was used to develop macro EWVA for automatized recognition of earlywood and effective analysis of vessels of ring porous species. Use of EWVA macro is presented in a case study of two pedunculate oaks from the Mlače stand. Advantages and disadvantages of the presented method are discussed

Nonlinear modelling of the relationship between xylem tree-rings and environment

Za analizo povezav med lesnimi branikami in okoljem so primerjane (multipla) linearna regresija (MLR) in izbrane nelinearne metode s področja strojnega učenja: umetne nevronske mreže z učnim algoritmom Bayesova regularizacija (ANN), modelna drevesa (MT), ansambli modelnih dreves (BMT) in naključni gozdovi regresijskih dreves (RF). Izbrane metode so bile primerjane na devetih podatkovnih množicah, ki so vključevale različne parametre branik in različne okoljske spremenljivke. Za nelinearne metode so bili v večini primerov izračunani boljši statistični kazalci za validacijsko množico, čeprav razlike v primerjavi z linearno regresijo niso bile velike. Dodatne analize so pokazale, da se metode večinoma razlikujejo pri napovedih ekstremnih vrednosti. Značilnost nelinearnih metod je, da sprememba odvisne spremenljivke ni premo sorazmerna spremembi ene ali več neodvisnih spremenljivk. Slednje pomeni zmanjšan razpon in variabilnost rekonstruiranih vrednosti, kar rekonstrukcijo naredi vizualno manj privlačno od linearne ekstrapolacije, čeprav v večini primerov statistično boljšo. Nobena izmed nelinearnih metod s področja strojnega učenja ni dala najboljših rezultatov na vseh podatkovnih množicah, zato je pred rekonstrukcijo klime z metodami strojnega učenja vedno smiselno primerjati več metod. Za ta namen smo razvili R funkcijo compare_methods() in jo vgradili v dendroTools R paket, ki je prosto dostopen na CRAN-repozitoriju.(Multiple) linear regression (MLR) and selected nonlinear methods from the field of machine learning were compared for the analysis of relationships between xylem tree-rings and the environment: artificial neural networks with a training algorithm that uses Bayesian regularization (ANN), model trees (MT), ensembles of model trees (BMT) and random forests of regression trees (RF). The selected methods were compared on nine datasets, which included different tree-ring parameters and different target environmental variables. For the nonlinear methods, better statistical metrics were calculated on validation data in most cases, but the differences in comparison to linear regression were minor. Additional analysis indicated that the methods mostly differ in predicting the extreme values. The characteristic of nonlinear methods is that the change in the dependent variable is not proportional to the change of one or more independent variables. The latter results in a reduced range and variability of reconstructed values, which makes the reconstruction visually less attractive as compared to linear extrapolation, even though in most cases statistically better. None of the nonlinear machine learning methods showed best results on all datasets, therefore it makes sense to always compare different machine learning regression methods prior to climate reconstruction. To do so, the R function compare_methods() was developed and implemented in the dendroTools R package, which is freely available on the CRAN repository

Pedunculate oak's (Quercus robur L.) conductive elements size dependence on temperature at two Querco-carpinetum sites in Slovenia

The aim of our study is to fully investigate the relationship between mean monthly temperatures and vessel features. Two vital and one declining groups of pedunculate oak from two Querco-Carpinetum sites in Slovenia are analyzed. Chronologies of mean vessel area and sum of vessel area were developed after previous high quality surface preparation and image analysis with macro EWVA in the ImageJ program. Declining group from Cigonca had the biggest average vessel and the largest amount of conductive tissue, which was linked to the dieback of this group. The analysis of temporal stability of correlation coefficients for declining group explained negative correlations, which were not stable in time. All groups were most responsive to the April temperatures. For all groups, climate signal was the strongest in the mean vessel area parameter. For vital group from Mlače we can expect, in the event of continuous rising of mean temperatures, bigger mean vessels that are more likely to be affected by cavitation. Lower ground water table in 1982 at Cigonca coincides with the reduced climate signal in the vessels

Dendrochronological and wood-anatomical features of differently vital pedunculate oaks (Quercus robur L.)

Razlike med različno vitalnimi skupinami dobov (Quercus robur) so bile ovrednotene v debelinskem priraščanju ter lesno-anatomskih značilnostih. Kronologije širin branik in ranega lesa so bile standardizirane z modificirano negativno eksponentno funkcijo. Velikopovršinska sprememba vodnega režima leta 1982 je pri drevesih iz Cigonce najprej povzročila spremembe v širini branike, širini kasnega lesa ter tudi v parametru "vsota površin trahej". Šele leta 1995 so znaki propadanja vidni tudi v zmanjšanih dimenzijah prevodnih elementov. Skupina "močno propadajoči" iz Cigonce se odziva le na povprečne mesečne in sezonske temperature. Odvisnost je vselej negativna in velja tako za dendrokronološke kot tudi za lesno-anatomske parametre. Skupini "zdravi" in "propadajoči" iz Mlač se odzivajo tako na temperature kot tudi na količine padavin. Lesno-anatomski parametri pri skupini "zdravi" iz Mlač so pokazali večjo odvisnost od temperatur kot dendrokronološki, ki se bolje odzivajo predvsem na junijske padavine. Večje količine dežja pozimi ter spomladi pomenijo manjše prevodne elemente pri skupini "zdravi", a ne vplivajo na skupno površino prevodnega tkiva. Parameter" povprečna površina maksimalne traheje" se je pokazal kot potencialen parameter za rekonstrukcijo povprečnih temperatur od marca do junija.Differences between differently vital groups of pedunculate oaks (Quercus robur) were determined in diameter increment and wood-anatomical features. Ring-width and latewood chronologies were standardized using modified negative exponential curve. Large-scale drainage manipulation in 1982 in forest stand from Cigonca first caused changes in ring width, latewood and parameter "total vessel area". Not until the year 1995 signs of dieback are also visible in smaller sizes of conductive elements. "Strongly Declining" group from Cigonca is responsive only to the mean monthly and seasonal temperatures. Dependence is strictly negative - for dendrochronological and wood-anatomical parameters. "Vital" and "Declining" groups from Mlače are responsive to the mean temperatures and the sum of precipitations. Wood-anatomical parameters from "Vital" group from Mlače showed higher responsive rate to temperatures than dendrochronological parameters, which are mostly responding to June precipitation. Higher winter and spring precipitation cause smaller conductive elements but do not affect the "total vessel area". Parameter "maximal vessel area" was recognized as a potential parameter for reconstruction of mean temperatures from March to June

New features in the dendroTools R package : bootstrapped and partial correlation coefficients for monthly and daily climate data

Climate-growth relationships are usually analysed using monthly climate data. The dendroTools R package also provides methodological approaches that enable climate-growth analysis for daily climate data. Such analysis reveals more complete climate signal patterns. In this article, new functions of the dendroTools R package are presented. Partial correlation coefficients are now implemented and can be used to calculate the strength of a linear relationship between two variables, while controlling for a third variable. Bootstrapped correlations can then be used to provide insights into the confidence intervals of statistical estimates. The calculation of partial and bootstrapped correlations is available for daily and monthly data. Finally, data transformation, S3 generic plotting and summary functions are also presented here

Daily climate data reveal stronger climate-growth relationships for an extended European tree-ring network

An extended European tree-ring network was compiled from various sources of tree-ring data from Europe, northern Africa and western Asia. A total of 1860 tree-ring chronologies were used to compare correlation coefficients calculated with aggregated day-wise and month-wise mean temperature, sums of precipitation and standardised precipitation-evapotranspiration index (SPEI). For the daily approach, climate data were aggregated over periods ranging from 21 to 365 days. Absolute correlations calculated with day-wise aggregated climate data were on average higher by 0.060 (temperature data), 0.076 (precipitation data) and 0.075 (SPEI data). Bootstrapped correlations are computationally expensive and were therefore calculated on a 69.4% subset of the data. Bootstrapped correlations indicated statistically significant differences between the daily and monthly approach in approximately 1% of examples. A comparison of time windows used for calculations of correlations revealed slightly later onset and earlier ending day of the year for the daily approach, while the largest differences between the two approaches arise from window lengths: Correlations calculated with day-wise aggregated climate data were calculated using fewer days than the monthly approach. Differences in the onset and ending dates of periods for the daily and monthly approaches were greater for precipitation and SPEI data than for temperature data