Principal Component Analysis Axes Research Articles

Changing soil properties influenced vegetation diversity along effluent‐dominated river courses in dry areas of north‐western India

AbstractImproving the environmental quality of effluent‐dominated seasonal rivers is a fundamental challenge for sustaining life in drylands, where people utilize contaminated water to produce food, which ultimately accumulates in the food chain. Preventing further contaminations and phytoremediation are needed to avoid environmental degradation and health risks. This study aimed at analysing water quality and its impacts on soil and vegetation at effluent‐impacted, river‐edge and non‐polluted (control) micro‐habitats at five sites along Luni, Bandi and Jojari Rivers each in western Rajasthan. Soil and water samples were collected and analysed, and vegetation was recorded. River water exhibited high pH (7.60–8.60), electrical conductivity (EC; 2.45–38.20 dS m−1), total dissolved solid (TDS; 1.26–30.86 g L−1), alkalinity (24.0–250.0 mg L−1) and Na (1.50–30.00 g L−1), K (29.0–1100.0 mg L−1), Ca (136.0–3800.0 mg L−1) and Mn (0.05–83.92 mg L−1) concentrations and low NH4‐N, NO3‐N, PO4‐P and heavy metals. Species numbers ranged between 32 along Luni and 20 along Jojari. Soil pH, EC, PO4‐P and shrub richness (R), diversity (H′) and evenness (e') were highest for Bandi, whereas NH4‐N, NO3‐N, K and tree R and H′ were highest for Jojari River. Soil variables decreased and plant diversity increased downstream. Concentrations of Cd, Zn, Cr, Cu and Pb were above the acceptable limit in leaf of Salvadora persica and Prosopis juliflora. Principal component analysis (PCA) revealed significant relationships between different variables of river water, soil, and vegetation and 11 PCA axes. Conclusively, industry effluents negatively affected water, soil and river ecology. Effluent‐impacted soils had high salinity and less diversity adapted by salt‐tolerant species, complementary effects of which contribute to restoring the modified ecosystem and urban greening. Although people utilize effluent‐contaminated water in irrigation, precautions should be taken to avoid environmental and animal/human health risks.

Recommendation of minimal distal tibial length for long axis coordinate system definitions

Accurate anatomical coordinate systems for the foot and ankle are critical for interpreting their complex biomechanics. The tibial superior-inferior axis is crucial for analyzing joint kinematics, influencing bone motion analysis during gait using CT imaging and biplane fluoroscopy. However, the lack of consensus on how to define the tibial axis has led to variability in research, hindering generalizability. Even as advanced imaging techniques evolve, including biplane fluoroscopy and weightbearing CT, there exist limitations to imaging the entire foot together with the full length of the tibia. These limitations highlight the need to refine axis definitions. This study investigated various superior-inferior axes using multiple distal tibia lengths to determine the minimal field of view for representing the full tibia long-axis. Twenty human cadaver tibias were imaged and segmented to generate 3D bone models. Axes were calculated based on coordinate definitions that required user manual input, and a gold standard mean superior-inferior axis was calculated based on the population’s principal component analysis axis. Four manually calculated superior-inferior tibial axes groups were established based on landmarks and geometric fittings. Statistical analysis revealed that geometrically fitting a cylinder 1.5 times the mediolateral tibial width, starting 5 cm above the tibial plafond, yielded the smallest angular deviation from the gold standard. From these findings, we recommend a minimum field of view that includes 1.5 times the mediolateral tibial width, starting 5 cm above the tibial plafond for tibial long-axis definitions. Implementing these findings will help improve foot and ankle research generalizability and impact clinical decisions.

Abstract PS02-05: Trajectories and predictors of peripheral neuropathy after neoadjuvant chemotherapy in a prospective cohort of 11,014 patients with early breast cancer

Abstract Background Peripheral neuropathy (PN) is a debilitating adverse event in patients with early breast cancer (BC) receiving (neo)adjuvant chemotherapy (CT). We harnessed the CANTO cohort study to detail clinical trajectories and explore clinical and genetic predictors of PN. Methods CANTO (CANcer TOxicities - NCT01993498) prospectively enrolled invasive stage I-III BC patients (pts) of 26 French comprehensive cancer centers. Pts were assessed at diagnosis, 3-6 (M6), 12 (M12), 36 (M36), and 60 (M60) months after treatment, defined as completion of surgery, CT or radiotherapy, whichever comes last. At each time point, PN events including paresthesia, sensory and motor neuropathy were collected according to NCI-CTC v4.0 criteria. A genome-wide association study (GWAS) was conducted to identify genetic predictors of PN, using Illumina GSA BeadChips. Minimac4/1000G was used to impute additional single nucleotide polymorphisms (SNPs). After stringent quality control measures, 1,894,475 SNPs with a minor allele frequency (MAF) >0.05 were evaluated. Longitudinal trajectories of PN events were descriptively examined. Statistical associations between each SNP and PN events measured at different time points, and between SNPs and trajectories, were performed with logistic regression assuming a log-additive genetic model. All analyses were adjusted for key clinical parameters and the first ten axes of principal component analysis of the genetic data to control for population stratification. Results Of 12,012 included pts (data lock Aug. 2022), 11,014 (91.7%) were analyzed. Age was < 50 and >65 in 3407 and 2759 pts (31% and 25%, respectively). Overweight/obesity and diabetes were recorded in 5328 (48%) and 458 pts (4%). A neurologic history was observed in 1360 pts (13%). Stage 0-I and II-III were observed in 5356 (49%) and 5512 pts (51%), and 4011 pts had an axillary dissection (37%). CT was administered in 5790 pts (53%), including a taxane (tax) in 5542 pts (96%). Shortly, all grade and grade 2+ PN was observed in 29% and 12%; 27% and 10%; 20% and 10%; 13% and 10% of pts at M6, M12, M36 and M60, respectively. We derived 5 trajectories of overall PN, deemed “never”, “always”, “appears”, “transient” and “disappears”, in respectively 54%, 10%, 9%, 7% and 19% of the pts. Similar trajectories were built for the 3 categories of PN events. We built 9 predictive nomograms including key clinical parameters and time of analysis. E.g., grade 2+ PN at M6 was independently predicted by a medical history of carpal tunnel syndrome, past neurologic history and exposure to tax. Grade 2+ PN at M36 was predicted by past neurologic history and exposure to tax, and largely by previous PN at M6 or M12. The GWAS analysis included 7633 pts (84%). Four independent SNPs adding predictive value to the clinical nomograms were identified at a suggestive level of association (p < 1e-6), including one SNP in the NCAM1 gene (involved in neurogenesis) for M6 PN (OR=1.40, 95%CI 1.23-1.60, p=4.8e-7, see table) and one SNP in the CLDN11 gene (regulates oligodendrocytes) for M12 sensory PN (OR=1.32; 95%CI 1.17-1.49, p=7.5e-6). For rare ( < 5%) toxicities, 10 independent suggestive SNPs were identified, including one SNP in the NELL1 gene (neural cell growth regulation and differentiation) for the “always” trajectory (OR=1.61, 95%CI 1.31-1.99, p=7.6e-6) and one SNP in the KCNIP1 gene (neuronal sensor) for M36 motor PN (OR=1.5, 95%CI 1.7-3.5, p=3.1e-07). Conclusions Risk of early peripheral neuropathy is associated with previous neurological history and taxane exposure. Patients with PN at M6 or M12 are highly exposed to long-term PN. Some key SNPs may add independent predictive value for specific PN endpoints. Exploratory results of interest were produced for rarer toxicities and typical clinical trajectories. Detailed results will be presented at the meeting. All PN, M6 Multivariate analyses of the risk of peripheral neuropathy, all grades, at M6, without and with GWAS input. Citation Format: Youenn Drouet, Emilie Thomas, Florence Lerebours, Barbara Pistilli, Olivier Trédan, Christelle Jouannaud, Marion Fournier, Philippe Rouanet, Laurence Vanlemmens, CHARLES COUTANT, Asma Dhaini Merimeche, Baptiste Sauterey, Christelle Levy, Mario Campone, Carole Tarpin, Marie-Ange Mouret-Reynier, Olivier Rigal, Thierry Petit, Sophie Guillermet, Antoine Arnaud, Mahmoud Ibrahim, Sylvie Giacchetti, Florence Dalenc, Johanna Wassermann, Olivier Arsène, Ariane Darut-Jouve, Sibille Everhard, Ines Vaz Luis, Anne-Laure Martin, Fabrice André, Jean-François Deleuze, Alain Viari, Matthieu Carton, Paul Cottu. Trajectories and predictors of peripheral neuropathy after neoadjuvant chemotherapy in a prospective cohort of 11,014 patients with early breast cancer [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PS02-05.

Abstract PO4-14-05: Germline and acquired genetic variants and long-term cancer-related fatigue among survivors of early-stage breast cancer (BC)

Abstract BACKGROUND: Previous studies suggested that bio-behavioral models explain part of the variability of cancer-related fatigue, and pro-inflammatory and age-related processes emerged as contributors to persistent fatigue. However, the biological underpinnings of this complex symptom, including its relevant genomic correlates, are still poorly understood. We aimed to comprehensively explore the association of genetic variants with long-term cancer-related fatigue. METHODS: We used the prospective, multicenter, longitudinal CANcer TOxicity cohort, enrolling patients at diagnosis of stage I-III BC (NCT01993498). Outcomes included severe (≥40/100) global (EORTC QLQ-C30) as well as physical, emotional, and cognitive (FA12) fatigue at year (Y)1, Y2, and Y4 after BC diagnosis. Applying a hypothesis-driven approach, we investigated (i) germline genetic variants in a pre-specified Genetic Risk Index (GRI) assaying expression-regulating single nucleotide polymorphisms (SNPs) in the promoter regions of 3 pro-inflammatory cytokine genes (IL1B [rs16944], IL6 [rs1800795], and TNF [rs1800629]; Bower J, JCO 2013; N=9035), and (ii) age-related expansions of hematopoietic clones carrying recurrent acquired mutations, commonly defined as clonal hematopoiesis of indeterminate potential (CHIP; NGS with unique molecular identifiers for 17 genes [including DNMT3A, TET2, ASXL1, PPM1D, ATM, JAK2, and TP53]; N=1219). The contribution of GRI and CHIP to fatigue was assessed by multivariable logistic regression models. Taking an agnostic approach, we then performed a genome-wide association study (GWAS) of fatigue and 1,894,511 germline SNPs (Illumina InfiniumExome24/Illumina GSA24; N=9056). All genetic variants were assessed at BC diagnosis. Tested associations were adjusted by validated clinical predictors (Di Meglio A, JCO 2022). RESULTS: In the overall cohort (N=9056) mean age was 56.5 years (SD 11.2), 51.0% had stage II or III BC, 52.6% received chemotherapy, and 82.1% endocrine therapy. The prevalence of severe fatigue was 26.1% at diagnosis and increased to 36.5%, 34.3%, and 32.6% at Y1, Y2, and Y4 after diagnosis, respectively. Most patients (77.4%) had 3-6 high-frequency alleles across the 3 SNPs in the pro-inflammatory GRI. Among patients with available CHIP data, 15.2% and 3.7% had a Variant Allele Frequency (VAF) >2% and >10%, respectively. The pro-inflammatory GRI was not associated with fatigue outcomes. We found significant associations between CHIP and severe long-term global fatigue at Y4 (adjusted OR [95%CI]: VAF ≥2% vs < 2%, 1.64 [1.08-2.51], p=0.021; VAF ≥10% vs < 10%, 2.22 [1.00-4.94], p=0.050). The GWAS identified several regions (each including ≥2 SNPs) as associated with severe fatigue outcomes (suggestive p-value cut-off < 5 × 10−5; see Table for number of identified regions by outcome and respective nearby genes). Overlap in biological pathways was observed in some of the gene regions associated with global and physical fatigue, but not for emotional or cognitive fatigue. Common biological processes that were associated (FDR < 0.05) with such genes included synaptic transmission, hemoglobin-oxygen binding, and response to stress. CONCLUSIONS: This study provides suggestive association data between gene variants and long-term cancer-related fatigue. While previously reported associations with pro-inflammatory GRI were not confirmed, some biological processes that may inform the mechanistic understanding of this symptom emerged, including associations with aging and response to stress that warrant further exploration. ///: marks different regions. All association analyses were adjusted by age, body mass index, smoke behavior, pre-treatment fatigue, pain, insomnia, and anxiety, and by the first ten axes of principal component analysis of the genetic data to control for population stratification. There was no overlap in biological pathways for the gene regions associated with emotional or cognitive fatigue (gene regions not shown). Table. Genes in proximity of regions associated with severe fatigue outcomes Citation Format: Antonio Di Meglio, Emilie Thomas, Youenn Drouet, Jean-Baptiste Micol, Davide Soldato, Maria Alice Franzoi, Martina Pagliuca, Julie Havas, Anne-Laure Martin, Sibille Everhard, Celine Besse, Anne Boland, Christophe Marzac, Nathalie Droin, Sandrine Boyault, Marina Rousseau, Olivier Trédan, Paul Cottu, Christelle Jouannaud, Marion Fournier, Laurence Vanlemmens, Charles Coutant, Asma Dhaini Merimeche, Baptiste Sauterey, Florence Joly, Mario Campone, Florence Lerebours, Marie-Ange Mouret-Reynier, Olivier Rigal, Thierry Petit, Sophie Guillermet, Antoine Arnaud, Mahmoud Ibrahim, Sylvie Giacchetti, Florence Dalenc, Johanna Wassermann, Olivier Arsène, Ariane Darut-Jouve, Aurélie Bertaut, Fabrice André, Jean-Francois Deleuze, Alain Viari, Ines Vaz Luis. Germline and acquired genetic variants and long-term cancer-related fatigue among survivors of early-stage breast cancer (BC) [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO4-14-05.

Hydroclimate Changes Based on Testate Amoebae in the Greater Khingan Mountains’ Peatland (NE China) during the Last Millennium

The driving force of climate change in the monsoon margin is complex, making it a key area for regional and global climate change research. Palaeohydrological studies in the monsoon margin have increased the resolution of research in the long term, transitioning from qualitative to quantitative studies to comprehend climate change processes, patterns, and mechanisms. Testate amoebae (TA) in peat sediments are used as a proxy indicator organism for quantitative reconstruction of palaeohydrology. Thus, their community changes are directly related to precipitation, and widely used to reconstruct the patterns of summer precipitation globally. We investigated TA species and reconstructed palaeohydrological changes in the Greater Khingan Mountains’ Hongtu (HT) peatland, located in the East Asian Summer Monsoon (EASM) margin. The result showed that the most abundant TA species were Assulina muscorum (12.4 ± 5.0%) and Nebela tincta (8.9 ± 4.9%) in the HT peat core. The increase in dry indicator species (e.g., A. muscorum and Alabasta militaris) indicated a drying pattern in the HT peatland since 150 cal yr BP. Principal component analysis (PCA) explained 47.6% of the variation in the selected TA assemblages. During 400 to 250 cal yr BP, PCA axis 1 scores ranged from 0.2 to −1.3 (reflecting a drier climate), associating with the Little Ice Age. The paleohydrology of the northern part of the Greater Khingan Mountains was mainly controlled by the EASM, which was associated with changes in North Atlantic Sea surface temperature and solar radiative forcing. The apparent drying pattern may be the result of the gradual intensification of anthropogenic activities and the increase in EASM intensity.

Tributary mitigates river discontinuity by dam depending on the distance from dam to the tributary confluence

AbstractRiver ecosystems host a continuum of various discontinuities, such as dams and tributary inflows, which shape the habitats of aquatic organisms; this makes it important to evaluate the interactions among discontinuities and effects of a single discontinuity point. Herein, we focused on tributaries in dammed rivers to elucidate a manner to mediate discontinuities and hypothesized that the effects of the tributary inflow on the downstream river were mediated by the (1) distance between the dam and tributary inflow, (2) size ratio between the dam and tributary, and (3) ability of the tributary to transport fine sediments, such as sand and gravel. We conducted field investigations to measure 24 environmental factors, including the water column, riverbed, and river topography, along eight dammed rivers to test the three hypotheses. Only five factors differed significantly between the upstream and downstream sites of the tributary confluence, whereas 12 factors differed significantly between the tributary and mainstem. We also classified the variation pattern using principal component analysis (PCA). The correlation between each PCA axis and environmental factors suggests that the modifications of the water quality factors by tributary inflow were significantly correlated with the distance between the dam and the tributary inflow, and that the flux of various riverbed factors, that is, was significantly correlated with the ability to resupply of fine riverbed sediments by the tributary. Overall, tributary‐inflow downstream of a dam has the potential to be applicable in environmental restoration, especially in terms of resupplying fine sediment.

Measurement of polychlorinated biphenyls in different high consumption canned foods, using the QuEChERS/GC-MS method

Polychlorinated biphenyls (PCBs) are organic pollutants containing chlorine, which can be carcinogenic to humans. The current research focused on the heart risk and determination of PCBs levels in canned foods using the modified QuEChERS (fast, easy, cheap, effective, resistant and safe) method and gas chromatograph/mass spectrometer (GC-MS) technique. In this study, LOD (limit of detection), LOQ (limit of quantification), and recovery ranged from 0.06 to 0.32, 0.18 to 1.07 ng/g, and 97.05 to 102.5 %, respectively. In canned foods, the highest median of PCBs was PCB 52 (0.27 ± 0.20 ng/g fat) and the lowest median were PCB 28 and 138 (not detected in samples). Also, the maximum median of PCB 28, 52, 101, 138, 153, and 180 were detected in eggplant samples (0.06 ng/g), haricot samples (0.49 ng/g), eggplant samples (0.36 ng/g), eggplant samples (0.19 ng/g), eggplant samples (0.11 ng/g) and lentiform samples (0.66 ng/g), respectively. The median PCBs levels of oral exposure were estimated to be in the range of 9.80E-07to 4.30E-05 ng/g.d for all population groups, which were meaningfully lesser than the Tolerable daily intake value. The Monte Carlo simulation (MCS) outcomes indicated that the rank order of PCBs in adults based on incremental lifetime cancer risk (ILCR) was Lentiform (7.05E-8) > canned fish (5.73E-8) > Eggplant (5.38E-8) > Haricot (4.33E-8) > pasta source (2.06E-8); and in children was Lentiform (3.40E-7) > canned fish (2.72E-7) > Eggplant (2.44E-7) > Haricot (2.06E-7) > pasta source (9.83E-8). The median values of the ILCR induced oral exposure for all groups were within safe limits (lower than 10−6). The heat map and multivariate principal component analysis (PCA) showed significantly different contributions of PCBs profile in samples as the PCA axis scores were correlated with the type of cans. Based on the obtained outcomes, it can be concluded that the PCBs of canned food do not potential health risks to Iranian consumers.

Root vascular anatomy predicts maximum growth rates in savanna trees and grasses

AbstractRoot‐based functional traits are relatively overlooked as drivers of savanna plant community dynamics, an important gap in water‐limited ecosystems. Recent work has shed light on patterns of trait coordination in roots, but less is known about the relationship between root functional traits, water acquisition, and plant demographic rates. Here, we investigated how fine‐root vascular and morphological traits are related in two dominant PFTs (C3 trees and C4 grasses from the savanna biome), whether root traits can predict plant relative growth rate (RGR), and whether root trait multivariate relationships differ in trees and grasses. We used root data from 21 tree and 18 grass species grown under greenhouse conditions, and quantified a suite of vascular and morphological root traits. We used a principal components analysis (PCA) to identify common axes of trait variation, compared trait correlation matrices between the two PFTs, and investigated the relationship between PCA axes and individual traits and RGR. We found that there was no clear single axis integrating vascular and morphological traits, but found that vascular anatomy predicted RGR in both trees and grasses. Trait correlation matrices differed in trees and grasses, suggesting potentially divergent patterns of trait coordination between the two functional types. Our results suggested that, despite differences in trait relationships between trees and grasses, root conductivity may constrain maximum growth rate in both PFTs, highlighting the critical role that water relations play in savanna vegetation dynamics and suggesting that root water transport capacity is an important predictor of plant performance in the savanna biome.

Responses of Bird Communities to Habitat Structure along an Aridity Gradient in the Steppes North of the Sahara

We explored the influence of habitat structure on bird density and species richness in the poorly known bird communities in the steppes of Eastern Morocco, along a 200 km long N–S gradient of increasing aridity. The birds were surveyed, and habitat structure was measured in 44 transects regularly distributed along the gradient and during the winter and spring seasons in two consecutive years. After applying a principal component analysis (PCA), five axes were identified, including one related to the latitude–altitude–soil-type gradient and another describing the development of herbaceous vegetation. Generalized linear models were used to explore the relations between bird density and species richness with PCA axes in each season, considering both the entire community and groups of granivorous, insectivorous, and mixed-diet species. More than 90% of the birds were year-round residents, with larks dominating the community in both seasons. We conclude that a distinct multifactorial response can be identified for each functional group of species. In the winter, the community is mainly affected by the structure of the habitat, while aridity (and its assumed relation to primary production) is less influential. In the spring, habitat structure continues to have the greatest explanatory power, but location along the aridity gradient becomes more relevant. These findings reveal the interaction of the negative effects of climatic and anthropogenic changes in the habitat available to these bird communities, with a greater impact expected on birds with diets that include seeds, as well as a general shift of optimal breeding conditions toward more northerly latitudes.

Does life form affect tree species assembly? A demographic study across the life history of a temperate forest in Japan

AbstractIn this study, the dominant mechanism that defines the species assembly in an old‐growth temperate forest was investigated by analyzing the species specificity of demographic parameters in relation to the life history stage, testing the hypotheses that early life stages should be more critical for sub‐canopy species than canopy species. Data for 17 major tree species in the Ogawa Forest Reserve (OFR) in Japan were analyzed, together with data from early stages (seed production, seed dispersal, and seedling emergence) to dbh‐based transition probability and survival stages (5–80 cm). Both datasets were subjected to principal components analysis (PCA): one included tree of dbh < 35 cm for all species (small‐sized trees of all species [SSAS]) and the other included tree species with dbh ≥ 55 cm (large‐sized species [LSS]). The most influential was the growth–survival trade‐off for trees at small‐to‐middle‐sized stages (dbh: 10–40 cm), which captured a moderate proportion of the demographic variation (24.3%–26.4%). At these stages, some Quercus species were characterized by higher growth, and some Fagus and Acer species by shade tolerance. Behavior during early‐to‐late life stages was the second most important dimension, for SSAS, sub‐canopy tree species showed high survival at early life stages than canopy species as the second important dimension, which differed between the SSAS‐ and LSS‐based PCAs. The relationship between functional traits and PCA axis dimensions varied with PCA type and dimension. The growth–survival trade‐off in the OFR was closely associated with maximum tree height, a proxy for life form, and specific leaf area a proxy for shade tolerance. This finding implies a significant role for the growth–survival trade‐off in stable species coexistence by maintaining mutual claims to vertical light resources and allowing the more efficient use of the forest canopy space. However, there was no significant association between wood density and demographic variables. Our study shows that interspecies relationships vary with the life history stage and that early life stages are more critical for sub‐canopy species than canopy species in temperate forests, where the entire life history of the trees must be considered focusing on the difference in life forms.

Adaptability of Wild-Growing Tulips of Greece: Uncovering Relationships between Soil Properties, Rhizosphere Fungal Morphotypes and Nutrient Content Profiles.

Wild-growing Greek tulips are protected plants but almost nothing is known about their natural nutrient status and rhizosphere fungal morphotypes in the wild, thus no insight is currently available into their growth and adaptation to their natural environment or artificial settings. To this end, several botanical expeditions were conducted with a special collection permit, and 34 tulip and soil samples were collected, representing 13 species from two phytogeographical regions of Greece (North Aegean Islands, Crete Island) and seven regions of mainland Greece. The tulips' content in essential macro- and micro-nutrients, respective physicochemical soil properties, and rhizosphere fungal morphotypes were assessed across samples, and all parameters were subjected to appropriate statistical analysis to determine their interrelationships. The results showed that soil variables played a significant role in shaping tulips' nutrient content, explaining up to 67% of the detected variability as in the case of phosphorus (P) in the above-ground plant tissue. In addition, significant correlations were observed (with an r value of up to 0.65, p < 0.001) between essential nutrients in the tulips, such as calcium (Ca) and boron (B). The principal component analysis (PCA) revealed that between the three spatial units examined, the total variability of tulips' nutrient content produced a clear distinction among sampled species, while the first two PCA axes managed to explain 44.3% of it. This was further confirmed by the analysis of variance (ANOVA) results which showed corresponding significant differences (at p < 0.05) in both the tulips' nutrient content and the studied soil properties as well (mean values of N, P, and K in the North Aegean Islands tulips' nutrient content, up to 53%, 119%, and 54% higher compared to those of the Crete Island, respectively). Our study sheds light on Greek tulips' adaptability and resilience in their original habitats, facilitating at the same time the undertaken efforts regarding their conservation and potential domestication in artificial settings.

DUS Characterization and Evaluation of Untapped French Bean (Phaseolus vulgaris L.) Genotypes

French bean is being considered as an important legume for human diet having rich source of dietary proteins, minerals and vitamins. Germplasm characterization and evaluation is having great contribution in breeding and crop improvement. Substantial phenotypic and genetic characterization of untapped French bean germplasm are still needed to unlock its breeding potential. Purposefully, 27 diverse French bean genotypes comprising primitive, cultivars, commercial cultivars, farmers grown varieties were collected from different parts of India, characterized as per Distinct, Uniformity and Stability (DUS) and evaluated for associated morpho-phenological traits in randomized complete block design. The screened panel revealed highly significant differences among French bean genotypes for all the traits under study which witnessed the existence of sufficient variability in the French bean genotypes in which first two Principal Component Analysis (PCA) explained 20.03% and 13.32% of the total morphological variability. The genotypes were well scattered in PCA axis forming groups with various traits as per contribution towards the variability. The genotype IC 632961 having desirable traits which could be an elite germplasm for future crop improvement.

Spatiotemporal Dynamics of Ecological Condition in Qinghai-Tibet Plateau Based on Remotely Sensed Ecological Index

The eco-system in the Qinghai-Tibet Plateau (QTP) is extremely fragile, and highly vulnerable to climate change. Knowledge of the changes in the ecological conditions is vital to mitigate the impact of climate change. In this study, we investigated the trend of ecological conditions of the QTP using the remotely sensed ecological index (RSEI), which is the first PCA (principal component analysis) axis of the four indexes derived from the MODIS (Moderate resolution Imaging Spectroradiometer) images captured in the growing season of 2000–2020. The four indexes, i.e., NDVI (normalized difference vegetation index), heat (land surface temperature, LST), wetness (tasseled cap wetness index, WET) and dryness (normalized difference impervious surface index, NDBSI), were calculated on the Google Earth Engine platform. Using land use cover change (LUCC) data, long-term meteorological records and the supplementary annual livestock production, we explored the drivers of spatiotemporal changes in the RSEI. The results show the following points: (1) the ecological conditions of the QTP have remarkable spatiotemporal variations. There were two ecological degradation periods, one of them occurred in the central region during 2005–2010, mainly attributed to the rising temperatures and decreasing precipitation. The other occurred during 2015–2020, driven primarily by overgrazing in the southwest. From 2000 to 2005, it was a period of rapid ecological restoration in the ecologically fragile northeast region. (2) The contribution rate of pc1 was stable at 60%, while the contribution rate of pc2 remained below 40%, indicating that pc1 demonstrated most of the characteristics of the four indexes. The correlation coefficients between NDVI and WET with pc1 are both positive, while LST and NDBSI have negative correlation coefficients, i.e., negative effects. This is consistent with the actual situation. (3) Overgrazing caused grass degradation in the southwest area of the QTP, which might be the main reason for the poor ecological conditions (i.e., low RSEI value) during 2015–2020. (4) Temperature and precipitation showed an increasing trend during the study period. A warmer and wetter climate is expected to have profound impacts on the ecosystems in QTP and practices should be concentrated on identifying climate-sensitive ecosystem components and designating adaptative options.

Morphological pattern of the dermal denticles of the Southern sawtail catshark Galeus mincaronei Soto, 2001.

Dermal denticles cover the skin of sharks for protection and may have additional functions, depending on the environment. The aim of the present study was to analyze the morphological pattern of dermal denticles across the body of the poorly known deep-water catshark Galeus mincaronei, which is endemic to Southern Brazil. Additionally, we aimed to identify differences between sexes and stages of sexual maturity. For this purpose, we analyzed patches of eight skin samples from body regions, that is, the head, body, and tail. Dermal denticles were imaged using scanning electron microscopy. Measurements of crown morphological variations (length and width) and density of dermal denticles were performed. Nine characters of dermal denticle morphology were selected to describe a morphological pattern using principal component analysis (PCA). The first PCA axis explained 45.2% of the variation, the second explained 33%, and the third explained 14.3%, together explaining 92.5% of the total variation in denticle morphology. We identified three groups of dermal denticle crown morphologies and their possible functions. The first was composed of nostril and snout denticles, which might suggest abrasion strength functions; the second was composed of most body denticles, such as those in the cranium, on the left side of the body, and on the pectoral, dorsal, and caudal fins, which might be related to generalized functions; and the third was composed of only caudal crest denticles, which might indicate defense functions with hydrodynamic properties in G. mincaronei. Likewise, our results reveal variations in dermal denticle morphology and arrangement along the three maturity stages considered in both sexes. Similarly, sexual dimorphism in the crown width and morphology of dermal denticles was observed in developing and mature individuals. Our results are the first to reveal the morphological variation of dermal denticles in relation to function, sex, and ontogeny of individual G. mincaronei.

Mapping functional tree regions of the Atlantic Forest: how much is left and opportunities for conservation

SummaryMany biomes still lack an overall view of their macro-functional structure (i.e., natural biogeographical regions and zones), including the Atlantic Forest biodiversity hotspot. The effective design of protected areas depends on the spatial identification of units with ecologically distinct content, whether it be floristic, phylogenetic or functional. This study used a regionalization approach to identify the potential functional regions of the Atlantic Forest by interpolating functional data from forest remnants into the entire original occurrence area of the biome, including deforested lands. Conservation status was then estimated. Analysis of seven traits of leaf, wood, seed and plant size revealed that the biome is structured over 14 functional regions and three zones (clusters of regions). Functional regions represented specific combinations of traits rather than being characterized by extremely high or low values of a single trait. They retained an average of 29.5% of forest remnants (range: 7.63–54.66%) and 10.82% of protected areas (range: 0.35–35.78%). By analysing the functional space occupied by all regions, captured by two principal component analysis axes using the pixel-level information contained in interpolated trait maps, we showed that large parts of this space were not covered by forest remnants or protected areas and that the most represented regions had serious deficits in protected areas. Although the Serra do Mar mountain range in the south and south-east Atlantic Forest is relevant as a centre of species endemism and richness and has received considerable attention for carrying out ecological studies and creating protection areas, this range does not fully encompass the functional biodiversity of such a rich biome. Our results demonstrate the potential for combining regionalization and conservation approaches to unravel the macro-structures of biomes.

Environment and space drive the community assembly of Atlantic European grasslands: Insights from multiple facets

AbstractAimEcological communities are assembled by regional and local processes. These processes select species through their traits, which are tied to species' evolutionary history. A multifaceted approach, encompassing taxonomic, functional and phylogenetic diversity can thus help us to better understand community assembly. We asked what the relative importance of geography, climate and soil parameters is in driving taxonomic, functional and phylogenetic diversities at local (alpha) and larger scales (beta diversity).LocationAtlantic Europe.TaxonPlant communities of Violion caninae grasslands.MethodsAlpha and beta taxonomic, functional and phylogenetic diversities were calculated for 153 sites. Traits were obtained from the LEDA database and phylogeny from Daphne. We summarized climatic (CHELSA database) and soil variables using principal component analysis (PCA), and geographical distance using Moran's Eigenvector Maps (MEMs). To assess the importance of environment and space on all three facets, we performed redundancy and distance‐based redundancy analyses for alpha and beta diversity, respectively, using the PCA and MEM axes as predictors.ResultsCompared to alpha diversity, beta diversity was relatively high in taxonomic diversity, but very low in functional and phylogenetic diversity. Geography and climate were relatively more important at larger scales, whereas soil conditions acted more strongly at the local scales, with alpha diversity of all facets decreasing towards richer and acidic soils.Main ConclusionsConsidering multiple biodiversity facets along environmental and spatial gradients enables advancing both theoretical and applied aspects of community assembly. Accordingly, the observed turnover across the study area was mediated by species that share similar suites of traits and evolutionary history. Towards richer and acidic soils, exclusion of weaker competitors was an important filter at local scales. In summary, assessing multiple biodiversity facets and broad scale environmental gradients is key to understand the relative importance of multi‐scale processes driving the community assembly of European grasslands.

Source and Optical Dynamics of Chromophoric Dissolved Organic Matter in the Watershed of Lake Qinghai

Lake Qinghai is the largest lake in China and is of great significance to maintain the ecological security of the Qinghai-Tibet Plateau. Few studies have been carried out to investigate the optical composition and source of chromophoric dissolved organic matter (CDOM) in large lakes on the Qinghai-Tibet Plateau. It is of great significance to study the source and optical dynamics of CDOM in Lake Qinghai watershed for water quality protection and filling in the gaps in the knowledge of CDOM variability in a remote area. Two sampling campaigns in the Lake Qinghai watershed were carried out, and excitation-emission matrices coupled with parallel factor analysis (EEMs-PARAFAC) were used to unravel the optical composition and the sources of CDOM. Our results indicated that the mean dissolved organic carbon (DOC) concentration, a250:a365, and the spectral slope of CDOM absorption S275-295 in the lake were significantly higher than that in the inflow river (P<0.0001, t-test), whereas the mean absorption coefficient of CDOM a350, humification index (HIX), fluorescence peak integration ratio IC:IT, and specific ultraviolet absorbance at 254 nm SUVA254 of CDOM were shown to be lower in the lake than in the inflow river (P<0.0001), indicating that compared with the lake itself, CDOM in the inflow was humic-rich and highly aromatic. Four fluorescent components were obtained using PARAFAC, including a terrestrial human-like component C1, a microbial human-like component C2, a tyrosine-like C3, and a tryptophan-like C4. The mean DOC concentration, S275-295, and a250:a365in the headwater streams of the Lake Qinghai watershed were lower than those in the downstream estuary, indicating that the CDOM abundance increased, and the molecular weight decreased, from the headwaters to the downstream river mouths. The mean of SUVA254, C1, and the first axis of principal component analysis were positively related to terrestrial input (i.e., the PC1 values were significantly higher in rivers than in lakes (P<0.001)), indicating that the aromaticity of CDOM in rivers was higher than that in lakes. Particularly, the contribution of terrestrial humic-like C1 was higher in the Quanji River, Shaliu River, and Khargai River compared with that in other tributaries due to an intensified cultivated land use at the downstream estuary of these rivers.

Evaluating Slow Pyrolysis of Parthenium hysterophorus Biochar: Perspectives to Acidic Soil Amelioration and Growth of Selected Wheat (Triticum aestivum) Varieties.

Application of biochar on acidic soils may improve soil fertility and crop productivity. This study aimed to explore the relevance of parthenium biochar-induced changes in the physicochemical properties and agronomic performance of the selected wheat varieties in acidic soils. A pot trial was used in determining the effect of slow pyrolysis parthenium biochar on acidic soils and the agronomic performance of wheat varieties. A general linear model (GLM) of multivariate analysis and principal component analysis (PCA) was used to compare functional variation among soil assayed parameters with biochar dosages and years. Biochar-treated acidic soils did not show significant differences in their physical properties. However, a significant incremental trend was observed in the soil moisture content. The biochar-amended acidic soils showed noticeable differences in the soil pH, available phosphorous, and exchangeable bases (Ca, K, and Na) compared to the control. In all soil samples, a decreasing trend in the soil micronutrients was observed with an increase in the biochar amounts. The analysis also unveiled significant changes in root length, root and shoot dry biomass, and plant height of wheat varieties in response to the biochar amendments. The application of 19.5 t/ha and 23 t/ha dosages of biochar gave the maximum changes in the agronomic performance of Kekeba and Ogolcha varieties, while the minimum was obtained in the 26.5 t/ha and the control. Furthermore, PCA axis 1 accounted for 74.34% of the total variance within a higher eigenvector value (10.4076), and most of the soil parameters were positively correlated with CEC (0.29), available phosphorous (0.29), and soil pH (0.28); however, the micronutrients were negatively correlated. In conclusion, Parthenium hysterophorus biochar has the potential to amend acidic soils, and thus, the application of 16.0, 19.5, and 23 t·ha−1 biochar dosages are considered suitable to reduce the soil acidity level and improve the agronomic performance of wheat varieties. However, extensive research will be needed to determine the effects of biochar on soil properties and crop production in field conditions.

Analysis of Calcareous Soils for Two Various Facies within the Nature Reserve of El-Mergueb (M’sila, Algeria)

Abstract This research was conducted on the protected area of El-Mergueb at M’sila province. The zone of El-Mergueb is located about 180 km south of the capital Algiers, at an altitude from 550 to 800 m, and is characterised by arid climate. The zone of El-Mergueb has a landscape from the steppe to Alfa that lies just as well in the flat ridges hills that in their slopes and in the top part of the ravines. Alfa tenacissima dominates the most geographical space of El-Mergueb. This study is based on the analysis of the homogenous and heterogeneous facies by the determination of the content of calcium carbonate (CaCO3), active calcium carbonate (ACCE) and gypsum through monitoring these chemical parameters during 3 years: 2017, 2018, 2019. Six soil profiles of 15 soil samples collected in the site of study were studied and several chemical soil properties were considered. These factors included: soil pH, calcium carbonate (CaCO3), active total carbonate (CA), gypsum (CaSO4) and electrical conductivity (EC). Principal component analysis (PCA) was used to identify the variations in soil properties. Results showed that there are significant relationships between some soil factors and two PCA axes. The results thus obtained showed that the content of CaCO3 and CA analysed ranged from average to high. The average of gypsum and salinity was low. Floristic diversity defined 284 species. The data on the chemical characteristics of the soil studied have been the subject of a detailed statistical analysis (PCA). Our database consisted of quantitative variables. The implementation of the PCA to the soils studied showed a major dominance of the limestone in the two stations, which explains the alkaline pH and the low concentration of gypsum. Finally, these types of high total limestone are the most observed in the majority of steppe and arid soils.

Testing the Sensitivity and Limitations of Frequently Used Aquatic Biota Indices in Temperate Mountain Streams and Plain Streams of China

Different biological groups show biased responses to similar or different environmental stressors on different scales. The selection of bioindicators based on pressure characteristics is the basis for accurately assessing ecological quality. In this study, we investigated the responses of common bioindicators, namely, macroinvertebrates and fish, to multiple stressors in temperate mountain and plain streams of northeast China. We used 56 indices, including the single biological evaluation index and biological evaluation index system, to analyze and compare characteristic response to different scales under varying environmental stressors. The principal component analysis (PCA) showed that PCA axis 1 in the catchment scale explained 83.6% and 96.1% of the variance in mountain and plain rivers, respectively, which characterized the comprehensive pressure gradient integrated by land-use development and water pollution. PCA axis 1 explained 40.7% and 53.9% of variance in mountain and plain rivers on the reach scale and 63.1% and 61.8% of variance on the site scale. The correlation analysis showed responses of different indices to abiotic variables which did not overlap. Macroinvertebrate and fish indices successfully explained the change in water chemistry on a small scale, whereas fish indices additionally explained the change in land use on a large scale. Macroinvertebrate and fish indices were recommended because of their rich responses to environmental stressors, particularly in plain rivers. For mountain stream biomonitoring programs, especially in the Taizi River of northeastern China, we suggest that macroinvertebrates and fish should be used separately or jointly according to the actual capacity and cost, Moreover, compared with the possible differences in the evaluation results of different single biological evaluation indexes, the biological evaluation index system shows more stable monitoring results, and the single sensitivity index is more significant in biological evaluation, and more sensitive to some special environmental factors.