Assessing fine-scale pondscape connectivity with amphibian eyes: An integrative approach using genomic and capture-mark-recapture data.

In the face of habitat loss, preserving functional connectivity is essential to maintain genetic diversity and the demographic dynamics required for the viability of biotic communities. This requires knowledge of the dispersal behaviour of target species, which can be modelled as kernels, or probability density functions of dispersal distances at increasing geographic distances. We present an integrative approach to investigate the relationships between genetic connectivity and demographic parameters in organisms with low vagility focusing on five syntopic pond-breeding amphibians. We genotyped 1056 individuals of two anuran and three urodele species (1732-3913 SNPs per species) from populations located in a landscape comprising 64 ponds to characterize fine-scale genetic structure in a comparative framework, and combined these genetic data with information obtained in a previous 2-year capture-mark-recapture (CMR) study. Specifically, we contrasted graphs reconstructed from genomic data with connectivity graphs based on dispersal kernels and demographic information obtained from CMR data from previous studies, and assessed the effects of population size, population density, geographical distances, inverse movement probabilities and the presence of habitat patches potentially functioning as stepping stones on genetic differentiation. Our results show a significant effect of local population sizes on patterns of genetic differentiation at small spatial scales. In addition, movement records and cluster-derived kernels provide robust inferences on most likely dispersal paths that are consistent with genomic inferences on genetic connectivity. The integration of genetic and CMR data holds great potential for understanding genetic connectivity at spatial scales relevant to individual organisms, with applications for the implementation of management actions at the landscape level.

Active and passive chlorophyll fluorescence measurements at canopy level on potato crops. Evidence of similitude of diurnal cycles of apparent fluorescence yields.

We performed active and passive measurements of diurnal cycles of chlorophyll fluorescence on potato crops at canopy level in outdoors conditions for 26 days. Active measurements of the stationary fluorescence yield (Fs) were performed using Ledflex, a fluorescence micro-LIDAR described in Moya et al. (Photosynth Res 142:1-15, 2019), capable of remote measurements of chlorophyll fluorescence under full sun-light in the wavelength range from 650 to 800 nm. Passive measurements of solar-induced fluorescence (SIF) fluxes were performed with Spectroflex, an instrument based on the method of filling-in in the O2A and O2B absorption bands at 760 nm (F760) and 687 nm (F687), respectively.Diurnal cycles of Fs showed significant variations throughout the day, directly attributed to changes in photosystem II yield. Contrasting patterns were observed according to illumination conditions. Under cloudy sky, Fs varied in parallel with photosynthetically active radiation (PAR). By contrast, during clear sky days, the diurnal cycle of Fs showed a "M" shape pattern with a minimum around noon.F687 and F760 showed different patterns, according to illumination conditions. Under low irradiance associated with cloudy conditions, F687 and F760 followed similar diurnal patterns, in parallel with PAR. Under high irradiance associated with clear sky we observed an increase of the F760/F687 ratio, which we attributed to the contributions in the 760 nm emission of photosystem I fluorescence from deeper layers of the leaves, on one end, and by the decrease of 687 nm emission as a result of red fluorescence re-absorption, on the other end.We defined an approach to derive a proxy of fluorescence yield (FYSIF) from SIF measurements as a linear combination of F687 and F760 normalized by vegetation radiance, where the coefficients of the linear combination were derived from the spectral transmittance of Ledflex. We demonstrated a close relationship between diurnal cycles of FYSIF and Fs, which outperformed other approaches based on normalization by incident light.

Active in situ and passive airborne fluorescence measurements for water stress detection on a fescue field.

Ledflex is a fluorometer adapted to measure chlorophyll fluorescence at the canopy level. It has been described in detail by Moya et al. (2019), Photosynthesis Research. https://doi.org/10.1007/s11120-019-00642-9 . We used this instrument to determine the effect of water stress on the fluorescence of a fescue field under extreme temperature and light conditions through a 12 days campaign during summer in a Mediterranean area. The fescue field formed part of a lysimeter station in "las Tiesas," near Albacete-Spain. In addition to the fluorescence data, the surface temperature was measured using infrared radiometers. Furthermore, "Airflex," a passive fluorometer measuring the filling-in of the atmospheric oxygen absorption band at 760 nm, was installed in an ultralight plane and flown during the most critical days of the campaign. We observed with the Ledflex fluorometer a considerable decrease of about 53% of the stationary chlorophyll fluorescence level at noon under water stress, which was well correlated with the surface temperature difference between the stressed and control plots. Airflex data also showed a decrease in far-red solar-induced fluorescence upon water stress in agreement with surface temperature data and active fluorescence measurements after correction for PS I contribution. Notwithstanding, the results from airborne remote sensing are not as precise as in situ active data.

Canopy chlorophyll fluorescence applied to stress detection using an easy-to-build micro-lidar.

LEDFLEX is a micro-lidar dedicated to the measurement of vegetation fluorescence. The light source consists of 4 blue Light-Emitting Diodes (LED) to illuminate part of the canopy in order to average the spatial variability of small crops. The fluorescence emitted in response to a 5-µs width pulse is separated from the ambient light through a synchronized detection. Both the reflectance and the fluorescence of the target are acquired simultaneously in exactly the same field of view, as well as the photosynthetic active radiation and air temperature. The footprint is about 1 m2 at a distance of 8 m. By increasing the number of LEDs longer ranges can be reached. The micro-lidar has been successfully applied under full sunlight conditions to establish the signature of water stress on pea (Pisum Sativum) canopy. Under well-watered conditions the diurnal cycle presents an M shape with a minimum (Fmin) at noon which is Fmin > Fo. After several days withholding watering, Fs decreases and Fmin < Fo. The same patterns were observed on mint (Menta Spicata) and sweet potatoes (Ipomoea batatas) canopies. Active fluorescence measurements with LEDFLEX produced robust fluorescence yield data as a result of the constancy of the excitation intensity and its geometry fixity. Passive methods based on Sun-Induced chlorophyll Fluorescence (SIF) that uses high-resolution spectrometers generate only flux data and are dependent on both the 3D structure of vegetation and variable irradiance conditions along the day. Parallel measurements with LEDFLEX should greatly improve the interpretation of SIF changes.

Remote sensing of solar-induced chlorophyll fluorescence (SIF) in vegetation: 50 years of progress.

Remote sensing of solar-induced chlorophyll fluorescence (SIF) is a rapidly advancing front in terrestrial vegetation science, with emerging capability in space-based methodologies and diverse application prospects. Although remote sensing of SIF - especially from space - is seen as a contemporary new specialty for terrestrial plants, it is founded upon a multi-decadal history of research, applications, and sensor developments in active and passive sensing of chlorophyll fluorescence. Current technical capabilities allow SIF to be measured across a range of biological, spatial, and temporal scales. As an optical signal, SIF may be assessed remotely using highly-resolved spectral sensors and state-of-the-art algorithms to distinguish the emission from reflected and/or scattered ambient light. Because the red to far-red SIF emission is detectable non-invasively, it may be sampled repeatedly to acquire spatio-temporally explicit information about photosynthetic light responses and steady-state behaviour in vegetation. Progress in this field is accelerating with innovative sensor developments, retrieval methods, and modelling advances. This review distills the historical and current developments spanning the last several decades. It highlights SIF heritage and complementarity within the broader field of fluorescence science, the maturation of physiological and radiative transfer modelling, SIF signal retrieval strategies, techniques for field and airborne sensing, advances in satellite-based systems, and applications of these capabilities in evaluation of photosynthesis and stress effects. Progress, challenges, and future directions are considered for this unique avenue of remote sensing.

Integrating dispersal, breeding and abundance data with graph theory for the characterization and management of functional connectivity in amphibian pondscapes.

Context: Robust assessment of functional connectivity in amphibian population networks is essential to address their global decline. The potential of graph theory to characterize connectivity among amphibian populations has already been confirmed, but the movement data on which modelled graphs rely are often scarce and inaccurate. While probabilistic methods that account for intraspecific variability in dispersal better reflect the biological reality of functional connectivity, they must be informed by systematically recorded individual movement data, which are difficult to obtain for secretive taxa like amphibians. Objectives: Our aim is to assess the applied potential of probabilistic graph theory to characterize overall connectivity across amphibian pondscapes using fine-scale capture-recapture data, and to inform conservation management based on the role of ponds on functional connectivity. Methods: We monitored an amphibian community in a pondscape located in a Spanish "dehesa" for 2 years. Photoidentification was used to build capture histories for individuals of six species, from which dispersal kernels and population sizes were estimated to model probabilistic graphs. Results: We obtained kernels of variable robustness for six species. Node importance for connectivity varied between species, but with common patterns such as shared road crossing areas and the presence of coincident interconnected pond clusters. Conclusions: The combination of photoidentification, capture-recapture data and graph theory allowed us to characterize functional connectivity across the pondscape of study accounting for dispersal variability and identify areas where conservation actions could be most efficient. Our results highlight the need to account for interspecific differences in the study and management of amphibian pondscapes. Supplementary Information: The online version contains supplementary material available at 10.1007/s10980-022-01520-x.

Quantitative study of fluorescence excitation and emission spectra of bean leaves.

A quantitative and comprehensive knowledge of leaf fluorescence is required for the interpretation of fluorescence signals at the canopy level and also for the modelling of leaf and canopy fluorescence. In this work we present full range fluorescence excitation and emission spectra of intact leaves, expressed in units of apparent spectral fluorescence yield, from both the adaxial and the abaxial sides of the leaves, and for both front-side and back-side geometries. Emission spectra were measured for incident radiations in the blue and the green spectral range. The red/far-red fluorescence ratio depended on the measurement geometry and on the excitation wavelength. Excitation spectra were measured for emissions at 687 and 760 nm. When the abaxial side was illuminated, the measured spectra always had a larger intensity compared to adaxial side that is explained by the higher scattering of the spongy tissues. At 760 nm, the spectra had the same shape for front-side and back-side geometry, indicating that scattering predominated. At 687 nm, the shape of the spectra was very different for front-side and back-side geometry due to re-absorption of red fluorescence within the leaf. The comparison of excitation spectra measured from the adaxial or the abaxial side revealed differences in carotenoid absorption.

Correlation between lifetime heterogeneity and kinetics heterogeneity during chlorophyll fluorescence induction in leaves: 2. Multi-frequency phase and modulation analysis evidences a loosely connected PSII pigment-protein complex.

We report the first direct decomposition of the fluorescence lifetime heterogeneity during multiphasic fluorescence induction in dark-adapted leaves by multi-frequency phase and modulation fluorometry (PMF). A very fast component, assigned to photosystem I (PSI), was found to be constant in lifetime and yield, whereas the two slow components, which are strongly affected by the closure of the reaction centers by light, were assigned to PSII. Based on a modified "reversible radical pair" kinetic model with three compartments, we showed that a loosely connected pigment complex, which is assumed to be the CP47 complex, plays a specific role with respect to the structure and function of the PSII: (i) it explains the heterogeneity of PSII fluorescence lifetime as a compartmentation of excitation energy in the antenna, (ii) it is the site of a conformational change in the first second of illumination, and (iii) it is involved in the mechanisms of nonphotochemical quenching (NPQ). On the basis of the multi-frequency PMF analysis, we reconciled two apparently antagonistic aspects of chlorophyll a fluorescence in vivo: it is heterogeneous with respect to the kinetic structure (several lifetime components) and homogeneous with respect to average quantities (quasi-linear mean tau-Phi relationship).

Correlation between lifetime heterogeneity and kinetics heterogeneity during chlorophyll fluorescence induction in leaves: 1. Mono-frequency phase and modulation analysis reveals a conformational change of a PSII pigment complex during the IP thermal phase.

The relationship between the fluorescence lifetime (tau) and yield (Phi) obtained in phase and modulation fluorometry at 54 MHz during the chlorophyll fluorescence induction in dark-adapted leaves under low actinic light has been investigated. Three typical phases have been identified: (i) linear during the OI photochemical rise, (ii) convex curvature during the subsequent IP thermal rise, and (iii) linear during the PS slow decay. A similar relationship has been obtained in the fluorescence induction for the fluorescence yield measured at 685 nm plotted versus the fluorescence yield measured at 735 nm. A spectrally resolved analysis shows that the curvature of the tau-Phi relationship is not due to chlorophyll fluorescence reabsorption effects. Several other hypotheses are discussed and we conclude that the curvature of the tau-Phi relationship is due to a variable and transitory nonphotochemical quenching. We tentatively propose that this quenching results from a conformational change of a pigment-protein complex of Photosystem II core antenna during the IP phase and could explain both spectral and temporal transitory changes of the fluorescence. A variable blue shift of the 685 nm peak of the fluorescence spectrum during the IP phase has been observed, supporting this hypothesis.

Time-resolved spectral studies of blue-green fluorescence of artichoke (Cynara cardunculus L. Var. Scolymus) leaves: identification of chlorogenic acid as one of the major fluorophores and age-mediated changes.

Synchrotron radiation and the time-correlated single-photon counting technique were used to investigate the spectral and time-resolved characteristics of blue-green fluorescence (BGF) of artichoke leaves. Leaves emitted BGF under ultraviolet (UV) excitation; the abaxial side was much more fluorescent than the adaxial side, and in both cases, the youngest leaves were much more fluorescent than the oldest ones. The BGF of artichoke leaves was dominated by the presence of hydroxycinnamic acids. A decrease in the percentage of BGF attributable to the very short kinetic component (from 42 to 20%), in the shape of the BGF excitation spectra, and chlorogenic acid concentrations indicate that there is a loss of hydroxycinnamic acid with leaf age. Studies on excitation, emission, and synchronized fluorescence spectra of leaves and trichomes and chlorogenic acid contents indicate that chlorogenic acid is one of the main blue-green fluorophores in artichoke leaves. Results of the present study indicate that 20-42% (i.e., the very short kinetic component) of the overall BGF is emitted by chlorogenic acid. Time-resolved BGF measurements could be a means to extract information on chlorogenic acid fluorescence from the overall leaf BGF.

Steady-state chlorophyll fluorescence (Fs) measurements as a tool to follow variations of net CO2 assimilation and stomatal conductance during water-stress in C3 plants.

Water stress experiments were performed with grapevines (Vitis vinifera L.) and other C3 plants in the field, in potted plants in the laboratory, and with detached leaves. It was found that, in all cases, the ratio of steady state chlorophyll fluorescence (Fs) normalized to dark-adapted intrinsic fluorescence (Fo) inversely correlated with non-photochemical quenching (NPQ). Also, at high irradiance, the ratio Fs/Fo was positively correlated with CO2 assimilation in air, with electron transport rate calculated from fluorescence, and with stomatal conductance, but no clear correlation was observed with qP. The significance of these relationships is discussed. The ratio Fs/Fo, measured with a portable instrument (PAM-2000) or with a remote sensing FIPAM system, provides a good method for the early detection of water stress, and may become a useful guide to irrigation requirements.

The anatomical components of the cardiac outflow tract of the gray bichir, Polypterus senegalus: their evolutionary significance.

It has been reported that in chondrichthyans the cardiac outflow tract is composed of the myocardial conus arteriosus, while in most teleosteans it consists of the nonmyocardial bulbus arteriosus. Classical studies already indicated that a conus and a bulbus coexist in several ancient actinopterygian and teleost groups. Recent work has shown that a cardiac outflow tract consisting of a conus and a bulbus is common to both cartilaginous and bony fishes. Nonetheless and despite their position at the base of the actinopterygian phylogenetic lineage, the anatomical arrangement of the cardiac outflow tract of the Polypteriformes remained uncertain. The present study of hearts from gray bichirs was intended to fill this gap. The cardiac outflow tract of the bichir consists of two main components, namely a very long conus arteriosus, furnished with valves, and a short, intrapericardial, arterial-like bulbus arteriosus, which differs from the ventral aorta because it is covered by epicardium, shows a slightly different spatial arrangement of the histological elements and is crossed by coronary arteries. Histomorphologically, the outflow tract consists of three longitudinal regions, distal, middle and proximal, an arrangement which has been suggested to be common to all vertebrates. The distal region corresponds to the bulbus, while the conus comprises the middle and proximal regions. The present findings reinforce the notion that the bulbus arteriosus of fish has played an essential role in vertebrate heart evolution as it is the precursor of the intrapericardial trunks of the aorta and pulmonary artery of birds and mammals.

Chlorophyll fluorescence emission spectrum inside a leaf.

Chlorophyll a fluorescence can be used as an early stress indicator. Fluorescence is also connected to photosynthesis so it can be proposed for global monitoring of vegetation status from a satellite platform. Nevertheless, the correct interpretation of fluorescence requires accurate physical models. The spectral shape of the leaf fluorescence free of any re-absorption effect plays a key role in the models and is difficult to measure. We present a vegetation fluorescence emission spectrum free of re-absorption based on a combination of measurements and modelling. The suggested spectrum takes into account the photosystem I and II spectra and their relative contribution to fluorescence. This emission spectrum is applicable to describe vegetation fluorescence in biospectroscopy and remote sensing.

Photochemistry, remotely sensed physiological reflectance index and de-epoxidation state of the xanthophyll cycle in Quercus coccifera under intense drought.

Quercus coccifera L. is a Mediterranean sclerophyllous shrub with a high capacity to resist intense drought stress. Therefore, it could be used in the study of physiological changes suffered by plants at very low water potentials. A remote sensing sensor was used to measure continuously the physiological reflectance index (PRI; defined as the changes in reflectance at 531 nm with respect to those at 570 nm; PRI = [(R531 - R570)/(R531 + R570)] at canopy level and under field conditions in an artificial carpet of seedlings of Q. coccifera during a drought cycle. Correlations between leaf level-measured chlorophyll fluorescence parameters as well as the de-epoxidation state of the xanthophyll cycle [(A + Z)/(V + A + Z)] and canopy level-measured PRI were reasonably good (R (2) = 0.57-0.63, P < 0.01), and quite interesting for water stress remote sensing purposes. The instrument's temporal resolution allowed us to follow the rapid response of PRI to changing photosynthetic active radiation, and to resolve, in response to cloud-induced changes in light intensity, a fast and a slow PRI component. We report the disappearance of the rapid one under conditions of intense drought in response to a sudden increase in light intensity. The underlying photoprotection mechanisms that Q. coccifera shows in response to intense drought stress periods seem to be related to the existence of a low intrathylakoid lumenal pH at the end of the drought cycle. Under intense drought, these mechanisms allow this species to avoid oxidative damage, which was evidenced by the maintenance of an unaltered photosynthetic pigment composition and constant photosystem II efficiency in the mornings. It is concluded that, contrary to early reports, PRI is a sensible, indirect, non-destructive water stress indicator, even in plants experiencing intense drought.

Dualex: a new instrument for field measurements of epidermal ultraviolet absorbance by chlorophyll fluorescence.

Dualex (dual excitation) is a field-portable instrument, hereby described, for the assessment of polyphenolic compounds in leaves from the measurement of UV absorbance of the leaf epidermis by double excitation of chlorophyll fluorescence. The instrument takes advantage of a feedback loop that equalizes the fluorescence level induced by a reference red light to the UV-light-induced fluorescence level. This allows quick measurement from attached leaves even under field conditions. The use of light-emitting diodes and of a leaf-clip configuration makes Dualex a user-friendly instrument with potential applications in ecophysiological research, light climate analysis, agriculture, forestry, horticulture, pest management, selection of medicinal plants, and wherever accumulation of leaf polyphenolics is involved in plant responses to the environment.

Early light-induced proteins protect Arabidopsis from photooxidative stress.

The early light-induced proteins (ELIPs) belong to the multigenic family of light-harvesting complexes, which bind chlorophyll and absorb solar energy in green plants. ELIPs accumulate transiently in plants exposed to high light intensities. By using an Arabidopsis thaliana mutant (chaos) affected in the posttranslational targeting of light-harvesting complex-type proteins to the thylakoids, we succeeded in suppressing the rapid accumulation of ELIPs during high-light stress, resulting in leaf bleaching and extensive photooxidative damage. Constitutive expression of ELIP genes in chaos before light stress resulted in ELIP accumulation and restored the phototolerance of the plants to the wild-type level. Free chlorophyll, a generator of singlet oxygen in the light, was detected by chlorophyll fluorescence lifetime measurements in chaos leaves before the symptoms of oxidative stress appeared. Our findings indicate that ELIPs fulfill a photoprotective function that could involve either the binding of chlorophylls released during turnover of pigment-binding proteins or the stabilization of the proper assembly of those proteins during high-light stress.