Comparison of nonlinear functions to describe lactation curves for cumulative milk production in buffalo.

The aim of this study was to examine the suitability of different growth functions (linear, sinusoidal, Gompertz, Schumacher and Richards) to fit cumulative milk production data from buffalo cows. Cumulative milk production at each day in milk was calculated from two published datasets reporting (i) fortnightly test-day milk yield records of the first lactation of Murrah buffalo that had calved during 1977-2012 and (ii) the first lactation records of Jaffarabadi buffalo collected from history-cum-pedigree registers for each quinquennium between 1991 and 2010. Each function was fitted to the lactation curves using nonlinear regression procedures. The Richards and sinusoidal equations provided the smallest root mean square error values, Akaike's and Bayesian information criteria and, therefore, the best fit for the cumulative lactation curves for milk yield. The Richards equation appeared to provide the most accurate estimate of the cumulative milk production at peak milk yield. Sinusoidal and flexible classical growth functions are appropriate to describe cumulative milk production curves and estimate lactation traits in buffalo.

Spatial genetic structure in European marbled newts revealed with target enrichment by sequence capture.

European marbled newts come in two species that have abutting ranges. The northern species, Triturus marmoratus, is found in France and the northern part of the Iberian Peninsula, whereas the southern species, T. pygmaeus, is found in the southwestern corner of the Iberian Peninsula. We study the intraspecific genetic differentiation of the group because morphological data show geographical variation and because the Iberian Peninsula is a recognized center of speciation and intraspecific genetic diversity for all kinds of organisms, amphibians included. We use target enrichment by sequence capture to generate c. 7 k nuclear DNA markers. We observe limited genetic exchange between the species, which confirms their distinctiveness. Both species show substantial genetic structuring that is only in part mirrored by morphological variation. Genetically differentiated groups are found in the south (T. marmoratus) and west (T. pygmaeus) of the species ranges. Our observations highlight the position of the Iberian Peninsula as a hotspot for genetic differentiation.

Fitting mathematical functions to extended lactation curves and forecasting late-lactation milk yields of dairy cows.

A 305-d lactation followed by a 60-d dry period has traditionally been considered economically optimal, yet dairy cows in modern intensive dairy systems are frequently dried off while still producing significant quantities of milk. Managing cows for an extended lactation has reported production, welfare, and economic benefits, but not all cows are suitable for an extended lactation. Implementation of an extended lactation strategy on-farm could benefit from use of a decision support system, based on a mathematical lactation model, that can identify suitable cows during early lactation that have a high likelihood of producing above a target milk yield (MY) at 305 d in milk (DIM). Therefore, our objectives were (1) to compare the suitability of 3 commonly used lactation models for modeling extended lactations (Dijkstra, Wood, and Wilmink) in primiparous and multiparous cows under a variety of lactation lengths, and (2) to determine the amount of early-lactation daily MY data needed to accurately forecast MY at d 305 by using the most suitable model and determine whether this is sufficient for identifying cows suitable for an extended lactation before the end of a typical voluntary waiting period (50-90 d). Daily MY data from 467 individual Holstein-Friesian lactations (DIM >305 d; 379 ± 65-d lactation length [mean ± SD]) were fitted by the 3 lactation models using a nonlinear regression procedure. The parameter estimates of these models, lactation characteristics (peak yield, time to peak yield, and persistency), and goodness-of-fit were compared between parity and different lactation lengths. The models had similar performance, and differences between parity groups were consistent with previous literature. Then, data from only the first i DIM for each individual lactation, where i was incremented by 30 d from 30 to 150 DIM and by 50 d from 150 to 300 DIM, were fitted by each model to forecast MY at d 305. The Dijkstra model was selected for further analysis, as it had superior goodness-of-fit statistics for i= 30 and 60. The data set was fit twice by the Dijkstra model, with parameter bounds either unconstrained or constrained. The quality of predictions of MY at d 305 improved with increasing data availability for both models and assisting the model fitting procedure with more biologically relevant constraints on parameters improved the predictions, but neither was reliable enough for practical use on-farm due to the high uncertainty of forecasted predictions. Using 90 d of data, the constrained model correctly classified 66% of lactations as being above or below a target MY at d 305 of 25 kg/d, with a probability threshold of 0.95. The proportion of correct classifications became smaller at lower targets of MY at d 305 and became greater when using more lactation days. Overall, further work is required to develop a model that can forecast late-lactation MY with sufficient accuracy for practical use. We envisage that a hybridized machine learning and mechanistic model that incorporates additional historical and genetic information with early-lactation MY could produce meaningful lactation curve forecasts.

Hybrid zone analysis confirms cryptic species of banded newt and does not support competitive displacement since secondary contact.

When two putatively cryptic species meet in nature, hybrid zone analysis can be used to estimate the extent of gene flow between them. Two recently recognized cryptic species of banded newt (genus Ommatotriton) are suspected to meet in parapatry in Anatolia, but a formal hybrid zone analysis has never been conducted. We sample populations throughout the range, with a focus on the supposed contact zone, and genotype them for 31 nuclear DNA SNP markers and mtDNA. We determine the degree of genetic admixture, introgression, and niche overlap. We reveal an extremely narrow hybrid zone, suggesting strong selection against hybrids, in line with species status. The hybrid zone does not appear to be positioned at an ecological barrier, and there is significant niche overlap. Therefore, the hybrid zone is best classified as a tension zone, maintained by intrinsic selection against hybrids. While the two banded newt species can evidently backcross, we see negligible introgression and the pattern is symmetric, which we interpret as supporting the fact that the hybrid zone has been practically stationary since its origin (while extensive hybrid zone movement has been suggested in other newt genera in the region). Our study illustrates the use of hybrid zone analysis to test cryptic species status.

Very large fluxes of methane measured above Bolivian seasonal wetlands.

Methane (CH4) mole fractions from the large semiseasonal Llanos de Moxos wetlands (∼70,000 km2) in northern Bolivia were measured by aircraft flights and ground sampling during early March 2019 (late wet season). Daily fluxes of CH4 determined from the measurements using box models and inverse modeling were between 168 (± 50) and 456 (± 145) mg CH4⋅m-2⋅d-1 for the areas overflown, very high compared with those of previous Amazon basin studies. If the seasonality of the CH4 emissions is comparable to other parts of the Amazon Basin, the region could contribute as much as 8% of annual Amazonian CH4 emissions.

A Holistic Approach to Evaluating Linear and Non-Linear Mixed Models to Predict Phosphorus Retention in Growing and Finishing Pigs.

The ability of four non-linear mixed models and one linear mixed model to describe phosphorus (P) retention as a function of dietary P intake, expressed on an available P (avP) basis, was assessed in growing and finishing pigs. Of the four non-linear models, the monomolecular and Michaelis-Menten describe diminishing returns behaviour, while the Richards and Morgan describe sigmoidal behaviour with the ability to also describe diminishing returns. Using a meta-analysis approach, models were fitted to avP intake vs. P retention data from P balance studies. Pig bodyweights (BW) ranged from 43.5 to 133 kg, P intake ranged from 0.055 to 0.468 g kg-1 BW0.75 d-1 for avP, and 0.151 to 0.806 g kg-1 BW0.75 d-1 for total P, with P retention ranging from 0.026 to 0.329 g kg-1 BW0.75 d-1. Models were evaluated using statistical measures of goodness-of-fit and inspection of residuals. The monomolecular and Michaelis-Menten best described the relationship between P retention and P intake. Endogenous P losses and P requirement for maintenance were found to be higher in finishing pigs compared to growing pigs as BW increased.

Modelling growth in dairy heifers based on linear body measurements (withers height) using non-linear functions.

This research communication reports a study to model the growth curves for withers height (WH) and body weight (BW) to withers height ratio (BW:WH) using monthly records (from 1 to 24 months of age) for three breeds of dairy heifer (Holstein, Jersey and Brown Swiss). The data sets used were those reported by the Dairy Heifer Evaluation Project of Penn State Extension (USA) between 1991 and 1992. Four growth functions (monomolecular and Michaelis-Menten, both with diminishing returns behaviour, and Schumacher and López, both with asymptotic sigmoidal behaviour) were fitted using the non-linear regression procedure of the SigmaPlot software and the parameters estimated. The models were judged for goodness of fit using adjusted coefficient of determination ($R_{{\rm adj}}^2 $), root mean square error (RMSE), Akaike's information criterion (AIC) and Bayesian information criterion (BIC). Assessing the goodness of fit by $R_{{\rm adj}}^2 $ (>0.99 in all cases) reveals the generally appropriate fit of the models to the data. The non-sigmoidal functions (i.e. Michaelis-Menten and monomolecular) provided the best fits giving the lowest values of RMSE, AIC and BIC. Based on the chosen statistical criteria, the Schumacher and López equations provided acceptable fits to the WH and BW:WH growth curves, but showed points of inflexion at times before birth, indicating that these growth curves are not sigmoidal. In conclusion, evaluation of the different non-linear growth functions used in this study indicated their potential for modelling growth patterns in dairy heifers.

On the Description of Equine Somatic Growth Using Nonlinear Functions.

A better knowledge of the growth of horses can facilitate sounder intervention in their health control, nutrition and management. This study compared five growth functions with either diminishing returns (monomolecular and Michaelis-Menten) or asymptotic sigmoidal (Gompertz, Richards and Lopez) behavior for describing the growth curves of horses, based on the relationship between a given somatic growth trait (body weight, withers height, or body weight to withers height ratio) and age. Data used in this study were those available in the literature for quarter horse males and thoroughbred foals and fillies from birth to maturity. Estimates of the model parameters were obtained using nonlinear regression procedures and the Marquardt-Levenberg algorithm. Functions were compared using goodness-of-fit statistics such as adjusted coefficient of determination and root mean square error. The results obtained with the Richards, Lopez and Gompertz equations suggest that curves are not sigmoidal, and that the diminishing returns models are adequate for describing the growth curves in horses.

Is the destruction or removal of atmospheric methane a worthwhile option?

Removing methane from the air is possible, but do the costs outweigh the benefits? This note explores the question of whether removing methane from the atmosphere is justifiable. Destruction of methane by oxidation to CO2 eliminates 97% of the warming impact on a 100-yr time scale. Methane can be oxidized by a variety of methods including thermal or ultraviolet photocatalysis and various processes of physical, chemical or biological oxidizers. Each removal method has energy costs (with the risk of causing embedded CO2 emission that cancel the global warming gain), but in specific circumstances, including settings where air with high methane is habitually present, removal may be competitive with direct efforts to cut fugitive methane leaks. In all cases however, great care must be taken to ensure that the destruction has a net positive impact on the total global warming, and that the resources required would not be better used for stopping the methane from being emitted. This article is part of a discussion meeting issue 'Rising methane: is warming feeding warming? (part 2)'.

Airborne quantification of net methane and carbon dioxide fluxes from European Arctic wetlands in Summer 2019.

Arctic wetlands and surrounding ecosystems are both a significant source of methane (CH4) and a sink of carbon dioxide (CO2) during summer months. However, precise quantification of this regional CH4 source and CO2 sink remains poorly characterized. A research flight using the UK Facility for Airborne Atmospheric Measurement was conducted in July 2019 over an area (approx. 78 000 km2) of mixed peatland and forest in northern Sweden and Finland. Area-averaged fluxes of CH4 and carbon dioxide were calculated using an aircraft mass balance approach. Net CH4 fluxes normalized to wetland area ranged between 5.93 ± 1.87 mg m-2 h-1 and 4.44 ± 0.64 mg m-2 h-1 (largest to smallest) over the region with a meridional gradient across three discrete areas enclosed by the flight survey. From largest to smallest, net CO2 sinks ranged between -513 ± 74 mg m-2 h-1 and -284 ± 89 mg m-2 h-1 and result from net uptake of CO2 by vegetation and soils in the biosphere. A clear gradient of decreasing bulk and area-averaged CH4 flux was identified from north to south across the study region, correlated with decreasing peat bog land area from north to south identified from CORINE land cover classifications. While N2O mole fraction was measured, no discernible gradient was measured over the flight track, but a minimum flux threshold using this mass balance method was calculated. Bulk (total area) CH4 fluxes determined via mass balance were compared with area-weighted upscaled chamber fluxes from the same study area and were found to agree well within measurement uncertainty. The mass balance CH4 fluxes were found to be significantly higher than the CH4 fluxes reported by many land-surface process models compiled as part of the Global Carbon Project. There was high variability in both flux distribution and magnitude between the individual models. This further supports previous studies that suggest that land-surface models are currently ill-equipped to accurately capture carbon fluxes inthe region. This article is part of a discussion meeting issue 'Rising methane: is warming feeding warming? (part 2)'.

δ13C methane source signatures from tropical wetland and rice field emissions.

The atmospheric methane (CH4) burden is rising sharply, but the causes are still not well understood. One factor of uncertainty is the importance of tropical CH4 emissions into the global mix. Isotopic signatures of major sources remain poorly constrained, despite their usefulness in constraining the global methane budget. Here, a collection of new δ13CCH4 signatures is presented for a range of tropical wetlands and rice fields determined from air samples collected during campaigns from 2016 to 2020. Long-term monitoring of δ13CCH4 in ambient air has been conducted at the Chacaltaya observatory, Bolivia and Southern Botswana. Both long-term records are dominated by biogenic CH4 sources, with isotopic signatures expected from wetland sources. From the longer-term Bolivian record, a seasonal isotopic shift is observed corresponding to wetland extent suggesting that there is input of relatively isotopically light CH4 to the atmosphere during periods of reduced wetland extent. This new data expands the geographical extent and range of measurements of tropical wetland and rice δ13CCH4 sources and hints at significant seasonal variation in tropical wetland δ13CCH4 signatures which may be important to capture in future global and regional models. This article is part of a discussion meeting issue 'Rising methane: is warming feeding warming? (part 2)'.

Isotopic signatures of methane emissions from tropical fires, agriculture and wetlands: the MOYA and ZWAMPS flights.

We report methane isotopologue data from aircraft and ground measurements in Africa and South America. Aircraft campaigns sampled strong methane fluxes over tropical papyrus wetlands in the Nile, Congo and Zambezi basins, herbaceous wetlands in Bolivian southern Amazonia, and over fires in African woodland, cropland and savannah grassland. Measured methane δ13CCH4 isotopic signatures were in the range -55 to -49‰ for emissions from equatorial Nile wetlands and agricultural areas, but widely -60 ± 1‰ from Upper Congo and Zambezi wetlands. Very similar δ13CCH4 signatures were measured over the Amazonian wetlands of NE Bolivia (around -59‰) and the overall δ13CCH4 signature from outer tropical wetlands in the southern Upper Congo and Upper Amazon drainage plotted together was -59 ± 2‰. These results were more negative than expected. For African cattle, δ13CCH4 values were around -60 to -50‰. Isotopic ratios in methane emitted by tropical fires depended on the C3 : C4 ratio of the biomass fuel. In smoke from tropical C3 dry forest fires in Senegal, δ13CCH4 values were around -28‰. By contrast, African C4 tropical grass fire δ13CCH4 values were -16 to -12‰. Methane from urban landfills in Zambia and Zimbabwe, which have frequent waste fires, had δ13CCH4 around -37 to -36‰. These new isotopic values help improve isotopic constraints on global methane budget models because atmospheric δ13CCH4 values predicted by global atmospheric models are highly sensitive to the δ13CCH4 isotopic signatures applied to tropical wetland emissions. Field and aircraft campaigns also observed widespread regional smoke pollution over Africa, in both the wet and dry seasons, and large urban pollution plumes. The work highlights the need to understand tropical greenhouse gas emissions in order to meet the goals of the UNFCCC Paris Agreement, and to help reduce air pollution over wide regions of Africa. This article is part of a discussion meeting issue 'Rising methane: is warming feeding warming? (part 2)'.

Atmospheric methane and nitrous oxide: challenges alongthe path to Net Zero.

The causes of methane's renewed rise since 2007, accelerated growth from 2014 and record rise in 2020, concurrent with an isotopic shift to values more depleted in 13C, remain poorly understood. This rise is the dominant departure from greenhouse gas scenarios that limit global heating to less than 2°C. Thus a comprehensive understanding of methane sources and sinks, their trends and inter-annual variations are becoming more urgent. Efforts to quantify both sources and sinks and understand latitudinal and seasonal variations will improve our understanding of the methane cycle and its anthropogenic component. Nationally declared emissions inventories under the UN Framework Convention on Climate Change (UNFCCC) and promised contributions to emissions reductions under the UNFCCC Paris Agreement need to be verified independently by top-down observation. Furthermore, indirect effects on natural emissions, such as changes in aquatic ecosystems, also need to be quantified. Nitrous oxide is even more poorly understood. Despite this, options for mitigating methane and nitrous oxide emissions are improving rapidly, both in cutting emissions from gas, oil and coal extraction and use, and also from agricultural and waste sources. Reductions in methane and nitrous oxide emission are arguably among the most attractive immediate options for climate action. This article is part of a discussion meeting issue 'Rising methane: is warming feeding warming? (part 1)'.

Carbon isotopic characterisation and oxidation of UK landfill methane emissions by atmospheric measurements.

Biological oxidation of methane in landfill cover material can be calculated from the carbon isotopic signature (δ13CCH4) of emitted CH4. Enhanced microbial consumption of methane in the aerobic portion of the landfill cover is indicated by a shift to heavier (less depleted) isotopic values in the residual methane emitted to air. This study was conducted at four landfill sites in southwest England. Measurement of CH4 using a mobile vehicle mounted instrument at the four sites was coupled with Flexfoil bag sampling of ambient air for high-precision isotope analysis. Gas well collection systems were sampled to estimate landfill oxidised proportion. Closed or active status, seasonal variation, cap stripping and site closure impact on landfill isotopic signature were also assessed. The δ13CCH4 values ranged from -60 to -54‰, with an average value of -57 ± 2‰. Methane emissions from active cells are more depleted in 13C than closed sites. Methane oxidation, estimated from the isotope fractionation, ranged from 2.6 to 38.2%, with mean values of 9.5% for active and 16.2% for closed landfills, indicating that oxidised proportion is highly site specific.

Investigating the Uptake and Fate of Poly- and Perfluoroalkylated Substances (PFAS) in Sea Ice Using an Experimental Sea Ice Chamber.

Poly- and perfluoroalkyl substances (PFAS) are contaminants of emerging Arctic concern and are present in the marine environments of the polar regions. Their input to and fate within the marine cryosphere are poorly understood. We conducted a series of laboratory experiments to investigate the uptake, distribution, and release of 10 PFAS of varying carbon chain length (C4-C12) in young sea ice grown from artificial seawater (NaClsolution). We show that PFAS are incorporated into bulk sea ice during ice formation and regression analyses for individual PFAS concentrations in bulk sea ice were linearly related to salinity (r2 = 0.30 to 0.88, n = 18, p < 0.05). This shows that their distribution is strongly governed by the presence and dynamics of brine (high salinity water) within the sea ice. Furthermore, long-chain PFAS (C8-C12), were enriched in bulk ice up to 3-fold more than short-chain PFAS (C4-C7) and NaCl. This suggests that chemical partitioning of PFAS between the different phases of sea ice also plays a role in their uptake during its formation. During sea ice melt, initial meltwater fractions were highly saline and predominantly contained short-chain PFAS, whereas the later, fresher meltwater fractions predominantly contained long-chain PFAS. Our results demonstrate that in highly saline parts of sea ice (near the upper and lower interfaces and in brine channels) significant chemical enrichment (ε) of PFAS can occur with concentrations in brine channels greatly exceeding those in seawater from which it forms (e.g., for PFOA, εbrine = 10 ± 4). This observation has implications for biological exposure to PFAS present in brine channels, a common feature of first-year sea ice which is the dominant ice type in a warming Arctic.

An Illustrative Analysis of Atypical Gas Production Profiles Obtained from In Vitro Digestibility Studies Using Fecal Inoculum.

Gas production profiles typically show a monotonically increasing monophasic pattern. However, atypical gas production profiles exist whereby at least two consecutive phases of gas production or additional extraneous features that distort the typical profile are present. Such profiles are more likely to occur with the use of a fecal inoculum and are much less well described. The presence of multiple phases or non-descript extraneous features makes it difficult to apply directly recommended modeling approaches such as standard response functions or classical growth functions. To overcome such difficulties, extensions of the Mitscherlich equation and a numerical modeling option also based on the Mitscherlich are explored. The numerical modeling option uses an estimate of relative rate obtained from the smoothed data profile and an estimate of maximum gas produced together with any lag time information drawn from the raw data to construct a simple Mitscherlich equation. In summary, this article illustrates the analysis of atypical gas production profiles obtained using a fecal inoculum and explores the methodology of numerical modeling to reconstruct equivalent typical growth-like trends.