Ecology

DEGs under low-temperature stressThe results from the field experiments indicated that the daily mean values of A, Fvʹ/Fmʹ, ETR and Fv/Fm decreased in the LT group, the PSII function was impaired, and the photosynthetic capacity was weakened. Through the specific analysis of the “Photosynthesis” pathway (pathway ID ko00195) in the LT group, it was found that PSII, the cytochrome b6f. complex (Cyt b6f.), PSI and ATPase exhibited differential gene expressions. Figure 9 shows the structural pattern diagram for photosynthesis. The parts marked by white boxes indicate that the structure has DEGs. The gene expressions of CP43, CP47, D1 protein and Cytb559 of PSII changed. The inner peripheral antenna pigment proteins, CP43 and CP47, of PSII bind to chlorophyll. They accept the excitation energy transferred from the surrounding antenna complex and transfer this energy to the reaction centre complex. Changes in CP43 and CP47 affect the absorption and transmission of light energy. In the PSII reaction centre, light energy is converted into chemical energy. P680 absorbs light and is excited to become P680*, and then transfers electrons to pheophytin (Pheo). At the same time, the PSII oxygen-evolving complex obtains electrons from water molecules, the water molecules are split and releases oxygen and protons. As one of the two core proteins that compose the reaction centre complex, the D1 protein combines with various cofactors that are related to the original charge separation and electron transfer. The D1 protein plays an important role in the process of photosynthetic electron transfer. Studies have found that low temperatures can induce allosteric inactivation of the D1 protein, which results in changes in the structure of thylakoid membranes and hinders electron transfer8. As part of the reaction centre, Cytb559 can adjust the photoinhibition sensitivity of PSII through redox changes so that the PSII reaction centre is protected from damage9. The light energy absorption, energy conversion and electron transfer functions of PSII are impaired, which result in significant decreases in Fv/Fm to levels far below the normal value. The results of Xiangchun Song are similar to those presented in this paper: the PS II reaction centre of A. mongolicus seedlings is irreversibly inactivated or the thylakoid membrane is damaged under subzero low temperature stress, which may produce serious photoinhibition. However, Song believes that the peripheral antenna component of the optical system is more affected than the core complex at low temperatures, which was not observed in the corresponding results in this study10.Figure 9Photosynthesis of A. mongolicus under low-temperature stress. The areas outlined by white boxes indicate the differentially expressed genes in these structures.Full size imageThe gene expressions of Cyt b6, PrtD and Cyt f in Cyt b6f. changed. Cyt b6f. changes not only affect the electron transport function of photosynthesis but also affect ATP synthesis. Pheo transfers the received electrons to plastid quinone (PQ). PQ receives electrons and protons to form plastid hydroquinone (PQH2). Then, the electrons of PQH2 are transferred to plastid cyanin (PC) on PSI through Cyt b6f., and hydrogen protons are released into the cavity of the thylakoid to form a transmembrane proton gradient. The transmembrane proton gradient is the driving force for ATP synthesis.The function of PSI is to transfer electrons from PC to ferredoxin for the reduction of NADP+. Recent studies have found that PSI is more sensitive to light and more prone to selective photoinhibition than PS II under low temperature and weak light conditions11,12. The KEGG analysis results indicated that the LHCI complex, PsaF and PsaE subunits of PSI showed differential gene expressions. The main function of the LHCI light-harvesting pigment protein complex is to capture light energy. PsaF is a low-molecular-weight protein that is distributed in the membrane. Some studies have suggested that the N-terminal amino acid sequence of eukaryotic PsaF is involved in the binding of PSI and PC13. PsaE, PsaD and PsaC together form the docking site of ferredoxin on the PSI receptor side14,15. Ferredoxin and ferredoxin-NADP+ reductase in the photosynthetic electron transport chain are also affected, which results in hindrance of NADPH synthesis. The F-type H+/Na+ transport ATPase subunits also show differential gene expressions, which lead to impaired ATP synthesis. Low temperatures affect the ability to absorb light energy, transfer electrons, convert light energy into electric energy, and synthesize NADPH as well as ATP, which ultimately lead to declines in Fv’/Fm’ and ETR and impair the photosynthesis capacity of A. mongolicus.Compared with the light reaction, low temperatures have a greater impact on the dark reaction. Because the dark reaction process is composed of many complex enzymatic reactions, the enzyme activity is very susceptible to temperature. The KEGG results show that 13 related enzymes were differentially expressed in the “carbon sequestration of photosynthesis” (ko00710). The Rubisco enzyme is a key enzyme that determines the direction and efficiency of photosynthetic carbon metabolism in C3 plants and is sensitive to temperature16. The results also show that the expression levels of 10 differentially expressed genes of Rubisco enzymes all declined. In the Calvin cycle, the gene expressions of only transketolase and glyceraldehyde-3-phosphate dehydrogenase are not sensitive to temperature. In addition, the reduction phase of the dark reaction requires the use of NADPH and ATP that are produced by the light reaction. The inhibition of NADPH and ATP synthesis will inevitably affect the normal progression of the Calvin cycle.Chloroplast respiration is an O2-dependent electron transport pathway in chloroplasts. Chloroplast respiration includes the nonphotochemical reduction of PQ by NAD(P) H and the reoxidation of PQ by terminal oxidase, which can consume excess electrons to protect plants from damage due to photooxidation.Figure 10 shows the partial KEGG enrichment metabolic pathway in the LT group. There were three significant enrichment pathways related to carbohydrate metabolism: fructose and mannose metabolism (ko00051), butanoate metabolism (ko00650) and C5-branched dibasic acid metabolism (ko00660). The metabolism of fructose and mannose includes the ascorbic acid biosynthetic pathway. Ascorbic acid (ASA), also known as vitamin C, can be used as a cofactor of violaxanthin de-epoxidase to participate in the lutein cycle and consume excess light energy and protect plants from harm.Figure 10The regulatory mechanism of A. mongolicus under low-temperature stress. The white ovals represent the enriched metabolic pathways. The blue rectangles represent significantly enriched KEGG metabolic pathways. The pathways are followed by the physiological structures and substances or physiological processes in which the expressions of related genes change.Full size imageLow temperatures damage cell membranes first. Increasing the mass fraction of unsaturated fatty acids in the membrane is beneficial to improve the stability and fluidity of the membrane. Some studies have shown that the degree of unsaturation of fatty acids in adult leaves of A. mongolicus that grow naturally in the field is lower in summer and higher in autumn and winter17. The significantly enriched pathways related to unsaturated fatty acid metabolism were alpha-linolenic acid metabolism (ko00592), linoleic acid metabolism (ko00591) and arachidonic acid metabolism (ko00590). Various proteins, such as linoleate 13S-lipoxygenase and cytochrome P450 family 2 subfamily J (CYP2J), which are involved in the metabolism of linoleic acid, showed differences in their gene expressions. Linoleate 13S-lipoxygenase is a common lipoxygenase in plants that can catalyse the production of precursors of several important compounds, including jasmonic acid. CYP2J is a group of P450 haem thiolate proteins, which are mainly distributed on the endoplasmic reticulum and inner mitochondrial membrane and are involved in the synthesis of sterol hormones, including brassinosteroids. Because light systems are distributed on the thylakoid membrane, damage to this membrane will affect the progress of plant photosynthesis.Plant hormone signal transduction (ko04075) plays an important role in plant resistance to stress. Studies have shown that JAs have physiological functions, such as inducing stomatal closure, inhibiting photosynthesis, promoting respiration and promoting leaf senescence18,19. Treating plants with exogenous methyl jasmonate can induce the transcription of the heat shock protein family, increase the synthesis of antioxidants, reduce lipoxygenase activity and enhance the ability of plants to resist cold damage20.Figure 11 shows the regulatory mechanism of A. mongolicus in the HL group. The MapMan analysis results show that the DEGs of the LHCII complex and those for the assembly and maintenance of PSII are significantly changed. LHCII contains chlorophyll and carotenoids, which can capture and transmit light energy. Chlorophyll is an important photosynthetic pigment that captures light energy and drives electrons to the reaction centre. The chlorophyll molecule in the reaction centre is related to photochemical quenching. The entire chlorophyll biosynthesis process (e.g., L-glutamyl-tRNA → chlorophyll a → chlorophyll b) involves 15 enzymes. The analysis found that 4/5 of the enzymes’ expression genes were changed. Carotenoids include carotene and lutein, and their synthesis is affected by high temperatures. Lutein participates in the lutein cycle, which can dissipate excess light energy and prevent membrane lipids from being peroxidized and thus maintain the stability of the thylakoid membrane structure and protect A. mongolicus. from high temperature stress and strong light stress.Figure 11The regulatory mechanism of A. mongolicus. under high-temperature stress. The white ovals represent enriched metabolic pathways. The red rectangles represent significantly enriched KEGG metabolic pathways. The pathways are followed by the physiological structures and substances or physiological processes in which the expressions of related genes change.Full size imageThe D1 protein in the PSII reaction centre is rapidly degraded under strong light conditions. To maintain the normal physiological needs of plants, the degraded D1 protein will be replaced by the new D1 protein that is produced by the repair mechanism. The reversible inactivation of the PSII reaction centre can protect the photosynthetic system and avoid destruction. This may be the reason for the significant changes in the DEGs that are involved in the assembly and maintenance of PSII.Rubisco is the main site for high-temperature inhibition of the Calvin cycle16. The KEGG analysis found that there were 7 (4↑, 3↓) DEGs of Rubisco. SBPase catalyses the conversion of sedum heptulose-1,7-diphosphate (SBP) into sedum heptulose-7-phosphate (S7P) in the renewal phase. Under low-temperature stress, only transketolase and glyceraldehyde-3-phosphate dehydrogenase remained unchanged in the Calvin cycle. In addition, NDH-mediated cyclic electron transfer may decreased the photooxidation damage that is caused by high-temperature stress by shunting the excess electrons that were generated by the inhibition of CO2 assimilation to the chloroplast respiratory pathway21.In the HT group, the net photosynthetic rates of the leaves showed two peaks on the diurnal change curves, and there was an obvious phenomenon of midday photosynthesis depression. The daily average A values were greater than those of the CK group. These results show that A. mongolicus has a complete photosynthetic structure protection mechanism and can adapt to high-temperature environments. The pathway of significant enrichment related to carbohydrate metabolism in the HT group was the same as that in the LT group. The enrichment degrees of the fructose and mannose metabolic pathways were higher only in the HT group, and C5-branched dibasic acid metabolism and butanoate metabolism were higher in the LT group.Under high temperature and strong light conditions, the balance between production and removal of reactive oxygen species (ROS) in plant cells was broken, and large amounts of reactive oxygen species accumulated in the cells. Active oxygen can cause lipid peroxidation of the biomembrane, enlarge membrane pores, increase the permeability, and affect the spatial structures of enzymes on the membrane, which thus leads to chloroplast destruction. In severe cases, ROS will cause serious injury or even death to plants22. The gene expressions of FabH and acetyl-CoA carboxylase (ACCase) changed during the synthesis of unsaturated fatty acids in the HT group.There are two types of active oxygen scavenging mechanisms in plants. (1) The enzymatic detoxification system: superoxide dismutase (SOD), ascorbate peroxidase (APX), and catalase (CAT). (2) Nonenzymatic antioxidants: ASA, carotenoids, glutathione, mannitol, and flavonoids23.Secondary metabolites result from long-term adaptation of plants to their environments. They can improve the ability of plants to protect themselves, compete for survival, and coordinate the relationship between plants and the environment. The significant enrichment pathways related to the biosynthesis of secondary metabolites in the HT group consisted of phenylpropane biosynthesis (ko00940), flavonoid biosynthesis (ko00941) and isoflavone biosynthesis (ko00943). The phenylpropanoid biosynthesis pathway is one of the three main secondary metabolic pathways in plants. It starts from phenylalanine and generates different phenylpropane metabolites through multistep reactions, such as flavonoids, isoflavones, anthocyanins and lignin24,25. Anthocyanins can protect plants from light damage by quenching free oxygen radicals and reducing the absorption of light energy. Hughes studied 10 species of evergreen broad-leaved trees and found that red leaves containing anthocyanins always maintained higher Fv/Fm levels than green leaves. Fv’/Fm’ is related to nonphotochemical quenching. This means that trees with red leaves rely more on the light-damage defence function of anthocyanins than on the light-damage defence mediated by lutein26.Riboflavin metabolism (ko00740) and biotin metabolism (ko00780) are two significantly enriched cofactors and vitamin metabolic pathways. Riboflavin is the precursor of flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD). As a prosthetic group of flavinases, FAD participates in multiple biochemical processes, such as mitochondrial electron transport, photosynthesis, fatty acid oxidation and folate metabolism, in plants27. Riboflavin can induce antioxidant accumulations in plant cells and can also promote plant growth by affecting the ethylene signalling pathway28. Biotin (e.g., VH or VB7), as an essential cofactor for biotin-dependent carboxylase, plays an important role in the life activities of plants. Common biotin-dependent carboxylase enzymes are pyruvate carboxylase (PC) and ACCase. PC is present in the mitochondria and participates in the replenishment mechanism of the tricarboxylic acid cycle. ACCase plays a pivotal role in the feedback regulation of fatty acid synthesis and is the site of action for the feedback regulation of fatty acid synthesis29.The four pathways related to amino acid metabolism showed differences in the HT group. The enrichment degrees of each pathway were as follows: valine, leucine and isoleucine biosynthesis (ko00290)  > biosynthesis of amino acids (ko01230)  > lysine biosynthesis (ko00300)  > glycine, serine and threonine metabolism (ko00260). The branched chain amino acids, valine, leucine and isoleucine and their derivatives, are beneficial to plant growth and plant responses to stress30. As an essential amino acid, lysine metabolism affects many physiological reactions, such as the tricarboxylic acid cycle, abiotic and biotic stress responses, and starch metabolism31. The glycine, serine and threonine metabolic pathways combined with the GO enrichment results showed that the genes related to glycine catabolism and glycine dehydrogenation/decarboxylase activity changed greatly. It is known that when the activity of mitochondrial glycine decarboxylase increases, both photorespiration and photosynthesis will increase32.In terms of hormones, salicylic acid, cytokinin, and abscisic acid (ABA) can improve plant active oxygen scavenging ability. Salicylic acid can decrease the damage to seedlings due to high temperatures by improving the ability of plants to resist oxidative stress and increasing the contents of osmotic adjustment substances in cells33. Salicylic acid also has the function of delaying the degradation of D1 protein and speeding up the recovery of D1 protein when high temperatures are no longer present34. ABA can improve the heat tolerance of plants by regulating the expressions of heat stress-induced genes at the transcriptional level35.In conclusion, A. mongolicus has weak resistance to low temperatures and good adaptation to high temperatures. At the physiological level, under low-temperature stress, the proportion of Y (NO) increased, the function of PSII was damaged, and photosynthesis was inhibited. A. mongolica maintains normal physiological activities by regulating the circadian rhythm, increasing the synthesis of unsaturated fatty acids and changing the effects of plant hormones. Under high-temperature stress, A. mongolicus maintains normal photosynthesis by adjusting gsw as well as water utilization and by increasing the proportion of Y (NPQ). At the same time, A. mongolicus uses LHCII to consume excess energy, continuously assembles and maintains the normal function of PSII, and changes the types of antioxidants, such as by synthesizing anthocyanins, flavonoids, and isoflavones, to protect itself from injury. In addition, the porphyrin and chlorophyll metabolisms, carotenoid metabolism, plant hormones, amino acid metabolism, unsaturated fatty acid synthesis and other metabolic pathways that are related to the differentially expressed genes changed greatly. More

The avian plumage color gamut is much more diverse than previously estimated2. We demonstrate that hummingbird barbule structural colors contribute substantially to the total color diversity of living birds, occurring in areas of the avian color space that were sparsely occupied in Stoddard and Prum2, which most notably included saturated blues, greens, and true purples (blue + red). Such regions of the avian color space were suggested to be unoccupied because these colors are challenging to create, rather than because they might function poorly for communication2. Our results support this hypothesis because hummingbird coloration densely occupies these regions of the avian color gamut (Fig. 2d), using plumage patches that generally play particularly important roles in hummingbird communication, such as throat and crown plumage patches (Supplementary Fig. 5)16,17. The greater color diversity uncovered by our study suggests that barbule structural coloration is the most versatile class of all plumage coloration mechanisms and poses the least constraints on the evolvability of plumage color diversity. Barbule structural colors evolve through changes in the size, shape, spacing, and refractive index of barbule melanosome nanostructures, but little is known about how changes in these parameters themselves evolve18.The UV/V + green region of avian color space remains mostly unoccupied (Fig. 2c, d). It is challenging to create colors with separate reflectance peaks within the wavelength sensitivities of non-adjacent color cones because the peaks must be highly saturated to avoid stimulating neighboring cones2. However, this idea does not explain why there are far more true purple (blue + red) than UV/V + green plumage colors. Notably, birds particularly fail to fill the more UV/V regions (those closer to the UV/V vertex) of UV/V + green color space, which might indicate that it is difficult to create spectra with uv/v wavelength peaks higher than those in the m wavelengths.The differences between our methods and those of Stoddard and Prum2 likely contribute in part to the larger gamut size when comparing species data but not overall data. While the number of species included in our study was comparable to that of Stoddard and Prum2 (114 vs 111 species, respectively), we measured almost twice as many plumage patches as they did (+1600 vs. 965 patches). To prevent erroneous distortion to iridescent colors we did not average the three measurements per patch. Both studies measured six standard patches for all species and additional patches if necessary to capture other plumage color variation. The larger number of plumage patches we measured reflects how color diverse hummingbird plumages are. Our methods preserved the natural variation in hue due to iridescence and avoided the distorted flattening caused by averaging highly saturated peaks with slightly different peak hues. Although our methods are biased toward increasing variation, they are necessary to accurately capture the phenomenon of iridescent hummingbird coloration.There are multiple reasons why the hummingbird color gamut is so diverse. The size of the hummingbird color gamut, like the achieved color gamut of any clade, constitutes a combination of the history of selection on color function, the clade’s evolved capacities for color production, the age of the clade, and the number of species. Hummingbirds excel at all these criteria. The 336 species of extant hummingbirds have radiated rapidly over the last 22 million years19. Hummingbird plumage color diversity has evolved through a long history of persistent sexual and social selection on plumage coloration. Hummingbirds have polygynous breeding systems characterized by female only parental care, female mate choice, and often elaborate male courtship displays. Intersexual selection in hummingbirds has contributed to elaborate radiation in brilliant plumage coloration as well as vocalizations and non-vocal feather sounds14,16,20. Hummingbird plumage color evolution rates have even been shown to positively correlate with hummingbird speciation rates14. Furthermore, in some species, brilliant monomorphic plumage ornaments apparently function in aggressive, intra- and interspecific defense of floral resources21 and appear to be associated with socioecological features related to resource competition19. Our finding that crown and throat patches, which flash brilliantly when the head of the bird is oriented toward the observer, are more diverse in coloration than other plumage regions highlights the role of plumage coloration in direct inter-individual communication and social interactions.The mechanistic properties of hummingbird barbule structural color further explain the exceptional diversity of hummingbird plumage coloration. Hummingbird barbule structural coloration is among the most complex plumage coloration mechanisms, comprised of stacks of hollow, air-filled melanosomes, surrounded by a thin superficial, solid keratin cortex as well as sometimes superficial, miniature melanin platelets which lie just beneath this cortex9,10,11,12,13. Complex nanostructures allow for independent tuning of multiple components, and, hence, greater achievable color diversity12,18,22. Barbule structural color permits the production of any peak-reflected wavelength by varying the thickness of melanosome arrays, which can produce a diversity of single-peak spectra-hues, such as the unusual diversity of greens, blues, and blue + greens seen in hummingbirds (Fig. 2b). Hummingbird melanosomes are among the most unusual in birds in being both disc-shaped and air-filled9,10,11,12,13,23. The air in the center of hummingbird melanosomes approaches the maximum possible biological difference in refractive index (air = 1.0, melanin = ~1.7), which results in the efficient production of brilliant colors with the fewest layers of melanosomes, such that resulting spectra are narrow and near saturation13,24. Such spectra can thereby create colors that extend further in color space (Fig. 2a–c).Barbule structural color also allows for the production of plumage spectra with multiple saturated peaks, creating saturated color combinations that are not as commonly produced via other plumage coloration mechanisms. However, researchers have yet to identify exactly how hummingbird multipeak spectra are produced12,13, emphasizing the need for further analyses of the optics of hummingbird feathers. Many hummingbird melanosome arrays are non-ideal– i.e., the products of the thicknesses and refractive indices of the melanin and air cavity layers are not equal25. Non-ideal thin films can create more highly saturated, pure tone colors of the primary peak while also introducing additional, harmonic spectral peaks at shorter wavelengths25, which allows for complex reflectance spectra with multiple bright peaks within the avian visible spectrum. Also, melanosome arrays with a large average layer thickness ( >~300 nm) can create colors with fundamental interference peaks in the infrared and multiple, harmonic peaks in the avian visible range (300–700 nm). The presence of minute, superficial melanin platelets below the cortex in hummingbird barbules is also correlated with secondary, lower wavelength reflectance peaks, but the precise optical mechanism remains to be established12. These different nanostructural elements all contribute to distinctive multipeak reflectance spectra that can stimulate non-adjacent color cone combinations, which Stoddard and Prum2 identified as particularly difficult to accomplish: UV/V-purple (uv/v + s + l wavelengths; Schistes geoffroyi cheek, Fig. 4g); true purple (s + l wavelengths; Atthis ellioti gorget, Fig. 4h); UV/V-green (uv/v + m; Schistes geoffroyi crown, Fig. 4a); and UV/V-red (uv/v + l; Heliangelus viola, Fig. 4b). With multipeak spectra the potential for creating new and different colors is greatly expanded, allowing for a more versatile evolution of novel colors.Unexpectedly, the hummingbird plumage color gamut is larger in volume when modeled with the VS-type (34.2%) than with the UVS-type (29.6%) visual system. This apparently unique result contrasts notably with both Stoddard and Prum’s2 and our revised estimate of the color gamut of all birds combined– VS gamut = 40.5%; UVS gamut = 47.3%. Multiple previous analyses have shown that the UVS cone-type visual system does a more efficient job of discriminating the colors of natural objects because of the broader separation between the peak spectral sensitivities of the uv and s (blue) cone types2,26,27. Because the UVS-type visual system produces an even greater increase in color volume for a diverse plant color data set over the VS-type visual system, Stoddard and Prum2 rejected the hypothesis that the UVS-type visual system had specifically evolved to expand the diversity of avian color stimuli.However, our observations that the hummingbird plumage gamut is substantially greater in volume with the VS-visual system than with the more efficient UVS-visual system strongly suggests another hypothesis: Hummingbird plumage may have specifically evolved to be more diverse within the hummingbird VS-type color visual system via selection for highly saturated plumage colors. Given diversity in hue, the way to achieve greater color gamut volume, i.e., greater plumage color diversity, is through highly chromatic color vectors that extend toward the limits of the color space. The two visual systems map variation in wavelength to different maximum potential chroma—i.e., wavelengths with color vectors that extend toward the edges, faces, and vertices of the tetrahedron6. Color vectors that extend towards the vertices, i.e., plumage that best corresponds to a singular cone type’s peak sensitivity, have the highest maximum potential chroma because vertices are the regions furthest away from the tetrahedron’s center. Thus, hummingbird plumages may have specifically evolved to have maximum chroma within their own VS-visual system via peaks that correspond most closely to the peak sensitivities of the VS- rather than the UVS-visual system. For example, when comparing the UVS and VS plumage color gamuts for hummingbirds, it is notable that hummingbird coloration extends much further into the UV/V regions of color space for the VS-visual system (Supplementary Fig. 2). While in the VS system these color points map toward the v vertex, in the UVS-visual system they map towards the uv-s edge and the uv-s-l face. Such color vectors that contribute to expanded color volume of the VS gamut could have evolved by sexual or social selection for highly saturated plumage colors that are near in hue to the specific sensitivity peaks of hummingbird receptor cone types. Such selection could note preferences within some hummingbird species for hues with maximally possible chroma, not merely for maximal chroma of a given hue.Hummingbirds have tetrachromatic color vision with substantial sensitivity in the near ultraviolet28,29. Recently, Stoddard et al.30 used a series of elegant experiments with hummingbird feeders and LED lights to demonstrate for the first time that hummingbirds can distinguish non-spectral colors distributed throughout the tetrachromatic color space. However, the presence of this remarkably proficient four-color vision in hummingbirds poses an interesting evolutionary conundrum. Recent phylogenetic analyses have established that hummingbirds and swifts are phylogenetically embedded within the nocturnal caprimulgiforms31,32. The most parsimonious hypothesis is that the immediate ancestors of swifts and hummingbirds were extensively nocturnal for approximately 8 million years before they re-evolved diurnal ecology and behavior31. Given that an evolutionary history of nocturnality can lead to the degradation or loss of opsin genes33,34, it should be a high priority to establish what effect that ancestral nocturnality may have had on the molecular physiology and anatomy of the hummingbird color visual system.Our attempt to document the color diversity of an avian family has revealed that current estimates of the total avian color gamut are likely inaccurately low. Similar studies sampling from other color-diverse families, such as sunbirds (Nectariniidae), parrots (Psittacidae), tanagers (Thraupidae), birds of paradise (Paradiseidae), manakins (Pipridae), and starlings (Sturnidae), most of which have already been studied for their plumage coloration35,36,37,38,39, would help us obtain a better estimate of the true avian color gamut. More

In their original description of V. rhodanica, Fischer & Riou16 determined that the previously undescribed genus was a Jurassic relative of V. infernalis. This assignment was based on the configuration of the arm crown and armature, fin type, presence of luminous organs, lateral eyes, and the absence of an ink sac. Assuming this assignment is correct, then V. rhodanica is a member of the suborder Vampyromorphina, which includes the family Vampyroteuthidae22,29.Reappraisal of the anatomy shows that V. rhodanica and V. infernalis both have 8 arms and uniserial suckers flanked by cirri. They both possess V. infernalis-like sucker attachments34,36, which are broader at the base and taper up to a radially symmetrical sucker.Both species have distinctly modified arms though the morphology differs in each. V. infernalis, has retractable filaments in the position of arm pair II27,33,34, though there is no evidence of these appendages in V. rhodanica. Instead, the species has elongate dorsal arms (arm pair I) with a unique configuration of suckers and cirri on the distal section.The suckers and cirri of V. rhodanica are more numerous than those of V. infernalis27,37. They are also more closely positioned. Proportionally, the suckers of both species have a consistent ratio to mantle length37, though the diameter of the cirri and infundibulum are greater in V. rhodanica. The V. infernalis-like attachment1,3,34 is present in both species, though in V. rhodanica, the distal part of the neck protrudes into the acetabular cavity. Of note, the sucker stalks on the dorsal arms of V. rhodanica are more elongate than those on the other arms (Figs. 2b,c, and 3a,b). This variation in suckers and their attachments suggests a specialized function between the dorsal and sessile appendages. On the longer dorsal arms, the larger sucker diameter, and more elongate stalks (Figs. 2b and 4) indicate the potential for increased mobility over their extant relatives, and possibly facilitated additional manipulation and prey capture capability.Figure 4Hypothesised reconstruction of V. rhodanica based on the data from this study (A. Lethiers, CR2P). The scale is based on measurements from the holotype (MNHN.B.74247) and the arm crown is completed using dimensions from MNHN.B.74244.Full size imageIn addition to the arm crown specialization, V. rhodanica has a more streamlined shape than V. infernalis, which is caused by a proportionally narrower head. Their muscular body is narrower and more elongate than the gelatinous V. infernalis16,27,37 suggesting a higher energy locomotory style. This is consistent with increased predation relative to the modern form. Observations in this study support many assertions of Fischer & Riou16 about the characters in V. rhodanica, though the presence of luminous organs cannot be confirmed. Rather than luminous organs much larger than those present in the deep-sea, extant V. infernalis, it is possible that these structures represent displaced cartilage prior to fossilization (Supplementary Fig. 6).Two other genera from the La Voulte-sur-Rhône locality, Gramadella and Proteroctopus are, like V. rhodanica, considered to be Incertae sedis Vampyromorpha22. All three share morphological similarities that include an elongated mantle fused with the head, and a longer dorsal arm pair with armature on the distal ends1,16,22,38. Neither the second nor fourth arm pair have been modified. Each has one pair of fins. In Gramadella, the fins are lateral and skirt-like16,38. In V. rhodanica and Proteroctopus these fins are located posteriorly1,16.V. rhodanica shows the greatest length variation between the dorsal and sessile arms (Fig. 4), though proportionally, Gramadella, and Proteroctopus have longer dorsal arms1,31. Fischer & Riou31 and Kruta et al.1 described biserial suckers in their descriptions of Gramadella, and Proteroctopus, respectively. In Proteroctopus, these suckers have a proportionally smaller diameter than the uniserial row in V. rhodanica, and do not exhibit the same tapered pattern.None of these specimens shows evidence of an ink sac, though it is present in contemporaneous genera from the same assemblage (Mastigophora, Rhomboteuthis and Romaniteuthis)8,16. That this character occurs only in some taxa from the same assemblage suggests variation in ecology, possibly associated with the steep, bathymetric relief in the La Voulte-sur-Rhône paleoenvironment11. The mosaic of characters found within the coleoid taxa at La Voulte-sur-Rhône suggests that Mesozoic vampyromorphs co-occurred in different ecological niches during the mid-Jurassic.Today, extant V. infernalis is uniquely adapted to a low-energy, deep-sea mode of life27,28,29,39, though the timing of character acquisition and progression of this ecology is unclear24. It is hypothesised that the vampyromorph Necroteuthis Kretzoi 1942 was already exploiting this niche by the Oligocene29, and that the initial shift to offshore environments was possibly driven by onshore competition24,29. The data obtained here suggests that V. rhodanica, the purportedly oldest-known genus of the Vampyromorphina group, was an active predator following a pelagic mode of life.Indeed, several anatomical details, mainly found in the brachial crown, seem to support this hypothesis. Though we cannot directly compare functionality of the arm crown elements with other Jurassic taxa, we can infer function based on observation in modern forms. In Octopoda, the sister group to Vampyromorpha, suckers are attached to the arm by a cylindrical layer of muscle, encircling oblique musculature40,41, that connects the arm musculature and the lateral margin of the acetabulum34,40,41,42. This facilitates a variety of functions including locomotion, manipulation, and prey retention43. The sucker attaches by flattening the infundibulum against the surface and then the encircling epithelium creates a watertight seal36,40,41,42,43,44,45. Contraction of the radial acetabular muscles provides the pressure differential required to create the suction force43,44,46.The stalked sucker attachments2,34 of decabrachians (Fig. 3d, and Supplementary Fig. 4) are muscular35 and connect the musculature of the arm with the base of the sucker, forming part of the acetabulum33,34. Tension on the sucker stretches this muscular attachment, which pulls locally on the acetabular base. This facilitates a greater pressure differential inside the sucker, allowing the teeth on the sucker ring to maintain the hold47.Extant V. infernalis lack decabrachian-like stalks2,18 and the neck of the attachment joins to the base of the acetabulum (Fig. 3c, and Supplementary Fig. 4), rather than being inserted into it18. The infundibulum is not distinct, and the suckers do not provide strong suction27. Instead, suckers function by secreting mucus to coat detritus—marine snow captured by retractable filaments—which is then moved to the mouth by cirri7,27.A mosaic of these characters is present in V. rhodanica (Fig. 3a,b), therefore, suggesting their potential for increased attachment and hold on prey over extant V. infernalis. These include a larger infundibular diameter, a neck attachment integrated with the acetabular muscles, and the elongated stalks of the dorsal suckers.Additionally, the paired, filamentous cirri observed in extant cirrates48 are present in V. rhodanica (Fig. 4, and Supplementary Fig. 2). In extant forms they are understood to have a sensory function and are used in the detection and capture of prey48. In V. infernalis, they serve to transport the food proximally along the arms to the mouth27. The greater diameters of cirri, and placement along the entire arm in V. rhodanica (Fig. 4), suggests an increased sensory function in these fossil forms.The shape of the arms also contributes to the suction potential49 in coleoids. Functional analysis in Octopoda highlights a positive correlation between distal tapering of the arms and their flexibility. A tapered, flexible arm facilitates more precise adhesion than a cylindrical-shaped one and requires a greater force for sucker detachment49. Suckers detach sequentially, rather than the more simultaneous release observed in models of arms with less taper variation. The tapered diameter of the suckers, like those seen on the sessile arms of V. rhodanica, potentially facilitated this kind of sequential detachment49 allowing them more adherence force and flexibility. Though V. rhodanica has just two suckers on the distal tips of their dorsal arms, the most distal is marginally smaller in diameter than the proximal one. On the dorsal arms, this tapering is observed in conjunction with a well-developed axial nerve cord (Fig. 2b). In extant forms, the nerve cord facilitates complex motor functions42. The combination of these characters in V. rhodanica suggests their arms had increased potential to be actively used in prey capture50 over extant V. infernalis.Though arm crown characters offer insight on the ecology of V. rhodanica, in fossil coleoid phylogenies only a few characters are based on the suckers1, 3. Two studies that have attempted to create a phylogeny using morphological characters that include both fossil and extant taxa return V. rhodanica and V. infernalis as sister taxa1,3. These matrices are, by necessity, heavily influenced by the gladius51 and more than 50% of the characters are based on this feature1,3. Indeed, the authors1 note that the lack of gladius data for some fossil forms, including V. rhodanica, creates an inherent bias in the phylogenetic matrix. Fischer & Riou16 suggested that V. rhodanica and V. infernalis are related on the basis of the observable morphological characters in the family Vampyroteuthidae, though without morphological information on the gladius, a recent systematic synthesis of fossil Octobrachia22 positioned V. rhodanica as Vampyromorpha Incertae sedis.X-ray CT analysis in this study did not allow a reconstruction of the gladius. Nevertheless, it does provide new data on soft tissues, and permits comparisons between extant and fossil taxa. Specifically, we can add distinct states to 4 of the 132 characters in the existing phylogenetic matrix from Sutton et al.3 that was modified and used in Kruta et al.1. These four characters (#89–#92) represent the suckers, and sucker attachments. Detailed examination revealed that the sessile and dorsal arms have the Vampyroteuthis-like attachment. In the dorsal arms, this is more elongated, though it cannot be considered pedunculate like those seen in modern decabrachians. Indeed, the attachment type (plug and base34) is the same, only the length varies. As previously discussed, this variation may have functional implications.When updated with these new data, the matrix from this study returns the same topology seen in Kruta et al.1 that supports the positioning of V. rhodanica and V. infernalis as sister taxa. Further, it strengthens their relationship as they both share a sucker attachment that is not clearly attached to the arm muscles, a state that was previously considered autapomorphic in V. infernalis. However, it is important to note that no additional characters were added for the gladius, which is the cornerstone of coleoid systematics52. Indeed, just 29 of the 132 matrix characters can so far be coded for V. rhodanica, with only 9 of these relating to the 74 states of the gladius.Assuming the phylogenetic work so far is correct, then both species belong to the family Vampyromorphina, and are joined by the Oligocene fossil Necroteuthis hungarica29. While the lack of gladius characters precludes a full phylogenetic understanding of this group, preservation and observation of the soft tissues allow us to infer information regarding palaeobiology.The data obtained in this study demonstrates that the characters observed in V. infernalis, including the sucker attachments and lack of ink sac, were present in Jurassic Vampyromorpha. Comparative anatomy of V. rhodanica and extant V. infernalis revealed that the fossil taxon displayed more morphological variation and were more diversified than previously understood. The assemblage of characters observed in V. rhodanica are consistent with a pelagic predatory lifestyle and corroborate the likelihood of a distinctly different ecological niche. These findings support the hypothesis that a shift towards a deep-sea environment occurred prior to the Oligocene5,29. More

Life cycle cost modelAn analysis of life cycle costs is an economic analysis of the assessment of the total cost of acquisition, ownership and liquidation of a product. It is applicable during the entire life cycle of the product or a life cycle stage or combination of different stages21 and22.There are five period phases of the vehicle life cycle:Generally, the total costs for the above listed phases are acquisition costs, ownership costs and liquidation costs21 and22. For the LCC model, I recommend to divide the life cycle costs into four categories:$$LCC={C}_{P}+{C}_{M}+{C}_{O}+{C}_{D},$$
(1)
$${LCC}_{s}=frac{LCC}{t},$$
(2)

where LCC—the life cycle cost of vehicles, LCCs—the specific life cycle cost of vehicles, CP—the vehicle purchase cost, CM—the maintenance cost, CO—operating state of vehicle cost, CD—the vehicle disposal cost, t—the time of vehicle operation.The model for evaluating the economic viability of products is based on the general LCC model which is based on acquisition and ownership costs$$LCC={C}_{P}+{C}_{OW},$$
(3)

where CP—purchase cost, COW—ownership costs.Acquisition cost (CP) is represented by the purchase price at the time of acquisition of the assessed passenger vehicle.Ownership cost (COW) is significant during the life cycle of a motor vehicle and varies according to the type of the vehicle. This cost includes the costs of maintenance and operation time can be defined as follows10$${C}_{Ow}={C}_{M}+{C}_{O},$$
(4)

where CM—cost of maintenance, CO—operation cost.The cost of ownership a vehicle (COW) can be defined as follows$${C}_{OW}={C}_{O}+{C}_{MC}+{C}_{MP},$$
(5)

where CO—operation cost, CMC—corrective maintenance cost, CMP—preventive maintenance cost.The cost of ownership (COW) may include the operating and maintenance costs which consist of the corrective maintenance cost (CMC) and the cost of preventive maintenance (CMP) of a motor vehicle.Calculation of operating costsOperating cost CO is determined by the price and amount consumed of conventional or alternative types of fuel. It cover the cost of fuel CF, operating fluids, oils and lubricants COL that are supplied during vehicle operation (not during service inspection), tyres CT, accumulator batteries CAB, vehicle insurance fee and road tax or other mandatory fees CIRT, cost of the motorway tax sticker CMT, mandatory vehicle inspection and emission measurement in special vehicles CETC. The costs are calculated according to$${C}_{O}={C}_{F}+{C}_{OL}+{C}_{T}+{C}_{AB}+{C}_{IRT}+{C}_{MT}+{C}_{ETC}.$$
(6)
Fuel costs (CF) are affected by the average consumption of a given type of propulsion vehicle. Then the comparative fuel costs (CF) can be expressed by the equation$${C}_{F}=frac{{bar{c}}_{aF}}{100}{p}_{F}{t}_{l},$$
(7)

where CF—total fuel costs (EUR), (bar{c})aF—average fuel consumption (l/100 km), pF—fuel price (EUR/l), tl—service life of a passenger vehicle (km).Costs for operating fluids, oils and lubricants (COL) are any costs for operating fluids, oils and lubricants that are replenished during operation and not during service maintenance; it can be expressed by the equation$${C}_{OL}=frac{{bar{c}}_{aOL}}{100}{p}_{OL}{t}_{l},$$
(8)

where (bar{c})aOL—average consumption of oil and lubricant (l/100 km), pOL—price of oil and lubricant (EUR/l).The cost of tyres (CT) can be expressed by the equation$${C}_{T}=frac{{t}_{l}}{{bar{d}}_{aT}}{n}_{T}{p}_{T},$$
(9)

where (bar{d})aT—average life of a passenger vehicle tyre (km), nt—number of tyres on the passenger vehicle (pc), pT—price of one piece of tyre (EUR).Accumulator battery costs (CAB) —can be expressed by the equation$${C}_{AB}=frac{{t}_{l}}{{bar{d}}_{aAB}}{n}_{AB}{p}_{AB},$$
(10)

where (bar{d}_{aB})—average life of one accumulator battery (km), nAB—number of accumulator batteries in the passenger vehicle (pc), pAB—price of an accumulator battery (EUR).Costs arising from laws (CIRT) are the costs of motor vehicle insurance (compulsory liability, accident insurance, or other). Some of them can be omitted in case of the same costs due to the simplification of the model. Otherwise, they can be expressed by the equation$${C}_{IRT}=left({C}_{SI}+{C}_{AI}+{C}_{RT}+{C}_{R}right){t}_{la},$$
(11)
where CS1—price of mandatory annual insurance of a passenger vehicle (EUR), CA1—price of the annual accident insurance of a passenger vehicle (EUR), CRT—price of annual road tax (EUR), CR—price of statutory fee (EUR), tla—operating time of the passenger vehicle until decommissioning (years).The cost of obtaining a motorway sticker (CMT) may be omitted if the same type of passenger vehicle is compared. Otherwise, the cost of a motorway sticker (CMT) can be expressed by the equation$${C}_{MT}={c}_{MT}{t}_{la},$$
(12)

where cMT—price of annual motorway sticker for the passenger vehicle (EUR).The costs of the mandatory vehicle inspection and emission measurement (CETC) include the costs incurred for the measurement of emissions of the drive engine unit (CE) and for the technical inspection of the passenger vehicle (CTC). For the proposed model, the costs of the mandatory technical inspections and emission measurements can be expressed by the equation$${C}_{ETC}=left({C}_{E}+{C}_{TC}right)frac{{y}_{n}}{{t}_{la}},$$
(13)

where CE—costs related to the measurement of passenger vehicle emissions (EUR), CTC—costs of mandatory technical inspection (EUR), yn—number of years of legal validity of emission measurement and technical condition for the given type of the passenger vehicle (years).Calculation of maintenance costThe total costs for vehicle maintenance CM consist of the cost of preventive maintenance CMP and the cost of corrective maintenance CMC10,11$${C}_{M}={C}_{MC}+{C}_{MP}.$$
(14)
Vehicle maintenance costs include the cost of material and the cost of labour$${C}_{M}={(C}_{MCM}+{C}_{MCL}+{C}_{MCF})+left({C}_{MPM}+{C}_{MPL}+{C}_{MPF}right),$$
(15)

where CM—cumulative maintenance costs, CMC—corrective maintenance costs, CMP—preventive maintenance costs, CMCM—costs of material used for corrective maintenance, CMCL—costs of labour force for corrective maintenance, CMCF—costs of workshop equipment used for corrective maintenance, CMPM—costs of material used for preventive maintenance, CMPL—costs of labour force for preventive maintenance, CMPF—costs of workshop equipment used for preventive maintenance.

Preventive maintenance costs (CMP) are costs that include all costs associated with preventive maintenance performed to reduce degradation and mitigate the likelihood of failure. At present, preventive maintenance is performed at predetermined time intervals (according to the manufacturer’s preventive maintenance program) or when a specified number of kilometres are not covered before the next service maintenance, depending on the time. In practice, for passenger cars, it is usually 1 or 2 years, depending on the use of engine oil. This mainly includes the cost of:

material consumed during preventive maintenance,

work spent on preventive maintenance,

workshop equipment, training of preventive maintenance specialists.$${C}_{MP}=frac{{t}_{l}}{MTB{M}_{p}}left({C}_{MPM}+{(bar{c}}_{p}{bar{t}}_{pm})right),$$
(17)

where MTBMp—mean operating time between preventive maintenances (km), CMPM—costs of material used for preventive maintenance (EUR), (bar{c})p—average hourly cost of labour and workshop equipment used for maintenance (EUR/hour), ̅tpm—mean time of labour-intensity per one preventive maintenance (hour).

Design of a model for the analysis of selected life cycle costs of a passenger motor vehicleThe model for performing an analysis of life cycle costs for the purchase of a new motor vehicle is based on the basic Eq. (3), (18). We will not count the costs of improvement (CE) and the costs of the decommissioning phase (CD) for the mentioned model due to the calculations of costs that are unnecessary for the analysis. Then the model can be expressed as follows$$LCC={C}_{P}+{C}_{O}+{C}_{M}.$$
(18)
Then, the following Eqs. (6), (7), (8), (9), (10), (11), (12), (13), (16) and (17) are substituted into the given equation, and the selected costs can be calculated for individual vehicles. The resulting model for calculating the LCC costs has the following form$$LCC={C}_{p}+frac{{bar{c}}_{aF}}{100}{p}_{F}{t}_{l}+frac{{bar{c}}_{aOL}}{100}{p}_{OL}{t}_{l}+frac{{t}_{l}}{{bar{d}}_{aT}}{n}_{T}{p}_{T}+frac{{t}_{l}}{{bar{d}}_{aAB}}{n}_{AB}{p}_{AB}+{C}_{SI}{t}_{la}+{c}_{MT}{t}_{la}+left({C}_{E}+{C}_{TC}right)frac{{y}_{n}}{{t}_{la}}+frac{{t}_{l}}{MTBF}left({bar{c}}_{m}+{(bar{c}}_{p}{bar{t}}_{pc})right)+frac{{t}_{l}}{MTB{M}_{p}}left({C}_{OMPM}+{bar{(c}}_{p}{bar{t}}_{pm})right).$$
(19)
It is presented in a Fig. 6.Figure 6Structure of model input parameters for LCC model calculation.Full size imageIn this way, the cumulative costs for each passenger motor vehicle are calculated. Since the passenger motor vehicles may have a different service life tl which is expressed in kilometres, it is recommended to convert this equation to specific costs which are related to one kilometre of use. The selected LCCS life cycle specific costs can be expressed by the following equation$${LCC}_{S}=frac{LCC}{{t}_{l}}.$$
(20)
LCC model input values and items affecting ownership costs for alternative drivesThe process of the calculation of selected life cycle costs for the propulsion of passenger vehicles and the structure of individual cost items is shown in Fig. 6. These are the input parameters to the LCC model.The total life cycle costs are divided into two main cost groups, which are the ownership and acquisition costs for a given drive type. Fuel costs are determined by the price and the quantity of conventional or alternative fuel consumed. For the calculation of the selected LCCs, the authors of the paper assume that the availability of conventional and alternative fuels is not limited in any way. It is assumed that the availability of fuels is ideal, which is not entirely true in practice. This is dependent on the support for each alternative fuel in each state.In practice, therefore, multiple costs may arise due to the distance to the refuelling station to provide alternative fuels such as E85, CNG, LPG and hydrogen. In addition, there is a distance to the charging station for electric drives.Another item that affects the cost of operation for hybrid passenger vehicles is the percentage of alternative fuel driving, which can have a significant impact on life cycle costs. Values for this item are given as a percentage, which is then converted into the number of kilometres driven on alternative and conventional fuel.One of the important parameters for calculating the life cycle operating costs for the hybrid-electric and electric drive is the setting of a threshold value for the capacity of the electric vehicle battery (EV battery) when the replacement is performed. For the model calculation, a limit value of 70% of the electric vehicle battery capacity at 20 °C was set.Return on investmentReturn on investment (ROI) is a performance measure used to evaluate the efficiency or profitability of an investment or compare the efficiency of a number of different investments. ROI tries to directly measure the amount of return on a particular investment, relative to the investment’s cost. To calculate ROI, the benefit (or return) of an investment is divided by the cost of the investment. The result is expressed as a percentage or a ratio12,23.For our calculation of the return on investment ROI on alternative and conventional passenger car propulsion the following formula is used, which is expressed as a percentage$$ROI=frac{{LCC}_{A}-{LCC}_{C}}{{LCC}_{C}}100,$$
(21)

where LCCA—selected live cycle costs of the alternative passenger car propulsion (EUR), LCCC—selected live cycle costs of the conventional passenger car propulsion (EUR).The return on investment of an alternative vehicle ROIAV purchase expresses after how many kilometres the increased cost of purchasing an alternative fuel vehicle compared to a conventional one is recovered. If the value is negative, the payback will not occur for various reasons. The following equation is used to calculate ROIAV$${ROI}_{AV}=frac{{C}_{{P}_{AV}}-{C}_{{P}_{CV}}}{frac{{C}_{O{W}_{CV}}-{C}_{O{W}_{AV}}}{{t}_{l}}}$$
(22)

where ({C}_{{P}_{AV}})—purchase cost on alternative vehicle (EUR), ({C}_{{P}_{CV}})—purchase cost on conventional vehicle (EUR), ({C}_{O{W}_{CV}})—ownership cost on conventional vehicle (EUR), ({C}_{O{W}_{AV}})—ownership cost on alternative vehicle (EUR), tl—service life of the passenger vehicle (km).Ownership costs on conventional vehicle are expressed by the following equation$${C}_{{OW}_{CV}}={left(frac{{bar{c}}_{aF}}{100}{p}_{F}{t}_{l}+frac{{bar{c}}_{aOL}}{100}{p}_{OL}{t}_{l}+frac{{t}_{l}}{{bar{d}}_{aT}}{n}_{T}{p}_{T}+frac{{t}_{l}}{{bar{d}}_{aAB}}{n}_{AB}{p}_{AB}+{C}_{SI}{t}_{la}+{c}_{MT}{t}_{la}+left({C}_{E}+{C}_{TC}right)frac{{y}_{n}}{{t}_{la}}+frac{{t}_{l}}{MTBF}left({bar{c}}_{m}+{(bar{c}}_{p}{bar{t}}_{pc})right)+frac{{t}_{l}}{MTB{M}_{p}}left({C}_{OMPM}+({bar{c}}_{p}{bar{t}}_{pm})right)right)}_{CV}.$$
(23)
Ownership costs on alternative vehicle are expressed by the following equation$${C}_{{OW}_{AV}}={left(frac{{bar{c}}_{aF}}{100}{p}_{F}{t}_{l}+frac{{bar{c}}_{aOL}}{100}{p}_{OL}{t}_{l}+frac{{t}_{l}}{{bar{d}}_{aT}}{n}_{T}{p}_{T}+frac{{t}_{l}}{{bar{d}}_{aAB}}{n}_{AB}{p}_{AB}+{C}_{SI}{t}_{la}+{c}_{MT}{t}_{la}+left({C}_{E}+{C}_{TC}right)frac{{y}_{n}}{{t}_{la}}+frac{{t}_{l}}{MTBF}left({bar{c}}_{m}+{(bar{c}}_{p}{bar{t}}_{pc})right)+frac{{t}_{l}}{MTB{M}_{p}}left({C}_{OMPM}+({bar{c}}_{p}{bar{t}}_{pm})right)right)}_{AV}.$$
(24)
The rate of return on investment for the purchase of an alternative vehicle depending on the kilometres travelled to is expressed by the following equation$${ROI}_{AV({t}_{o})}={(C}_{{P}_{AV}}-{C}_{{P}_{CV}})-({C}_{O{W}_{CV}left({t}_{o}right)}-{C}_{O{W}_{AV}left({t}_{o}right)}) quad text{when} ;to = (0-tl)$$
(25)

where to—operation of the passenger vehicle (km). More

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Study areaThe NCA encompasses an area of 8292 km2 and in 2020 had approximately 87,000 inhabitants23, who are primarily dependent on livestock for their livelihoods. It is a multiple-use area where people coexist with wildlife and livestock, and practise pastoralism with transhumance, characterised by seasonal movements of livestock for accessing resources such as grazing areas and water. The NCA comprises eleven administrative wards: Alailelai, Endulen, Eyasi, Laitole, Kakesio, Misigiyo, Ngorongoro, Naiyobi, Nainokanoka, Ngoile and Olbalbal (Fig. 1). The NCA was chosen for our study as it is known to be hyperendemic for anthrax4,17,20. In addition, informal consultations we held prior to the study, as well as tailored data collection at the community and household level, indicated that local communities have a good understanding of the disease in humans and animals, and of practices around carcass and livestock management that increase risks, particularly in certain locations and periods of the year24.Figure 1Locations of participatory mapping. Map showing the 11 administrative wards of the Ngorongoro Conservation Area in northern Tanzania and the locations where participatory mapping sessions took place (red dots). The maps were produced in QGIS 2.18.2 using data from the National Bureau of Statistics, Tanzania (http://www.nbs.go.tz/).Full size imageEthics approval and consent to participateThe study received approval from the National Institute for Medical Research, Tanzania, with reference number NIMRJHQ/R.8a/Vol. IX/2660; the Tanzania Commission for Science and Technology (numbers 2016-94-NA-2016-88 (O. R. Aminu), 2016-95-NA-2016-45 (T. L. Forde) and 2018-377-NA-2016-45 (T. Lembo)); Kilimanjaro Christian Medical University College Ethics Review Committee (certificate No. 2050); and the University of Glasgow College of Medical Veterinary & Life Sciences Ethics Committee (application number 200150152). Approval and permission to access communities and participants were also obtained from relevant local authorities. Written informed consent was obtained from all participants involved in the study. All data collected were analysed anonymously, ensuring the confidentiality of participants. All research activities were performed in accordance with relevant guidelines and regulations.Participatory mappingA participatory mapping approach based on methodology previously tested in East Africa25 was employed to define areas of anthrax risk for animals in the NCA based on community knowledge. Georeferenced maps of the NCA were produced using data from Google and DigitalGlobe (2016). The maps used datum Arc 1960/UTM zone 36S and grid intervals of 1000 km and were produced at 1:10,000 and 1:50,000 scales, in order to provide participants with a choice. Ten participatory mapping focus groups were held at ward administrative level (Fig. 1) in order to identify areas in the NCA that communities perceive as posing a high risk of anthrax. One mapping exercise was held in each ward. Ngoile and Olbalbal wards were covered at the same time and treated as one, as they had only recently (in 2015) been split from one ward (Olbalbal). Each session had between ten and thirteen participants, who consisted of village and ward administrators, animal health professionals (including community animal health workers and livestock field officers), community leaders, and selected community members. These participants represented members of the community concerned with animal health and owning livestock and, as such, were likely to hold in-depth knowledge relating to community experience of animal health and disease, including anthrax. Participants were recruited by consulting with animal health professionals as well as village and ward administrators, who gave permission to conduct the mapping sessions.The mapping sessions were conducted in Swahili and translated into English by an interpreter. Participants’ general knowledge of the area was first verified by testing whether they could correctly identify popular locations such as health centres, places of worship, markets and schools. Subsequently, participants discussed among themselves and came to a consensus about areas they considered to be at high risk of anthrax. Specifically, we asked them to identify locations they perceived as areas where they considered their animals to be at risk of being exposed to anthrax. These areas were drawn on the maps provided (Fig. 2). While they did not locate areas where the animals had succumbed to disease, we also asked for generic information on locations where anthrax outbreaks had occurred in the past to define areas that could be targeted for active surveillance of cases. In order to improve the fidelity of the data, participants defined risk areas in relation to their own locality (ward) and locations where their animals access resources. Therefore, the areas were not defined by administrative boundaries, as communities may access locations outside their wards, for instance for grazing or watering. The resulting maps were scanned, digitised and analysed as detailed in the following sections. Further detail on the participatory mapping process is provided in the Supplementary Methods (Additional File 1).Figure 2Participatory mapping of anthrax risk areas in the Ngorongoro Conservation Area. Images show (A) the set-up of a mapping session, (B) participants engaged during a session and (C) an example of a 1:50,000 scale map annotated by participants. The map was created with QGIS opensource mapping software. The basemap used was a scanned and geo-referenced full colour 1:50,000 scale topographic map produced by the Surveys & Mapping Division, Ministry of Lands, Housing & Human Settlements, Dar es Salaam, Tanzania. The grid is based on the Arc1960 UTM 36S projection and datum. The map was exported from QGIS in Acrobat Pdf format to enable it to be printed at suitable sizes for using in the fieldwork and to be manually annotated during the participatory mapping.Full size imageDigitisation of maps and generation of random pointsScanned maps were saved as PDF files and converted to high resolution TIFF files for digitisation in QGIS 2.18.2-Las Palmas free OpenSource software26. All maps were georeferenced with geographical coordinates during production and reference points were available to enable the precise mapping of all locations. The digitization was carried out using the QGIS digitizing tools and by creating polygon layers of the defined risk areas.Sourcing data on the environmental predictors of anthraxAvailable soil and environmental data (250 m grid) for Tanzania were obtained from various sources (Table 1). From the available data, we selected the following seven variables which have previously been shown to contribute to or explain the risk of anthrax based on the biology of B. anthracis (Table 1).Table 1 Environmental factors with potential to influence anthrax occurrence.Full size tableCation exchange capacity (CEC)Measured in cmol/kg, CEC is the total capacity of the soil to retain exchangeable cations such as Ca2+, Mg2+ etc. It is an inherent soil characteristic and is difficult to alter significantly. It influences the soil’s ability to hold on to essential nutrients and provides a buffer against soil acidification27. CEC has been reported to be positively correlated with anthrax risk. In addition, CEC is a proxy for calcium content, which may contribute to anthrax risk in a pH-dependent manner as explained below19,22.Predicted topsoil pH (pH)Soil pH below 6.0 (acidic soil) is thought to inhibit the viability of spores19 thus a positive effect of higher pH on the risk of anthrax is expected. It has been suggested that the exosporium of B. anthracis is negatively charged in soils with neutral to slightly alkaline pH. This negative charge attracts positively charged cations in soil, mainly calcium, enabling the spores to be firmly attached to soil particles and calcium to be maintained within the spore core, thereby promoting the viability of B. anthracis19,28.Distance to inland water bodies (DOWS)Both the distance from water and proximity to water may increase anthrax risk. Distance to inland water may indicate the degree to which an area is dry/arid. Anthrax outbreaks have been shown to occur in areas with very dry conditions19. Although anthrax occurrence has also been associated with high soil moisture, this relates more to the spore germination in the environment (a mechanism that is disputed) and the concentration of spores in moist humus that amount to an infectious dose18,29. Spores will survive much longer in soils with low moisture content19. Low moisture may also be associated with low vegetation which results in animals grazing close to the soil, increasing the risk of ingesting soil with spores. Hampson et al. reported that anthrax outbreaks occurred close to water sources in the Serengeti ecosystem of Tanzania in periods of heavy rainfall20, and Steenkamp et al. found that close proximity to water bodies was key to the transmission of B. anthracis spores in Kruger National Park, South Africa22. Water is an important resource for livestock and a large number of animals may congregate at water sources during dry seasons. The close proximity of a water source to a risk area may increase the chance of infection, particularly during periods of high precipitation which might unearth buried spores.Average enhanced vegetation index (EVI)Vegetation density may influence the likelihood of an animal ingesting soil or inhaling dust that may be contaminated with spores. Grazing animals are more likely to encounter bacteria in soil with low vegetation density20, although there is a possibility that spores can be washed onto higher vegetation by the action of water19. Vegetation index may also reflect the moisture content of soil. Arid/dry conditions favour the formation and resistance of spores in the environment, thus lower vegetation may be associated with the occurrence of anthrax.Average daytime land surface temperature (LSTD)Anthrax has been more commonly reported to occur in regions with warmer climates worldwide. Minett observed that under generally favourable conditions and at 32 °C to 37 °C, sporulation of B. anthracis occurs readily but vegetative cells are more likely to disintegrate at temperatures below 21 °C30. Another hypothesis for the association of high temperature with anthrax occurrence is altered host immune response to disease due to stress caused by elevated temperatures19. In addition, elevated temperatures are usually associated with arid areas where vegetation is low, limiting access to adequate nutrition, which in turn affects immunity. Similarly, in hotter climates where infectious diseases occur more often, host interactions with other pathogens may modulate immune response to anthrax31. In this case, a lower infectious and lethal dose of spores would be sufficient to cause infection and death, respectively19. Contact with and ingestion of soil, spores and abrasive pasture is also higher with low vegetation in hot and arid areas19,32. In boreal regions such as in northern Canada, where anthrax occurs in wood bison, and Siberia, the disease is more commonly reported in the summer19. We therefore hypothesised a positive effect of LSTD on the risk of anthrax.SlopeSpores of B. anthracis are hypothesized to persist more easily in flat landscapes that are characterised by shallow slopes19, as it is thought that wind and water may disperse spores more easily along areas with a higher slope gradient, thereby decreasing the density of spores to levels that may be insufficient to cause infection in a susceptible host. Therefore, we expected a negative relationship between slope and the risk of anthrax.Predicted topsoil organic carbon content (SOC)Organic matter (g/kg) may aid spore persistence by providing mechanical support. The negatively charged exosporium of spores is attracted to the positive charges on hummus-rich soil, thus anthrax is thought to persist in soil rich in organic matter18. Based on available evidence, we expected a positive effect of SOC on the risk of anthrax.Creating the datasetThe annotated and digitised maps yielded polygons of high-risk areas within the NCA (Fig. 3). After digitization, 5000 random points were generated33 to cover the 8292 km2 area of the NCA. This enabled us to obtain distinct points allowed by the 250 m grid resolution of the environmental variables. Points falling within the defined risk areas were selected to represent risk areas while those falling outside represented low-risk areas. Measures of the environmental characteristics associated with individual points were obtained with the ‘add Raster data to points’ feature in QGIS.Figure 3Ngorongoro Conservation Area map showing (A) defined risk areas (in red) and (B) distance to settlements. For analysis, 5000 random points were generated throughout the area; points falling within 4.26 km of human settlements (the average distance herds are moved from settlements in a day as determined through interviews of resident livestock owners) were retained for analysis (n = 2173, shown in blue in 3a). The maps were created in QGIS 2.18.2 using data from the National Bureau of Statistics, Tanzania (http://www.nbs.go.tz/).Full size imageIn order to focus on areas of greatest risk to humans and livestock and to exclude locations that are not accessible, only points within a certain range of distance from settlements were included (Fig. 3). On average, herders in the NCA move their livestock 4.26 km away from settlements for grazing and watering during the day (unpublished data obtained through a cross-sectional survey of 209 households). Thus, only points falling within this distance from settlements were selected, providing us with data on areas where infection is most likely to occur. Data on locations of settlements were obtained from satellite imagery and included permanent residences as well as temporary settlements (e.g. seasonal camps set up after long distance movement away from permanent settlements, typically in the dry season, in search of pasture and water). These data were collated from the Center for International Earth Science Information Network (CIESIN).After adjusting for accessibility of resource locations using the average distance moved by livestock, 2173 points were retained for analysis, of which 239 (11%) fell within high-risk areas.Data analysisAll statistical analyses were carried out in R (v 4.1.0) within the RStudio environment34. The aims of the statistical analysis were to infer the relationship between anthrax risk areas as determined through participatory mapping and the environmental factors identified in Table 1, and to use this relationship to make spatial predictions of anthrax risk across the study area. We achieved both aims by modelling the binary risk status (high or low) of the randomly generated points as a function of their environmental characteristics in a Bayesian spatial logit-binomial generalised linear mixed-effects model (GLMM), implemented in the package glmmfields35. Spatial autocorrelation (residual non-independence between nearby points) was accounted for by including spatial random effects in the GLMM. We chose relatively non-informative priors for the intercept and the covariates, using Student’s t-distributions centred at 0 and wide variances (intercept: df = 3, location = 0, scale = 10; betas: df = 3, location = 0, scale = 3). For the spatial Gaussian Process and the observation process scale parameters, we adopted the default glmmfields settings and used half-t priors (both gp_theta and gp_sigma: df = 3, location = 0, scale = 5), and 12 knots. To achieve convergence, the models were run for 5000 iterations35.First, univariable models were fitted to estimate unadjusted associations between each environmental factor (CEC, pH, DOWS, EVI, LSTD, slope, and SOC; Table 1; Supplementary Table S1) and high- and low-risk areas. Second, we constructed multivariable models by fitting multiple environmental variables (Supplementary Table S2). Three variables, SOC, slope and EVI showed a strongly right-skewed distribution and were therefore log-transformed prior to GLMM analysis to prevent excessive influence of outliers. All predictor variables were centred to zero mean and scaled to unit standard deviation for analysis, and odds ratios were rescaled back to the original units for ease of interpretation. Prior to fitting the multivariable GLMM, the presence of collinearity among the predictor variables—which were all continuous—was assessed using variance inflation factors (VIFs)36, calculated with the car package and illustrated using scatter plots (Supplementary Fig. S1)36. Three predictor variables showed a VIF greater than 3 (LSTD, ln EVI and pH with VIFs of 6.8, 4.2 and 3.5, respectively). Removal of LSTD and ln EVI reduced all VIFs to below 3, therefore these two variables were excluded from the multivariable regression analysis37.The model performance was assessed by calculating the area under the receiver operating characteristic curve. The predicted probability of being an anthrax high-risk area was determined and depicted on a map of the NCA using a regular grid of points generated throughout the NCA with one point sampled every 500 m.Consent for publicationPermission to publish was granted by the National Institute for Medical Research, Tanzania. More

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