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This section provides an overview of methods. The Supplementary Information provides additional detailed descriptions of the leech collections, laboratory processing, bioinformatics pipeline, and site-occupancy modelling. Code for our bioinformatics pipeline is available at Ji72 and Yu73. Code for our site-occupancy modelling and analysis is available at Baker et al.74.Leech collectionsSamples were collected during the rainy season, from July to September 2016, by park rangers from the Ailaoshan Forestry Bureau. The nature reserve is divided into 172 non-overlapping patrol areas defined by the Yunnan Forestry Survey and Planning Institute. These areas range in size from 0.5 to 12.5 km2 (mean 3.9 ± sd 2.5 km2), in part reflecting accessibility (smaller areas tend to be more rugged). These patrol areas pre-existed our study, and are used in the administration of the reserve. The reserve is divided into six parts, which are managed by six cities or autonomous counties (NanHua, ChuXiong, JingDong, ZhenYuan, ShuangBai, XinPing) which assign patrol areas to the villages within their jurisdiction based on proximity. The villages establish working groups to carry out work within the patrol areas. Thus, individual park rangers might change every year, but the patrol areas and the villages responsible for them are fixed.Each ranger was supplied with several small bags containing tubes filled with RNAlater preservative. Rangers were asked to place any leeches they could collect opportunistically during their patrols (e.g. from the ground or clothing) into the tubes, in exchange for a one-off payment of RMB 300 ( ~USD 45) for participation, plus RMB 100 if they caught one or more leeches. Multiple leeches could be placed into each tube, but the small tube sizes generally required the rangers to use multiple tubes for their collections.A total of 30,468 leeches were collected in 3 months by 163 rangers across all 172 patrol areas. When a bag of tubes contained  More

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The Willmott similarity indices, over the first 4 months, for outside and inside temperatures, in sunny and shaded environments, with values close to 1, confirm that A. sexdens colonies were exposed to significantly different temperatures. The lowest values of this index for irradiance, differing between the sunny and shaded environments for internal temperature (in the initial chamber), indicates variation in this parameter between environments. Irradiance values close to 0 between environments represent differences between sunny and shaded areas, but the temperature of the initial chamber did not vary. The selection pressure from irradiance and, consequently, temperature, defines the ideal depth of the initial chamber for the founding queens16 to keep this parameter at values adequate for the fungus garden and the offspring8 in the field. The similar temperature, in the nests in the shaded environment, agrees with that reported for this leaf-cutting ant, of 24°C3, but this varies between species of these insects, being 25–28 °C for A. sexdens17, 27.5 °C for A. vollenweideri18 and 27 °C for A. heyeri19. This adaptation of an ideal depth to construct the initial chamber allows A. sexdens to adapt to different habitats in full sun and shade. The nesting process, habits and foraging strategies differ between A. bisphaerica and A. sexdens, with the former normally establishing their nests in full sun in areas with predominantly grass forages and the latter in shaded areas where it cuts dicot leaves14. Furthermore, differences in nest depth between these species may be related to soil temperature, which is lower in shaded areas7. For this reason, fungal chambers in exposed nests in pastures are deeper than in shaded areas in forests, as soil temperature is negatively correlated with depth7. Soil humidity and temperature act simultaneously due to the thermo preference of workers, resulting in the construction of shallower nests in cold soils and deeper nests in warmer ones7. Soil moisture also varies according to depth, affecting the nest-digging behavior of leaf-cutting ants7,15.The temperature in the shaded environment was higher than that reported for A. sexdens rubropilosa, from 24.82 ± 3.14 to 24.11 ± 1.30 °C at a depth of 5–25 cm underground, for optimal offspring development and, consequently, reduction in the lipid content of queens at high temperatures, without affecting their survival20. This is because the depth of the initial chamber excavated by the queen is adequate for colony success8,16.The different habitats occupied by the ant A. sexdens21, from dense forests to cerrado and caatinga may explain the greater depth and volume of the initial chamber of the nests in shaded than in sunny environments. However, the depth of the initial nests varies between Atta species with 7.5–12 cm, 6.5–13 cm, 15–25 cm, 10–30 cm, 10–15 cm, 11–34 cm, and 9–15 cm for A. colombica, A. cephalotes, A. texana, A. sexdens rubropilosa, A bisphaerica, A capiguara, and A. insulares, respectively1,13,15,22,23,24. The initial chamber volume is within the expected range for A. sexdens1,13 in both environments, with a chamber volume of 24.88 cm3 in a shaded area with eucalyptus plantation13. Different excavation efforts with the removal of small soil particles by the founding queen using her jaws in repeated biting motions25, subsequently discarded outside the nest8,16,26 may explain the greater volume of the initial chamber in the shaded area. The greater solar irradiation in sunny areas increases the temperature, with the higher soil temperature generating greater excavation effort and oxidative damage27,28, in addition to water loss, as described for seed-collecting ants29,30. Further, humid soils are easier to dig, which explains the greater volume of the initial chamber in the shaded area as found for the excavation behavior by Atta spp. in soils with different densities and moistures15,16,31.The higher mass of A. sexdens queens in the first month of the claustral phase than in the fourth, in both sunny and shaded environments, stems from a reduction in their body mass, due to the metabolism of the lipid content during the first 6 months following the flight, but with recovery in the subsequent months1. The mass loss is due to the use of body reserves by the queens to prepare and maintain the colony in the claustral phase, as stored lipids are important in the evolutionary history of the Attini tribe, from semi-claustral to claustral foundation32. The queen, with a claustral foundation, does not feed, remaining enclosed in the nest and rearing her initial offspring by metabolizing her own body reserves33, as reported for this ant species1. The selection pressure on the evolution of claustral foundation tends to minimize risk during foraging33 with a more viable adaptation being the storing of reserves in the body, as observed in our study. The greater biomass of the fungus garden in the fourth month is due to growth, but its values were lower than those reported for 4-month-old A. sexdens nests, from 2000 to 3000 mg1.The lower number of A. sexdens eggs in the first than in the third month is similar to that observed in laboratory colonies of this ant8. The irregularity in the egg production by the queen is due to hormone fluctuations regulated by the endocrine system, and is correlated with the activity cycle of the corpora allata during the 3 or 4 months of colony life34. This gland synthesizes the juvenile hormone, which acts in the oviposition of founding queens, as verified for females that underwent alatectomy34. This hormone acts in the fat body, initiating the synthesis of vitellogenin (glycolipophosphoproteins, with lipids and carbohydrates in its composition) to be deposited in the oocyte35. Thus, the production of offspring depends on body reserves (fatty body lipids and muscle mass protein), as the queen does not feed during the foundation period (claustral foundation). The lower production of small and medium workers in the first month than in the second, third or fourth months, agrees with that reported in A. sexdens nests1. The similar number of larvae over the 4 months is due to the duration of the larval period of A. sexdens, of around 25 days8, with new immature individuals produced monthly with overlapping generations, common in social insects. This overlap begins with larvae in the first month of nests and pupae, usually in the second month of ant nests in the laboratory8.The lower values of fungus biomass and number of eggs, larvae, pupae and small and medium workers of A. sexdens in nests in the sunny environment may be due to a higher incidence of solar irradiance increasing the variation in the internal temperature of the initial chamber. This agrees with reports that a lower incidence of solar irradiance improved the stability of the internal temperature of the initial chamber, favoring A. sexdens with narrow thermal tolerance range as it is a thermally protected underground species11. However, frequent heat peaks, with habitat-specific physiological consequences for subterranean ectothermic animals, are common in sunny areas11. The queen’s body mass, similar between environments, indicates a similar reduction of this parameter between them and their tolerance to temperature variations in this type of foundation. A reduction in the mass of A. sexdens queens is expected from the nuptial flight to the end of the claustral phase. The energy expenditure of A. sexdens queens, in carbohydrates and body lipids for the nuptial flight and nest excavation, was estimated at 0.58 J36 and during the claustral phase, they metabolize body lipids and proteins to survive and form the initial colony26,37.The higher mortality of A. sexdens nests in the sunny environment, during the claustral foundation, is due to a higher incidence of solar irradiance, increasing the variation in the internal temperature of the initial chamber and, consequently, the excavation effort and oxidative damage to the founding queens27,28, in addition to water losses as reported for seed-collecting ants29,30. This mortality may also be related to entomopathogens, unsuccessful symbiotic fungus regurgitation, excavation effort, density and soil moisture1,9,38,39.Atta sexdens founder queens were exposed to sunny and shaded environments with greater solar irradiance and, consequently, a greater variation range in the internal temperature of the initial chamber in the first environment. The shaded environment, with lower incidence of solar irradiance and greater stability of the internal temperature of the initial chamber, was more favorable for colony development, as confirmed by the biological parameters and greater survival of A. sexdens queens.
Atta sexdens female collection methods- after the nuptial flightAtta sexdens queens were collected at the Experimental Farm Lageado in Botucatu, Brazil in 2019 (22°50′37.3″S 48°25′38.3″W) on sunny days after heavy rains from late October to early November. Two hundred queens were collected using tweezers. They were stored separately in 250 ml pots with 1 cm wet plaster for 60 min prior to use. We had permission to collect Atta sexdens queen specimens.Experimental areasThe A. sexdens queens were individualized in two experimental areas: sunny—an open area exposed to Global Horizontal Irradiation with exclusive coverage of Paspalum notatum Flügge grass (N = 100) and shaded – an area exposed to Diffuse Horizontal Irradiation (50% shade screen—1.50 × 50 MT), in a plowed environment (N = 100). The soil is a superficial horizon of oxisols.The founding A. sexdens queens were individualized in the center of a square of land (50 × 50 cm) covered with a transparent bottle measuring 20 cm in diameter by 12 cm in height, delimiting the space to be drilled in the soil by the ant queens per experimental area of 25 m2 (Fig. S1).Development of early nests during the claustral phaseAtta sexdens queens were evaluated over 4 months following nest foundation, to monitor its development. A total of 25% of the successfully established nests were excavated per month by removing the colony with a gardening shovel. The number of eggs, larvae, pupae and adults was counted and the mass of the queen and the biomass of the fungus garden determined. The depth, width, length, and height of each nest were measured with the aid of a caliper. The estimated volume of each fungus chamber was based on a cylinder. A correction factor was used to calculate the volume of the chamber because they are rounded: V = πr2 (ch + r0.67), in which ‘r’ is the chamber base radius and ‘ch’ the cylinder height, measured by subtracting the maximum height of the chamber from its radius, ch = h − r40. Queen mortality was evaluated during the excavation of their nests.Temperature and radiation measurementThe temperatures of the external and internal environments (15 cm deep), in each area, were measured for 4 months, with Data loggers (Testo), after the foundation of the nest by the leaf-cutting ant. Global Horizontal Irradiation (GHI) was measured using an Eppley PSP Pyranometer and Diffuse Horizontal Irradiation by a Kipp & Zonen CM3 Pyranometer (Table 3). Solar measurements were obtained over a five-minute time scale (mean of 60 readings with scanning time every five seconds) in W/m2 by a CR300041 model data logger and stored in an ASCII file.Table 3 Instruments used to measure solar irradiance in nests of Atta sexdens (Hymenoptera: Formicidae) in sunny and shaded environments.Full size tableThe measurements were submitted to a quality control procedure to verify if their values were in accordance with pre-defined solar irradiance thresholds. This procedure consists of a series of checks on physically possible limits per component measured (Table 4). These checks were carried out according to the process created by the International Commission on Illumination (CIE) discarding erroneous measures to avoid compromising the processes of numerical integration or data processing.Table 4 Physically possible minimum and maximum values for each measurement of solar irradiance.Full size tableMeasures accepted as possible were those above 0 W/m2 and lower than the maximum stipulated limit, per component, according to the extraterrestrial solar irradiance (IE) (Eq. 1). This represents the maximum value reaching the top of the atmosphere, without attenuation by atmospheric elements (clouds, particles, among others). Values measured at the earth’s surface are lower than those at the top of the atmosphere. However, the phenomenon of multireflection when scattered clouds near the apparent location of the sun reflect part of the solar irradiance onto the sensor, increase the value measured even higher than the extraterrestrial irradiance over short periods45. For this reason, the global irradiance value can be up to 20% higher than that of the extraterrestrial one.The 1361 of Eq. (1), to calculate the extraterrestrial irradiance, represents the solar constant in W/m246, R the relation of the average dimensionless distance between the Earth and the Sun (Eq. 2) and Z the zenithal angle of the Sun (Eq. 3) in degrees47.$${text{I}}_{{text{E}}} = {1361}left( {text{1/R}} right) ,{{cos}}, left( {text{Z}} right)$$
(1)
$$begin{aligned} {text{R}} & = {1} – 0.000{9467};{text{sen}} left( {text{F}} right) – 0.0{1671};{text{cos}},left( {text{F}} right) – 0.000{1489}left( {{text{2F}}} right) \ & quad – 0.0000{2917};{text{sen}}left( {{text{3F}}} right) – 0.000{3438};{text{cos}},left( {{text{4F}}} right) \ end{aligned}$$
(2)
$${text{Z}} = {text{sen}} ,left(updelta right);{text{sen}}left(upphi right) + cos left(updelta right);cos left(upphi right);cos left(upomega right)$$
(3)
F, in Eq. (4), is the angular fraction of the date of interest in degrees, δ, at 5, the solar declination in degrees, Φ, at 6, the geographic latitude of the location in degrees (22.85) and ω, at 6, the clockwise angle in degrees.$${mathbf{F}} = {36}0^circ ;{text{D/365}}$$
(4)
$$begin{aligned} {{varvec{updelta}}} & = 0.{3964} + {3}.{631};{text{sen}}left( {text{F}} right) – {22}.{97};{text{cos}}left( {text{F}} right) + 0.0{3838};{text{sen}}left( {{text{2F}}} right) – 0.{3885};{text{cos}};left( {{text{2F}}} right) \ & quad + 0.0{7659};{text{sen}};left( {{text{3F}}} right) – 0.{1587};{text{cos}}left( {{text{3F}}} right) – 0.0{1}0{21};{text{cos}}left( {{text{4F}}} right) \ end{aligned}$$
(5)
$${{varvec{upomega}}} = left( {{12} – {text{Hd}}} right){15}$$
(6)
The d, in the previous expression, represents the day of the year, from 1 to 365 and the Hd, the hour and the tenth of an hour in degrees of the moment of interest.The values were numerically integrated, after applying the measurement quality control procedure, obtaining a solar irradiation value for the day in MJ/m2 representing the total energy received daily, on a horizontal surface of 1 m2.Statistical analysisThe null hypothesis that the mortality proportions (probabilities of success) of the founding queens of both groups are the same was submitted to the test of equal proportions.The null hypothesis that a data sample came from a normally distributed population was submitted to the Shapiro–Wilk test.Data structure fitting the ANOVA (completely randomized factorial scheme) assumptions were submitted to this analysis and to Tukey’s test for multiple comparisons of means. The Scheirer Ray Hare test is a nonparametric test used for a two-way completely randomized factorial design49. This procedure is an extension of the Kruskal–Wallis rank test allowing for calculation of the interaction effects and linear contrasts and were used for data structure that did not fit the ANOVA assumptions. Dunn’s test50 of multiple median comparisons was performed with a correction (the false discovery rate method) to control the experiment-wise error rate.The Willmott’s Index of Similarity (d) is a standardized measure of the degree of similarity between two data series ranging from 0.0 to 1.0 with the value 1.0 indicating a perfect match (two identical data sets), and 0 no agreement at all51. As an example, in the sunny environment, the indoor and outdoor temperature data were identical, which results in 1.0. The more identical, close, and concordant two data sets are, the closer to 1.0 they will be. The calculation of the index is presented with A and B representing two data sets whose agreement is to be evaluated.$$begin{aligned} A^{prime}_{i} & = A_{i} – overline{B} \ B^{prime}_{i} & = B_{i} – overline{B} \ d & = 1 – frac{{sumnolimits_{i = 1}^{N} {left( {A_{i} – B_{i} } right)^{2} } }}{{sumnolimits_{i = 1}^{N} {left[ {left| {A_{i} } right| – left| {B_{i} } right|} right]^{2} } }} \ end{aligned}$$The R companion package, ggplot252, FSA53, tidyverse54, and hydroGOF55 used is a free software environment for statistical computing and graphics R version 4.0.456. More

Study area and dateIn the north-west of France, the macrotidal Bourgneuf Bay (1°-2° W, 46°-47° N; total area ~340 km2; Fig. 1) has an intertidal zone largely dominated by mudflats (exposed surface area ~100 km2). Bourgneuf Bay is situated south of the Loire estuary and is open to the sea along 12 km from the west to the north-west. C. gigas aquaculture here is of national importance and wild C. gigas reefs can account for over double the biomass of their farmed conspecifics65. Analysis of satellite observations covering 30 years of MPB biomass in the bay confirmed the co-occurrence of high MPB biomass with wild oyster reefs and cultivated stocks16 (Supplementary Methods: Wider Situation of the Reefs). Two small (each  > 750 m2) wild C. gigas reefs and their immediate surroundings (10–100 m) in the north of Bourgneuf Bay were deemed suitable for experimental manipulation (yellow and orange regions in Fig. 1). Méléder et al.18 described MPB biomass as mostly concentrating around the 2 m isobath, the Falleron river channel (closest point ~400 m NNE from the eastern reef), and oyster farms. Covering this isobath, we superimposed a 350 * 350 m grid (12.25 hectares) to cover the two wild oyster reefs, orientated so that the ‘Y’ axis runs parallel to the slope of bathymetry (Fig. 1). The grid was split regularly into 49 ‘grand-cells’ of 50 * 50 m (i.e., n = 49) and each of those split into 25 cells of 10 * 10 m (i.e., n = 1225; Fig. 1). Four cells per grand-cell were chosen randomly for the sampling of meiofauna, granulometry, OM (see Table 3 for specific methodology), and macrofauna. Of these cells, only every second cell was processed for meiofauna because of time constraints in assessing their abundance.Table 3 Summary of study variables and their sampling methodologies.Full size tableAlthough there were only two oyster reef complexes (‘reefs’, hereon) in this study, multiple sampling cells fell on, or in close proximity to, each reef, so that each reef had many potential (though not independent) distance decay transects running from it capturing natural variation in spatial structure66. Comparing the ecological change following the experimental burning of oyster reefs (described below) against ecological change occurring at these two reefs over the previous 25 years16 also allowed us greater confidence to disentangle the treatment effects from typical variation. Through the centres of five grand-cells to the south of the extent, a transect forming an ‘L’ shape (Fig. 1) was sampled every 10 m for in situ MPB pigment composition and biomass. We used these data to complete the remote sensing approach for MPB biomass estimation (see below, Microphytobenthos). The western reef was slightly larger than the eastern reef and contained a large rock, ‘Roche Bonnet’, rising 0.5–1 m from the sediment. Outside the grid, another larger (200 * 80 m) wild oyster reef lies WSW at ~260 m distance from the western reef. The grid was sampled for the variables listed in Table 3 during the winter MPB low and early autumn peak seasons (see also ground-truthing in16), on the dates 18-19th September 2013 and 17-18th March 2014, before treatment, and on 7-8th October 2014 after treatment.MicrophytobenthosWe mapped MPB biomass by satellite remote sensing, following the method described in detail in Echappé et al. (2018). We used the same long-term record of high-resolution satellite images to analyse the spatial distribution of the normalised difference vegetation index (NDVI), a proxy of MPB chlorophyll a concentration at the sediment’s surface18,67, before and after treatment (individual image details in captions of Fig. 2 and Supplementary Figs. S4–S7). After atmospheric correction (FLASH and US40 aerosol model), the satellite-derived NDVI was validated against associated field measurements (r2 = 0.85, root-mean-square deviation, RMSE = 0.04, n = 57, P 20°) was limited (Supplementary Results: Additional MPB Images). An optimal image was chosen as representative of MPB biomass patterns per season16. The study area would ideally be tidally uncovered for ~2 h before the image was taken, whereupon MPB biomass is concentrated at the sediment surface. The optimal images met this condition (i.e., Fig. 2).To complete NDVI maps, in situ MPB pigment composition and biomass were retrieved by HPLC analysis from the 25 triplicates of sediment. These had been sampled using contact-cores to freeze the top 2 mm of sediment in situ with liquid nitrogen, with a metal surface 56 mm in diameter. Biomass was expressed by Chl a concentration (mg m−2), and dominance of MPB taxa was broadly assessed by ratio of pigment sources to Chl a: Fucoxanthin (Fuco), Diadinoxanthin (DD), Diatoxanthin (DT) and Chl c for diatoms. The ratio of unknown carotenoids (interpreted as by-products due to the low resolution of their absorption spectra) to Chl a was also analysed for ecological purposes (dominant taxa), whereas grazing pressure was investigated using the ratio of pheophorbid a to Chl a (methodological discussion in28).Sediment variablesFor laser granulometry, we sampled two depths, 0–5 cm and 5–10 cm, in triplicate at each cell. Each of the triplicate samples was put in a vial with water and sonicated. The particle size distribution was determined on a Mastersizer 3000 with a reporting range 50 nm to 3 mm. We also determined sediment percentage OM at two depths by mass loss on ignition in comparison to the oven-dried original (procedure as described for Macrofauna, also Table 3).MacrofaunaWe sampled macrofauna by a single 200 * 200 mm (depth * diameter) core per cell. Contents were placed into labelled buckets and sieved onshore (1 mm mesh). Soft-bodied polychaetes were picked out with forceps and preserved in buffered formalin during sieving. All material left on the sieve was bagged and preserved in formalin at the laboratory. Individuals were counted and measured by the longest axis (accuracy 0.1 mm, calipers); the deep-burrowing polychaete Diopatra biscayensis was counted by the presence of visible tubes above the sediment. Calibration curves from length to mass per species per season were built by identifying size classes by Sturges rule. Multiple individuals per size class (ideally n = 100) were measured to estimate mean organic mass per individual of each size class. Shell matter was physically separated from tissue, before both being dried in aluminium foil cups for 48 h at 60 °C and weighed (g) for tissue dry mass using a mass balance. Dry mass was then incinerated for four hours at 450 °C and reweighed (g; decrease in mass of the aluminium cup was also accounted for), the difference giving the organic matter mass (including residue in the shell matter), or ash free dry weight (AFDW). This number was divided by number of individuals. Calibration curves per species used first order polynomial curves for bivalves, unless numbers of size classes and individuals were small (1% of the total abundance. All mapping and analyses were performed in the statistical computing environment R (v4.0.2)73.Reporting summaryFurther information on research design is available in the Nature Research Reporting Summary linked to this article. More

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doi: https://doi.org/10.1038/d41586-022-00832-x

ReferencesLiu, J. et al. Conserv. Biol. https://doi.org/10.1111/cobi.13907 (2022).Article 

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Siver et al.19 identified three categories of fossil Mallomonas species uncovered in the extensive Giraffe Pipe locality. One group of species had scales with morphological characteristics similar to, and difficult to separate from, modern congeners. Based on a morphological species concept, these could be viewed as representing the same species. A second group had morphologically different scales, but ones that could be linked to one or more modern species. The third group possessed scales that could not be directly linked to any modern species. The majority of the species contained in the latter group lacked a V-rib and well developed dome, and were considered as stem organisms within the broad section Planae. Siver et al.19 further reported that the mean size of scales in the group containing the extinct stem taxa was larger than those fossil taxa grouped with modern congeners.The current study adds additional modern and fossil species to the database used by Siver et al.19, including the oldest known taxon from the Cretaceous Wombat locality, and provides the first attempt to reconstruct cell size for fossil Mallomonas species. Based on the expanded database, several trends with respect to the evolution of scale and cell size of Mallomonas taxa can be made. First, there is a strong relationship between scale width and scale length that was similar for both fossil and modern forms. Second, as a group, fossil taxa had scales that are significantly larger than those produced by modern species, especially with respect to surface area. The five species with the largest scales belong to extinct fossil species, four of which belong to the group of stem taxa within section Planae. These scales are massive compared with modern forms, and support the concept of scale gigantism for early members of the Mallomonas clade containing species with scales that lack a V-rib and dome (Fig. 1; subclade A2). Third, assuming the model relating scale and cell size can be applied to the geologic record, fossil species produced significantly larger cells than modern forms.Because the models relating scale length to scale width were similar for modern and fossil species, the assumption is that the models developed relating scale size to cell size are appropriate for fossil taxa. In addition, the precise overlapping pattern of scales comprising the cell covering on modern species has recently been documented for Eocene fossil species22, indicating that this architectural design was well evolved by at least the early Eocene. Thus, making the assumption that other fossil taxa had similarly constructed cell coverings is reasonable, and further supports the application of the models relating scale and cell size to these fossil forms.Based on the model estimates, the mean cell size of the fossil species is approximately twice as large as the average cell produced by modern organisms. This doubling of cell size was also observed for the smallest species. The mean size of the five smallest modern species (M. canina, M. mangofera, M. dickii, M. madagascariensis, and M. gutata) was 9.3 × 5 µm, compared to the mean cell size estimated for the five smallest fossil taxa (M. pseudohamata, M. preisigii, M. dispar, M. bakeri and M. GP4) of 18 × 8.7 µm. The cell size discrepancy is even greater for fossil species that lack modern congeners, and especially for the extinct stem species within section Planae that possessed an average cell size of 69.2 × 20.8 µm, with a maximum cell size of 81.7 × 22.7 µm for M. GP13. The scales produced by these large fossil cells were not only massive in size, but also robust and heavily silicified. It is likely that these large cells covered with large, heavy and cumbersome scales would have been slow swimmers that expended significantly more energy to maintain their position in the water column than modern species. Perhaps these cells were also more prone to predation by larger zooplankton, and a combination of decreased motility and greater predation provided the evolutionary pressure for smaller and faster cells with less dense siliceous components, and ultimately caused the demise of the large-celled fossil species. In contrast, it is also possible that the stimulus initially resulting in the evolution of the larger species was the fact that they were too big to be preyed upon by smaller invertebrates.Several points regarding the models used to estimate cell size are warranted. First, it is important to note that because the scale sizes used to estimate cell sizes for the larger fossil taxa are at the end of the range used to produce the model, caution needs to be exercised. The assumption is being made that the linear relationship of the model holds for the larger scales, and that the linear relationship does not begin to flatten and reach a maximum cell size. However, there is no indication that the relationship is reaching an asymptote, nor reason to assume that the model would not hold for organisms that produce larger siliceous components. Second, the scale and cell size data used to produce the models consisted of the midpoint values of the ranges given in the literature. Thus, the cell sizes inferred from the models represent a midpoint estimate of the range for each species, and not an upper size limit. Third, there is more data available in the literature documenting scale size than there is for cell size for most modern Mallomonas species. Additional data on cell size, especially inclusion of mean values, may help to further fine-tune the models. Lastly, the formula of an ellipse was used to estimate scale surface area for the few species with “square-shaped” scales. Although this may slightly underestimate the surface area, using a formula for a square or rectangle would have resulted in an overestimation. Because the few species with square-shaped scales were primarily the extinct fossil taxa lacking modern congeners, their cell size may actually have been slightly larger than estimated in this study.Interestingly, fossil scales that have morphologically similar (identical) modern counterparts were not significantly different in size from each other, implying that their corresponding cells were also of similar size. These taxa have significantly smaller scales compared to those species with gigantic scales, and closer to the mean of modern species. Perhaps, this is why the lineages of these morphologically-identical species have survived for tens of millions of years. Despite maintaining virtually identical scale types, the degree of genetic difference from a physiological or reproductive perspective between taxa with virtually identical siliceous components remains unknown19,23.The extinct scale types are not only significantly larger than those of species with modern congeners, but some have a tendency of being more rectangular to square-shaped. In contrast, fossil scale types that can be linked to modern species, along with their contemporary counterparts, tend to have elliptical-shaped scales. This is especially true of body scales15,16,19. Although a few smaller species of Mallomonas form spherical cells, the vast majority of species produce ellipsoidal-shaped cells, and this is especially true of species forming larger cells15,16. Smaller elliptical-shaped scales would be more efficient in covering a curving ellipsoidal cell surface than larger and square-shaped scales, and allow for a closer fitting cell covering. Jadrná et al.26 recently reported that scales of the closely related synurophyte genus, Synura, have also become smaller and more elongate over geologic time, complementing the observations for Mallomonas. Taken together, these findings support the idea that the evolutionary trend for synurophyte organisms has been towards smaller, elliptical scales.Cyanobacteria, a prokaryotic group of organisms estimated to have evolved by 3.5–3.4 Ga, represent one of the earliest known and smallest life forms on Earth27. Since the evolution of these early prokaryotes, Smith et al.28 estimated that the maximum body size of subsequent life forms has increased approximately 18-fold, with large jumps occurring with the evolution of eukaryote cells, and another concurrent with the advent of multicellularity. In contrast, shifts in the sizes of siliceous scales and corresponding cells of Mallomonas species are small in comparison, within an order of magnitude, and similar to changes observed for prokaryote organisms and other unicellular protists over the Geozoic28,29.Despite the overall lack of historical information on cell size for the majority of unicellular eukaryote lineages, there are data for some organisms that build resistant cell walls or coverings that are taxonomically diagnostic and become incorporated into the fossil record. Diatoms produce a siliceous cell wall known as the frustule, a structure composed of top and bottom pieces called valves that are held together with additional structures called girdle bands. Frustules, or their valve components, can be uncovered from the fossil record and used to provide a direct measure of cell size. Using this technique, Finkel et al.29 reported that the size of planktic marine diatoms declined over the Cenozoic, and correlated the shift with abiotic forcing factors, including a rise in sea surface temperature and water column stratification. Foraminifera are heterotrophic marine protists that build shells out of calcium carbonate, the latter of which can also become part of the fossil record. Changes in the size of foraminifera shells over the Cenozoic have also been correlated with shifts in the intensity of water column stratification30. At this time, it is not known if the decline in cell size for Mallomonas species in the section Planae lineage recorded in the current study was the result of abiotic variables (e.g. energy expenditure or temperature), biotic factors (e.g. predation), or a combination of forcing variables.The current study has provided a means to link scale size to cell size for Mallomonas that, in turn, can be used to trace shifts in cell size over geologic time. As additional scales of Mallomonas species are uncovered from the fossil record, the scale-to-cell size model will be a valuable tool for continuing to unravel the evolutionary history of cell size for this important photosynthetic organism. Other groups of unicellular protists, including euglyphids, heliozoids and rotosphaerids, are similar to synurophytes in that they build cell coverings using numerous overlapping siliceous scales or plates that can become fossilize. Perhaps the same technique of relating scale size to cell size could be used to develop models for these protist organisms, and similarly applied to the fossil record.It is interesting to note that most modern Mallomonas species with large body scales are found in warm tropical regions, including M. bronchartiana Compère, M. pseudobronchartiana Gusev, Siver & Shin, M. velari Gusev, Siver & Shin31, M. vietnamica Gusev, Kezlya & Trans32, M. gusakovii33 and several varieties of M. matvienkoae16. In addition, the modern tropical taxa M. neoampla Gusev & Siver and M. vietnamica share several rare features of their scales and bristles with fossil species recorded from the Giraffe locality, suggesting a possible link between the modern tropical and fossil floras. During the early to middle Eocene, the Earth experienced warm greenhouse conditions and lacked a cryosphere34. The Giraffe locality, positioned near the Arctic Circle, had an estimated mean annual temperature 17 °C warmer, and a mean annual precipitation over four times higher, than present conditions35. In fact, the assemblage of plants and animals in the Eocene Arctic has been described as analogous to those found today in eastern Asia36. Perhaps tropical regions, especially in southeastern Asia, offered refugia for some of the ancient Mallomonas lineages.In summary, multiple extinct fossil species of the diverse and common synurophyte genus, Mallomonas, are reported here to have possessed gigantic scales that are significantly larger than those found on modern species. Based on a model relating scale to cell size, cells of fossil Mallomonas species were estimated to be, on average, twice as large as modern species. A combination of larger cells with heavy siliceous scales that fit less effectively around the cell may have resulted in slower cells more prone to predation, heavier cells requiring more energy resources to maintain their position in the water column, and ultimately their demise. Additional fossil species, especially representing other localities and time periods, will ultimately strengthen our understanding of the evolution of scale and cell size in synurophyte algae. More