Data from: Demographic responses underlying eco-evolutionary dynamics as revealed with inverse modelling

Data from a field experiment in which the dynamics of green peach aphid (Myzus persicae) populations consisting of one clone (non-evolving) were compared to the dynamics of populations consisting of two clones (potentially evolving). A total of three aphid clones were used, which were all tested individually and in each combination. At the start of the experiment, 20 third-instar individuals were placed on a caged host plant. For half of the populations, cages were removed at day 13, allowing competitors to access the plants. Rapid evolutionary responses were observed, which increased population growth rates by 33% to 42% compared to non-evolving populations. These results have been published in Turcotte, Reznick & Hare (Ecology Letters, 2011). Data have been reanalyzed to estimate which demographic rates were underlying different dynamics among clones, and between non-evolving and evolving populations, making use of changes in stage structure through time. These results have been published in Bruijning, Jongejans & Turcotte (Journal of Animal Ecology, forthcoming)

Data of 'Relating plant height to demographic rates and extinction vulnerability'

This dataset was developed for our study on plant allometry and extinction vulnerabilities. In this study we gathered plant demographic data from various sources and related this to maximum plant height. We derived allometric relationships with maximum plant height for the intrinsic population growth rate, variance in population growth rate due to environmental stochasticity and the maximum plant density. These relationships were used to relate maximum plant height to the Mean time to extinction and the Probability of extinction. The results of this research will soon be published as ‘Relating plant height to demographic rates and extinction vulnerability’ (forthcoming). In this repository we provide only the processed data from this study because the original data was gathered from existing open access and semi-open access databases. Original data for this project was gathered from the following databases: (1) TRY Plant Trait Database, (2) COMPADRE Plant Matrix Database Version 4.0.1, (3) Biomass allocation and growth data of seeded plants The processed data is stored in two files: - 2017_deJonge_MaximumPlantDensity.csv: This file contains 230 datapoints with maximum plant density (per square meter) and average individual plant mass (grams). A description of the methodology used to obtain the processed data is given in a PDF file called ‘2017_deJonge_Methodology.pdf’. Additionally, a description file called 'description.pdf' is added, which includes the information mentioned above

Population-level responses to temperature, density and clonal differences in 'Daphnia magna' as revealed by Integral Projection Modeling

Data on individual survival, growth and reproduction of 'Daphnia magna' individuals, as collected during a laboratory experiment. The aim of this study was to quantify effects of temperature, genetic background and population density on the dynamics of 'Daphnia magna' populations. In this experiment, 40 populations of 'Daphnia magna', starting with 20 individuals, were followed during 80 days. Twice a week, three individuals were arbitrarily picked from each population, and isolated for three or four days in transparent tubes that were placed inside each aquarium. Results of this study have been published in ‘Population-level responses to temperature, density and clonal differences in 'Daphnia magna' as revealed by Integral Projection Modeling’ (Bruijning et al., 'Functional Ecology' 2018)

Trackdem: Automated particle tracking to obtain population counts and size distributions from videos in R

This dataset includes two example videos on Daphnia magna populations with each containing 12 individuals and the R-package trackdem. This package automatically counts and tracks moving individuals, and version 0.3.1 of the package is included. See https://CRAN.R-project.org/package=trackdem and https://github.com/marjoleinbruijning/trackdem for more information and the most recent version of the package. The Daphnia were recorded in the lab at KU Leuven (Belgium) in September 2017. The aim of trackdem is to obtain unbiased, automated estimates of population densities and body size distributions, using video material or image sequences as input. It is meant to assist in evolutionary and ecological studies, which often rely on accurate estimates of population size, population structure and/or individual behaviour. The package trackdem includes a set of functions to convert a short video into an image sequence, background detection, particle identification and linking, and the training of an artificial neural network for noise flltering. A tutorial is included, providing a step-by-step introduction on the usage of all functions to analyse image sequences of moving organisms

Data from: Long-term effects of liming on soil physico-chemical properties and micro-arthropod communities in Scotch pine forest

This dataset contains the results of long-term liming on soil micro-arthropods in a stand of Scotch pine on a former drift sand. To counteract the effects of acidification liming was applied in triplicate in increasing quantities from 0 (control), 3, 6, 9 and 18 ton per ha on experimental plots in 1985 and 1986. Soil samples for chemical analyses and soil samples for extraction of soil micro-arthropods were taken in October 2017, 32 years after application. The study site is a 55 years old forest stand of Scotch Pine on a typic quarzipsamment (afforested former drift sand) near de city of Harderwijk, the Netherlands. Soil taxonomy is according to Soil Survey Staff (1999). The forest stand is on a flat plane at 17.5 m above sea level. In 1985 a series of experiments have been conducted here, varying from application of several types of manure (from calves and ducks), a factorial experiment with additions of P, Ca, Mg and K and a range of added carbonated lime in quantities of 3, 6, 9 and 18 ton per ha and an untreated control. All experimental fields are triplicated and 22 x 25 = 550m2 in size. At the start of the experiment pH[CaCl] was around 4.1-4.2 in the mineral soil (mixed top 25 cm) (Hekstra et al. 1990). Carbonated lime for agricultural use, having around 2% Mg, was added in autumn of 1985 (3 ton and all other plots first gift), in autumn 1986 (final gift 6 and 9 ton and second gift 18 ton) and additionally in spring 1987 (final gift to 18 ton). Thinning of the canopy was done in 2001 as regular forest management measure, no other management activities have been conducted ever since. On 16 October 2017 samples have been taken for soil chemical analyses. Each sample has been taken from the mixed top 25 cm mineral soil. We determined organic matter content (weight loss on ignition), pH (in NaCl 0.2 mol per liter), POlsen (plant available P), Cation Exchange Capacity and base saturation (Strontium extraction method). Total quantities of Ca, Mg, Al, Fe, Mn, P, S, Si and Zn (after grinding and extraction with 65% HNO3) were measured with an Inductively Coupled Plasma Spectrophotometer (ICP-OES, ICAP 6300 ARCOS MV, Spectro). NO3-, NH4+ and PO43- concentrations were determined colorimetrically with a Seal auto-analyser III with resp. reagens of salicylate, hydrazin sulphate and ammoniummolybdate/ascorbic acid. Cl- was determined colorimetrically with a Bran+Luebbe auto-analyser III system with mercuritiocynide. Na+ and K+ were determined with a flame spectrophotometer Sherwood Model 420 Flame Photometer. On 17 October 2017, in each of the limed plots and the control plots (green and yellow cadres) four soil cores of 5 cm depth: 100 cm3 content plus litter were sampled and extracted on a Tullgren funnel for 7 days. During that period temperature was increased from 35 to 45 0C. Ethanol 70% was used as conservation fluid and micro-arthropods obtained were put into lactic acid 40% for clarification and identification (Siepel and van de Bund, 1988). Nomenclature and identification for the main groups is according to Weigmann (2006) for Oribatida, Karg (1993) for Gamasina, Karg (1989) for Uropodina and Bretfeld (1999), Potapow (2001), Dunger and Schlitt (2011) and Jordana (2012) for Collembola. Species were grouped to feeding guilds after Siepel & de Ruiter-Dijkman (1993) in herbivorous grazers, herbivorous browsers, fungivorous grazers, fungivorous browsers (grazers feed on the cell walls as well and have resp. cellulase and chitinase activities, browsers on the contents only), opportunistic herbofungivores (plants incl. cell walls and fungal cell contents, i.e. trehalase activity), herbofungivorous grazer (plant and fungal cell walls) and predators (general or specialized on nematods or arthropods). Data files guildData.csv - limeTreatment: number of tons of lime added per hectare - plotNumber: experimental plot identifier - fb: number of individuals in the ‘fungivorous browsers’ category - fg: number of individuals in the ‘fungivorous grazers’ category - hfg: number of individuals in the ‘herbofungivorous grazers’ category - ohf: number of individuals in the ‘opportunistic herbofungivores’ category - hg: number of individuals in the ‘herbivorous grazers’ category - hb: number of individuals in the ‘herbivorous browsers’ category - o: number of individuals in the ‘omnivores’ category - gp: number of individuals in the ‘general predators’ category soilChemistryData.csv - limeTreatment: number of tons of lime added per hectare - plotNumber: experimental plot identifier - organicMatter: soil organic matter percentage, determined by weight loss on ignition - pH: pH in NaCl 0.2 mol.l-1 - Ca: calcium concentration [µmol per kg dry weight] - Mg: magnesium concentration [µmol per kg dry weight] - Al: aluminium concentration [µmol per kg dry weight] - NH4: ammonium concentration [µmol per kg dry weight] - NO3: nitrate concentration [µmol per kg dry weight] - Polsen: plant available phosphorus concentration [µmol per kg dry weight] - Fe: iron concentration [µmol per kg dry weight] - K: kalium concentration [µmol per kg dry weight] - Mn: manganese concentration [µmol per kg dry weight] - S: sulphur concentration [µmol per kg dry weight] - Si: silicon concentration [µmol per kg dry weight] - Zn: zinc concentration [µmol per kg dry weight] - moistureContent: soil moisture content percentage References Bretfeld G (1999) Symphypleona. Synopses on Palaearctic Collembola, Vol. 2 (Dunger), Staatliches Museum für Naturkunde Görlitz Dunger W, Schlitt, B (2011) Tullbergiidae. Synopses on Palaearctic Collembola, Vol. 6/1 (Dunger), Senckenberg Museum of Natural History Görlitz Hekstra A, Dilz K, van Diest A, van den Burg J (1990) Jaarverslag 1989-1990 Bosbemestingsonderzoek in het gemeentebos van Harderwijk. Report [in Dutch] Gemeente Harderwijk, CAS Dronten, LU Wageningen and NMI Den Haag Jordana R (2012) Capbryinae and Entomobryini. Synopses on Palaearctic Collembola, Vol. 7/1 (Dunger), Senckenberg Museum of Natural History Görlitz Karg W (1989) Acari (Acarina), Milben, Unterordnung Parasitiformes (Anactinoichaeta), Uropodina Kramer, Schildkrötchenmilben. Die Tierwelt Deutschlands 67. Teil, VEB Gustav Fischer Verlag, Jena Karg W (1993) Acari (Acarina), Milben, Parasitiformes (Anactinochaeta), Cohors Gamasina Leach, Raubmilben. Die Tierwelt Deutschlands 59. Teil, 2. Überarbeitete Auflage, VEB Gustav Fischer Verlag, Jena Potapow M (2001) Isotomidae. Synopses on Palaearctic Collembola, Vol. 3 (Dunger), Staatliches Museum für Naturkunde Görlitz Siepel H, de Ruiter-Dijkman EM (1993) Feeding guilds of oribatid mites based on carbohydrase enzyme activities. Soil Biol Biochem 25:1491-1497 Siepel H, van de Bund CF (1988) The influence of management practices on the microarthropod community of grassland. Pedobiologia 31:339-354 Soil Survey Staff (1999) Soil Taxonomy: A basic system of soil classification for making and interpreting soil surveys. 2nd Ed. United States Department of Agriculture, Agriculture handbook 436 Weigmann G (2006) Hornmilben (Oribatida). Die Tierwelt Deutschlands 76. Teil, Goecke & Evers, Kelter

Data from: Reproduction probabilities and size distributions of the smooth snake Coronella austriaca in the Netherlands and Norway

The goal of our study was to compare the morphology, survival and frequency of reproduction of Smooth snakes (Coronella austriaca) between The Netherlands and Norway. Individuals caught in the field were measured and identified using photographs. We here archive the raw measurements and individual encounter histories used in the analyses of Dalessi et al. (2021, Amphibia-Reptilia). Field observations were done in the Eindhoven area in The Netherlands (51°27′0″N, 5°28′0″E), and the Oslo area (59°54′41″N, 10°45′29″E) in Norway. In The Netherlands the study area consists of a number of remaining nature fragments of De Peel, a once large moorland area in the South-east of The Netherlands. Fragmentation is largely due to peat extraction and transformation of the former peat bog into farmland. De Peel is located across and along the border of the provinces Noord-Brabant and Limburg. Two large and a number of smaller geographical elements can be distinguished that still show most of the original natural conditions and features of a peat-bog moor. De Groote Peel (1500 ha; a national park) is one of these, the other is a combined area consisting of the Deurnsche Peel (1400 ha) and the adjacent Mariapeel (1400 ha). The vegetation in these sites is dominated by Purple moor-grass (Molinea caerulea). Other plants species that are mainly found are common heather (Calluna vulgaris), cross-leaved heath (Erica tetralix), small trees and different species of peat moss (Sphagnum spp.). In this study we included six locations within these two nature reserves: Groote Peel Yellow track, Groote Peel summer biotope, Groote Peel Noordoostpad, Mariapeel East, and in the Deurnsche Peel: Leegveld and Eikenlaan. In the South of Norway, Coronella austriaca is found mainly in a narrow area along the southwestern coastline. Typical habitat is more or less isolated open areas (surrounded by forest varying in density) with south-facing rocky slopes. Patches of small trees and shrubs are present in these areas and particularly crevices and parts where cracks filled with plant material, loose rocks and stones occur, are the spots where smooth snakes were found. Typical plant species are Scotch pine (Pinus silvestris), juniper (Juniperus communis) and birch (Betula verrucosa). Heather (Calluna vulgaris) is dominating the lower vegetation (Sørensen 2014). This study includes data from 8 different locations (mainly fjord-related habitats) south of Oslo (Sørensen 2014): Pollevannet, Skjelvik, Emmerstad, Bunnefjorden, Eineåsen, Digerud, Tofte and Bleikslitjern. In The Netherlands we searched for smooth snakes during their reproductive season (April/May to August/September) from 2011 until 2015. Visiting frequencies were higher from 2012 onwards (ranging from approximately 40 visits in 2011, 60 visits in 2012, 80 visits in 2013 to around 130 visits during 2014 and 150 visits during 2015, for at least once a week in all years), and were higher in Leegveld and Mariapeel East than in the other areas. Observations in Norway were collected with frequencies varying from 1 to 20 visits per year varying with weather conditions and available time. In The Netherlands, we constructed encounter histories for a total of 110 distinguished individual female snakes. A number of these individuals were observed during multiple years, adding up to a total of 157 observations, 142 of which involved pregnant females and 9 observations non-pregnant females. In 6 cases the pregnancy status was not established with certainty. Females were determined to be pregnant or non-pregnant visually (in many cases the unborn snakes can readily be observed) or by means of palpating in both Norway and The Netherlands (Reading 2004). A number of pregnant females was temporarily held in captivity to determine the number of offspring. Physical traits such as sex, total body length (summation of the snout-vent length and tail length; measured with measuring tape) were recorded. Body mass was determined by use of a scale-beam (Super Samson, 200 g max., increments 2 g). Temperature was recorded as well. Photographs of the heads of all snakes (from above) and first 5-15 cm of dorsal side of the body were taken in order to be able to distinguish individual snakes, based on coloration and markings present on the skin (Sauer, 1994). Each individual was marked with a small dot of green nail polish on the head and thereafter released at the exact same spot where it was captured. In Norway, measurements of participation in reproduction of female snakes were carried out during a varying number of consecutive years between 1982 and 2015. Generally, more observations were made per individual, but for fewer individuals than in The Netherlands. Exact locations of the found individuals were determined and measurements such as total body length, body mass and whether females were pregnant or not were taken using the same methods as in The Netherlands. Females were photographed in order to distinguish between individuals. Encounter histories were constructed for a total of 87 distinguished individual female snakes from Norway. A number of these snakes were observed during multiple years, adding up to a total of 184 observations, 148 of which were determined pregnant, and 29 observations were determined non-pregnant. In 7 cases pregnancy status was not established with certainty

Data from: Predation and survival in reintroduced populations of the Common hamster Cricetus cricetus in the Netherlands

We studied the survival Common hamster Cricetus cricetus in reintroduced populations (La Haye et al. 2020). The dataset contains information about observation intervals based on transmitter data collected during frequent visit to the studied populations. The study was performed in the southernmost part of the Netherlands, in the province of Limburg, in three areas: South (Amby-Heer-Sibbe; 50°50’18’’N, 5°48’32’’E), Centre (Sittard-Puth-Jabeek; 50°57’42’’N, 5°52’45’’E) and North (Koningsbosch; 51°02’41’’N, 5°57’35’’E), further referred to as areas 1, 2 and 3. These are typical agricultural landscapes: relatively open, with a mosaic of grassland, arable fields, small woods, little villages and small roads. Arable fields are approximately a few hectares in size and cereals are cultivated on 15-20% of all fields. Harvest of cereals starts at the beginning of July and continues till the first half of August. In the Netherlands the common hamster is found on arable land with loess or loamy soils, which is only present in Limburg and therefore restricting its range (Kuiters et al. 2010). In our study areas adaptive ‘hamster-friendly’ agricultural management has been established through the implementation of ‘hamster-friendly’ agri-environmental schemes (AES) on several hundreds of hectares. Hamster-friendly management implies cultivation of suitable crops on arable fields like cereals and alfalfa, in combination with harvest restrictions, giving hamsters the chance to survive and reproduce over a longer time period than on regular managed cereal and alfalfa fields (La Haye et al. 2014). This study on hamsters was strongly biased to arable fields with ‘hamster-friendly’ management, arable fields with an AES-scheme, and farmland nature reserves, because almost no hamsters live on regular managed agriculture fields anymore. Transmitters Hamsters in the wild were trapped at the entrance of their burrow from approximately the end of March until the end of October, although trapping was minimal in June-August to prevent damage in standing crops. Hamsters trapped in the wild were brought to a wildlife veterinarian at Burgers Zoo (Arnhem, the Netherlands) for implanting a transmitter. For individual identification all trapped hamsters in the wild also received a pit tag. Normally a wild hamster was released at its burrow within 48 hours after being trapped. Each year about 25% of released captive-bred hamsters were operated to implant a radio transmitter. Implantation of a transmitter was at least five days before their release in the wild. Released captive-bred hamsters were one or two years old, depending on whether they had been used in the breeding program (La Haye et al. 2017). Implantation of transmitters in captive-bred hamsters was done by veterinarians at Blijdorp Zoo (Rotterdam, the Netherlands) and GaiaZOO (Kerkrade, the Netherlands). From 2002 to 2016 a total of 879 different common hamsters, wild and captive-bred, were equipped with a radio-transmitter and followed until their death or loss of the radio-signal. Hamsters that could not be monitored anymore as a result of a failing transmitter/low battery for more than 60 days before eventually being re-trapped alive, were, once re-trapped, treated in our analysis as being new individuals. This specific treatment of re-trapped hamsters is done to prevent overestimation of survival rates. Re-trapping hamsters after more than 60 days mainly happened in early spring directly after the hibernation period. During hibernation hamsters stay underground, which makes re-trapping literally impossible. It is not possible to exactly ascertain the age of a wild-born hamster, but only hamsters weighing at least 200 grams were equipped with a transmitter. We assumed that all trapped hamsters were therefore at least (sub)adults and capable of reproduction. Monitoring survival All hamsters with a transmitter were located once a week or once every two weeks during the active season, from mid March till mid October, and at least once in every two or three weeks during winter months (November till February). Each hamster was tracked at its burrow during daylight hours, after dawn and before sunset. Hamsters which could not be located during regular monitoring events, were searched for extensively around the last known location as soon as possible. Most of the missing hamsters or transmitters, were relocated within 500 meters from the last known location (van Wijk et al. 2011). Electric fences and spotlight hunting of foxes In some areas and years enclosures were made with an electric fence around suitable fields to protect hamsters inside these enclosures. These enclosures excluded foxes and other large ground-dwelling predators like badgers and dogs, but enclosures were open for aerial predators and small mustelids (Kuiters et al. 2010; Villemey et al. 2013). The number of enclosures with an electric fence ranged from one to four per year and enclosures were randomly distributed over all areas, but with a mean of two enclosures per year. On average, these enclosures with an electric fence protected an area of two till three hectares. Regular daylight hunting of foxes was allowed in all years in all areas, but spotlight hunting during the nightly hours, after sunset and before sunrise, was only allowed with a special permit. The intensity of spotlight hunting therefore varied between years and areas. Spotlight hunting was intensified in the last four years of the project. hamsterdata.csv The dataset contains 9083 records of intervals over which hamster survival is assessed. We explain each of the variables here: ID = individual identifier of the studied hamsters male = sex of the hamster: 0 = female, 1 = male year = year of (the midpoint of) the observation interval midDay = midpoint of the observation interval, in day of the year (1 Jan = 1) isSummer = whether (1) or not (0) the midpoint of the interval was in summer (midDay>74 & midDay<289) days = length of the observation interval in days area = identity of the study area (1, 2 or 3) captiveBred = whether the hamster was captive bred (1) or wild (0) daySinceRelease = number of days since the release of the hamster (at the time of the midpoint) enclosure = whether (1) or not (0) the hamster was last observed within an enclosure with electric fencing (unknown in 1 case: NA) spotlight = whether (1) or not (0) spotlight hunting of foxes was allowed at the site and time of the observation interval surv = whether (1) or not (0) the hamster survived the observation interval; NAs signal the 238 cases in which we could not determine the fate of the hamster References Kuiters L, La Haye M, Müskens G, van Kats R (2010) Perspectieven voor een duurzame bescherming van de hamster in Nederland. Rapport Alterra, Wageningen La Haye MJJ, Reiners TE, Raedts R, Verbist V, Koelewijn HP (2017) Genetic monitoring to evaluate reintroduction attempts of a highly endangered rodent. Conserv Genet 18:877–892 La Haye MJJ, Swinnen KRR, Kuiters AT, Leirs H, Siepel H (2014) Modelling population dynamics of the common hamster (Cricetus cricetus): timing of harvest as a critical aspect in the conservation of a highly endangered rodent. Biol Conserv 180:53–61 La Haye MJJ, van Kats RJM, Müskens GJDM, Hallmann CA, Jongejans E (2020) Predation and survival in reintroduced populations of the Common hamster Cricetus cricetus in the Netherlands. In preparation van Wijk R, La Haye MJJ, van Kats RJM, Müskens GJDM (2011) Movement characteristics of the common hamster (Cricetus cricetus) in Limburg, the Netherlands. Säugetierkundliche Informationen Band 8, Heft 42, pp 79-92. Proceedings of the 16t and 17th Meeting of the International Hamster Workgroup; Ranis, Germany (2009), Gödöllö, Hungary Villemey A, Besnard A, Grandadam J, Eidenschenck J (2013) Testing restocking methods for an endangered species: Effects of predator exclusion and vegetation cover on common hamster (Cricetus cricetus) survival and reproduction. Biol Conserv 158:147–15