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R scripts and associated data files
No full textThis dataset is composed of the R Markdown files that contain the R scripts for preparing the data, estimating and evaluating ecological niches, randomization tests to explore the effect of time period assignment on the niche overlap tests, and evaluating the relationships between lithic technology and environmental suitability. All of the data files called in the various R scripts are included in this dataset
Seine: Le chemin de halage de Chatou au Pecq (1774)
No full textCarte géoréférencée portant la date du 2 août 1774.
Elle a pour visée d'informer de l'emplacement du chemin de halage sur une partie en aval de la Seine à partir de Chatou. Le chemin est lavé de rouge, ce qui signifie qu'il est construit en maçonnerie. La ligne et le sens de navigation sont figurés. Ce chemin de halage permettait la traction des bateaux pour remonter le cours d'eau, soit par des hommes soit par des animaux. Les îles bordant la Seine sont déjà reliées par des digues à Chatou et à Croissy.
Service des Cartes et Plans des Archives Nationales. Cote AN F/14/10078/1/14
Numérisation en 2014. Géoréférencement en 2014 par Julie DAVODET. Mise en ligne en avril 2015. Métadonnées par Julie DAVODET et Juliette AUDET.</p
Replication data for: Fig 11.1, Top right, GPDs, Colony sizes and compositions by year, 18 Dec 2025
No full textFILE DESCRIPTION
Keywords: Gunnison's prairie dog, Colony sizes and colony compositions by year
File name = Fig 11.1, Top right, GPDs, Colony sizes and compositions by year, 18 Dec 2025
SM males = sexually mature GPD males, some of them yearlings
SM females = yearling and adult fems, all of which copulated,
with 1-2 possible exceptions
SIM yrl males = sexually immature yearling males, for which
we found no evidence for copulation from either behavior
or reproductive condition
SOME gunnison males DID copulate as yearlings. If so, then I
show these sexually active yearlings males as SM males
These data have been checked TWO TIMES on 13 April 2020
SM = Sexually Mature = Sexually Active
SI = Sexually Immature = Sexually Inactive
YRL = Yearling
Colony sizes are and other counts are for May of each year. If a GPD was alive for any
part of May, then I used him or her in my calculation of Colony
size--unless the UPD disappeared in the first day or two of May
OLDFile name = GPDs, Colsize, colcomps, babies, 13 April 2020
This file checked TWO TIMES by JLH on 31 March 2020.
Note: These three GPD data sets are from THREE DIFFERENT STUDY SITES.
PEFO = Petrified Forest National Park
RMC = Redondo Meadow Colony of Valles Caldera National Preserve
VCC = Visitor Colony of Valles Caldera National Preserve
Remember: For all three GPD colonies, I studied PART OF ONE LARGE COLONY
I call that part the "Study site" or "Study area. "For more details on this point, see Chapters 4, 9, and 11.
On 24 June 2020, I deleted 91 and BB6 from 31-R19A in 1994
This change affected colony size and colony density
and also clan size and clan density and also number of SM females
OLD File name = GPDs, Colsize, colcomps, babies, 25 June 2020
These data used for Fig 11.1 in Hoogland 2026.
This file ready for longterm storage on 15 Feb 2025.
Note: Counts of emergent juveniles in this EXCEL file INCLUDE babies never captured
Weanling = juvenile at first emergence from the natal burrow entrance = baby
Colony size = number of adults and yearlings in May
For this EXCEL file, adult = prairie dog that was >=2 years old
For this EXCEL file, yearlings were young adults that emerged from the natal nursery-burrow >9 months ago, but <20 months ago.
File name = Fig 11.1, Top right, GPDs, Colony sizes and compositions by year, 18 Dec 202
Aisne: Plan d'un canal en aval de Neufchâtel (1837)
No full textPlan détaillé d'un tracé d'un canal latéral projeté pour le prolongement de la navigation du canal des Ardennes dans la vallée de l'Aisne en aval de Neufchâtel. Portion comprise entre l'écluse de Brienne (dernière écluse du canal des Ardennes) et la fin du coteau de Pignicourt.
Carte réalisée par Marcilly, ingénieur en chef des Ponts et Chaussées, publiée à Soissons le 3 janvier 1837.
La carte indique un projet qui a effectivement été en partie réalisé : autorisés en 1837, les travaux ont débuté en 1838. Le canal a été ouvert à la navigation entre 1841 et 1843. Il a été modifié par les travaux effectués dans le cadre du plan Freycinet à la fin du XIXe siècle.
Ici les teintes conventionnelles sont légendées, ce qui est rare. On remarque que les couleurs se sont atténuées avec le temps car la différence entre les couleurs des bois et des prés est plutôt ténue.
Raster GeoTIFF : EAT_Aisne_Neufchatel_1837.tif
Service des Cartes et Plans des Archives Nationales. Cote AN F/14/10049/1/14.
Numérisation en 2014. Géoréférencement en 2014 par Julie DAVODET. Métadonnées par Julie DAVODET et Juliette AUDET. Mise en ligne en avril 2015.</p
Chronic: HTML template with JavaScript for social-ecological timelines
No full textThis small HTML file allows for the representation of events on a timeline.
It serves as a replacement for ZATimeline, a tool for visualizing timelines.
Users can use this template to plot their own data on a webpage.
Short version of the user guide (full version in the file):
Open the HTML file using Visual Studio Code or any other text editor.
Update the data using the same format.
View the result in an internet browser.
Please keep the citation to assist readers and future users
Seine: Plan général du cours de la Seine à Paris (19ème siècle)
No full textPlan général du cours de la Seine à Paris, en vue de l'amélioration de la navigation de celle-ci.
Cette carte, qui date du 19ème siècle, a été réalisée à l'encre, au lavis et à l'aquarelle. Elle est non signée.
Il manque un morceau de la carte mais cela n'entrave pas la représentation du cours de la Seine.
Certains édifices ou quartiers sont indiqués en noir, comme l'ancienne Halle aux vins, le Louvre et la cathédrale Notre-Dame.
Raster GeoTIFF : EAT_Seine_Paris_Plan_General_1850.tiff
Service des Cartes et Plans des Archives Nationales. Cote AN F/14/10078/2/55.
Numérisation en 2015. Géoréférencement en 2015 par Juliette AUDET. Métadonnées par Juliette AUDET. Mise en ligne en juin 2015
Herbicide-induced metabolic changes in a plant-aphid system: How soil bacteria drive the fate and impact of an environmental dose of Isoproturon
No full textThe intensification of agriculture, based on massive use of pesticides, led to the widespread contamination of terrestrial ecosystems. Although soil contaminations with pesticide residues have been demonstrated, their impacts on terrestrial biotic interactions remain unclear. To address this matter, we studied the effects of an environmental dose of a photosynthesis inhibitor herbicide (isoproturon) on an isoproturon-degrading soil bacteria-poacea-aphid system in the lab, mimicking below and aboveground interactions within buffer strips. We found that isoproturon and its main degradation product flow through this system, accumulating in plant shoots. No macroscopic effect of the herbicide was observed but metabolic shifts occurred in both plants (especially when exposed for a short time) and phytophages. Inoculation of isoproturon-degrading bacteria in the substrate suppressed most of these effects but some metabolic reshuffles in the longer run suggest secondary effects of Isoproturon degradation products. Moreover, inoculation of the non-degrading bacterial strain also impacted plant metabolism, underlying the close link between soil microbiota and aboveground organisms. This study shows that pesticide residues can transfer in terrestrial trophic networks, altering the physiology of each biological level, and highlights the importance of considering plant-bacteria interactions when assessing the response of semi-natural ecosystems to chronic contamination
Marne: Cours de la Marne de Bercy à Troissy (1836)
No full textEnsemble de sept feuilles qui présentent le cours de la Marne depuis l'embouchure de la Seine à Bercy jusqu'à Troissy. Les cartes ont été élaborées en 1836. La feuille 5 entre Ussy-sur-Marne et Nanteuil-sur-Marne n'existe plus.
Feuille 1/7 : de Bercy à Bry-sur-Marne : EAT_Marne_Bercy_Troissy_1836_1.tif
Feuille 2/7 : de Joinville-le-Pont à Cornetin : EAT_Marne_Bercy_Troissy_1836_2a.tif et EAT_Marne_Bercy_Troissy_1836_2b.tif
Feuille 3/7 : de Chessy à Meaux : EAT_Marne_Bercy_Troissy_1836_3.tif
Feuille 4/7 : de Meaux à Saint-Jean-les-Deux-Jumeaux : EAT_Marne_Bercy_Troissy_1836_4.tif
Feuille 6/7 : de Crouttes-sur-Marne à Fossoy : EAT_Marne_Bercy_Troissy_1836_6a.tif et EAT_Marne_Bercy_Troissy_1836_6b.tif
Feuille 7/7 : de Fossoy à Troissy : EAT_Marne_Bercy_Troissy_1836_7a.tif et EAT_Marne_Bercy_Troissy_1836_7b.tif
Service des Cartes et Plans des Archives Nationales. Cote AN F/14/10068/1/15a.
Numérisation et géoréférencement en 2015 par Juliette AUDET dans le cadre du projet Archiseine (PIREN-Seine - Archives Nationales).</p
Replication Data for: "Genomic Signatures of Microgeographic Adaptation in Anopheles coluzzii Across Urban, Rural, and Forested Environments in Gabon"
No full textThese data are accompanying the manuscript: "Genomic Signatures of Microgeographic Adaptation in Anopheles coluzzii Across Urban, Rural, and Forested Environments in Gabon" by Daron J, Bouafou L, Tennessen J, Rahola N, Makanga B, Ousman, A-E, Ngangue MF, Longo Pendy, NM, Paupy C, Neafsey, DE, Fontaine MC*, & Ayala D*. (Co-last authors).
Codes and scripts supporting this study are available here: https://github.com/jdaron/wilding.git .
Raw sequencing data generated as part of this project are available on NCBI under the Bioproject PRJNA1261573
Replication data for: Fig 7.2, Focal samples, WTPDs, male-0 and female-RR2, 05 Nov 2025
No full textFILE DESCRIPTION
Keywords: focal samples, WTPDs, for male-0 and female-RR2
Filename = Fig 7.2, Focal samples, WTPDs, male-0 and female-RR2, 05 Nov 2025
OLD Filename = WTPDs, focal times from 2012, 26 April 2022
I used data from this file WTPD for male-0 and WTPD female-RR2 in 2012.
All these focal times from spring 2012
This file checked by Julia Phillip in Fall 2021
I checked Julia's entries, and made only a few trivial changes on 26 April 2022
I did a another quick check of this file in December 2021.
For statistical analyses of focal samples, I used data from a single overall percentage for the entire field season
calculated from single percentages of vigilance from focal samples per day per individual.
WTPD marker = Nyanzol dye marker. No information from eartags in this file.
Note, however, that all data are from a single year (2012).
These data used for Fig 7.2 in Hoogland 2026 for WTPD male-0 and WTPD female-RR2 in 2012.
To do that, I did searches for data for male-0 and female-RR2
This file ready for longterm storage on 30 May 2025.
This file does NOT include data from focal samples from Hoogland 1979 = The effect of colony size on individual
alertness of prairie dogs (Sciuridae: Cynomys spp.). Animal Behaviour 27:394-407.
Also, this file does NOT include information from Hoogland et al 2013 = Individual variation in vigilance
among white-tailed prairie dogs (Cynomys leucurus). Southwestern Naturalist 58:279-285.
Hoogland et al. 2013 has information from SCAN SAMPLES, and that information is in a different EXCEL file.
I have NOT purlished these data on WTPD focal times previously.
Notice that this file is not sorted BY INDIVIDUAL WTPD. I did that to get the "Single estimate per individual of
vigilance from focal samples = 8.75%+ 3.03 % (Mean + SD) depicted in Figure 7.1.
This file thus contains ALL RAW DATA for WTPD focal samples for Fig 7.1.
The raw data in this file comes from 50 different WTPDs. Note that N = 105 for SCAN SAMPLES.
These data used for Fig 7.2 in Hoogland 2026.
This file ready for longterm storage on 27 May 2025.
For sex, M = male and F = female
Filename = Fig 7.2, Focal samples, WTPDs, male-0 and female-RR2. 05 Nov 202