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Replication data for: Fig 10.3, BGUW, Percentage of males of Multi-male coteries and clans with close kinship, 11 Dec 2025
No full textFILE DESCRIPTION
Keywords: BGUW, Kinship of males in multi-male coteries or multi-male clans
File name = Fig 10.3, BGUW, Percentage of males of Multi-male coteries and clans with close kinship, 11 Dec 2025
OLD File name BGUW, Percentage of males in multi-male clans with close kinship (r >= 0.2500), 12 Feb 2025
Data are only from Multi-male coteries and clans for which I could be confident
about possible kinship of the copulating males; for several other coteries and
I could not be confident about possible kinships of the copulating males
(N = 0 for black-tailed prairie dogs, N = 7 for Gunnison’s prairie dogs,
N = 34 for Gunnison’s, prairie dogs, and N = 0 for white-tailed prairie dogs).
The number above each bar is the number of dyads of copulating males for which I knew kinships.
These data checked TWO times.
These data used for Figure 10.3 in Hoogland 2026.
This file ready for longterm storage on 12 Feb 2025.
For this figure, I paired each copulating male with every other copulating male in the home Multi-male coterie or clan.
A two-male Multi-male coterie or clan had only one dyad (A x B),
a three male Multi-male coterie or clan had three dyads (A x B, A x C, B x C), and so on.
File name = Fig 10.3, BGUW, Percentage of males of Multi-male coteries and clans with close kinship, 11 Dec 202
Containerised programs used in "Combining Annotation Software to Identify Orthologous genes (CASIO) provides a new dataset of orthologous genes for swallowtail butterflies"
No full textThese are Singularity containers used in the Snakemake pipeline CASIO: Combining Annotation Software to Identify Orthologous genes. This pipeline is described in the manuscript “Combining Annotation Software to Identify Orthologous Genes (CASIO) Provides a New Dataset of Orthologous Genes for Swallowtail Butterflies” by Vigo et al. (2025).
The Snakemake workflow and instructions for its use are available at :
https://github.com/Gwenaelle-Vigo/CASIO.
The containers are called directly by CASIO and are automatically downloaded by the installation script provided in the GitHub repository. Please read the full documentation on how to use CASIO here:
https://github.com/Gwenaelle-Vigo/CASIO.
repeatM.sif : contains RepeatModeler 2.0.7, RepeatMasker 4.2.0 and BRAKER2
Busco.sif : BISCO 5.8.2
miniprot_scipio.sif : Miniprot 0.13, Scipio 1.4
cleaning_orthology.sif : see https://github.com/Gwenaelle-Vigo/CASIO
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Replication data for Fig 5.3, Middle , BGUW, fleas per adult in May or June,13 Oct 2025
No full textFILE DESCRIPTION
Keywords: BGUW, fleas per adult, May-June
File name = Fig 5.3, Middle, BGUW, fleas per adult in May or June, 17 Sept 2025
I used these data for Fig 5.3, middle graph, of Hoogland 2026
Numbers shown are means + one standard error (SEM)
The number above each SE line indicates the number of adult prairie dogs
examined for fleas during marking and handling (details in Hoogland 2026)
WTPD = white-tailed prairie dog BTPD = black-tailed prairie dog
GPD = Gunnison's prairie dog WTPD = white-tailed prairie dog
BGUW = black-tails, gunnisons, utahs, and white-tails
All data for flea-counts in this figure are from ADULT prairie dogs only--i.e., no data from juveniles.
Data from flea counts from JUVENILE prairie dogs are in Fig 5.3, Bottom Graph
I used only one flea-count per adult prairie dog per time-period.
These data ready for longterm storage on 17 Sept 2025.
Note: these data are summaries only. Most of the raw data are in
EXCEL file = BGUW, Final flea and body masses, 14 Jan 2025.
See figures 3.5 and 3.6 for intersexual differences in flea-counts for adults and juveniles.
Note: these data are summaries only. Most of the raw data are in
EXCEL file = BGUW, Final flea and body masses, 14 Jan 2025
Replication data for: Fig 9.7. BTPDs, copulating males and copulating females vs coterie size, 04 Dec 2025
No full textFILE DESCRIPTION
Keywords: BTPDs, coterie size, copulating males, copulating females
File name: Fig 9.7. BTPDs, copulating males and copulating females vs coterie size, 04 Dec 2025
OLDFile name = BTPDs, Revised, SM and SI fems per coterie, 02 May 2020
* = Change made on 14 or 15 April 2020
Note well: These numbers are for MAY. Prior to today, most of my BTPD counts are from APRIL.
For example, all data for coterie sizes in Hoogland 1995 are for APRIL rather than May.
For this table, SM male = sexually mature male, including some BTPD yearling males that copulated.
Adfem = >=2 year old female. I do NOT score yearlings that copulated as Adfems for this table.
If a BTPD male was >=2 years old but showed not evidence of sexual activity (No PS [Pigmented Scrotum],
No DT [Descended Testes] or no observed copulations), then I scored that male as a SI male.
SI male = sexually inactive in year of observation
On 15 April 2020, I check everything in this table TWO TIMES.
On 01 May 2020, I include fems that did not cop, and I add yearling fems that copped or weaned a litter
On 01 May 2020 I also compute the column of SM-Allfems. This column includes (a) adult BTPD fems
that copped; (b) subtracts fems that did NOT cop; and (c)adds yearling fems that either copped or weaned
a litter.
Adfems-No cop = adult BTPD fems that did not cop--to be subtracted to compute SM-Allfems
Yrlfens w/cop = yearling BTPD females that either copped or weaned a litter.
This file has been checked TWO TIMES on 01 May 2020
SM = Sexually Mature
SI = Sexually Immature
YRL = yearling = one-year old
In 1986, R51 and R76 came into estrus two times. In 1987, R71 came
into estrus two times. I score each of these double-estrus females
one time only in this file. I also scored several double-estrous
ADULT FEMALES one time only in this file.
This file has been checked TWO TIMES on 02 May 2020
This file does NOT contain data for the 48 coterie in 1978 or the 49A coterie in 1980
For the 00 clan in 1985, I only use data for coterie size and coterie type
These data used for Figure 9.7 in Hoogland 2026.
This file ready for longterm storage on 04 Feb 2025.
coterie size = number of adults and yearlings in home coterie territory
cottype = type of coterie
cottype = 0 = no-male coterie
cottype = 0.5 = half-male coterie
cottype = 1 = one-male coterie
cottype = 2 = multi-male coterie
See Chapter 10 of Hoogland 2026 for descriptions of coterie types
File name: Fig 9.7. BTPDs, copulating males and copulating females vs coterie size, 04 Dec 2025
76 = 1976, 80 = 1980, 87 = 1987, etc
Extant Ethiopian Cercopithecids
No full textThis dataset contains dental microwear surfaces (on both crushing and shearing molar facets) of extant wild-sampled specimens of 4 species cercopithecids from Ethiopia and stored in different institutions. details are given in Read.me file. See also "Template" and "List of specimens"
Replication data for: Fig 11.1, Lower right, WTPDs, Colony sizes and compositions by year, 18 Dec 2025
No full textFILE DESCRIPTION
Keywords: white-tailed prairie dog, Colony sizes and colony compositions by year
File name = Fig 11.1, Lower right, WTPDs, Colony sizes and compositions by year, 18 Dec 2025
OLDFile name = WTPDs, Colony sizes + babies, 15 Oct 2021
Revisions on 15 May 2021
On 15 October 2021, I change Sexually inactive males in 2011 to 9 (from 10)
On 15 October 2021, I change colony size in 2011 to 49 (from 50)
SM = Sexually Mature = Sexually Active
SI = Sexually Immature = Sexually Inactive
Yrl = Yearling
Colony sizes are for May of each year. If a WTPD was alive for any
part of May, then I used him or her in my calculation of Colony
size--unless the WTPD disappeared in the first day or two of May
OLDFile name = WTPDs, Colony sizes and babies, 31 March 2020
Sexually mature/active males = sexually mature WTPD males, some of them yearlings
Sexually mature females = yearling and adult WTPD female, all of which copulated,
with 1-2 possible exceptions
Sexually immature yearling WTPD males = yearling WTPD male for which
we found no evidence for copulation from either behavior
or reproductive condition
SOME WTPD males DID copulate as yearlings. If so, then I
show these sexually active yearlings males as Sexually mature males
Colony size = number of adults at yearlings at colony-site in May.
These data used for Fig 11.1 in Hoogland 2026.
This file ready for longterm storage on 15 Feb 2025.
All data from the WTPD Study-colony at Arapaho National Wildlife Refuge in Colorado.
Note: Counts of emergent juveniles = weanlings in this EXCEL file INCLUDE weanlings never captured
Weanling = juvenile at first emergence from the natal burrow entrance = baby
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, Lower left, UPDs, Colony sizes and compositions by year, 18 Dec 202
Replication data for: Fig 8.14, Bottom, Submergers vs nonsubmergers, WTPDs, 21 Nov 2025
No full textFILE DESCRIPTION
Keywords: alarm call, submerger vs nonsubmerger, WTPDs
File name = Fig 8.14, Bottom, Submergers vs nonsubmergers, WTPDs, 21 Nov 2025
Date = 10 April 2019 = date of creation for this file
These data are from WTPDs at the Arapaho National Wildlife Refuge
from 2006 through 2012
292/956 WTPD submergers = 30.54 % DID give alarm call
664/956 WTPD submergers = 69.46% DID give alarm call
804/1536 WTPD NON-submergers = 52.34 % DID give alarm call
732/1536 WTPD NON-submergers = 47.66% DID give alarm call
Variable = Frequency = number of observations of calling or non-calling for
each class of WTPD
All data were summarized by Judy, and checked by Judy and John TWO TIMES
File name = Fig 8.14, Bottom, Submergers vs nonsubmergers, WTPDs, 21 Nov 2025
For statistical analysis, I did a 2x2 chi-square test
These data used for Fig 8.14, Bottom, in Hoogland 2026.
This file ready for longterm storage on 04 June 2025.
Counts for this file come from study of alarm call raw data sheets.
I considered data from the same prairie dog
on the same day and on different days and in different years to be independent.
Data in this file represents SUMMATION OF UPD DATA FROM ALL YEARS
Variable = Frequency = number of observations of calling or non-calling for
WTPDs that did and did not submerge during experiments with the moving stuffed badger
Submerger = 1 = prairie dog DID submerge
Submerger = 2 = prairie dog did NOT submerge
Alarm call = 1 = prairie dog DID give alarm call
Alarm call = 2 = prairie dog did NOT give alarm cal
multiCAFE Protocol, data sample, analysis tools and 3D experimental cages
No full textSet of tools and data samples illustrating how to measure the feeding behavior in insects like Drosophila melanogaster, the fruit fly. Individual flies contained in small 3D printed cages are given access to calibrated capillaries containing a colored liquid. A webcam is used to take images at regular intervals. The stack of images is then analyzed to extract how much liquid is ingested by the flies. This collection regroup files describing how to run such experiments (called multiCAFE), how to analyze the images and stl files to 3D-print the cages used to collect data. This collection is associated with a STAR Protocols manuscript in preparation
Replication data for: Fig 5.11, BTPDs, Intercolony synchrony, 22 Oct 2025
No full textFILE DESCRIPTION
Keywords: BTPDs, Intercolony synchrony, weaning dates
File name = Fig 5.11, BTPDs, Intercolony synchrony, 22 Oct 2025
Numbers are for dates in May or June 1979 and three BTPD colonies:
Monte, Pringle, and Rankin Ridge
Numbers show number of first emergences for each date at each colony
These data were double-checked and revised on 05 July 2025
This file ready for longterm storage on 25 January 2025
This file used for Fig 5.11 of Hoogland 2026
Date = first juvenile emergence = approximate date of weaning
I do not have comparable data on intercolony for any other species
For date in May or June, 14 = 14 May, 15 = 15 May, 31= 31 May,
32 = 01 June, 33 = 02 June, 44 = 13 June, etc.
Pringle and Rankin Ridge colonies were about 1 kilometer apart,
and Monte colony was about 7 kilometers away from Pringle colony
Data in this EXCEL file are RAW DATA.
Mean dates of first juvenile emergences are shown within Fig 5.11
Data used in the article: "Phenotypic plasticity as a function of genetic polymorphism: thermal dominance reversal in Drosophila species with contrasting melanism"
No full textThis archive contains the data used in the following article: "Phenotypic plasticity as a function of genetic polymorphism: thermal dominance reversal in Drosophila species with contrasting melanism". It is composed of 15 data text files, 16 text files describing commands and statistical analyses in R, 4 perl script text files, 81 photo files in jpg format, and 1 readme text file describing the content of the archive