DOI: 10.5281/zenodo.7614878
title: MicromAsia: small mammal surveys in Western China and Kyrgyzstan (1994-2014)

description: This dataset corresponds to surveys carried out in Asia (western China and Kyrgyzstan) between May 1994 and August 2014 as part of the research expeditions of Patrick Giraudoux and his team. It includes:



Traplines set up and small mammal captured. The corresponding collection of skulls, specimens and tissues has been donated to the Museum National d'Histoire Naturelle, Paris since the 22nd of November 2022.

Activity index transect walked to provide abundance estimates over a larger range than possible using trapping methods

Miscellaneous supplementary files and trapline photos.


Main files

Traplines.txt   This file is a table that describes the 787 traplines or trap clusters or circumstances by which small mammal specimens have been captured. Some traplines can have  no capture. This is a point to consider when trapping success is computed joining the trapline table to the capture table. Those two tables can be joined using the field 'idLine'. For more details about sampling design, trap types, distance between two traps, etc. please refer to the articles published using those data (see references on this web page).



nameStudysite, name of the survey site

country, country ISO code

countryName, country name

province, province name

idLine, trapline ID code: digits #1-2 location ID, digits #3-4 year, digits  #5-6 month, digits #7-8 line number. The two latter digits can be coded on numbers 01, 02, 03... or on letters AA, AB, AC,...

sLongitude, longitude of the trapline beginning (for surveys carried out before 1998 included, GPS receivers were not available: geographical coordinates are those of the nearest village, whose name is given in the field 'nameStudysite', and the position of trapline is given relative to this village (see field 'emplacementMethod' = CoordCloserVillage and 'distVillage' and 'azimuthVillage')

sLatitude, latitude of the trapline beginning (for surveys carried out before 1998 included, GPS receivers were not available: geographical coordinates are those of the nearest village, whose name is given in the field 'nameStudysite', and the position of trapline is given relative to this village (see field 'emplacementMethod' = CoordCloserVillage and 'distVillage' and 'azimuthVillage')

eLongitude, longitude of the trapline end

eLatitude, latitude of the trapline beginning

cLongitude, longitude of the trapline centroid (for surveys carried out before 1998 included, GPS receivers were not available: geographical coordinates are those of the nearest village, whose name is given in the field 'nameStudysite', and the position of trapline is given relative to this village (see field 'emplacementMethod' = CoordCloserVillage and 'distVillage' and 'azimuthVillage')

cLatitude, latitude of the trapline beginning (for surveys carried out before 1998 included, GPS receivers were not available: geographical coordinates are those of the nearest village, whose name is given in the field 'nameStudysite', and the position of trapline is given relative to this village (see field 'emplacementMethod' = CoordCloserVillage and 'distVillage' and 'azimuthVillage')

altitude, altitude

emplacementMethod, way location is recorded: CoordCloserVillage, distance and direction of the nearest village (used on a time when GPS receivers were nor available); GPS, geographical coordinates; unknown

distVillage, distance to the nearest village (in m)

azimuthVillage, bearing direction to the nearest village

habitat, habitat description

campagneObs, month and year of the survey

campagneObsBegin, date of the beginning of the survey

campagneObsEnd, date of the end of the survey

traptype, trap type (see e.g. Traptypes.pdf for some  illustrations):



INRA, INRA trap

sbbt, small break back trap

apporté, brought by people

apporté (?), possibly brought by people

BBBT, big break back trap

sSherman, small Sherman trap

BSHERMAN, big Sherman trap

CAGE, cage trape

tong, tong trap

attrapé à la main, caught by hand

road, found dead along a road

trouvés, found

assommoir, deadfall trap

tong trap, tong trap

bbbt, small break back trap

child, brought by a child

collet, snare

BBBT ou jaw, big break back trap or jaw trap

jaw, jaw trap



remarks, remarks

nbControlNights, number of control nights (traps were set up during the day and controlled every morning)

nbTrapsInstal1, number of traps set up

nbTrapsRecov1, number of traps recovered on first control

nbTrapsRecov2, number of traps recovered on control #2

nbTrapsRecov3, number of traps recovered on control #3

nbTrapsRecov4, number of traps recovered on control #4

nbTrapsRecov5, number of traps recovered on control #5


CapturesV2.txt

This file is a table that describes the 2178 animals captured.  As a  table, it can be joined to the trapline table using the field 'idLine'. Animals with an idMNHN have had their skulls and sometimes other body parts deposited at the Museum National d'Histoire Naturelle in Paris.



country, country ISO code

idCapture, Capture ID code: digits #1-8 trapline ID, see field 'idLine' of Traplines.txt for details, digits #9-10 capture ID in the trapline

numControlNight, number of the control night

dateControlNight, date of the control night

labCode, code for the laboratory

speciesField, species as identified in the field; for abbreviations see SpeciesNames.txt 

species, species as confirmed in the lab

sex, M male; F female.

reproducing T true; F False

remarks

HeadBodyLength, head-body length

UterusDiameter (mm)

WholeBodyWetmass, body mass (g)

EarLength (mm)

ToesForelegNb, number of toes (foreleg)

ToesHindlegNb, number of toes (hintleg)

ClawLength (mm)

TailLength (mm)

TailQuiffLength (mm)

HindFootLength (mm)

CristallineLensNb, number of crystalline lens weighed (sometimes only one could be taken)

CristallineLensDrymass, dry mass of the crystalline lens weighed (one or two together according to 'CristallineLensNb'

TesticleLength (mm)

TesticleWidth (mm)

SeminalVesicleLength (mm)

SeminalVesicleWidth (mm)

PlacentaScarsNb, number of placental scares

EmbryosNb, number of embryos

idLine, ID of the trapline where the animal was caught

idMNHN, MNHN ID


Parasites.txt 

Livers and general cavity were generally examined visually to identify macroparasites such as cestode kysts or nematodes with a particular attention for Echinococcus multilocularis metacestodes. Additionnal informations on parasites might have been reported in the field 'remarks' of Captures.txt. As a  table, it can be joined to the capture table using the field 'idCapture'



country, country ISO code

idCapture, Capture ID code see field idCapture of Captures.txt 

species, parasite species name: "?" or  "99" = unknown (generally a small unidentifiable white dot);  "CH" =  Capillaria hepatica  (sometimes in full "Capillaria hepatica"); "Em"  =  Echinococcus multilocularis (sometimes in full "Echinococcus multilocularis");   "Taenia" ;  "Taenia crassiceps"; "Taenia taeniformis"

number


Transects.zip 

Transects were used to sample open habitats such as grassland, arable fields etc., for species that leave conspicuous activity indices on the ground surface, in order to provide abundance estimates over a larger range than possible using trapping methods. For each transect, 10 paces intervals were surveyed with activity indicators identifiable to species or genus level (including foraging corridors, ground holes, earth tumuli and small mammal faeces) recorded. Except for Sary Mogol, Kyrgyzstan, where transect were walked on twenty 10-paces intervals centred on the nodes of a grid, transect routes were selected opportunistically under accessibility constraints in order to cross the largest portion of each habitat patch. They were recorded via Global Positioning System receivers with an approximate 15 m accuracy. The zip file includes the followings:



Transect file descriptions.rtf, the description of the fields of each transect table

Transects_Honlong_2007_09.txt, transects walked near HongLong, China, in September 2007

Transects_Narati_2006_09.txt, transects walked near Narati, China, in September 2006

Transects_Ningxia_2003_09.txt, transects walked in Ningxia, China, in September 2003

Transects_SaryMoghul_2012_2014.txt, transects walked near Sary Moghul, Kyrgyzstan, in May 2012 and August 2014

Transects_Serxu_2002_07.txt, transects walked near Serxu, China, in July 2002

Transects_Tuotuohe_2006_07.txt, transects walked on the way from Xining to Tuotuo He, China, in July 2006


Supplementary files

1MapStudyAreas.jpg Map of the main areas surveyed

DNA_sequencing.txt table of the specimens whose DNA has been sequenced



ind_number, Capture ID code: see field 'idCapture' in Captures.txt 

ID_lab, lab identification label

Species_DNA, species as identified by DNA sequencing

laboratory, people and/or lab who performed the analysis

ID morphometry/karyotype, species as identified by morphology + karyotype


Photos_traplines.zip Photos of traplines and habitats for the following surveys



Honglong, CN, September 2007

Maerkang, CN, September 2005

Narati, CN, September 2006

Ningxia, CN, September 2003, July 2012

Rantang, CN, June 2004

Sary Mogol, KG, April 2008

Serxu, CN, July 2002


SpeciesNames.txt Abbreviations, latin, English, French names of species



Code, code on 4 digits

Nom latin, latin name

Nom commun (Anglais), common name (English)

Nom commun (Français), common name (French)

Remark


Small_mammal_measurements.pdf Method for small mammal sampling and measurements.

TrapLocationCodes.txt Codes for the location of traplines



Location, location name

Symbol, symbol (first two digits of idLine in Traplines.txt 

Province, province name

Trapping, remarks about sampling design


Traptypes.pdf  Samples of small and big break back traps, tong trap and INRA trap. 
description: Sample collection has been undertaken with the help of countless people who have regularly or occasionally participated. Among them (alphabetical order of the surname): Eve Afonso, Bao GenShu, Nadine Bernard, Carole Bodin, Michael Coeurdassier, Thomas Déforêt, Pierre Delattre, Kurt E. Galbreath, Patrick Giraudoux, Akira Ito, Li Li, Li TiaoYing, Li WenKe, Wulamu Mamuti, David Pleydell, Qi XinWei, Qiu Jiamen, Jean-Pierre Quéré, Francis Raoul, Dominique Rieffel, Thomas Romig, Renaud Scheifler, Kenichi Takahashi, Nicolas Tete, Amélie Vaniscotte, Wang Junli, Wang Qian, Wang XiaoMing, Torsten Wassermann, Yang Yurong, Jean-Christophe Weidmann, Wen Hao, Yang Wen, Zhou Hongxia, Iskender Ziadinov. Thanks go also to countless people who have regularly provided invaluable support and aid in villages in China and Kyrgyzstan. [The following grants contributed to the surveys but could not be entered in the "Grants" dialog box of the Zenodo system: + 1995-1997 Programme européen DG XII "Human cystic and alveolar echinococcosis in northwest China : community screening, patient treatment/follow-up and transmission studies" STD TS3-CT94-0270. [UK - France - Chine] + 1996-1997 Programme de l'Association franco-chinoise pour la recherche scientifique et technique, programme de recherche avancée franco-chinois PRA95. "Gestion du paysage et structure des peuplements de rongeurs: incidence sur la transmission de l'échinococcose alvéolaire". N° E-95-1 + 2004 Transmission ecology and eco-epidemiology of Echinococcus sp. in the Yili valley. Grant n° XJDX0202-2004-01 du Xinjiang Key Lab of fundamental research on echinococcosis, first affiliated hospital of the Xinjiang Medical University, République Populaire de Chine. + 2013 - 2014 Institut Universitaire de France + 2013 - 2014 CNRS - INEE, Groupement de Recherche International Ecosystem Health and Environmental Disease Ecology https://gdri-ehede.univ-fcomte.fr]. Special thanks to Phil S. Craig who has been at the initiative, one of the principal investigators, and the friendly companion and supporter of most of the research programmes that permitted data collection.