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Simple rules for an efficient use of Geographic Information Systems in molecular ecology [article]

Kevin Leempoel, Solange Duruz, Estelle Rochat, Ivo Widmer, Pablo Orozco-terWengel, Stephane Joost
2017 bioRxiv   pre-print
Geographic Information Systems (GIS) are becoming increasingly popular in the context of molecular ecology and conservation biology thanks to their display options efficiency, flexibility and management of geodata. Indeed, spatial data for wildlife and livestock species is becoming a trend with many researchers publishing genomic data that is specifically suitable for landscape studies. GIS uniquely reveal the possibility to overlay genetic information with environmental data and, as such,
more » ... us to locate and analyze genetic boundaries of various plant and animal species or to study gene-environment associations (GEA). This means that, using GIS, we can potentially identify the genetic bases of species adaptation to particular geographic conditions or to climate change. However, many biologists are not familiar with the use of GIS and underlying concepts and thus experience difficulties in finding relevant information and instructions on how to use them. In this paper, we illustrate the power of free and open source GIS approaches and provide essential information for their successful application in molecular ecology. First, we introduce key concepts related to GIS than are too often overlooked in the literature, for example coordinate systems, GPS accuracy and scale. We then provide an overview of the most employed open-source GIS-related software, file formats and refer to major environmental databases. We also reconsider sampling strategies as high costs of Next Generation Sequencing (NGS) data currently diminish the number of samples that can be sequenced per location. Thereafter, we detail methods of data exploration and spatial statistics suited for the analysis of large genetic datasets. Finally, we provide suggestions to properly edit maps and to make them as comprehensive as possible, either manually or trough programming languages.
doi:10.1101/113225 fatcat:zr3yg67rvjdutpo2aq2k5r6qra

A WebGIS platform for the monitoring of Farm Animal Genetic Resources (GENMON)

Solange Duruz, Christine Flury, Giona Matasci, Florent Joerin, Ivo Widmer, Stéphane Joost, Roberta Davoli
2017 PLoS ONE  
The code is available on GitHub: https://github.com/SolangeD/GENMON. Supporting information Fig 1 . 1 Simplified overview of the GENMON Process.  ... 
doi:10.1371/journal.pone.0176362 pmid:28453561 pmcid:PMC5408993 fatcat:q56tzp36crexveok3ptzc4aqha

Simple Rules for an Efficient Use of Geographic Information Systems in Molecular Ecology

Kevin Leempoel, Solange Duruz, Estelle Rochat, Ivo Widmer, Pablo Orozco-terWengel, Stéphane Joost
2017 Frontiers in Ecology and Evolution  
Geographic Information Systems (GIS) are becoming increasingly popular in the context of molecular ecology and conservation biology thanks to their display options efficiency, flexibility and management of geodata. Indeed, spatial data for wildlife and livestock species is becoming a trend with many researchers publishing genomic data that is specifically suitable for landscape studies. GIS uniquely reveal the possibility to overlay genetic information with environmental data and, as such,
more » ... us to locate and analyze genetic boundaries of various plant and animal species or to study gene-environment associations (GEA). This means that, using GIS, we can potentially identify the genetic bases of species adaptation to particular geographic conditions or to climate change. However, many biologists are not familiar with the use of GIS and underlying concepts and thus experience difficulties in finding relevant information and instructions on how to use them. In this paper, we illustrate the power of free and open source GIS approaches and provide essential information for their successful application in molecular ecology. First, we introduce key concepts related to GIS that are too often overlooked in the literature, for example coordinate systems, GPS accuracy and scale. We then provide an overview of the most employed open-source GIS-related software, file formats and refer to major environmental databases. We also reconsider sampling strategies as high costs of Next Generation Sequencing (NGS) data currently diminish the number of samples that can be sequenced per location. Thereafter, we detail methods of data exploration and spatial statistics suited for the analysis of large genetic datasets. Finally, we provide suggestions to properly edit maps and to make them as comprehensive as possible, either manually or trough programming languages.
doi:10.3389/fevo.2017.00033 fatcat:xsr546gjoffm5iuyzixu6m7u3y

Big dairy data to disentangle the effect of geo-environmental, physiological and morphological factors on milk production of mountain-pastured Braunvieh cows [article]

Solange Duruz, Elia Vajana, Alexander Burren, Christine Flury, Stephane Joost
2020 bioRxiv   pre-print
interested in 405 performing studies on these data may contact directly the association (see contact information homepage.braunvieh.ch). 406 The code used for this article is available at https://github.com/SolangeD  ... 
doi:10.1101/2020.04.16.042028 fatcat:isogp6c6kferfha6x36akqrvh4

Relationship between land cover type and Body Mass Index in Geneva

Estelle Rochat, Solange Duruz, Ivo Widmer, Alain Clemence, Olivier Desrichard, Daniel Rappo, Olivier Ertz, Jens Ingensand, Jean-Marc Theler, Idris Guessous, Stephane Joost
2015 2015 Joint Urban Remote Sensing Event (JURSE)  
Past studies conducted in urban areas analyzed the impact of the presence of green spaces on public health, and highlighted in particular the psychological benefits of interacting with nature. To investigate a supposed relationship between overweight and dense built environment, we focused on the State of Geneva, Switzerland, and calculated the correlation between Body Mass Index (BMI) in a representative sample of 6663 adults and the percentage of natural areas at the locations where these
more » ... viduals were living. To this end, we used populationbased health data from the "Bus Santé" study (Geneva University Hospitals) and multi-scale land cover maps obtained by means of satellite images and LiDAR data classification. We found little correlation between BMI (as a proxy for health) and land cover data and were not able to verify the working hypothesis at local and regional scales. However, an important phenomenon highlighted here is the difference in the results obtained between the city center and the whole State.
doi:10.1109/jurse.2015.7120542 dblp:conf/jurse/RochatDWCDREITG15 fatcat:yk72nodw5jge5jiu7rl7rwvl64

Indication of spatially random infection of chlamydia-like organisms in Bufo bufo tadpoles from ponds located in the Geneva metropolitan area [article]

Elia Vajana, Ivo Widmer, Estelle Rochat, Solange Duruz, Oliver Selmoni, Severine Vuilleumier, Sebastien Aeby, Gilbert Greub, Stephane Joost
2018 bioRxiv   pre-print
Occurrence of bacteria belonging to the order Chlamydiales was investigated for the first time in common toad (Bufo bufo) tadpole populations collected from 41 ponds in the Geneva metropolitan area, Switzerland. A Chlamydiales-specific Real-Time PCR was used to detect and amplify the Chlamydiales 16S rRNA-encoding gene from the tails of 375 tadpoles. We found the studied amphibian populations to be infected by "Chlamydia-like organisms" (CLOs) attributable to the genera Similichlamydia,
more » ... ydia, Protochlamydia and Parachlamydia (belonging to the family Parachlamydiaceae), Simkania (family Simkaniaceae) and Estrella (family Criblamydiaceae); additionally, DNA from the genus Thermoanaerobacter (family Thermoanaerobacteriaceae) was detected. A global autocorrelation analysis did not reveal a spatial structure in the observed CLOs infection rates, and association tests involving land cover characteristics did not evidence any clear effect on CLOs infection rates in B. bufo. Despite preliminary, these results suggest a random and ubiquitous distribution of CLOs in the environment, which would support the biogeographical expectation "everything is everywhere" for the concerned microorganisms and their amoeba vectors.
doi:10.1101/402487 fatcat:ib5qxywb7fez3a2hsisykzwquu

Big dairy data to unravel effects of environmental, physiological and morphological factors on milk production of mountain-pastured Braunvieh cows

Solange Duruz, Elia Vajana, Alexander Burren, Christine Flury, Stéphane Joost
2020 Royal Society Open Science  
The transhumance system, which consists in moving animals to high mountain pastures during summer, plays a considerable role in preserving both local biodiversity and traditions, as well as protecting against natural hazard. In cows, particularly, milk production is observed to decline as a response to food shortage and climatic stress, leading to atypical lactation curves that are barely described by current lactation models. Here, we relied on 5 million monthly milk records from over 200 000
more » ... raunvieh and Original Braunvieh cows to devise a new model accounting for transhumance, and test the influence of environmental, physiological and morphological factors on cattle productivity. Counter to expectations, environmental conditions in the mountain showed a globally limited impact on milk production during transhumance, with cows in favourable conditions producing only 10% more compared with cows living in detrimental conditions, and with precipitation in spring and altitude revealing to be the most production-affecting variables. Conversely, physiological factors such as lactation number and pregnancy stage presented an important impact over the whole lactation cycle with 20% difference in milk production, and alter the way animals respond to transhumance. Finally, the considered morphological factors (cow height and foot angle) presented a smaller impact during the whole lactation cycle (10% difference in milk production). The present findings help to anticipate the effect of climate change and to identify problematic environmental conditions by comparing their impact with the effect of factors that are known to influence lactation.
doi:10.1098/rsos.200638 pmid:32874658 pmcid:PMC7428251 fatcat:46fpzirbkngejjfrdwihkbutzu

Sup. Mat. S1 from Big dairy data to unravel effects of environmental, physiological and morphological factors on milk production of mountain-pastured Braunvieh cows

Solange Duruz, Elia Vajana, Alexander Burren, Christine Flury, Stéphane Joost
2020 Figshare  
For each criterion and calving month, the between-group difference in milk production in the alp and over the total lactation cycle is reported, together with the Δd (reflecting how differently the two groups are impacted by alping) and its associated significance.
doi:10.6084/m9.figshare.12570728 fatcat:izurn5jzlzhj5iuq64fyibcpz4

Rapid identification and interpretation of gene‐environment associations using the new R.SamBada landscape genomics pipeline

Solange Duruz, Natalia Sevane, Oliver Selmoni, Elia Vajana, Kevin Leempoel, Sylvie Stucki, Pablo Orozco‐terWengel, Estelle Rochat, Susana Dunner, Michael W. Bruford, Stéphane Joost
2019 Molecular Ecology Resources  
The package is available in the r CRAN package repository and on GitHub (github.com/SolangeD/R.SamBada).  ...  SO F T WA R E AVA I L A B I LIT Y R.SamBada package is available in the r CRAN package repository and on GitHub (github.com/SolangeD/R.SamBada).  ... 
doi:10.1111/1755-0998.13044 pmid:31136078 pmcid:PMC6790591 fatcat:vpcjgeycfnbtlmel2bt5pgj4oy

Persistent spatial clusters of high body mass index in a Swiss urban population as revealed by the 5-year GeoCoLaus longitudinal study

Stéphane Joost, Solange Duruz, Pedro Marques-Vidal, Murielle Bochud, Silvia Stringhini, Fred Paccaud, Jean-Michel Gaspoz, Jean-Marc Theler, Joël Chételat, Gérard Waeber, Peter Vollenweider, Idris Guessous
2016 BMJ Open  
Swiss urban population as revealed by the 5-year GeoCoLaus longitudinal study Stéphane Joost,1,2,3 Solange  ...  index in a Swiss urban population as revealed by the 5-year GeoCoLaus longitudinal study Stéphane Joost, Solange  ... 
doi:10.1136/bmjopen-2015-010145 pmid:26733572 pmcid:PMC4716152 fatcat:vroznt45tjafxcik3sw6ibdc5i

Prospects and challenges for the conservation of farm animal genomic resources, 2015-2025

Michael W. Bruford, Catarina Ginja, Irene Hoffmann, Stéphane Joost, Pablo Orozco-terWengel, Florian J. Alberto, Andreia J. Amaral, Mario Barbato, Filippo Biscarini, Licia Colli, Mafalda Costa, Ino Curik (+31 others)
2015 Frontiers in Genetics  
Livestock conservation practice is changing rapidly in light of policy developments, climate change and diversifying market demands. The last decade has seen a step change in technology and analytical approaches available to define, manage and conserve Farm Animal Genomic Resources (FAnGR). However, these rapid changes pose challenges for FAnGR conservation in terms of technological continuity, analytical capacity and integrative methodologies needed to fully exploit new, multidimensional data.
doi:10.3389/fgene.2015.00314 pmid:26539210 pmcid:PMC4612686 fatcat:e3hfzgdqinafrmqprel4trlqea

A WebGIS platform for the monitoring of Farm Animal Genetic Resources (GENMON)

Solange Duruz, Christine Flury, Giona Matasci, Florent Joerin, Ivo Widmer, Stéphane Joost, Roberta Davoli
2017
The code is available on GitHub: https://github.com/SolangeD/GENMON. Supporting information Fig 1 . 1 Simplified overview of the GENMON Process.  ... 
doi:10.24451/arbor.8503 fatcat:lgpqgdv6qnfs5mh7lswogtyvra

Le numéro

Brigitte Waternaux
2009 Thérapie Familiale  
L'anorexie mentale, elle aussi, met à mal les relations fraternelles et Solange Cook-Darzens, après une étude détaillée de la littérature, décrit, exemples à l'appui, l'impact de la maladie sur les frères  ...  La place de la thérapie individuelle dans la systémique, une question en suspens… L'étude de la littérature faite par Christel Vaudan, Barbara Tripet, Antoinette Corboz-Warnery et Nicolas Duruz montre  ... 
doi:10.3917/tf.093.0313 fatcat:buk3ho7ftzegdj6cik7uuxayj4

Le numéro

2005 Thérapie Familiale  
Alors, dans le dernier article de ce numéro, Nicolas Duruz s'interroge sur la nature paradoxale du lien du couple.  ...  Partant de ce constat Solange Cook-Darzens, Catherine Doyen, Florence Brunaux, Françoise Rupert, Marie-José Bouquet, Florence Bergametti, et Marie-Christine Mouren, à l'Hôpital Robert Debré à Paris, ont  ... 
doi:10.3917/tf.053.0217 fatcat:64pe5flrergjzfx62dq74fimry

Notes de lecture

2003 Cliniques méditerranéennes  
da psicanalise », n°156, sous la direction de Sud Nord, « humanitaires humanitaireries », n°17, revue sous la direction de Sébastien Giudicelli (érès) Thérapie familiale de l'adolescent anorexique par Solange  ...  L'esprit du temps) Topique « La dette », n°79, revue sous la direction de Sophie de Mijolla-Mellor et Jean-Paul Valabrega (L'esprit du temps) Traité de psychothérapie comparée sous la direction de Nicolas Duruz  ... 
doi:10.3917/cm.067.0284 fatcat:h3ud4qqr6fg5te3krficbaccku
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