,
,
,
,
fatigo: A web tool for finding significant associations of Gene Ontology terms with groups of genes, Bioinformatics, vol.20, pp.578-580, 2004. ,
Evolution of population genetic structure of the British roe deer by natural and anthropogenic processes (Capreolus capreolus), Ecology and Evolution, vol.3, pp.89-102, 2013. ,
Influence of Holocene environmental change and anthropogenic impact on the diversity and distribution of roe deer, Heredity, vol.112, pp.607-615, 2014. ,
The red deer Cervus elaphus genome CerEla1.0: Sequencing, annotating, genes, and chromosomes, Molecular Genetics and Genomics, vol.293, pp.665-684, 2018. ,
Asynchronous glaciations in arid continental climate, Quaternary Science Reviews, vol.182, pp.1-19, 2018. ,
Description of post-implantation embryonic stages in European roe deer (Capreolus capreolus) after embryonic diapause, Anatomia Histologia and Embryologia, vol.46, pp.582-591, 2017. ,
GeneWise and Genomewise, Genome Research, vol.14, pp.988-995, 2004. ,
trimmomatic: A flexible trimmer for Illumina sequence data, Bioinformatics, vol.30, pp.2114-2120, 2014. ,
Lineage-specific profiling delineates the emergence and progression of naive pluripotency in mammalian embryogenesis, Developmental Cell, vol.35, pp.366-382, 2015. ,
Roe deer population and harvest changes in, Europe. Estonian J. Ecol, vol.58, pp.169-180, 2009. ,
Prediction of complete gene structures in human genomic DNA, Journal of Molecular Biology, vol.268, pp.78-94, 1997. ,
Evolution of Drosophila on the newer Hawaiian volcanos, Heredity, vol.48, pp.3-25, 1982. ,
stacks: Building and Genotyping Loci De Novo from shortread Sequences, vol.3, pp.171-182, 2011. ,
Large-scale ruminant genome sequencing provides insights into their evolution and distinct traits, Science, vol.364, p.6446, 2019. ,
Deer from late Miocene to Pleistocene of western Palearctic: Matching fossil record and molecular phylogeny data, Zitteliana B, vol.32, pp.115-153, 2014. ,
The variant call format and VCFtools, Bioinformatics, vol.27, pp.2156-2158, 2011. ,
Evidence of adaptation from ancestral variation in young populations of beach mice, Evolution, vol.66, pp.3209-3223, 2012. ,
muscle: Multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Research, vol.32, pp.1792-1797, 2004. ,
Quaternary glations -extent and chronology, Developments in Quaternary Science, vol.15, pp.2-1108, 2011. ,
The genome sequence of taurine cattle: A window to ruminant biology and evolution, Science, vol.324, pp.522-528, 2009. ,
URL : https://hal.archives-ouvertes.fr/hal-02667039
lea: An R package for landscape and ecological association studies, Methods in Ecology and Evolution, vol.6, pp.925-929, 2015. ,
URL : https://hal.archives-ouvertes.fr/hal-02004815
Deciphering the wisent demographic and adaptive histories from individual whole-genome sequences, Molecular Biology and Evolution, vol.33, pp.2801-2814, 2016. ,
URL : https://hal.archives-ouvertes.fr/hal-02506852
RAD-sequencing for estimating genomic relatedness matrix-based heritability in the wild: A case study in roe deer, Molecular Ecology Resources, vol.19, pp.1205-1217, 2019. ,
URL : https://hal.archives-ouvertes.fr/hal-02349032
Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies, Nucleic Acids Research, vol.31, pp.5654-5666, 2003. ,
Genetic drift at expanding frontiers promotes gene segregation, Proceedings of the National Academy of Sciences USA, vol.104, 2007. ,
URL : https://hal.archives-ouvertes.fr/hal-00321262
Improved pairwise alignment of genomic DNA, 2007. ,
The confounding effect of population structure on Bayesian skyline plot inferences of demographic history, PLoS ONE, vol.8, 2013. ,
Conservation of adaptive potential and functional diversity, Cons. Genet, vol.20, pp.1-5, 2019. ,
adegenet: A R package for the multivariate analysis of genetic markers, Bioinformatics, vol.24, pp.1403-1405, 2008. ,
URL : https://hal.archives-ouvertes.fr/hal-00428105
adegenet 1.3-1: New tools for the analysis of genome-wide SNP data, Bioinformatics, vol.27, pp.3070-3071, 2011. ,
Discriminant analysis of principal components: A new method for the analysis of genetically structured populations, BMC Genetics, vol.11, 2010. ,
URL : https://hal.archives-ouvertes.fr/hal-00539267
InterProScan 5: Genome-scale protein function classification, Bioinformatics, vol.30, pp.1236-1240, 2014. ,
Gene finding in novel genomes, BMC Bioinformatics, vol.5, p.59, 2004. ,
ANGSD: Analysis of next generation sequencing data, BMC Bioinformatics, vol.15, p.35610, 2014. ,
SOX9 duplication linked to intersex in deer, PLoS ONE, vol.8, 2013. ,
Mutation rates in mammalian genomes, Proceedings of the National Academy of Sciences USA, 99, pp.803-808, 2002. ,
Fast gapped-read alignment with Bowtie 2, Nature Methods, vol.9, pp.357-354, 2012. ,
Synchroneity of tropical and high-latitude Atlantic temperatures over the last glacial termination, Science, vol.301, pp.1361-1364, 2003. ,
Genetic diversity and phylogeography of Siberian roe deer, Caproulus pygargus, in central and peripheral populations, Ecology and Evolution, vol.6, pp.7286-7297, 2016. ,
SimRAD: An R package for simulation-based prediction of the number of loci expected in RADseq and similar genotyping by sequencing approaches, Molecular Ecology Resources, vol.14, pp.1314-1321, 2014. ,
URL : https://hal.archives-ouvertes.fr/hal-02633536
Statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data, Bioinformatics, vol.27, pp.2987-2993, 2011. ,
Inference of human population history from individual whole-genome sequences, Nature, vol.475, pp.493-496, 2011. ,
Draft genome of the reindeer, Gigascience, vol.6, pp.1-5, 2017. ,
pgdspider: An automated data conversion tool for connecting population genetics and genomics programs, Bioinformatics, vol.28, pp.298-299, 2012. ,
The European Roe Deer: The biology of success, pp.23-46, 1998. ,
Exploring population size changes using SNP frequency spectra, Nature Genetics, vol.47, pp.1099-1099, 2015. ,
Breaking RAD: An evaluation of the utility of restriction site-associated DNA sequencing for genome scans of adaptation, Molecular Ecology Research, vol.17, pp.142-152, 2017. ,
High-resolution carbon dioxide concentration record 650,000-800,000 years before present, Nature, vol.453, pp.379-382, 2008. ,
URL : https://hal.archives-ouvertes.fr/insu-00378509
Evolution of the mutation rate, Trends in Genetics, vol.26, pp.345-352, 2010. ,
tigrscan and glimmerhmm: Two open source ab initio eukaryotic gene-finders, Bioinformatics, vol.20, pp.2878-2879, 2004. ,
Unexpected population genetic structure of European roe deer in Poland: An invasion of the mtDNA genome from Siberian roe deer, Molecular Ecology, vol.23, pp.2559-2572, 2014. ,
Bony labyrinth morphology clarifies the origin and evolution of deer, Sci. Rep-uk, vol.7, 2017. ,
URL : https://hal.archives-ouvertes.fr/hal-01625495
Why time matters: Codon evolution and the temporal dynamics of dN/dS, Molecular Biology and Evolution, vol.31, pp.212-231, 2012. ,
BCFtools/RoH: A hidden Markov model approach for detecting autozygosity from next-generation sequencing data, Bioinformatics, vol.32, pp.1749-1751, 2016. ,
A slow life in hell or a fast life in heaven: Demographic analyses of contrasting roe deer populations, Journal of Animal Ecology, vol.78, issue.3, pp.585-594, 2009. ,
ape: Analyses of phylogenetics and evolution in R language, Bioinformatics, vol.20, pp.289-290, 2004. ,
URL : https://hal.archives-ouvertes.fr/ird-01887318
Contemporary demographic reconstruction methods are robust to genome assembly quality: A case study in Tasmanian devils, Molecular Biology and Evolution, vol.36, issue.12, pp.2906-2921, 2019. ,
A southern African origin and cryptic structure in the highly mobile plains zebra, Nature Ecology & Evolution, vol.2, pp.491-498, 2018. ,
URL : https://hal.archives-ouvertes.fr/hal-02348420
stampp: An R package for calculation of genetic differentiation and structure of mixedploidy level populations, Molecular Ecology Resources, vol.13, pp.946-952, 2013. ,
Double digest RADseq: An inexpensive method for de novo SNP discovery and genotyping in model and non-model species, PLoS ONE, vol.7, 2012. ,
Identification of European (Capreolus capreolus L.) and Siberian (C. pygargus Pall.) roe deer hybrids by microsatellite marker analysis, Genetika, vol.50, pp.862-867, 2014. ,
Embryonic diapause is conserved across mammals, PLoS ONE, vol.7, 2012. ,
PLINK: A tool set for whole-genome association and population-based linkage analyses, American Journal of Human Genetics, vol.81, pp.559-575, 2007. ,
Genome variation associated with local adaptation of weedy rice during de-domestication, Nature Communications, vol.8, p.15323, 2017. ,
BEDTools: A flexible suite of utilities for comparing genomic features, Bioinformatics, vol.26, pp.841-842, 2010. ,
Mitochondrial DNA polymorphism in populations of Siberian and European roe deer (Capreolus pygargus and C. capreolus), Heredity, vol.80, pp.429-437, 1998. ,
Genome-wide polymorphism and comparative analyses in the white-tailed deer (Odocoileus virginianus): A model for conservation genomics, PLoS ONE, vol.6, 2011. ,
Role of positive selection in the retention of duplicate genes in mammalian genomes, Proceedings of the National Academy of Sciences USA, vol.103, pp.2232-2236, 2006. ,
BUSCO: Assessing genome assembly and annotation completeness with single-copy orthologs, Bioinformatics, vol.31, pp.3210-3212, 2015. ,
, , 2018.
Quaternary history of the European roe deer Capreolus capreolus, Mammal Reviews, vol.39, pp.1-16, 2009. ,
raxml version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies, Bioinformatics, vol.30, pp.1312-1313, 2014. ,
augustus: Ab initio prediction of alternative transcripts, Nucleic Acids Research, vol.34, pp.435-439, 2006. ,
Seven million years of wind and precipitation variability on the Chinese Loess Plateau, Earth and Planetary Science Letters, vol.297, pp.525-535, 2010. ,
Using RepeatMasker to identify repetitive elements in genomic sequences, Current Protocols Bioinformatics Chapter, p.10, 2009. ,
The reality and importance of founder speciation in evolution, BioEssays, vol.30, pp.470-479, 2008. ,
The evolution of the Dutch and Belgian coasts and the role of sand supply from the North Sea, Global and Planetary Change, vol.27, issue.01, pp.68-74, 2000. ,
The genetic structure of natural and reintroduced roe deer (Capreolus capreolus) populations in the Alps and central Italy, with reference to the mitochondrial DNA phylogeography of Europe, Molecular Ecology, vol.11, pp.1285-1297, 2002. ,
, , 2011.
, Genotyping of Capreolus pygargus fossil DNA from Denisova cave reveals phylogenetic relationships between ancient and modern samples, PLoS ONE, vol.6, p.24045
Genetic basis of ruminant headgear and rapid antler regeneration, Science, vol.364, 2019. ,
On the number of segregating sites in genetical models without recombination, Theoretical Population Biology, vol.7, pp.90020-90029, 1975. ,
Estimating F-statistics for analysis of population structure, Evolution, vol.38, issue.6, pp.1358-1370, 1984. ,
Bayesian inference of recent migration rates using multilocus genotypes, Genetics, vol.163, pp.1177-1191, 2003. ,
TreeSAAP: selection on amino acid properties using phylogenetic trees, Bioinformatics, vol.19, issue.5, pp.671-672, 2003. ,
ltr _ finder: An efficient tool for the prediction of full-length LTR retrotransposons, Nucleic Acids Research, vol.35, pp.265-268, 2007. ,
Phylogenetic analysis by maximum likelihood, Molecular Biology and Evolution, vol.4, pp.1586-1591, 2007. ,
zoo: S3 infrastructure for regular and irregular time series, Journal of Statistical Software, vol.14, issue.6, pp.1-27, 2005. ,
, , 2018.
,
Comparative genomics and metagenomics analyses of endangered Père David's deer (Elaphurus davidianus) provide insights into population recovery, 2016. ,
Endangered Pere David's deer genome provides insights into population recovering, Evolutionary Applications, vol.11, pp.2040-2053, 2018. ,
Demography and adaptation promoting evolutionary transitions in a mammalian genus that diversified during the Pleistocene, Mol Ecol, vol.00, pp.1-16, 2020. ,