Adaptive protein evolution at the Adh locus in Drosophila, Nature, vol.351, pp.652-654, 1991. ,
Estimating the rate of adaptive molecular evolution in the presence of slightly deleterious mutations and population size change, Mol. Biol. Evol, vol.26, pp.2097-2108, 2009. ,
Frequent adaptation and the McDonald-Kreitman test, Proc. Natl Acad. Sci. USA, vol.110, pp.8615-8620, 2013. ,
DOI : 10.1073/pnas.1220835110
URL : http://www.pnas.org/content/110/21/8615.full.pdf
Adaptive protein evolution in animals and the effective population size hypothesis, PLoS Genet, vol.12, 2016. ,
DOI : 10.1371/journal.pgen.1005774
URL : https://hal.archives-ouvertes.fr/hal-01900669
Inference of distribution of fitness effects and proportion of adaptive substitutions from polymorphism data, Genetics, vol.207, pp.1103-1119, 2017. ,
Changing effective population size and the McDonald-Kreitman test, Genetics, vol.162, pp.2017-2024, 2002. ,
On the probability of fixation of mutant genes in a population, Genetics, vol.47, pp.713-719, 1962. ,
Post-glacial re-colonization of European biota, Biol. J. Linn. Soc, vol.68, pp.87-112, 1999. ,
Cryptic northern refugia and the origins of the modern biota, Trends Ecol. Evol, vol.16, pp.2338-2340, 2001. ,
Ecological and evolutionary responses to recent climate change, Annu. Rev. Ecol. Evol. Syst, vol.37, pp.637-669, 2006. ,
SLiM 2: flexible, interactive forward genetic simulations, Mol. Biol. Evol, vol.34, pp.230-240, 2017. ,
Mutation rates in mammalian genomes, Proc. Natl Acad. Sci. USA, vol.99, pp.803-808, 2002. ,
Variation in recombination frequency and distribution across eukaryotes: patterns and processes, Phil. Trans. R. Soc. B, vol.372, 2017. ,
URL : https://hal.archives-ouvertes.fr/hal-01945363
The distribution of fitness effects of new deleterious amino acid mutations in humans, Genetics, vol.173, pp.891-900, 2006. ,
Data from: Overestimation of the adaptive substitution rate in fluctuating populations, Dryad Digital Repository, vol.14, p.20180055, 2018. ,
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, Literature Cited
The Glanville fritillary genome retains an ancient karyotype and reveals selective chromosomal fusions in Lepidoptera, Nat. Commun, vol.5, pp.1-9, 2014. ,
A test for faster X evolution in Drosophila, Mol. Biol. Evol, vol.19, pp.1816-1819, 2002. ,
Faster-X effects in two Drosophila lineages, Genome Biol. Evol, vol.6, pp.2968-2982, 2014. ,
The effects of sex-biased gene expression and X-linkage on rates of adaptive protein sequence evolution in Drosophila, Biol. Lett, vol.11, p.20150117, 2015. ,
Male-biased mutation rate and divergence in autosomal, Z-linked and W-linked introns of chicken and turkey, Mol. Biol. Evol, vol.21, pp.1538-1547, 2004. ,
Male monarch butterfly spermatophore mass and mating strategies, Anim. Behav, vol.36, pp.1384-1388, 1988. ,
DOI : 10.1016/s0003-3472(88)80208-2
Reference-free transcriptome assembly in nonmodel animals from next-generation sequencing data, Mol. Ecol. Resour, vol.12, pp.834-845, 2012. ,
URL : https://hal.archives-ouvertes.fr/hal-01267810
The relation between recombination rate and patterns of molecular evolution and variation in Drosophila melanogaster, Mol. Biol. Evol, vol.31, pp.1010-1028, 2014. ,
Evidence for widespread positive and purifying selection across the european rabbit (Oryctolagus cuniculus) genome, 2012. ,
URL : https://hal.archives-ouvertes.fr/hal-01313718
, Mol. Biol. Evol, vol.29, pp.1837-1849
The relative rates of evolution of sex chromosomes and autosomes, Am. Nat, vol.130, pp.113-146, 1987. ,
The role of background selection in shaping patterns of molecular evolution and variation: evidence from variability on the Drosophila X chromosome, Genetics, vol.191, pp.233-246, 2012. ,
Using comparative genomic data to test for fast-X evolution, Evolution, vol.58, pp.656-660, 2004. ,
DOI : 10.1554/03-413
Multi-platform Next-Generation sequencing of the domestic Turkey (Meleagris gallopavo): genome assembly and analysis, PLoS Biol, vol.8, p.1000475, 2010. ,
Why highly expressed proteins evolve slowly, Proc. Natl Acad. Sci. U S A, vol.102, pp.14338-14343, 2005. ,
DOI : 10.1073/pnas.0504070102
URL : http://www.pnas.org/content/102/40/14338.full.pdf
Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution, Cell, vol.134, pp.341-352, 2008. ,
The genomic landscape of species divergence in Ficedula flycatchers, Nature, vol.491, pp.756-760, 2012. ,
Estimating the rate of adaptive molecular evolution in the presence of slightly deleterious mutations and population size change, Mol. Biol. Evol, vol.26, pp.2097-2108, 2009. ,
Karyotype and achiasmatic female meiosis in Helicoverpa armigera (Hü bner) and H. punctigera (Wallengren) (Lepidoptera: Noctuidae), Gé nome, vol.32, pp.967-971, 1989. ,
Adaptive protein evolution in animals and the effective population size hypothesis, PLoS Genet, vol.12, p.1005774, 2016. ,
URL : https://hal.archives-ouvertes.fr/hal-01900669
Genome diversity and divergence in Drosophila mauritiana: multiple signatures of faster X evolution, Genome Biol. Evol, vol.6, pp.2444-2458, 2014. ,
Next-generation sequencing of transcriptomes: a guide to RNA isolation in nonmodel animals, Mol. Ecol. Resour, vol.11, pp.650-661, 2011. ,
Reference-free population genomics from NextGeneration transcriptome data and the vertebrate-invertebrate gap, PLoS Genet, vol.9, p.1003457, 2013. ,
Mating systems and the efficacy of selection at the molecular level, Genetics, vol.177, pp.905-916, 2007. ,
Full-length transcriptome assembly from RNA-seq data without a reference genome, Nat. Biotechnol, vol.15, pp.644-652, 2011. ,
DOI : 10.1038/nbt.1883
URL : http://europepmc.org/articles/pmc3571712?pdf=render
Bio ++: efficient extensible libraries and tools for computational molecular evolution, Mol. Biol. Evol, vol.30, pp.1745-1750, 2013. ,
A mathematical theory of natural and artificial selection, Part I. Trans. Cambridge Phil. Soc, vol.23, pp.19-41, 1924. ,
DOI : 10.1017/s0305004100011750
Incomplete sex chromosome dosage compensation in the Indian meal moth, Plodia interpunctella, based on de novo transcriptome assembly, Genome Biol. Evol, vol.4, pp.1118-1126, 2012. ,
CAP3: a DNA sequence assembly program, 1999. ,
DOI : 10.1101/gr.9.9.868
URL : http://europepmc.org/articles/pmc310812?pdf=render
, Genome Res, vol.9, pp.868-877
Extensive X-linked adaptive evolution in central chimpanzees, Proc. Natl Acad. Sci. U S A, vol.109, pp.2054-2059, 2011. ,
DOI : 10.1073/pnas.1106877109
URL : http://www.pnas.org/content/109/6/2054.full.pdf
The rate of adaptive evolution in animal mitochondria, Mol. Ecol, vol.25, pp.67-78, 2016. ,
URL : https://hal.archives-ouvertes.fr/hal-01246333
,
, Genome Biol. Evol, vol.8, issue.10, pp.3108-3119, 2016.
Mechanisms and evolutionary patterns of mammalian and avian dosage compensation, PLoS Biol, vol.10, p.1001328, 2012. ,
DOI : 10.1371/journal.pbio.1001328
URL : https://journals.plos.org/plosbiology/article/file?id=10.1371/journal.pbio.1001328&type=printable
Faster-X adaptive protein evolution in house mice, Genetics, vol.196, pp.1131-1143, 2014. ,
DOI : 10.1534/genetics.113.158246
URL : http://www.genetics.org/content/196/4/1131.full.pdf
Fast and accurate short read alignment with Burrows-Wheeler transform, Bioinformatics, vol.25, pp.1754-1760, 2009. ,
Subgroup 1000 Genome Project Data Processing 2009. The Sequence Alignment/Map format and SAMtools, Bioinformatics, vol.25, pp.2078-2079 ,
Adaptive protein evolution at the Adh locus in Drosophila, Nature, vol.385, pp.652-654, 1991. ,
The Drosophila melanogaster Genetic Reference Panel, Nature, vol.482, pp.173-178, 2012. ,
Faster-Z evolution is predominantly due to genetic drift, Mol. Biol. Evol, vol.27, pp.661-670, 2010. ,
The evolution of dosage-compensation mechanisms, BioEssays, vol.22, pp.1106-1114, 2000. ,
The faster-X effect: integrating theory and data, Trends Genet, vol.29, pp.537-544, 2013. ,
Maledriven molecular evolution: a model and nucleotide sequence analysis, Cold Spring Harb. Symp. Quant. Biol, vol.52, pp.863-867, 1987. ,
Mapping and quantifying mammalian transcriptomes by RNA-Seq, Nat. Methods, vol.5, pp.621-628, 2008. ,
Extreme selective sweeps independently targeted the X chromosomes of the great apes, Proc. Natl Acad. Sci. U S A, vol.112, 2015. ,
Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene, Genetics, vol.148, pp.929-936, 1998. ,
Gene expression, chromosome heterogeneity and the fast-X effect in mammals, Biol. Lett, vol.11, p.20150010, 2015. ,
URL : https://hal.archives-ouvertes.fr/hal-01815517
MACSE: Multiple Alignment of Coding SEquences accounting for frameshifts and stop codons, PLoS One, vol.6, p.22594, 2011. ,
URL : https://hal.archives-ouvertes.fr/hal-01773250
Sex chromosomes and the evolution of sexual dimorphism, Evolution, vol.38, pp.735-742, 1984. ,
Fast and robust characterization of time-heterogeneous sequence evolutionary processes using substitution mapping, PLoS One, vol.7, p.33852, 2012. ,
URL : https://hal.archives-ouvertes.fr/hal-00965722
Comparative population genomics in animals uncovers the determinants of genetic diversity, Nature, vol.515, pp.261-263, 2014. ,
URL : https://hal.archives-ouvertes.fr/hal-01313724
Positive selection drives faster-Z evolution in silkmoths, Evolution, vol.68, pp.2331-2342, 2014. ,
ABySS: a parallel assembler for short read sequence data, Genome Res, vol.19, pp.1117-1123, 2009. ,
X-linked genes evolve higher codon bias in Drosophila and Caenorhabditis, Genetics, vol.171, pp.145-155, 2005. ,
Estimation of the neutrality index, Mol. Biol. Evol, vol.28, pp.63-70, 2011. ,
Achiasmatic oogenesis in the Heliconiine butterflies, Hereditas, vol.74, pp.302-304, 1973. ,
DOI : 10.1111/j.1601-5223.1973.tb01134.x
URL : https://doi.org/10.1111/j.1601-5223.1973.tb01134.x
Efficient purging of deleterious mutations in plants with haploid selfing, Genome Biol. Evol, vol.6, pp.1238-1252, 2014. ,
Butterfly genome reveals promiscuous exchange of mimicry adaptations among species, Nature, vol.487, pp.94-98, 2012. ,
Rapid divergence of gene duplicates on the Drosophila melanogaster X chromosome, Mol. Biol. Evol, vol.19, pp.918-925, 2002. ,
A study of recombination, formation of chiasmata and synaptonemal complexes in female and male meiosis of Ephestia kuehniella (Lepidoptera), Genetica, vol.47, pp.135-142, 1977. ,
The population genomics of a fast evolver: high levels of diversity, functional constraint, and molecular adaptation in the tunicate Ciona intestinalis, Genome Biol. Evol, vol.4, pp.740-749, 2012. ,
Absence of crossing-over in female butterflies (Heliconius), Heredity, vol.34, pp.265-269, 1975. ,
Evidence for increased levels of positive and negative selection on the X chromosome versus autosomes in humans, Mol. Biol. Evol, vol.31, pp.2267-2282, 2014. ,
Effective population size and the faster-X effect: an extended model, Evolution, vol.63, pp.2413-2426, 2009. ,
DOI : 10.1111/j.1558-5646.2009.00719.x
URL : https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1558-5646.2009.00719.x
Sex chromosome dosage compensation in Heliconius butterflies: global yet still incomplete?, Genome Biol. Evol, vol.7, pp.2545-2559, 2015. ,
DOI : 10.1093/gbe/evv156
URL : https://academic.oup.com/gbe/article-pdf/7/9/2545/17925030/evv156.pdf
Whole genome sequencing of the black grouse (Tetrao tetrix): reference guided assembly suggests faster-Z and MHC evolution, BMC Genomics, vol.15, p.180, 2014. ,
Variation in promiscuity and sexual selection drives avian rate of Faster-Z evolution, Mol. Ecol, vol.24, pp.1218-1235, 2015. ,
Dosage analysis of Z chromosome genes using microarray in silkworm, Bombyx mori, Insect Biochem. Mol. Biol, vol.39, pp.315-321, 2009. ,
DOI : 10.1016/j.ibmb.2008.12.003
, Associate editor: Judith Mank Fast-Z Evolution in Satyrine Butterflies GBE
, Genome Biol. Evol, vol.8, issue.10, pp.3108-3119, 2016.