Comparative population genomics in animals uncovers the determinants of genetic diversity

J Romiguier, P Gayral, M Ballenghien, A Bernard… - Nature, 2014 - nature.com
Genetic diversity is the amount of variation observed between DNA sequences from distinct
individuals of a given species. This pivotal concept of population genetics has implications …

[HTML][HTML] Reference-free population genomics from next-generation transcriptome data and the vertebrate–invertebrate gap

…, JM Lourenco, PC Alves, M Ballenghien… - PLoS …, 2013 - journals.plos.org
In animals, the population genomic literature is dominated by two taxa, namely mammals
and drosophilids, in which fully sequenced, well-annotated genomes have been available for …

Reference‐free transcriptome assembly in non‐model animals from next‐generation sequencing data

…, J Melo‐Ferreira, M Ballenghien… - Molecular ecology …, 2012 - Wiley Online Library
Next‐generation sequencing (NGS) technologies offer the opportunity for population genomic
study of non‐model organisms sampled in the wild. The transcriptome is a convenient and …

[HTML][HTML] Patterns of cross-contamination in a multispecies population genomic project: detection, quantification, impact, and solutions

M Ballenghien, N Faivre, N Galtier - BMC biology, 2017 - Springer
… We created a between-species contamination matrix M in which cell m ij contained zero
in the absence of evidence for contamination of species j by species i, one in case of the …

Next‐generation sequencing of transcriptomes: a guide to RNA isolation in nonmodel animals

…, G Tsagkogeorga, M Ballenghien… - Molecular ecology …, 2011 - Wiley Online Library
… ) (4 m guanidinium thiocyanate; 50 mm sodium citrate; 1 m Tris, pH 8.0), which was obtained
from a slightly modified protocol of Triant & Whitehead 2009. After phase separation using …

Population genomics of sexual and asexual lineages in fissiparous ribbon worms (Lineus, Nemertea): hybridization, polyploidy and the Meselson effect

…, E Figuet, M Ballenghien… - Molecular …, 2016 - Wiley Online Library
Comparative population genetics in asexual vs. sexual species offers the opportunity to
investigate the impact of asexuality on genome evolution. Here, we analyse coding sequence …

Population genomics of eusocial insects: the costs of a vertebrate‐like effective population size

…, LA Weinert, S Ravel, M Ballenghien… - Journal of …, 2014 - academic.oup.com
The evolution of reproductive division of labour and social life in social insects has lead to
the emergence of several life‐history traits and adaptations typical of larger organisms: social …

Biased gene conversion and GC-content evolution in the coding sequences of reptiles and vertebrates

E Figuet, M Ballenghien, J Romiguier… - Genome Biology and …, 2015 - academic.oup.com
Mammalian and avian genomes are characterized by a substantial spatial heterogeneity of
GC-content, which is often interpreted as reflecting the effect of local GC-biased gene …

Development of SNP‐genotyping arrays in two shellfish species

…, C Donnadieu, P Gayral, M Ballenghien… - Molecular ecology …, 2014 - Wiley Online Library
Use of SNP s has been favoured due to their abundance in plant and animal genomes,
accompanied by the falling cost and rising throughput capacity for detection and genotyping. …

Population genomics of the introduced and cultivated Pacific kelp Undaria pinnatifida: Marinas—not farms—drive regional connectivity and establishment in natural …

J Guzinski, M Ballenghien… - Evolutionary …, 2018 - Wiley Online Library
… We, thus, used a minimal stack depth of five (-m parameter), up to two mismatches within a
locus at the sample level (-M parameter), up to two mismatches when merging loci across the …