Thierry Gosselin

RAD genotyping reveals fine-scale genetic structuring and provides powerful population assignment in a widely distributed marine species, the American lobster (Homarus americanus)

Deciphering genetic structure and inferring connectivity in marine species have been challenging due to weak genetic differentiation and limited resolution offered by traditional genotypic methods. The main goal of this study was to assess how a population genomics framework could help delineate the genetic structure of the American lobster (Homarus americanus) throughout much of the species’ range and increase the assignment success of individuals to their location of origin. We genotyped 10 156 filtered SNPs using RAD sequencing to delineate genetic structure and perform population assignment for 586 American lobsters collected in 17 locations distributed across a large portion of the species’ natural distribution range. Our results revealed the existence of a hierarchical genetic structure, first separating lobsters from the northern and southern part of the range (FCT = 0.0011; P‐value = 0.0002) and then revealing a total of 11 genetically distinguishable populations (mean FST = 0.00185; CI: 0.0007–0.0021, P‐value < 0.0002), providing strong evidence for weak, albeit fine‐scale population structuring within each region. A resampling procedure showed that assignment success was highest with a subset of 3000 SNPs having the highest FST. Applying Andersons (Molecular Ecology Resources, 2010, 10, 701) method to avoid ‘high‐grading bias’, 94.2% and 80.8% of individuals were correctly assigned to their region and location of origin, respectively. Lastly, we showed that assignment success was positively associated with sample size. These results demonstrate that using a large number of SNPs improves fine‐scale population structure delineation and population assignment success in a context of weak genetic structure. We discuss the implications of these findings for the conservation and management of highly connected marine species, particularly regarding the geographic scale of demographic independence.

Geographic variation of multiple paternity in the American lobster, Homarus americanus

We studied the frequency of multiple paternity for American lobster (Homarus americanus) at three Canadian sites differing in exploitation rate and mean adult size. The probability of detecting multiple paternity using four microsatellite loci and 100 eggs per female was in excess of 99% under various scenarios of paternal contribution. Overall, 13% of the 108 examined females carried a clutch sired by two or three males. Multiple paternity was observed at the two most exploited sites (11% at Magdalen Islands and 28% at Grand Manan Island), whereas single paternity only was observed at the least exploited site (Anticosti Island). Within populations females with a clutch sired by more than one male tended to be smaller than females with a clutch sired by a single male. Based on these and other findings, we postulate a link between female promiscuity and sperm limitation in the American lobster.

Patterns of sexual cohabitation and female ejaculate storage in the American lobster (Homarus americanus)

Little is known of the time and ejaculate allocation strategies during mating of American lobster, Homarus americanus. This study investigated sexual cohabitation and female ejaculate accumulation patterns in a laboratory mating experiment, as well as female seminal receptacle load in exploited populations in the waters of the Magdalen and Anticosti Islands, in eastern Canada. In the laboratory experiment, the length of sexual cohabitation was proportionate to female size for large but not for small males. Also, large males cohabited with pre- and postmolt females longer than small males. These different time investment strategies can be explained by different mutual benefits. In the field and laboratory, larger females accumulated more ejaculate than smaller ones. This suggests that male lobsters tailor ejaculate to female size, a reliable index of her reproductive potential. Moreover, similarly-sized females accumulated more ejaculate when mated with large compared to small males. Comparison of receptacle loads between wild-mated and laboratory-mated females suggests that the former were mating mainly with smaller males, although some evidence of positive size-assortative mating existed, especially at the less exploited Anticosti site. The results are discussed in the context of evolutionary theory and of proposed management measures to increase egg production in exploited populations.

Salmonid chromosome evolution as revealed by a novel method for comparing RADseq linkage maps

Whole genome duplication (WGD) can provide material for evolutionary innovation. Family Salmonidae is ideal for studying the effects of WGD as the ancestral salmonid underwent WGD relatively recently, ∼65 Ma, then rediploidized and diversified. Extensive synteny between homologous chromosome arms occurs in extant salmonids, but each species has both conserved and unique chromosome arm fusions and fissions. Assembly of large, outbred eukaryotic genomes can be difficult, but structural rearrangements within such taxa can be investigated using linkage maps. RAD sequencing provides unprecedented ability to generate high-density linkage maps for nonmodel species, but can result in low numbers of homologous markers between species due to phylogenetic distance or differences in library preparation. Here, we generate a high-density linkage map (3,826 markers) for the Salvelinus genera (Brook Charr S. fontinalis), and then identify corresponding chromosome arms among the other available salmonid high-density linkage maps, including six species of Oncorhynchus, and one species for each of Salmo, Coregonus, and the nonduplicated sister group for the salmonids, Northern Pike Esox lucius for identifying post-duplicated homeologs. To facilitate this process, we developed MapComp to identify identical and proximate (i.e. nearby) markers between linkage maps using a reference genome of a related species as an intermediate, increasing the number of comparable markers between linkage maps by 5-fold. This enabled a characterization of the most likely history of retained chromosomal rearrangements post-WGD, and several conserved chromosomal inversions. Analyses of RADseq-based linkage maps from other taxa will also benefit from MapComp, available at: https://github.com/enormandeau/mapcomp/

Linking genomics and population genetics with r.

Population genetics and genomics have developed and been treated as independent fields of study despite having common roots. The continuous progress of sequencing technologies is contributing to (re‐)connect these two disciplines. We review the challenges faced by data analysts and software developers when handling very big genetic data sets collected on many individuals. We then expose how r, as a computing language and development environment, proposes some solutions to meet these challenges. We focus on some specific issues that are often encountered in practice: handling and analysing single‐nucleotide polymorphism data, handling and reading variant call format files, analysing haplotypes and linkage disequilibrium and performing multivariate analyses. We illustrate these implementations with some analyses of three recently published data sets that contain between 60 000 and 1 000 000 loci. We conclude with some perspectives on future developments of r software for population genomics.

Towards an integrated ecosystem of R packages for the analysis of population genetic data

EMMANUEL PARADIS,* THIERRY GOSSELIN,† NIKLAUS J. GR € UNWALD,‡ ,§ THIBAUT JOMBART,¶ ST EPHANIE MANEL** and HILMAR LAPP†† *Institut des Sciences de l’ Evolution, Universit e Montpellier CNRS IRD EPHE, Place Eug ene Bataillon – CC 065, Montpellier c edex 05 34095, France, †Institut de Biologie Int egrative et des Syst emes (IBIS), Universit e Laval, Qu ebec, QC G1V 0A6, Canada, ‡Horticultural Crops Research Unit, USDA-ARS, Corvallis, OR 97330, USA, §Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA, ¶MRC Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College, London W2 1PG, UK, **EPHE, CNRS, UM, SupAgro, IRD, INRA, UMR 5175, PSL Research University, Montpellier CEFE F-34293, France, ††Center for Genomic and Computational Biology (GCB), Duke University, 101 Science Drive, Durham, NC 27708, USA

Novel Method for Comparing RADseq Linkage Maps Reveals Chromosome Evolution in Salmonids

Genome duplication can provide material for evolutionary innovation, and much remains unknown about its functional effects. Assembly of large, outbred eukaryotic genomes is difficult, but structural rearrangements within such taxa can be investigated using linkage maps. RAD sequencing provides unprecedented ability to generate high-density linkage maps for non-model species. However, these methods often result in a low number of homologous markers between species due to phylogenetic distance or technical differences in library preparation. Family Salmonidae is ideal for studying the effects of whole genome duplication. The ancestral salmonid underwent whole genome duplication around 65 million years ago and the tetraploid genome has undergone rediploidization during the salmonid diversification. In the salmonids, synteny occurs between orthologous chromosomes, but each species exhibits conserved and unique chromosome arm fusions and fissions. In this study, we identify orthologous chromosome arms within the salmonids using available RADseq salmonid linkage maps along with a new high-density linkage map (3826 markers) constructed for the Salvelinus genera (Brook Charr S. fontinalis ). We developed MapComp, a program that identifies identical and proximal markers between linkage maps using a reference genome of a related species as an intermediate (e.g. Rainbow Trout Oncorhynchus mykiss ). We greatly increased the number of comparable markers between linkage maps relative to that obtained using only identical markers. This enabled a characterization of the most likely history of retained chromosomal rearrangements post-whole genome duplication in five species of Oncorhynchus , and one species of each of Salvelinus , Salmo , and Coregonus , representing all of the main salmonid genera. Additionally, integration with the genetic map of the pre-duplicated sister species Northern Pike Esox lucius permitted the identification of homeologous chromosomes in all species. Putative conserved inversions within chromosome arms were also identified among species. Analyses of RADseq-based linkage maps from other taxa are likely to benefit from MapComp, available at: https://github.com/enormandeau/mapcomp/.Whole genome duplication (WGD) can provide material for evolutionary innovation. Assembly of large, outbred eukaryotic genomes can be difficult, but structural rearrangements within such taxa can be investigated using linkage maps. RAD sequencing provides unprecedented ability to generate high-density linkage maps for non-model species, but can result in low numbers of homologous markers between species due to phylogenetic distance or differences in library preparation. Family Salmonidae is ideal for studying the effects of WGD as the ancestral salmonid underwent WGD relatively recently, around 65 million years ago, then rediploidized and diversified. Extensive synteny between orthologous chromosomes occurs in extant salmonids, but each species has both conserved and unique chromosome arm fusions and fissions. Here we generate a high-density linkage map (3826 markers) for the Salvelinus genera (Brook Charr S. fontinalis), and then identify orthologous chromosome arms among the other available salmonid high-density linkage maps, including six species of Oncorhynchus, and one species for each of Salmo and Coregonus, as well as the sister group for the salmonids, Esox lucius for homeolog designation. To this end, we developed MapComp, a program that identifies identical and proximal markers between linkage maps using a reference genome of a related species as an intermediate. This approach increases the number of comparable markers between linkage maps by 5-fold, enabling a characterization of the most likely history of retained chromosomal rearrangements post-WGD, and identifying several conserved chromosomal inversions. Analyses of RADseq-based linkage maps from other taxa will also benefit from MapComp, available at: https://github.com/enormandeau/mapcomp/