Despite the importance of polyploidy and the increasing availability of new genomic data, there remain important gaps in our knowledge of polyploid population genetics. These gaps arise from the complex nature of polyploid data (e.g. multiple alleles and loci, mixed inheritance patterns, association between ploidy and mating system variation). Furthermore, many of the standard tools for population genetics that have been developed for diploids are often not feasible for polyploids. This review aims to provide an overview of the state-of-the-art in polyploid population genetics and to identify the main areas where further development of molecular techniques and statistical theory is required. We review commonly used molecular tools (amplified fragment length polymorphism, microsatellites, Sanger sequencing, next-generation sequencing and derived technologies) and their challenges associated with their use in polyploid populations: that is, allele dosage determination, null alleles, difficulty of distinguishing orthologues from paralogues and copy number variation. In addition, we review the approaches that have been used for population genetic analysis in polyploids and their specific problems. These problems are in most cases directly associated with dosage uncertainty and the problem of inferring allele frequencies and assumptions regarding inheritance. This leads us to conclude that for advancing the field of polyploid population genetics, most priority should be given to development of new molecular approaches that allow efficient dosage determination, and to further development of analytical approaches to circumvent dosage uncertainty and to accommodate 'flexible' modes of inheritance. In addition, there is a need for more simulation-based studies that test what kinds of biases could result from both existing and novel approaches.

Summary1. According to their geographical distribution, most Drosophila species may be classified as either temperate or tropical, and this pattern is assumed to reflect differences in their thermal adaptation, especially in their cold tolerance. We investigated cold tolerance in a global collection of D. melanogaster by monitoring the time adults take to recover from chill coma after a treatment at 0 °C. Flies grown at an intermediate temperature (21 °C)showed a significant linear latitudinal cline: recovery was faster in populations living in colder climates. 3. The role of growth temperature was analysed in a subset of tropical and temperate populations. In all cases, recovery time decreased when growth temperature was lowered, and linear reaction norms were observed. This adaptive phenotypic plasticity explained more than 80% of the total variation, while genetic latitudinal differences accounted for less than 4%. 4. The beneficial effect observed in adults grown at a low temperature contrasts with other phenotypic effects which, like male sterility, appear as harmful and pathological. Our results point to the difficulty of finding a general interpretation to the diversity of plastic responses that are induced by growth temperature variations.

The study of species complexes is of particular interest to understand how evolutionary young species maintain genomic integrity. The Daphnia pulex complex has been intensively studied as it includes species that dominate freshwater environments in the Northern hemisphere and as it is the sole North American complex that shows transitions to obligate parthenogenesis. Past studies using mitochondrial markers have revealed the presence of 10 distinct lineages in the complex. This study is the first to examine genetic relationships among seven species of the complex at nuclear markers (nine microsatellite loci and one protein-coding gene). Clones belonging to the seven species of the Daphnia pulex complex were characterized at the mitochondrial NADH dehydrogenase (ND5) gene and at the Lactate dehydrogenase (LDH) locus. K-means, principal coordinate analyses and phylogenetic network analyses on the microsatellite data all separated European D. pulicaria, D. tenebrosa, North American D. pulex, D. pulicaria and their hybrids into distinct clusters. The hybrid cluster was composed of diploid and polyploid hybrids with D. pulex mitochondria and some clones with D. pulicaria mitochondria. By contrast, the phylogeny of the D. pulex complex using Rab4 was not well resolved but still showed clusters consisting mostly of D. pulex alleles and others of D. pulicaria alleles. Incomplete lineage sorting and hybridization may obscure genetic relationships at this locus. This study shows that hybridization and introgression have played an important role in the evolution of this complex.

Genome size was estimated in 49 clones of the Daphnia pulex complex from temperate and subarctic locations using flow cytometry and microsatellite DNA analyses. Significant genome size differences were found in diploid species belonging to the two genetically distinct groups (the pulicaria and the tenebrosa groups), with clones from the tenebrosa group having genome sizes 22% larger than those in the pulicaria group. Combined flow cytometry and microsatellite DNA analyses revealed that nearly all polyploid clones in the D. pulex complex are triploid and not tetraploid, as was previously suggested. Sequencing analyses of the ND5 gene to position clones in their respective clades within the D. pulex complex have uncovered three triploid clones of Daphnia middendorffiana with a D. pulex maternal parent. This result was unexpected because Daphnia pulicaria has always been identified as the maternal parent of these hybrid polyploid clones. Triploid clones likely owe their origins to interactions between sexual and asexual populations. Further interactions in the tenebrosa group have generated tetraploid clones but these events have been rare.

BackgroundCo-dispersal of sperm-dependent hybrids and their sexual relatives is expected to result in consistent spatial patterns between assemblages of hybrids and genetic structure of parental species. However, local hybridization events may blur this signal as assemblages could be organized under different connectivity constraints. This study aims at testing the hypothesis of local hybridization events by comparing the assemblage of hybrid fish Chrosomus eos-neogaeus to the genetic diversity of one of its parental species, Chrosomus eos.ResultsAn extensive survey performed on a total of 132 sites located in two regions of Southern Quebec (West-Qc and East-Qc) revealed a distinct organization of hybrid lineages. One of the six hybrid lineages detected in West-Qc is widespread throughout this region resulting in a low α-diversity (1.38) and β-diversity (4.35). On the other hand, 36 hybrid lineages were detected in East-Qc and displayed narrow geographic distributions leading to a high α-diversity (2.30) and β-diversity (15.68). In addition, the C. eos multilocus haplotype of several of these hybrids is assigned to their respective sympatric C. eos population. Finally, contrasting with hybrids, the paternal species C. eos displayed a higher ρST in West-Qc (0.2300) than in East-Qc (0.0734).ConclusionThe unusually high diversity of hybrid lineages in East-Qc as well as the spatial organization and the close genetic relationship with C. eos sympatric populations support the hypothesis that multiple hybridization events occurred in situ. These findings coupled to the near absence of the maternal species Chrosomus neogeaus suggest that the decline of this species could be the trigger event at the origin of the high rates of spontaneous hybridization in this region.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-016-0754-5) contains supplementary material, which is available to authorized users.