The Population Genetic Group meetings have been a key forum in the last half century for discussion of the maintenance and distribution of genetic variation in natural populations, the genetic basis and evolution of quantitative traits, mechanisms of adaptation, sexual selection and speciation, and much more. The small selection of papers in this Special Issue illustrates the diversity and vibrancy of the 'PopGroup' community and helps to mark this anniversary.

Recent advances in sequencing technologies, statistics and theory have advanced the field of population genetics. This special issue deals with the effective population size (Ne), an important parameter to predict evolutionary trajectories and to plan conservation actions. The effective size of populations can be estimated from genetic or from life history data and depends on a variety of parameters, such as the neighborhood of a population, or its mode of reproduction. Estimation methods have benefited from genome-wide genotyping and new estimation methods may be more precise and balanced. The contributions of this special issue provide improved ways to predict and estimate the effective population size in different situations and present applied studies where Ne was estimated in different natural settings. As such the special issue may serve as a resource and guideline, or as inspiration to population geneticists, researchers interested in microevolution and conservationists.

Due to their extensive gene flow, long lifespans and flexible mating systems, many forest trees are resilient to most of the population genetic consequences of habitat fragmentation, but may still exhibit increased inbreeding and correlated paternity. Here we present five studies that advance our understanding of forest fragmentation genetics and make it clear that: (a) in impacted landscapes, it is the diversity and fitness of progeny that matters; (b) mating system, breeding system and landscape context determine sensitivity to fragmentation. A focus on these research areas will help deliver better management outcomes for trees in impacted landscapes.

This special issue reflects the recent advances in the field of environmental genomics and exposes the attractive prospects in the light of the new, rapidly-evolving tools that are next generation sequencing (NGS) approaches. Understanding the ecology, evolution, adaptation and biodiversity of organisms in their ecosystems is one of the most challenging scientific issues to which NGS and other “omics” may contribute. The papers deal with a broad range of organisms (eukaryotes and prokaryotes) and environments, including biotic interactions and methodological enhancements. The special issue highlights the exciting paths opened by NGS in environmental genomics and the novel opportunities to go deeper in the understanding and characterization of complex biological systems.

The epigenetic phenomenon of genomic imprinting, whereby the maternally and paternally inherited copies of a gene are differentially expressed, has long intrigued both theorists and empiricists. In particular there has been a great deal of interest in understanding why such a peculiar pattern of gene expression has evolved, and what implications it has for our understanding of evolutionary processes. This special issue presents a series of papers that have addressed these fundamental questions through various approaches. We aimed in these papers for the latest data to better inform and test the various theories for the evolution of imprinting, perhaps suggesting modifications to existing theories or the development of new ones.

As illustrated in this special issue, quantitative genetics is a dynamic and expanding field. New developments in methodologies (molecular and statistical) coupled with new theoretical approaches (such as associative effects models where members of a group influence the trait value of a focal individual) have significant implications for evolutionary biologists, breeders, and human geneticists. Papers highlight recent findings on the genetic architecture of traits, the limitations of genomic selection, the nature of selection on QTLs in natural populations, the behaviour of additive variance in fitness, and the stability of G matrices.

This special issue is focused on how polyploidy and hybridization affect the ability of organisms to adapt to novel or changing environments. By combining papers describing classic cases of invasions dominated by allopolyploids, methodological challenges of working with polyploid and hybrid genomes, physiological consequences of polyploidy, and application of the latest genomic advances to investigating the evolutionary dynamics of polyploid genomes, a central purpose is to highlight the new insights that can arise from readdressing old questions in ecology and evolution with new tools. Although more data are needed, results suggest that genome duplication or combination could play a creative evolutionary role in changing environments.

This special issue reflects the intersection between molecular cytogenetics and comparative genomics and emphasizes their use to confirm and refine syntenies, identify breakpoints, neocentromeres and other chromosomal features that are responsible for the myriad of karyotypes that characterize biological lineages. It features papers that discuss chromosomal diversification at different phylogenetic levels and presents new and exciting insights to some of the molecular mechanisms that are thought to underpin the structural modification of karyotypes (including the evolution of sex chromosomes and dosage compensation in amniotes), and new technologies that may impact on the precision by which we identify and characterize chromosomal rearrangements in future.

Local adaptation has been suggested to be especially common in salmonid fishes. However, evidence supporting the local adaptation paradigm is still lacking in many cases. This special issue brings together reviews and primary articles showcasing the variety of genetic approaches that can be used to study local adaptation at differing geographical and temporal scales. Salmonid fishes are the focus as, in part due to their commercial importance, they have a number of special features making them amenable to the study of local adaptation, but the results and conclusions are certain to be of relevance to a broad range of taxa.