Mammalian genomes encode tens of thousands of long non-coding RNAs (lncRNAs), which are long transcripts that do not give rise to proteins. To date, only a minuscule fraction of lncRNAs have been experimentally characterized and their functions remain uncertain. Evolutionary studies can provide important insights into the functionality of lncRNAs, by revealing the selective pressures that act on these genes. In this talk, I will present recent insights into the evolution of lncRNAs, stemming from large-scale comparative transcriptomics studies. To study the dynamics of lncRNAs in mammalian development and evolution, we generated and analyzed RNA-seq profile in a series of five developmental stages from mid-gestation embryo to aged individuals, for four major organs, in mouse and rat. We find that lncRNA repertoires, sequences and expression patterns evolve very rapidly. However, we show that there is increased functional constraint on lncRNAs expressed in somatic organs and early in development, and we identify several evolutionarily conserved lncRNAs with potential important roles in developmental processes. [more]

The view of species as entities amenable to evolutionary change elaborated by Charles Darwin laid the conceptual foundation for our current understanding of how biodiversity can be generated. Initially marred by a rudimental understanding of hereditary principles, evolutionists gained appreciation of the mechanistic underpinnings of adaptation and speciation following the merger of Mendelian genetic principles with Darwinian evolution. By the late 20th century a mature framework in theoretical and empirical evolutionary genetic research had been developed to investigate the genetic basis of species diversification. Spurred by a recent revolution in nano-sequencing technology speciation genetic research has become increasingly open to genetic non-model organisms. Genome-wide processes can now be investigated at unprecedented resolution in essentially any eco-evolutionary model species of interest. This development has expanded speciation research beyond the traditional boundaries and unveils the genetic basis of speciation from manifold perspectives and at various stages of the splitting process. In this talk I will give an overview on recent work in the growing field of ‘speciation genomics’ unraveling the genetic underpinnings of adaptation and speciation from a micro-evolutionary perspective. While providing examples from a variety of taxa, I will capitalize on own recent work in the Eurasian crow species complex. This system is characterized by parallel evolution of a sexually selected plumage phenotype and lends itself to studying population differentiation across the speciation continuum at different time points in the evolutionary trajectory. Population genomic analyses of >100 re-sequenced genomes from across the species’ range combined with transcriptome data and other functional assays provide first insight into processes underlying the built-up of genomic differentiation and its relationships to reproductive isolation. [more]

Most bird species have a diploid genome comprising around 80 chromosomes. Nearly all of these are relatively repeat-poor and gene-rich, and have been largely accessible with short-read sequencing technologies. There are, however, some chromosomes in the avian karyotype with considerable accumulation of selfish genetic elements such as transposable elements and endogenous viruses, which may imply that these chromosomes are in genetic conflict with the rest of the genome. Here I discuss ongoing research in our group focusing on two likely selfish chromosomes, the female-specific W chromosome in birds-of-paradise and the germline-specific chromosome in zebra finches. A combination of single-molecule technologies (such as long-read and linked-read sequencing) made it possible to access large parts of these highly repetitive chromosomes, showing that the birds-of-paradise W chromosome is highly enriched in endogenous retroviruses and the zebra finch germline-specific chromosome is highly enriched in tandemly repeated genes. These results raise the question of how much of the total genetic variation has previously been missed in avian genomics studies. [more]

Cooperative breeding is an extreme form of cooperation that evolved in birds, insects, fish, mammals, and humans. Although cooperative breeding in birds is well-studied, the conditions that favoured its evolution are still unclear. My presentation highlights the importance of family living for the evolution of cooperative breeding, explores its adaptive benefits, and assesses its life-history consequences. Phylogenetic comparative work showed that family living is a critical steppingstone for evolutionary transitions from pair breeding to cooperative breeding. The evolution of families is associated with productive environments, which facilitate prolonged parent-offspring associations. The subsequent evolution of cooperative breeding, however, is associated with environmental variability, where helpers can prevent reproductive failure in harsh years. My experiments with the family-living Siberian jay demonstrated that parents provide independent offspring with nepotistic food access, predator protection, and social learning opportunities to acquire vital life skills, for example to learn recognizing predators. Comparative work suggests that these benefits allow individuals in family living species to allocate more resources into their immune system or sexually selected traits. Thus, considering family living as an own social system changes our understanding of the evolution of sociality and cooperation, and provide novel insights into life-history evolution. [more]

In evolutionary ecology, the process of mate sampling is often considered as a secondary problem compared to the more important question of co-evolution between the traits expressed in one sex and the preferences in the other sex. Since there are direct benefits from choosing a partner, the processes of pair formation have been overlooked as a somewhat trivial question. Yet, the question of the choice between several partners of varying quality is not as simple and immediate as it may seem at first look. Difficulties arise at several levels. The study of mating strategies often begins with field observations at the group or population level, but it is not straightforward to identify the actual choice criterion. If non-random pairing is observed, many authors are tempted to conclude to the existence of an underlying sexual preference. Yet, one cannot directly link the pattern of assortative mating at the population level to a given process of individual choice. Indeed, simple models show that one can easily generate such a pattern without assuming any sexual preference for the individuals. On the contrary, a pattern apparently resulting from random choices can be generated from assumptions in which the individuals actually rely on explicit sexual preferences. More generally, the scramble competition (always arising when there is a limited number of sexual partners) is a sufficiently strong constraint to severely impair the evolution of any choosy decision rules. In most cases, the evolutionary stable strategy is to use very low acceptance threshold. We also provide experimental mechanisms in favour of the adaptive value of this apparent absence of choice. These results emphasize the urgent need for carefully considering the pairing process in sexual selection. [more]

What generates and maintains biological diversity? This major question in evolutionary biology has fascinated scientists for centuries and continues to drive new and exciting research. Explore recent findings that examine avian hybridization in chickadees and wagtails, species boundaries in redpoll finches, and the genetic basis of spatial cognition, to gain a better understanding of divergence and speciation in birds. From the genetic basis of feather color to metabolic pathways that differ between closely related species, this work is helping us better understand what makes species different, and how those differences contribute to the maintenance of avian biodiversity [more]