Teaching transposon classification as a means to crowd source the curation of repeat annotation - a tardigrade perspective.

BACKGROUND: The advancement of sequencing technologies results in the rapid release of hundreds of new genome assemblies a year providing unprecedented resources for the study of genome evolution. Within this context, the significance of in-depth analyses of repetitive elements, transposable elements (TEs) in particular, is increasingly recognized in understanding genome evolution. Despite the plethora of available bioinformatic tools for identifying and annotating TEs, the phylogenetic distance of the target species from a curated and classified database of repetitive element sequences constrains any automated annotation effort. Moreover, manual curation of raw repeat libraries is deemed essential due to the frequent incompleteness of automatically generated consensus sequences. RESULTS: Here, we present an example of a crowd-sourcing effort aimed at curating and annotating TE libraries of two non-model species built around a collaborative, peer-reviewed teaching process. Manual curation and classification are time-consuming processes that offer limited short-term academic rewards and are typically confined to a few research groups where methods are taught through hands-on experience. Crowd-sourcing efforts could therefore offer a significant opportunity to bridge the gap between learning the methods of curation effectively and empowering the scientific community with high-quality, reusable repeat libraries. CONCLUSIONS: The collaborative manual curation of TEs from two tardigrade species, for which there were no TE libraries available, resulted in the successful characterization of hundreds of new and diverse TEs in a reasonable time frame. Our crowd-sourcing setting can be used as a teaching reference guide for similar projects: A hidden treasure awaits discovery within non-model organisms.

Genomic signatures of the evolution of a diurnal lifestyle in Strigiformes.

Understanding the targets of selection associated with changes in behavioral traits represents an important challenge of current evolutionary research. Owls (Strigiformes) are a diverse group of birds, most of which are considered nocturnal raptors. However, a few owl species independently adopted a diurnal lifestyle in their recent evolutionary history. We searched for signals of accelerated rates of evolution associated with a diurnal lifestyle using a genome-wide comparative approach. We estimated substitution rates in coding and noncoding conserved regions of the genome of seven owl species, including three diurnal species. Substitution rates of the noncoding elements were more accelerated than those of protein-coding genes. We identified new, owl-specific conserved noncoding elements as candidates of parallel evolution during the emergence of diurnality in owls. Our results shed light on the molecular basis of adaptation to a new niche and highlight the importance of regulatory elements for evolutionary changes in behavior. These elements were often involved in the neuronal development of the brain.

Local selection signals in the genome of blue tits emphasize regulatory and neuronal evolution.

Understanding the genomic landscape of adaptation is central to understanding microevolution in wild populations. Genomic targets of selection and the underlying genomic mechanisms of adaptation can be elucidated by genome-wide scans for past selective sweeps or by scans for direct fitness associations. We sequenced and assembled 150 haplotypes of 75 blue tits (Cyanistes caeruleus) of a single Central European population by a linked-read technology. We used these genome data in combination with coalescent simulations (i) to estimate an historical effective population size of ~250,000, which recently declined to ~10,000, and (ii) to identify genome-wide distributed selective sweeps of beneficial variants probably originating from standing genetic variation (soft sweeps). The genes linked to these soft sweeps, but also those linked to hard sweeps based on new beneficial mutants, showed a significant enrichment for functions associated with gene expression and transcription regulation. This emphasizes the importance of regulatory evolution in the population's adaptive history. Soft sweeps were further enriched for genes related to axon and synapse development, indicating the significance of neuronal connectivity changes in the brain potentially linked to behavioural adaptations. A previous scan of heterozygosity-fitness correlations revealed a consistent negative effect on arrival date at the breeding site for a single microsatellite in the MDGA2 gene. Here, we used the haplotype structure around this microsatellite to explain the effect as a local and direct outbreeding effect of a gene involved in synapse development.

Female extra-pair behavior is not associated with reduced paternal care in Thorn-tailed Rayadito.

Extra-pair behavior is present in 76% of socially monogamous bird species with biparental care. This behavior may produce costs to females related to a reduction in paternal care. We estimated the percentage of extra-pair offspring and quantified paternal care in 44 nests of Thorn-tailed Rayadito (Aphrastura spinicauda) to assess whether males reduce their parental care when females obtain extra-pair fertilizations. We used data from a sub-Antarctic population of Rayadito located on Navarino Island (55°4'S, 67°40'W), southern Chile. We found no statistical support for a relationship between variation in paternal care and the percentage of extra-pair offspring. We discuss how the inability of breeding males to assess their genetic paternity and potential restrictions on behavioral flexibility may explain this result. Additionally, if paternal care is subjected to sexual selection, this could limit a facultative response to female extra-pair behavior by males. Finally, it is possible that a reduction in paternal care might not have evolved in this particular locality given the low frequency of extra-pair paternity in our study population.

On the relationship between baseline corticosterone levels and annual survival of the thorn-tailed rayadito.

Baseline concentrations of glucocorticoids (i.e., cortisol and/or corticosterone) can moderately increase with the degree of energy demands that an individual faces. This could be a mechanism based on which glucocorticods (GCs) can mediate life history trade-offs, and therefore fitness. The 'cort-fitness hypothesis' predicts a negative relationship between GCs and fitness, meanwhile the 'cort-adaptation hypothesis' predicts the opposite pattern. Field studies on the relation between baseline GCs and survival rate have shown mixed results, supporting both positive and negative effect. These ambiguous results could be partially consequence of the short time frame in that most of the studies are carried on. In this study, we tested the predictions of the 'cort-fitness hypothesis' and 'cort-adaptation hypothesis' by using long-term data (eight-year of capture-mark-recapture) of Thorn-tailed Rayadito (Aphrastura spinicauda) in two populations at different latitudes. We assessed whether survival varied as a function of Cort levels and whether it varied in a linear (positive: 'cort-adaptation hypothesis' or negative: 'cort-fitness hypothesis') or curvilinear way. The two populations in our study had different baseline Cort levels, then we evaluated whether the association between baseline Cort and survival probability varied between them. In the high latitude population (i.e., lower baseline Cort levels), we observed a marginally quadratic relationship that is consistent with the cort-fitness hypothesis. In contrast, in the low altitude population we did not find this relation. Our findings suggests that the association between baseline Cort and survival probability is context-dependent, and highlights the importance of comparing different populations and the use of long-term data.

Genomic Evidence for Sensorial Adaptations to a Nocturnal Predatory Lifestyle in Owls.

Owls (Strigiformes) evolved specific adaptations to their nocturnal predatory lifestyle, such as asymmetrical ears, a facial disk, and a feather structure allowing silent flight. Owls also share some traits with diurnal raptors and other nocturnal birds, such as cryptic plumage patterns, reversed sexual size dimorphism, and acute vision and hearing. The genetic basis of some of these adaptations to a nocturnal predatory lifestyle has been studied by candidate gene approaches but rarely with genome-wide scans. Here, we used a genome-wide comparative analysis to test for selection in the early history of the owls. We estimated the substitution rates in the coding regions of 20 bird genomes, including 11 owls of which five were newly sequenced. Then, we tested for functional overrepresentation across the genes that showed signals of selection. In the ancestral branch of the owls, we found traces of positive selection in the evolution of genes functionally related to visual perception, especially to phototransduction, and to chromosome packaging. Several genes that have been previously linked to acoustic perception, circadian rhythm, and feather structure also showed signals of an accelerated evolution in the origin of the owls. We discuss the functions of the genes under positive selection and their putative association with the adaptation to the nocturnal predatory lifestyle of the owls.