Supplementary feeding increases nestling feather corticosterone early in the breeding season in house sparrows

Several studies on birds have proposed that a lack of invertebrate prey in urbanized areas could be the main cause for generally lower levels of breeding success compared to rural habitats. Previous work on house sparrows Passer domesticus found that supplemental feeding in urbanized areas increased breeding success but did not contribute to population growth. Here, we hypothesize that supplementary feeding allows house sparrows to achieve higher breeding success but at the cost of lower nestling quality. As abundant food supplies may permit both high-and low-quality nestlings to survive, we also predict that within-brood variation in proxies of nestling quality would be larger for supplemental food broods than for unfed broods. As proxies of nestling quality, we considered feather corticosterone (CORTf), body condition (scaled mass index, SMI), and tarsus-based fluctuating asymmetry (FA). Our hypothesis was only partially supported as we did not find an overall effect of food supplementation on FA or SMI. Rather, food supplementation affected nestling phenotype only early in the breeding season in terms of elevated CORTf levels and a tendency for more variable within-brood CORTf and FA. Early food supplemented nests therefore seemed to include at least some nestlings that faced increased stressors during development, possibly due to harsher environmental (e.g., related to food and temperature) conditions early in the breeding season that would increase sibling competition, especially in larger broods. The fact that CORTf was positively, rather than inversely, related to nestling SMI further suggests that factors influencing CORTf and SMI are likely operating over different periods or, alternatively, that nestlings in good nutritional condition also invest in high-quality feathers

Developing the Protocol Infrastructure for DNA Sequencing Natural History Collections

Intentionally preserved biological material in natural history collections represents a vast repository of biodiversity. Advances in laboratory and sequencing technologies have made these specimens increasingly accessible for genomic analyses, offering a window into the genetic past of species and often permitting access to information that can no longer be sampled in the wild. Due to their age, preparation and storage conditions, DNA retrieved from museum and herbarium specimens is often poor in yield, heavily fragmented and biochemically modified. This not only poses methodological challenges in recovering nucleotide sequences, but also makes such investigations susceptible to environmental and laboratory contamination. In this paper, we review the practical challenges associated with making the recovery of DNA sequence data from museum collections more routine. We first review key operational principles and issues to address, to guide the decision-making process and dialogue between researchers and curators about when and how to sample museum specimens for genomic analyses. We then outline the range of steps that can be taken to reduce the likelihood of contamination including laboratory set-ups, workflows and working practices. We finish by presenting a series of case studies, each focusing on protocol practicalities for the application of different mainstream methodologies to museum specimens including: (i) shotgun sequencing of insect mitogenomes, (ii) whole genome sequencing of insects, (iii) genome skimming to recover plant plastid genomes from herbarium specimens, (iv) target capture of multi-locus nuclear sequences from herbarium specimens, (v) RAD-sequencing of bird specimens and (vi) shotgun sequencing of ancient bovid bone samples

Developmental Stability Covaries with Genome-Wide and Single-Locus Heterozygosity in House Sparrows

Fluctuating asymmetry (FA), a measure of developmental instability, has been hypothesized to increase with genetic stress. Despite numerous studies providing empirical evidence for associations between FA and genome-wide properties such as multi-locus heterozygosity, support for single-locus effects remains scant. Here we test if, and to what extent, FA co-varies with single- and multilocus markers of genetic diversity in house sparrow (Passer domesticus) populations along an urban gradient. In line with theoretical expectations, FA was inversely correlated with genetic diversity estimated at genome level. However, this relationship was largely driven by variation at a single key locus. Contrary to our expectations, relationships between FA and genetic diversity were not stronger in individuals from urban populations that experience higher nutritional stress. We conclude that loss of genetic diversity adversely affects developmental stability in P. domesticus, and more generally, that the molecular basis of developmental stability may involve complex interactions between local and genome-wide effects. Further study on the relative effects of single-locus and genome-wide effects on the developmental stability of populations with different genetic properties is therefore needed

Relating phenotypic and genetic variation to urbanization in avian species: a case study on house sparrows (Passer domesticus)

Urbanization is expected to increase at staggering rates in the near future underpinning the importance of the urban habitat as a source of biodiversity. One of the urban species, the house sparrow, has always been living and thriving well in highly built-up areas. Yet, since a few decades this commensal of man has showed marked reductions in population size and numbers to such an extent that it has been vanished from sight in many large European cities. Home range size varied significantly along an urban-rural gradient where urban house sparrows were characterized by the smallest home ranges. Home range size in the urban habitat was linked to the spatial distribution of key vegetation (bushes, hedges). In contrast, patch connectivity did not affect home range size in neither suburban nor rural areas. Finally, urban sparrows were in poorest nutritional condition and these indices were positively associated with estimates of home range size. According to the heterzygosity hypothesis genetic diversity promotes homeostatic mechanisms to buffer developmental pathways against random perturbations. Our results corroborated this hypothesis as, in contrast to environmental stress, FA was inversely related to levels of heterozygosity. Heterozygosity at population-level was able to explain as much as 34% of the observed variation in FA but a single key locus was the main driver underlying this pattern, although we could not entirely rule out genome-wide effects. Population genetic analyses could not reveal strong urban bottleneck signatures although these could have been masked by ongoing dispersal events. Principal coordinate analyses showed a moderate distinction between either the urban/suburban populations and the rural ones. Hierarchical Dest values further suggested genetic drift as an important determinant of spatial genetic variation. Urban areas were characterized by a higher average relatedness and higher proportion of close kin. Spatial autocorrelograms further supported small-scale population structure but also reported a smaller extent of positive genetic structure in highly urbanized areas, suggesting genetic drift might be stronger here due to small population sizes. These results advocate to integrate both individual and population-based analyses when attempting to visualize small-scale population structures

Calo_Enolase_haplos.info

List of individuals in which each enolase haplotype was found

Data from: Persistent inter- and intraspecific gene exchange within a parallel radiation of caterpillar hunter beetles (Calosoma sp.) from the Galápagos

When environmental gradients are repeated on different islands within an archipelago, similar selection pressures may act within each island, resulting in the repeated occurrence of ecologically similar species on each island. The evolution of ecotypes within such radiations may either result from dispersal, that is each ecotype evolved once and dispersed to different islands where it colonized its habitat, or through repeated and parallel speciation within each island. However, it remains poorly understood how gene flow during the divergence process may shape such patterns. In the Galápagos islands, three phenotypically similar species of the beetle genus Calosoma occur at higher elevations of different islands, while lowlands are occupied by a fourth species. By genotyping all major populations within this radiation for two nuclear and three mitochondrial gene fragments and seven microsatellite markers, we found strong support that the oldest divergence separates the highland species of the oldest island from the remaining species. Despite their morphological distinctness, highland species of the remaining islands were genetically closely related to the lowland population on each island and within the same magnitude as lowland populations sampled at different islands. Repeated evolution of highland ecotypes out of the lowland species appears the most likely scenario and estimates of geneflow rates revealed extensive admixture among ecotypes within islands, as well as between islands. These findings indicate that gene exchange among the different populations and species may have shaped the phylogenetic relationships and the repeated evolution of these ecotypes

Calo_µsats

Raw micosatellite genotype

Data from: Sex-biased dispersal at different geographical scales in a cooperative breeder from fragmented rainforest

Dispersal affects both social behavior and population structure and is therefore a key determinant of long-term population persistence. However, dispersal strategies and responses to spatial habitat alteration may differ between sexes. Here we analyzed spatial and temporal variation in ten polymorphic microsatellite DNA loci of male and female Cabanis’s greenbuls (Phyllastrephus cabanisi), a cooperative breeder of Afrotropical rainforest, to quantify rates of gene flow and fine-grained genetic structuring within and among fragmented populations. We found genetic evidence for female-biased dispersal at small spatial scales, but not at the landscape level. Local autocorrelation analysis provided evidence of positive genetic structure within 300 m distance ranges, which is consistent with behavioral observations of short-distance natal dispersal. At a landscape scale, individual-based autocorrelation values decreased over time while levels of admixture increased, possibly indicating increased gene flow over the past decade