The great tit HapMap project: a continental-scale analysis of genomic variation in a songbird

A major aim of evolutionary biology is to understand why patterns of genomic diversity vary within taxa and space. Large-scale genomic studies of widespread species are useful for studying how environment and demography shape patterns of genomic divergence. Here, we describe one of the most geographically comprehensive surveys of genomic variation in a wild vertebrate to date; the great tit (Parus major) HapMap project. We screened ca 500,000 SNP markers across 647 individuals from 29 populations, spanning ~30 degrees of latitude and 40 degrees of longitude - almost the entire geographic range of the European subspecies. Genome-wide variation was consistent with a recent colonisation across Europe from a South-East European refugiam, with bottlenecks and reduced genetic diversity in island populations. Differentiation across the genome was highly heterogeneous, with clear “islands of differentiation”, even among populations with very low levels of genome-wide differentiation. Low local recombination rates were a strong predictor of high local genomic differentiation (), especially in island and peripheral mainland populations, suggesting that the interplay between genetic drift and recombination causes highly heterogeneous differentiation landscapes. We also detected genomic outlier regions that were confined to one or more peripheral great tit populations, probably as a result of recent directional selection at the species’ range edges. Haplotype-based measures of selection were related to recombination rate, albeit less strongly, and highlighted population-specific sweeps that likely resulted from positive selection. Our study highlights how comprehensive screens of genomic variation in wild organisms can provide unique insights into spatio-temporal evolutionary dynamics

The great tit HapMap project: a continental‐scale analysis of genomic variation in a songbird

A major aim of evolutionary biology is to understand why patterns of genomic diversity vary within taxa and space. Large-scale genomic studies of widespread species are useful for studying how environment and demography shape patterns of genomic divergence. Here, we describe one of the most geographically comprehensive surveys of genomic variation in a wild vertebrate to date; the great tit (Parus major) HapMap project. We screened ca 500,000 SNP markers across 647 individuals from 29 populations, spanning ~30 degrees of latitude and 40 degrees of longitude – almost the entire geographical range of the European subspecies. Genome-wide variation was consistent with a recent colonisation across Europe from a South-East European refugium, with bottlenecks and reduced genetic diversity in island populations. Differentiation across the genome was highly heterogeneous, with clear ‘islands of differentiation’, even among populations with very low levels of genome-wide differentiation. Low local recombination rates were a strong predictor of high local genomic differentiation (FST), especially in island and peripheral mainland populations, suggesting that the interplay between genetic drift and recombination causes highly heterogeneous differentiation landscapes. We also detected genomic outlier regions that were confined to one or more peripheral great tit populations, probably as a result of recent directional selection at the species' range edges. Haplotype-based measures of selection were related to recombination rate, albeit less strongly, and highlighted population-specific sweeps that likely resulted from positive selection. Our study highlights how comprehensive screens of genomic variation in wild organisms can provide unique insights into spatio-temporal evolutionary dynamics

Data from: Does nest predation risk affect the frequency of extra-pair paternity in a socially monogamous passerine?

While considerable variations in both the frequency of extra-pair paternity (EPP) and the behavioral events that produce it are recognized among species, populations, individuals, and breeding attempts, the determinants of these variations are surprisingly difficult to establish. Nest predation may be one such determinant, since it is the most important source of reproductive failure, and past studies have suggested a variety of reproductive flexibilities under nest predation risk. However, despite its potentially significant effect on mating behaviors, nest predation risk has rarely been discussed in association with variations in intraspecific EPP patterns. Here, we examined the effect of naturally occurring nest predation, which varied between sites, years, and breeding attempts, on patterns of EPP in 92 broods (132 adults and 710 nestlings) of the Japanese great tit Parus major minor. We found that the frequency of extra-pair offspring was positively correlated with the nest predation rate, along with a correlation to breeding attempts in a season, but not with other factors such as individual quality or breeding density. Under high nest-predation risk, it may be adaptive for males to search for additional extra-pair copulation to spread the risk of losing all offspring and to invest less in mate-guarding, which also enables females to seek additional extra-mating. The results of this study suggest that nest predation risk, among other factors, may significantly influence paternity allocation in birds

Seasonal change in sexual differences in nestling size and survival: a framework to evaluate sex-dependent environmental sensitivity in the wild

Abstract Background Sexual size dimorphism (SSD) occurs in a wide range of species in birds and other animals, but the magnitude of SSD often varies with environmental conditions. In general, in the developmental stages, the larger sex is more vulnerable to adverse environmental conditions because the larger sex requires more energy than the smaller sex. However, this may not hold true for birds with large brood sizes; the larger sex can acquire more food by suppressing the smaller sex. In addition, most previous studies have been experimental, such as by manipulating clutch size and ectoparasites, which may not reflect natural conditions. Methods In the present study, we propose a general framework to assess sexual differences in environmental sensitivity in natural populations. Because environmental conditions change throughout the breeding season, seasonal changes of nestling SSD and sex ratio should reflect sexual differences in environmental sensitivity. We applied this approach to a large dataset (1555 nestlings over 5 years) of Japanese Tits (Parus minor). In this population, the male nestling is generally larger than the female (5% SSD in body weight). Results We found that the magnitude of SSD (weight, tarsus, wing) and fledgling sex ratio increased both in the beginning and the end of the breeding season. Conclusion Our study suggested that female nestlings are more valuable to poor environmental conditions in the relatively fecund species. This study underscores the importance of brood size on sexual differences in environmental stochasticity and our framework encourages comparative analysis among different bird species

Specific alien plant species predominantly deliver nectar sugar and pollen but are not preferentially visited by wild pollinating insects in suburban riparian ecosystems

Abstract The invasion of alien plants has been rapidly proceeding worldwide due to urbanisation. This might be beneficial to wild pollinating insects, since some alien plant species have large flowers and/or long flowering periods, which can increase nectar sugar and pollen availability. To determine the relative contribution of alien plants to floral resource supply and whether resource‐rich alien plants, if any, serve as an important food source of pollinating insects, we performed year‐round field observations in suburban riverbanks. We quantified the per‐unit‐area availability of nectar sugar and pollen delivered by alien and native flowering species and counted wild flower visitors (bees and wasps, hoverflies and butterflies) per plant species. The available nectar sugar and pollen per area were predominantly delivered by a few specific alien species, and the relative contribution of other species to floral resource provision was low throughout the period that wild flower visitors were observed. Nonetheless, the resource‐rich alien plants were not visited by as many insects as expected based on their contribution to resource provision. Rather, on a yearly basis, these plants received equal or even fewer visits than other flowering species, including resource‐poor natives. We show that despite their great contribution to the gross floral resource supply, resource‐rich alien plants do not serve as a principal food source for wild pollinating insects, and other plants, especially natives, are still needed to satisfy insect demand. For the conservation of pollinating insects in suburban ecosystems, maintaining floral resource diversity would be more beneficial than having an increase in gross floral resources by allowing the dominance of specific alien plants

EPO-predation data (T. Yuta & I. Koizumi 2015)

data for predation risk on extra-pair paternity in the Japanese great tit (10.1111/jav.00713

dataBEHECO-2018-0119

dataBEHECO-2018-011

Data from: Simulated hatching failure predicts female plasticity in extra-pair behavior over successive broods

While many studies have investigated the occurrence of extra-pair paternity (EPP) and its adaptive significance in wild population of birds, we still know surprising little about the plasticity in mating behavior of females at the individual level and how it affects the patterns of paternity. To address this question, we focused on the direct fertility benefit hypothesis for the function of EPP and studied if female birds react in extra-pair mating behavior after reproductive failures using a wild population of the Japanese great tit, Parus minor, a socially monogamous passerine with a moderate frequency of EPP and a high multiple brooding rate. We simulated hatching failure by replacing with artificial eggs during the egg laying period to investigate if females subsequently altered their mating behavior and became more promiscuous to improve reproductive success in their following clutches. The proportion of extra-pair offspring per clutches of both experimental and control pairs increased in the second clutches (replacement and repeat), but compared to the control pairs, the increase in the experimental pairs was significantly greater. The present study suggests that individual females appear to be making decisions based on specific cues and flexibly altering mating behavior in adaptive ways. Also, our results are compatible with one of the long-debated hypotheses for the evolutionary maintenance of EPP which predicts females gain direct fitness benefit through increased reproductive success from mating multiply