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Abstract Rails are a phenotypically diverse family of birds that includes 130 species and displays a wide distribution around the world. Here we present annotated genome assemblies for four rails from Aotearoa New Zealand: two native volant species, pūkeko Porphyrio melanotus and mioweka Gallirallus philippensis, and two endemic flightless species takahē Porphyrio hochstetteri and weka Gallirallus australis. Using the sequence read data, heterozygosity was found to be lowest in the endemic flightless species and this probably reflects their relatively small populations. The quality checks and comparison with other rallid genomes showed that the new assemblies were of good quality. This study significantly increases the number of available rallid genomes and will enable future genomic studies on the evolution of this family.

Abstract The physiological demands of flight exert strong selection pressure on avian morphology and so it is to be expected that the evolutionary loss of flight capacity would involve profound changes in traits. Here, we investigate morphological consequences of flightlessness in a bird family where the condition has evolved repeatedly. The Rallidae include more than 130 recognized species of which over 30 are flightless. Morphological and molecular phylogenetic data were used here to compare species with and without the ability to fly in order to determine major phenotypic effects of the transition from flighted to flightless. We find statistical support for similar morphological response among unrelated flightless lineages, characterized by a shift in energy allocation from the forelimbs to the hindlimbs. Indeed, flightless birds exhibit smaller sterna and wings than flighted taxa in the same family along with wider pelves and more robust femora. Phylogenetic signal tests demonstrate that those differences are independent of phylogeny and instead demonstrate convergent morphological adaptation associated with a walking ecology. We found too that morphological variation was greater among flightless rails than flighted ones, suggesting that relaxation of physiological demands during the transition to flightlessness frees morphological traits to evolve in response to more varied ecological opportunities.

City-dwellers are often confronted with the presence of many spontaneous animal species which they either like or dislike. Using a questionnaire, we assessed the appreciation and perception of the pigeon (Columba livia), the rat (Rattus norvegicus), and the hedgehog (Erinaceus europaeus) by people in parks, train stations, tourist sites, community gardens, and cemeteries in Paris, France. Two hundred individuals were interviewed between May 2017 and March 2018. While factors such as age, gender, level of education or place or location of the survey did not appear to be decisive in analyzing the differential appreciation of these species by individuals, there was a clear difference in appreciation based on the species and the perceived usefulness of the animal, which is often poorly understood. The rat was disliked (with an average appreciation score of 2.2/10), and the hedgehog was liked (with an average appreciation score of 7.7/10). The case of the pigeon is more complex, with some people loving or hating it, and many others being indifferent (with an average appreciation score of 4.7/10). The most common descriptor associated with pigeons and rats is the word "dirty", while for for hedgehogs it is "cute". Like Driscoll (1995) who found a positive correlation between perceived usefulness an appreciation given to the species, we assume that providing information to the citizens about the ecosystem services provided by unappreciated urban species could improve their perception of these animals, thus enabling better coexistence.

Abstract Recently, urban agriculture has spread rapidly in occidental cities taking the form of plant cultivation on the rooftops of urban buildings. In this context, it would be interesting to use a natural fertilizer present in cities like the pigeon (Columba livia) guano. In this study, we tested the effects of pigeon guano on the cherry tomato plant in an urban environment. On a rooftop at Ivry‐sur‐Seine (near Paris, France), we set up 30 cultivation bags (58.9 L volume) with two cherry tomato plants in each bag. In June 2017, we added about 15 g of pigeon guano in 1.5 L of water to each of the 15 “guano” bags and 1.5 L of water to each of the 15 “control” bags. After 15 days, we observed that the tomato plants were higher and tend to have more flowers in the guano treatment than in the control group. Finally, regarding the total number of cherry tomatoes harvested (total mass and number), it was around one to two times higher in the guano treatment than in the control. However, the average mass per fruit was not affected by the treatment. Overall, we showed that pigeon guano is an efficient local fertilizer for cherry tomato plants in urban areas.

Abstract The trade‐off between reproduction and self‐maintenance is a cornerstone of life history theory, yet its proximate underpinnings are elusive. Here, we used an artificial selection approach to create replicated lines of Japanese quail (Coturnix japonica) that differ genetically in their reproductive investment. Whole transcriptome sequencing revealed that females from lines selected for high reproductive output show a consistent upregulation of genes associated with reproduction but a simultaneous downregulation of immune genes. Concordant phenotypic differences in immune function (i.e., specific antibody response against keyhole limpet hemocyanin) were observed between the selection lines, even in males who do not provide parental care. Our findings demonstrate the key role of obligate transcriptional constraints in the maintenance of life history variation. These constraints set fundamental limits to productivity and health in natural and domestic animal populations.

Abstract Wildlife inhabiting urban environments exhibit drastic changes in morphology, physiology, and behavior. It has often been argued that these phenotypic responses could be the result of micro‐evolutionary changes following the urbanization process. However, other mechanisms such as phenotypic plasticity, maternal effects, and developmental plasticity could be involved as well. To address maternal effects as potential mechanisms, we compared maternal hormone and antibody concentrations in eggs between city and forest populations of European blackbirds (Turdus merula), a widely distributed species for which previous research demonstrated differences in behavioral and physiological traits. We measured egg and yolk mass, yolk concentrations of androgens (androstenedione [A4], testosterone [T], 5α‐dihydrotestosterone [5α‐DHT], and immunoglobulins [IgY]) and related them to population, clutch size, laying order, embryo sex, and progress of breeding season. We show (a) earlier onset of laying in the city than forest population, but similar egg and clutch size; (b) higher overall yolk androgen concentrations in the forest than the city population (sex‐dependent for T); (c) greater among‐female variation of yolk T and 5α‐DHT concentrations in the forest than city population, but similar within‐clutch variation; (d) similar IgY concentrations with a seasonal decline in both populations; and (e) population‐specific positive (city) or negative (forest) association of yolk A4 and T with IgY concentrations. Our results are consistent with the hypotheses that hormone‐mediated maternal effects contribute to differences in behavioral and physiological traits between city and forest individuals and that yolk androgen and immunoglobulin levels can exhibit population‐specific relationships rather than trade‐off against each other.

Recent evidence of the occurrence of atypical Chlamydiaceae strains in pigeons, different from the established Chlamydiaceae, requires the development of a specific and rapid detection tool to investigate their prevalence and significance. Here is described a new real-time PCR assay that allows specific detection of atypical Chlamydiaceae from pigeons. The assay has been used to assess the dissemination of these strains in field samples collected from Parisian pigeon populations in 2009. The results suggest a limited dissemination compared to the usually higher prevalence of Chlamydia psittaci that is the main species associated with avian chlamydiosis.

The ability of mothers to transfer antibodies (Abs) to their young and the temporal persistence of maternal Abs in offspring constitute important life-history traits that can impact the evolution of host-parasite interactions. Here, we examined the effects of food availability and parental immunization on the transfer and persistence of maternal antibodies in nestling pigeons (Columba livia). This species can transmit maternal Abs to offspring before hatching through the egg yolk and potentially after hatching through crop milk. However, the role of this postnatal substance in immunity remains elusive. We used a full cross-fostering design to disentangle the effects of food limitation and parental immunization both before and after hatching on the levels and persistence of maternal Abs in chicks. Parents were immunized via injection with keyhole limpet hemocyanin antigens. Using an immunoassay that specifically detected the IgY antibodies that are known to be transmitted via the yolk, we found that the levels of anti-KLH Abs in newly hatched chicks were positively correlated with the levels of anti-KLH Abs in the blood of their biological mothers. However, this correlation was not present between chicks and their foster parents, suggesting limited IgY transfer via crop milk to the chick's bloodstream. Interestingly, biological mothers subjected to food limitation during egg laying transferred significantly fewer specific maternal Abs, which suggests that the transfer of antibodies might be costly for them. In addition, the persistence of maternal Abs in a chick's bloodstream was not affected by food limitation or the foster parents' anti-KLH Ab levels; it was only affected by the initial level of maternal anti-KLH Abs that were present in newly hatched chicks. These results suggest that the maternal transfer of Abs could be costly but that their persistence in an offspring's bloodstream may not necessarily be affected by environmental conditions.