Efficacy of created and restored nesting sites for the conservation of colonial Laridae in the South of France

By rapidly modifying key habitat components, habitat restoration is at risk of producing attractive cues for animals without providing habitats of sufficient quality. As such, individual fitness components, such as reproduction, could be reduced and restored habitats could become ecological traps. This risk notably appears by using artificial constructions in restoration projects, yet few studies have evaluated their efficacy in a robust way. We investigated this by analyzing 154 islets that were created or restored to improve the conservation status of 7 colonial Laridae species in the South of France. From 2007 to 2016, we compared occupancy dynamics and breeding parameters of these species between the restored sites and 846 unmanaged nesting sites. We also explored species' preference for different nesting site characteristics and their respective effect on breeding parameters. Restored nesting sites were 2-9 times as attractive as unmanaged sites for all species except the Black-headed Gull (Chroicocephalus ridibundus). Colonization probability was up to 100 times higher in sites already used by other species the previous year and increased with distance to the shore until >0.2 when distance was over 250 m. Abandonment probability was 29-70% lower when breeding was successful the previous year in all species except the Sandwich Tern (Thalasseus sandvicensis). Productivity and breeding success probability were 2 times higher on managed sites. Distance from the shore was an important attractive characteristic of artificial nesting sites in all species. Other nesting site characteristics had species-specific effects on colonization, abandonment, and breeding success. Our results indicate that managed nesting sites are successful conservation tools for colonial Laridae in the Mediterranean and do not act as ecological traps. Our study showed that testing the ecological trap hypothesis is a robust way to evaluate the success of restoration projects of breeding habitats.

The color of greater flamingo feathers fades when no cosmetics are applied

Greater flamingos use cosmetic coloration by spreading uropygial secretions pigmented with carotenoids over their feathers, which makes the plumage redder. Because flamingos inhabit open environments that receive direct solar radiation during daytime, and carotenoids bleach when exposed to solar radiation, we expected that the plumage color would fade if there is no maintenance for cosmetic purposes. Here, we show that the concentrations of pigments inside feathers and on the surface of feathers were correlated, as well as that there was a correlation between the concentrations of pigments in the uropygial secretions and on the surface of feathers. There was fading in color (becoming less red) in feathers that received direct solar radiation when there was no plumage maintenance, but not so in others maintained in darkness. When we controlled for the initial color of feathers, the feathers of those individuals with higher concentration of pigments on the feather surfaces were those that lost less coloration after experimental exposure of feathers to sunny conditions. These results indicate that exposure to sunlight is correlated with the fading of feather color, which suggests that individuals need to regularly apply makeup to be more colorful. These results also reinforce the view that these birds use cosmetic coloration as a signal amplifier of plumage color. This may be important in species using highly variable habitats, such as wetlands, since the conditions experienced when molting may differ from those when the signal should be functional, usually months after molting.

Phylogeny- and Abundance-Based Metrics Allow for the Consistent Comparison of Core Gut Microbiome Diversity Indices Across Host Species

The filtering of gut microbial datasets to retain high prevalence taxa is often performed to identify a common core gut microbiome that may be important for host biological functions. However, prevalence thresholds used to identify a common core are highly variable, and it remains unclear how they affect diversity estimates and whether insights stemming from core microbiomes are comparable across studies. We hypothesized that if macroecological patterns in gut microbiome prevalence and abundance are similar across host species, then we would expect that increasing prevalence thresholds would yield similar changes to alpha diversity and beta dissimilarity scores across host species datasets. We analyzed eight gut microbiome datasets based on 16S rRNA gene amplicon sequencing and collected from different host species to (1) compare macroecological patterns across datasets, including amplicon sequence variant (ASV) detection rate with sequencing depth and sample size, occupancy-abundance curves, and rank-abundance curves; (2) test whether increasing prevalence thresholds generate universal or host-species specific effects on alpha and beta diversity scores; and (3) test whether diversity scores from prevalence-filtered core communities correlate with unfiltered data. We found that gut microbiomes collected from diverse hosts demonstrated similar ASV detection rates with sequencing depth, yet required different sample sizes to sufficiently capture rare ASVs across the host population. This suggests that sample size rather than sequencing depth tends to limit the ability of studies to detect rare ASVs across the host population. Despite differences in the distribution and detection of rare ASVs, microbiomes exhibited similar occupancy-abundance and rank-abundance curves. Consequently, increasing prevalence thresholds generated remarkably similar trends in standardized alpha diversity and beta dissimilarity across species datasets until high thresholds above 70%. At this point, diversity scores tended to become unpredictable for some diversity measures. Moreover, high prevalence thresholds tended to generate diversity scores that correlated poorly with the original unfiltered data. Overall, we recommend that high prevalence thresholds over 70% are avoided, and promote the use of diversity measures that account for phylogeny and abundance (Balance-weighted phylogenetic diversity and Weighted Unifrac for alpha and beta diversity, respectively), because we show that these measures are insensitive to prevalence filtering and therefore allow for the consistent comparison of core gut microbiomes across studies without the need for prevalence filtering.

Bioaccumulation of trace elements affects chick body condition and gut microbiome in greater flamingos

Elevated concentrations of trace elements represent a major concern to wetland ecosystems, since river estuaries are geochemical endpoints that accumulate pollution. Although the negative impact of environmental exposure of highly toxic elements such as Pb and Hg has received substantial attention, we still lack a comprehensive understanding of the effects that these and other common trace elements have on natural populations. We used greater flamingos as a study system within three sites that represent a gradient of pollution. Controlling for environmental sediment exposure, we assessed if signatures of bioaccumulation in feathers for ten trace elements (As, Cd, Cr, Cu, Hg, Ni, Pb, Se, Sn and Zn) are associated with two known proxies of health: body condition and the gut bacterial microbiome. We found evidence of an adverse effect of Se, Hg, and Pb bioaccumulation on body condition. Furthermore, bioaccumulation of the elements As, Cu, Se, Pb and Zn influenced different aspects of the gut microbiome. Bioaccumulation of Se led to a shift in the microbiome composition, largely driven by an enrichment of Bacteroides plebeius, which is linked to the breakdown of sulphated polysaccharides of algae. Bacteroides plebeius was negatively associated with chick body condition, suggesting an adverse effect of a microalgae diet rich in Se. Pb bioaccumulation was linked with a decrease in microbial diversity (adjusted-R² = 10.4%) and an increase in heterogeneity of the microbial community (adjusted-R² = 10.5%), an indication of impaired gut homeostasis. As, Cu and Zn had more nuanced effects on gut microbiome heterogeneity according to breeding site and bioaccumulation concentration. Our results therefore suggest that in addition to well-studied elements, bioaccumulation of poorly studied elements also adversely affect health of natural populations.

The dimensions of evolutionary potential in biological conservation

It is now well admitted by ecologists that the conservation of biodiversity should imply preserving the evolutionary processes that will permit its adaptation to ongoing and future environmental changes. This is attested by the ever-growing reference to the conservation of evolutionary potential in the scientific literature. The impression that one may have when reading papers is that conserving evolutionary potential can only be a good thing, whatever biological system is under scrutiny. However, different objectives, such as maintaining species richness versus ecosystem services, may express different, when not conflicting, underlying values attributed to biodiversity. For instance, biodiversity can be intrinsically valued, as worth it to be conserved per se, or it can be conserved as a means for human flourishing. Consequently, both the concept of evolutionary potential and the prescriptions derived from the commitment to conserve it remain problematic, due to a lack of explicit mention of the norms underlying different conservation visions. Here, we contend that those who advocate for the conservation of evolutionary potential should position their conception along four dimensions: what vehicles instantiate the evolutionary potential relevant to their normative commitment; what temporality is involved; how measurable evolutionary potential is, and what degree of human influence is tolerated. We need to address these dimensions if we are to determine why and when the maintenance of evolutionary potential is an appropriate target for the conservation of biodiversity.

Foraging niche shift maintains breeding parameters of a colonial waterbird during range expansion

Relating the effects of foraging niche variation to reproductive dynamics is critical to understand species response to environmental change. We examined foraging niche variations of the slender-billed gull (Chroicocephalus genei), a nomadic colonial waterbird species during its range expansion along the French Mediterranean coast over a 16-year period (1998-2013). We investigated whether range expansion was associated with a change in chick diet, breeding success, and chicks body condition. We also examined whether breeding success and chicks body condition were explained by diet and colonial characteristics (number of pairs, laying phenology, habitat, and locality). Diet was characterized using dual-stable isotopic proxies (δ 13C and δ 15N) of feather keratin from 331 individuals subsampled from a total of 4,154 chicks ringed and measured at 18 different colonies. δ 13C decreased and δ 15N increased significantly during range expansion suggesting that chicks were fed from preys of increasing trophic level found in the less salty habitat colonized by the end of the study period. Niche shift occurred without significant change of niche width which did not vary among periods, habitats, or localities either. Breeding success and chick body condition showed no consistent trends over years. Breeding success tended to increase with decreasing δ 13C at the colony level while there was no relationship between stable isotope signatures and chick body condition. Overall, our results suggest that even if range expansion is associated with foraging niche shift toward the colonization of less salty and more brackish habitats, the shift had marginal effect on the breeding parameters of the Slender-billed gull. Niche width appears as an asset of this species, which likely explains its ability to rapidly colonize new locations.

Offspring Microbiomes Differ Across Breeding Sites in a Panmictic Species

High dispersal rates are known to homogenize host’s population genetic structure in panmictic species and to disrupt host local adaptation to the environment. Long-distance dispersal might also spread micro-organisms across large geographical areas. However, so far, to which extent selection mechanisms that shape host’s population genetics are mirrored in the population structure of the enteric microbiome remains unclear. High dispersal rates and horizontal parental transfer may homogenize bacterial communities between breeding sites (homogeneous hypothesis). Alternatively, strong selection from the local environment may differentiate bacterial communities between breeding sites (heterogeneous hypothesis). Furthermore, selection from age-specific environmental or physiological factors may differentiate the microbiome between juveniles and adults. Here, we analyzed the cloacal bacterial 16S rRNA gene of fledgling greater flamingos, Phoenicopterus roseus, across nine western Mediterranean breeding sites and four breeding seasons (n = 731) and adult birds (n = 27) from a single site. We found that fledgling cloacal microbiome, as measured by alpha diversity, beta diversity, the relative abundance of assigned sequence variants (ASVs) belonging to a phylum and genus composition within phylum, varied significantly between sampling sites and across time within site despite high adult dispersal rates. The spatio-temporal effects were stronger on individual ASV absence/presence than on ASV abundance (i.e., than on core microbiome composition). Spatial effects had a stronger effect than temporal effects, particularly on ASV abundance. Our study supports the heterogeneous hypothesis whereby local environmental conditions select and differentiate bacterial communities, thus countering the homogenizing effects of high-dispersing host species. In addition, differences in core microbiome between adult vs. fledgling samples suggests that differences in age-specific environmental and/or physiological factors result in differential selection pressure of core enteric microbiome between age classes, even within the same environment. In particular, the genus Corynebacterium, associated with both seasonal fat uptake and migration in previous studies, was much more abundant in high-dispersing fledglings than in more resident adults. To conclude, selection mechanisms that shape the host’s genetic structure cannot be extended to the genetic structure of the enteric microbiome, which has important implications regarding our understanding of both host local adaptation mechanisms and enteric microbiome population genetics.

Correction to: Insights on dispersal and recruitment paradigms: sex- and age-dependent variations in a nomadic breeder

Unfortunately, Table 1 was incorrectly.

Very high MHC Class IIB diversity without spatial differentiation in the mediterranean population of greater Flamingos

Background

Selective pressure from pathogens is thought to shape the allelic diversity of major histocompatibility complex (MHC) genes in vertebrates. In particular, both local adaptation to pathogens and gene flow are thought to explain a large part of the intraspecific variation observed in MHC allelic diversity. To date, however, evidence that adaptation to locally prevalent pathogens maintains MHC variation is limited to species with limited dispersal and, hence, reduced gene flow. On the one hand high gene flow can disrupt local adaptation in species with high dispersal rates, on the other hand such species are much more likely to experience spatial variation in pathogen pressure, suggesting that there may be intense pathogen mediated selection pressure operating across breeding sites in panmictic species. Such pathogen mediated selection pressure operating across breeding sites should therefore be sufficient to maintain high MHC diversity in high dispersing species in the absence of local adaptation mechanisms. We used the Greater Flamingo, Phoenicopterus roseus, a long-lived colonial bird showing a homogeneous genetic structure of neutral markers at the scale of the Mediterranean region, to test the prediction that higher MHC allelic diversity with no population structure should occur in large panmictic populations of long-distance dispersing birds than in other resident species.

Results

We assessed the level of allelic diversity at the MHC Class IIB exon 2 from 116 individuals born in four different breeding colonies of Greater Flamingo in the Mediterranean region. We found one of the highest allelic diversity (109 alleles, 2 loci) of any non-passerine avian species investigated so far relative to the number of individuals and loci genotyped. There was no evidence of population structure between the four major Mediterranean breeding colonies.

Conclusion

Our results suggest that local adaptation at MHC Class IIB in Greater Flamingos is constrained by high gene flow and high MHC diversity appears to be maintained by population wide pathogen-mediated selection rather than local pathogen-mediated selection. Further understanding of how pathogens vary across space and time will be crucial to further elucidate the mechanisms maintaining MHC diversity in species with large panmictic populations and high dispersal rates.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-017-0905-3) contains supplementary material, which is available to authorized users.

Sexual display complexity varies non-linearly with age and predicts breeding status in greater flamingos

The long-lived greater flamingo (Phoenicopterus roseus) is famous for performing conspicuous group displays during which adults try to acquire a new mate each year with varying success. We examined variation in the sexual display complexity (SDC) of wild flamingos aged between 4 and 37 yrs. SDC was defined as the product of richness (the number of different display movements) and versatility (the number of transitions between movements) within a 5 min behavioral sequence. In both sexes, date in the pairing season had a linear and positive effect on SDC, whereas age had a quadratic effect, with SDC increasing until about age 20yrs, and declining afterwards. SDC better explained pairing patterns than age, and positively influenced the probability of becoming a breeder. Our results thus support the idea that SDC is an honest signal of individual quality and further suggest that senescence in display could be an overlooked aspect of reproductive decline in species with no or weak pair bonding.

Impacts of extreme climatic events on the energetics of long-lived vertebrates: the case of the greater flamingo facing cold spells in the Camargue

Most studies analyzing the effects of global warming on wild populations focus on gradual temperature changes, yet it is also important to understand the impact of extreme climatic events. Here we studied the effect of two cold spells (January 1985 and February 2012) on the energetics of greater flamingos (Phoenicopterus roseus) in the Camargue (southern France). To understand the cause of observed flamingo mass mortalities, we first assessed the energy stores of flamingos found dead in February 2012, and compared them with those found in other bird species exposed to cold spells and/or fasting. Second, we evaluated the monthly energy requirements of flamingos across 1980–2012 using the mechanistic model Niche Mapper™. Our results show that the body lipids of flamingos found dead in 2012 corresponded to 2.6±0.3% of total body mass, which is close to results found in woodcocks (Scolopax rusticola) that died from starvation during a cold spell (1.7±0.1%), and much lower than in woodcocks which were fed throughout this same cold spell (13.0±2%). Further, Niche Mapper™ predicted that flamingo energy requirements were highest (+6–7%) during the 1985 and 2012 cold spells compared with ‘normal’ winters. This increase was primarily driven by cold air temperatures. Overall, our findings strongly suggest that flamingos starved to death during both cold spells. This study demonstrates the relevance of using mechanistic energetics modelling and body condition analyses to understand and predict the impact of extreme climatic events on animal energy balance and winter survival probabilities.

Combining correlative and mechanistic habitat suitability models to improve ecological compensation

Only a few studies have shown positive impacts of ecological compensation on species dynamics affected by human activities. We argue that this is due to inappropriate methods used to forecast required compensation in environmental impact assessments. These assessments are mostly descriptive and only valid at limited spatial and temporal scales. However, habitat suitability models developed to predict the impacts of environmental changes on potential species' distributions should provide rigorous science-based tools for compensation planning. Here we describe the two main classes of predictive models: correlative models and individual-based mechanistic models. We show how these models can be used alone or synoptically to improve compensation planning. While correlative models are easier to implement, they tend to ignore underlying ecological processes and lack accuracy. On the contrary, individual-based mechanistic models can integrate biological interactions, dispersal ability and adaptation. Moreover, among mechanistic models, those considering animal energy balance are particularly efficient at predicting the impact of foraging habitat loss. However, mechanistic models require more field data compared to correlative models. Hence we present two approaches which combine both methods for compensation planning, especially in relation to the spatial scale considered. We show how the availability of biological databases and software enabling fast and accurate population projections could be advantageously used to assess ecological compensation requirement efficiently in environmental impact assessments.

Evidence for an association between post-fledging dispersal and microsatellite multilocus heterozygosity in a large population of greater flamingos

Dispersal can be divided into three stages: departure, transience and settlement. Despite the fact that theoretical studies have emphasized the importance of heterozygosity on dispersal strategies, empirical evidence of its effect on different stages of dispersal is lacking. Here, using multi-event capture-mark-recapture models, we show a negative association between microsatellite multilocus heterozygosity (MLH; 10 loci; n = 1023) and post-fledging dispersal propensity for greater flamingos, Phoenicopterus roseus, born in southern France. We propose that the negative effects of inbreeding depression affects competitive ability and therefore more homozygous individuals are more likely to disperse because they are less able to compete within the highly saturated natal site. Finally, a model with the effect of MLH on propensity of post-fledgling dispersers to disperse to the long-distance sites of Africa was equivalent to the null model, suggesting that MLH had low to no effect on dispersal distance. Variations in individual genetic quality thus result in context-dependent heterogeneity in dispersal strategies at each stage of dispersal. Our results have important implications on fitness since sites visited early in life are known to influence site selection later on in life and future survival.

Non-linear feeding functional responses in the Greater Flamingo (Phoenicopterus roseus) predict immediate negative impact of wetland degradation on this flagship species

Accurate knowledge of the functional response of predators to prey density is essential for understanding food web dynamics, to parameterize mechanistic models of animal responses to environmental change, and for designing appropriate conservation measures. Greater flamingos (Phoenicopterus roseus), a flagship species of Mediterranean wetlands, primarily feed on Artemias (Artemia spp.) in commercial salt pans, an industry which may collapse for economic reasons. Flamingos also feed on alternative prey such as Chironomid larvae (e.g., Chironomid spp.) and rice seeds (Oryza sativa). However, the profitability of these food items for flamingos remains unknown. We determined the functional responses of flamingos feeding on Artemias, Chironomids, or rice. Experiments were conducted on 11 captive flamingos. For each food item, we offered different ranges of food densities, up to 13 times natural abundance. Video footage allowed estimating intake rates. Contrary to theoretical predictions for filter feeders, intake rates did not increase linearly with increasing food density (type I). Intake rates rather increased asymptotically with increasing food density (type II) or followed a sigmoid shape (type III). Hence, flamingos were not able to ingest food in direct proportion to their abundance, possibly because of unique bill structure resulting in limited filtering capabilities. Overall, flamingos foraged more efficiently on Artemias. When feeding on Chironomids, birds had lower instantaneous rates of food discovery and required more time to extract food from the sediment and ingest it, than when filtering Artemias from the water column. However, feeding on rice was energetically more profitable for flamingos than feeding on Artemias or Chironomids, explaining their attraction for rice fields. Crucially, we found that food densities required for flamingos to reach asymptotic intake rates are rarely met under natural conditions. This allows us to predict an immediate negative effect of any decrease in prey density upon flamingo foraging performance.

Breeding experience might be a major determinant of breeding probability in long-lived species: the case of the greater flamingo

The probability of breeding is known to increase with age early in life in many long-lived species. This increase may be due to experience accumulated through past breeding attempts. Recent methodological advances allowing accounting for unobserved breeding episodes, we analyzed the encounter histories of 14716 greater flamingos over 25 years to get a detailed picture of the interactions of age and experience. Survival did not improve with experience, seemingly ruling out the selection hypothesis. Breeding probability varied within three levels of experience : no breeding experience, 1 experience, 2+ experiences. We fitted models with and without among-individual differences in breeding probabilities by including or not an additive individual random effect. Including the individual random effect improved the model fit less than including experience but the best model retained both. However, because modeling individual heterogeneity by means of an additive static individual random effect is currently criticized and may not be appropriate, we discuss the results with and without random effect. Without random effect, breeding probability of inexperienced birds was always [Formula: see text] times lower than that of same age experienced birds, and breeding probability increased more with one additional experience than with one additional year of age. With random effects, the advantage of experience was unequivocal only after age 9 while in young having [Formula: see text] experience was penalizing. Another pattern, that breeding probability of birds with [Formula: see text] experiences dropped after some age (8 without random effect; up to 11 with it), may point to differences in the timing of reproductive senescence or to the existence of a sensitive period for acquiring behavioral skills. Overall, the role of experience appears strong in this long-lived species. We argue that overlooking the role of experience may hamper detection of trade-offs and assessment of individual heterogeneity. However, manipulative experiments are desirable to confirm our finding.

From adaptive management to adjustive management: a pragmatic account of biodiversity values

The conservation of biodiversity poses an exceptionally difficult problem in that it needs to be effective in a context of double uncertainty: scientific (i.e., how to conserve biodiversity) and normative (i.e., which biodiversity to conserve and why). Although adaptive management offers a promising approach to overcome scientific uncertainty, normative uncertainty is seldom tackled by conservation science. We expanded on the approach proposed by adaptive-management theorists by devising an integrative and iterative approach to conservation that encompasses both types of uncertainty. Inspired by environmental pragmatism, we suggest that moral values at stake in biodiversity conservation are plastic and that a plurality of individual normative positions can coexist and evolve. Moral values should thus be explored through an experimental process as additional parameters to be incorporated in the traditional adaptive-management approach. As such, moral values should also be monitored by environmental ethicists working side by side with scientists and managers on conservation projects. Acknowledging the diversity of moral values and integrating them in a process of collective deliberation will help overcome the normative uncertainty. We used Dewey's distinction between adaptation and adjustment to offer a new paradigm built around what we call adjustive management, which reflects both the uncertainty and the likely evolution of the moral values humans attribute to biodiversity. We illustrate how this paradigm relates to practical conservation decisions by exploring the case of the Sacred Ibis (Threskiornis aethiopicus), an alien species in France that is the target of an eradication plan undertaken with little regard for moral issues. We propose that a more satisfying result of efforts to control Sacred Ibis could have been reached by rerouting the traditional feedback loop of adaptive management to include a normative inquiry. This adjustive management approach now needs to be tested in real-case conservation programs.