Does interspecific competition with a stronger competitor explain the rarity of an endangered snake on a Mediterranean island?

Interspecific competition has been demonstrated to be an important shaping force for snake communities worldwide, but relatively few studies have investigated its occurrence and extent with island assemblages of snakes. In Sardinia (Mediterranean Sea), two species of whip snakes (Colubridae) co-occur, one of them being abundant and widespread (Hierophis viridiflavus) and the other being localized and critically endangered (Hemorrhois hippocrepis). A previous hypothesis suggested that the latter species would be confined to suboptimal habitats by the former species, which is a stronger competitor for food. As a consequence, He. hippocrepis would not only be rare but would also be smaller in body size in Sardinia than in other regions of its range where Hi. viridiflavus does not occur. In 1999?C2010, we studied habitat selection, food habits, and body sizes of these two snakes in sympatric populations, applying a suite of statistical tools including null models and Monte Carlo simulations. We observed that dietary habits were different between species (compared to Hi. viridiflavus, He. hippocrepis more frequently preyed upon rodents and less frequently on lizards, and within rodent prey, more frequently upon Rattus and less frequently upon Mus), but not in a way compatible with competitively induced trophic niche partitioning. The two species were similar in terms of prey size and predator-size?Cprey-size relationships. They also differed in habitat selection (maquis was the preferred habitat for both, but Hi. viridiflavus was found significantly more often than He. hippocrepis in grasslands, cultivations, and artificial pinewoods) but again in a non-competitively directed way. In addition, there was no evidence for the hypothesis that He. hippocrepis was confined to suboptimal habitats. Body sizes were similar between species (with males being significantly larger than females), and Sardinian He. hippocrepis were not smaller than conspecifics inhabiting regions without Hi. viridiflavus. Overall, our study showed that the two species differed in some aspects of their ecology, but these differences could not be due to competitive interactions. The conservation implications of these results are also discussed.     

Do assortative mating and immigrant inviability help maintain population genetic structuring of an herbivore on a crop and a wild relative?

Population genetic structuring is common among herbivorous insects and frequently is associated with divergent host plants, such as crops and their wild relatives. Previous studies showed population genetic structuring in corn leafhopper Dulbulus maidis in Mexico, such that the species consists of two sympatric, host plant-associated populations: an abundant and widespread "pestiferous” population on maize (Zea mays mays), and a small and localized "wild" population on perennial teosinte (Zea diploperennis). a maize wild relative with a limited distribution. This study addressed whether assortative mating and immigrant inviability mediate genetic structuring of corn leafliopper by comparing the mating and reproductive successes of pestiferous and wild females that colonize their nonassociated host plants against the successes of females colonizing their associated host plants. Assortative mating was assessed by comparing mating frequencies and premating and mating times among females of each population on each host plant: immigrant inviability was assessed by comparing, across two generations, the fecundity, survival, development time, sex ratio, and population growth rate among leafhopper populations and host plants. Our results showed that on maize, and compared to resident, pestiferous females, wild females were more likely to mate, and greater proportions of their offspring survived to adult stage and were daughters;consequently, the per-generation population growth rate on maize was greater for immigrant, wild leafhoppers compared to resident, pestiferous leafhoppers. Our results suggested that wild leafhoppers emigrating to maize have a fitness advantage over resident, pestiferous leafhoppers, while immigrant pestiferous and resident wild leafhoppers on teosinte have similar fitnesses.     

Does higher connectivity lead to higher genetic diversity? Effects of habitat fragmentation on genetic variation and population structure in a gypsophile

Habitat fragmentation is a major threat to the maintenance of genetic diversity in many plant populations. Genetic effects of population size have received far more attention than the effects of isolation—or connectivity—but both are key components of the fragmentation process. To analyze the consequences of fragment size and connectivity on the neutral genetic variation and population genetic structure of the dominant gypsophile Lepidium subulatum, we selected 20 fragments along two continuous gradients of size and degree of isolation in a fragmented gypsum landscape of Central Spain. We used eight polymorphic microsatellite markers, and analyzed a total of 344 individuals. Populations were characterized by high levels of genetic diversity and low inbreeding coefficients, which agrees with the mainly outcrossing system of L. subulatum and its high abundance in gypsum landscapes. Bayesian clustering methods, pairwise F _ST values and analysis of molecular variance revealed low among-population differentiation, with no significant isolation by distance. However, several genetic diversity indices such as allelic richness, number of effective alleles, expected heterozygosity and number of private alleles were negatively related to population isolation. The higher genetic diversity found on more connected fragments suggests higher rates of gene flow among more connected populations. Overall, our results highlight that fragmentation can have important effects on intra-population genetic processes even for locally abundant, dominant species. This, together with previously documented effects of connectivity on fitness of gypsophile species highlights the importance of including habitat connectivity in management and conservation strategies of this type of semiarid systems.     

Is life history a barrier to dispersal? Contrasting patterns of genetic differentiation along an oceanographically complex coast

Extreme variation in early life‐history strategies is considered a moderately good predictor of genetic subdivision and hence dispersal for a range of marine species. In reality, however, a good deal of population differentiation must reflect historical effects, more subtle variation in life histories, and, particularly, the interaction of larvae with oceanographic processes. Using a combination of allozyme and microsatellite markers, we show that the large‐scale genetic structure of populations of three species (direct and planktonically developing cushion stars and a planktonic developing sea anemone that is also asexually viviparous) varies consistently, in line with the predicted capacity for dispersal within three geographic regions. We detected high levels of genetic subdivision for the direct developing cushion star (F_ST = 0.6), low levels for the planktonically developing cushion star (F_ST = 0.009), and intermediate levels for the sexual/asexual sea anmone (F_ST = 0.19). These patterns are exhibited despite the highly variable patterns of current movement and the presence of biogeographic barriers. Our results suggest that, although there is large scale genetic differentiation for two species, patterns of population connectivity are remarkably consistent within major regions and do not reflect variation in major oceanographic processes or genetic discontinuity coincident with biogeographic boundaries. © 2008 The Linnean Society of London, Biological Journal of the Linnean Society, 2008, 95 , 106–116.     

Are indirect genetic benefits associated with polyandry? Testing predictions in a natural population of lemon sharks

Multiple mating has clear fitness benefits for males, but uncertain benefits and costs for females. We tested for indirect genetic benefits of polyandry in a natural population, by using data from a long-term genetic and demographic study of lemon sharks ( Negaprion brevirostris ) at Bimini, Bahamas. To do so, we followed the fates of individuals from six cohorts (450 age-0 and 254 age-1 fish) in relation to their individual level of genetic variation, and whether they were from polyandrous or monoandrous litters. We find that offspring from polyandrous litters did not have a greater genetic diversity or greater survival than did the offspring of monoandrous litters. We also find no evidence of positive associations between individual offspring genetic diversity metrics and our surrogate measure of fitness (i.e. survival). In fact, age-1 individuals with fewer heterozygous microsatellite loci and more genetically similar parents were more likely to survive to age-2. Thus, polyandry in female lemon sharks does not appear to be adaptive from the perspective of indirect genetic benefits to offspring. It may instead be the result of convenience polyandry, whereby females mate multiply to avoid harassment by males. Our inability to find indirect genetic benefits of polyandry despite detailed pedigree and survival information suggests the need for similar assessments in other natural populations.     

How large a managed area is needed to protect a threatened animal species? Combining simple dispersal and population models

The size and shape of the managed area for a threatened species to have a stable or growing population is a central issue for conservation management, for example for kiwi, Apteryx sp. Combining geometric probability results for retention of juveniles to breed in the protected area with a standard matrix population model allows the creation of an explicit relationship between the minimum area needed and how far juveniles of the species disperse to establish breeding territories. For a given set of demographic parameters for the population, and a rectangular protected area, there is a quadratic relationship between area and dispersal distance. Extensions for a circular protected area, and for a probability distribution on dispersal distance, are considered. The results are applied to kiwi, using established population parameters, giving results that match closely those from a previously published simulation. This approach can provide simple tools, readily implemented in a spreadsheet, for assessment of the size and shape of protected areas needed in conservation management of animals that disperse before breeding.     

Sewage pollution and extinction risk: an endangered limpet as a bioindicator?

The mollusc Patella ferruginea, endemic to the Mediterranean, is the most endangered marine species on the list of the European Council Directive 92/43/EEC and it is under serious risk of extinction. In spite of the low abundances and restricted distribution of this limpet, important populations have been found in the harbour of Ceuta, north Africa. The main objective of the present study was to characterise, for the first time, the effects of sewage pollution on P. ferruginea and related limpet species, and to evaluate the potential value of these limpet assemblages as bioindicators, using univariate and multivariate analyses. Physicochemical parameters and limpets were sampled in nine stations located at 0, 1, 2, 4, 8, 16, 32, 64 and 128 m away from the discharge point of a sewage effluent in Ceuta harbour. The stations closer to the outfall (0, 1, 2, 4 and 8) were characterised by higher values of turbidity, phosphate and ammonia in the water column, and organic matter, faecal coliforms and faecal Streptococci in sediments. A total of six limpet species were found and studied (Patella ferruginea, P. caerulea, P. nigra, P. rustica, P. ulyssiponensis and Siphonaria pectinata); the number of limpet species increased with increasing distance from the outfall, while diversity and evenness reached the highest values at intermediate sites. Siphonaria pectinata and P. caerulea were the most resistant and abundant species, while P. ferruginea was the most sensitive species to sewage pollution, only found at stations from 32 to 128 m. The distribution of this endangered limpet seems mainly affected by the pollution gradient, and not by the competition with the remaining limpets. The results of this study should be taken into account in future programmes of management and conservation of P. ferruginea.     

Does a top predator reduce the predatory impact of an invasive mesopredator on an endangered rodent?

The mesopredator release hypothesis (MRH) predicts that reduced abundance of top‐order predators results in an increase in the abundance of smaller predators (mesopredators) due to a reduction in intra‐guild predation and competition. The irruption of mesopredators that follows the removal of top‐order predators can have detrimental impacts on the prey of the mesopredators. Here we investigated the mechanisms via which the presence of a top‐order predator can benefit prey species. We tested predictions made according to the MRH and foraging theory by contrasting the abundances of an invasive mesopredator (red fox Vulpes vulpes) and an endangered prey species (dusky hopping mouse Notomys fuscus), predator diets, and N. fuscus foraging behaviour in the presence and absence of a top‐predator (dingo Canis lupus dingo). As predicted by the MRH, foxes were more abundant where dingoes were absent. Dietary overlap between sympatric dingoes and foxes was extensive, and fox was recorded in 1 dingo scat possibly indicating intra‐guild predation. Notomys fuscus were more likely to occur in fox scats than dingo scats and as predicted by the MRH N. fuscus were less abundant in the absence of dingoes. The population increase of N. fuscus following rainfall was dampened in the absence of dingoes suggesting that mesopredator release can attenuate bottom‐up effects, although it remains conceivable that differences in grazing regimes associated with dingo exclusion could have also influenced N. fuscus abundance. Notomys fuscus exhibited lower giving‐up densities in the presence of dingoes, consistent with the prediction that their perceived risk of predation would be lower and foraging efficiency greater in the presence of a top‐predator. Our results suggest that mesopredator suppression by a top predator can create a safer environment for prey species where the frequency of fatal encounters between predators and prey is reduced and the non‐consumptive effects of predators are lower.     

Paternal effects on seed germination: a barrier to the genetic assimilation of an endemic plant taxon?

We used a crossing experiment to investigate post-zygotic barriers that might limit introgression between a pair of closely-related, gynodioecious plant species--the widespread weed Silene vulgaris and the local Swedish endemic S. uniflora ssp. petraea. The study not only considered the effects of hybridization on conventionally-used (primary) fitness components such as seed set and progeny survival, but also provided a test for the effects of interspecific hybridization on characters with more subtle or habitat-specific effects on fitness. We detected highly significant paternal effects on seed germination properties, with the germination characteristics of hybrid seed resembling those of the species that served as the pollen donor. These paternal effects on germination represent a potentially strong barrier to interspecific introgression in the two species' natural habitats, where an inappropriate germination response in the habitat of the maternal parent may lead to the failure of seedling establishment. Interspecific crosses had weak or variable effects on progeny survival, flowering and sex ratio, but these effects could not be interpreted in terms of barriers to introgression. Our results indicate that nuclear restorers in S. vulgaris have the capacity to suppress cytoplasmic male-sterility genes in its endemic congener.     

Estimating fitness consequences of dispersal: a road to 'know-where'? Non-random dispersal and the underestimation of dispersers' fitness

1. Many studies investigating fitness correlates of dispersal in vertebrates report dispersers to have lower fitness than philopatric individuals. However, if dispersers are more likely to produce dispersing young or are more likely to disperse again in the next year(s) than philopatric individuals, there is a risk that fitness estimates based on local adult survival and local recruitment will be underestimated for dispersers. 2. We review the available empirical evidence on parent-offspring resemblance and individual lifelong consistency in dispersal behaviour, and relate these studies to recent studies of fitness correlates of dispersal in vertebrates. 3. Of the 12 studies testing directly for parent-offspring resemblance in dispersal propensity, five report a significant resemblance. The average effect size (r) of parent-offspring resemblance in dispersal was 0.15 [95% confidence interval (CI) = 0.07-0.22], with no difference between the sexes (average weighted effect size of 0.12 (0.08-0.16) and 0.16 (0.11-0.20) for females and males, respectively). Only three studies report data on within-individual consistency in dispersal propensity, of which two suggest dispersers to be more likely to disperse again. 4. To assess the magnitude of fitness underestimation expected for dispersing individuals depending on the heritability of dispersal distance and study area size, we used a simulation approach. Even when study area size is 10 times the mean dispersal distance, local recruitment per breeding event may be underestimated by 4-10%, generating a potential difference of 4-60% in average lifetime production of recruits between dispersing and philopatric individuals, with larger differences in long-lived species. 5. Estimates of both fitness correlates of dispersal and parent-offspring resemblance or within-individual consistency in dispersal behaviour have been reported for 11 species. Although some comparisons suggest genuine differences in fitness components between philopatric and dispersing individuals, others, based on adult and juvenile survival, are open to the alternative explanation of biased fitness estimates. 6. We list three potential ways of reducing the risk of making wrong inferences on biased fitness estimates due to such non-random dispersal behaviour between dispersing and philopatric individuals: (a) diagnosing effects of non-random dispersal, (b) reducing the effects of spatially limited study area and (c) performing controlled experiments.     

When and where to count? Implications of migratory connectivity and nonbreeding distribution to population censuses in a migratory bird population

Migratory connectivity is a metric of the co-occurrence of migratory animals originating from different breeding sites, and like their spatial dispersion, can vary substantially during the annual cycle. Together, both these properties affect the optimal times and sites of population censusing. We tracked taiga bean geese (Anser fabalis fabalis) during 2014–2021 to study their migratory connectivity and nonbreeding movements and determine optimal periods to assess the size of their main flyway population. We also compared available census data with tracking data, to examine how well two existing censuses covered the population. Daily Mantel's correlation between breeding and nonbreeding sites lay between 0 and 0.5 during most of the nonbreeding season, implying birds from different breeding areas were not strongly separated at other times in the annual cycle. However, the connectivity was higher among birds from the westernmost breeding areas compared to the birds breeding elsewhere. Daily Minimum Convex Polygons showed tracked birds were highly aggregated at census times, confirming their utility. The number of tracked birds absent at count sites during the censuses however exceeded numbers double-counted at several sites, indicating that censuses might have underestimated the true population size. Our results show that connectivity can vary in different times during the nonbreeding period, and should be studied throughout the annual cycle. Our results also confirm previous studies, which have found that estimates using marked individuals usually produce higher population size estimates than total counts. This should be considered when using total counts to assess population sizes in the future.     

Gene flow in environmental Legionella pneumophila leads to genetic and pathogenic heterogeneity within a Legionnaires’ disease outbreak

Background

Legionnaires’ disease is a severe form of pneumonia caused by the environmental bacterium Legionella pneumophila. Outbreaks commonly affect people with known risk factors, but the genetic and pathogenic complexity of L. pneumophila within an outbreak is not well understood. Here, we investigate the etiology of the major Legionnaires’ disease outbreak that occurred in Edinburgh, UK, in 2012, by examining the evolutionary history, genome content, and virulence of L. pneumophila clinical isolates.

Results

Our high resolution genomic approach reveals that the outbreak was caused by multiple genetic subtypes of L. pneumophila, the majority of which had diversified from a single progenitor through mutation, recombination, and horizontal gene transfer within an environmental reservoir prior to release. In addition, we discover that some patients were infected with multiple L. pneumophila subtypes, a finding which can affect the certainty of source attribution. Importantly, variation in the complement of type IV secretion systems encoded by different genetic subtypes correlates with virulence in a Galleria mellonella model of infection, revealing variation in pathogenic potential among the outbreak source population of L. pneumophila.

Conclusions

Taken together, our study indicates previously cryptic levels of pathogen heterogeneity within a Legionnaires’ disease outbreak, a discovery that impacts on source attribution for future outbreak investigations. Furthermore, our data suggest that in addition to host immune status, pathogen diversity may be an important influence on the clinical outcome of individual outbreak infections.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-014-0504-1) contains supplementary material, which is available to authorized users.     

Predator identification and effects of habitat management and fencing on depredation rates of simulated nests of an endangered population of Hermann’s tortoises

Nest predation has been identified as the main threat behind the negative population dynamics in chelonian species and in particular in the native Iberian population of the Western Hermann’s tortoise Testudo hermanni hermanni. This endangered subspecies is found within the Albera Nature Reserve, where this study was performed. We selected three formerly high-density tortoise areas to carry out different trials whose aims were to: (1) identify nest predator species, (2) test the success of reducing the shrub cover to reduce nest predation in potential new nesting areas, and (3) assess fencing efficiency to exclude predators. For the first objective, camera-trapping was used to identify nest predators, with sardines and artificial tortoise nests as lures. We obtained 825 pictures of possible predators and demonstrated that the beech marten was the most abundant predator in the study areas, followed by the badger and the wild boar. For the second objective, predation of artificial nests was compared between plots managed for shrub reduction (27 plots of 4, 25, and 100?m²) and a natural nesting area (nine control plots of 100?m²). Predation was strong in the managed plots (43.6% after 48?h and 99.6% after 144?h) but highest in the control area (100% after 48?h). Surprisingly, predation occurred at an even faster pace when we repeated the trial with a single artificial nest (in order to reduce odor intensity). Finally, we compared predation rates between eight fenced and eight unfenced plots of 100?m². Fencing was partially effective to control nest predation because it excluded all the main predator species except the beech marten, which learned to go through it. Since the nest predation threat to this endangered population is critical, new strategies are needed to control nest predation by taking into account the ability of predators to learn nest location.     

Maternal modulation of natal dispersal in a passerine bird: an adaptive strategy to cope with parasitism?

The decision of how far to disperse from the natal territory has profound and long-lasting consequences for young animals, yet the optimal dispersal behavior often depends on environmental factors that are difficult or impossible to assess by inexperienced juveniles. Natural selection thus favors mechanisms that allow the adaptive and flexible adjustment of the offspring's dispersal behavior by their parents via either paternal or maternal effects. Here we show that different dispersal strategies maximize the reproductive success of young great tits (Parus major) originating from a parasite-infested or a parasite-free nest and demonstrate that differential transfer of maternal yolk androgens in response to parasitism can result in a modification of the offspring's dispersal behavior that appears adaptive. It demonstrates that prenatal maternal effects are an important yet so far neglected determinant of natal dispersal and highlights the potential importance of maternal effects in mediating coevolutionary processes in host-parasite systems.