Catarina Ferreira

Ecosystem Effects of Variant Rabbit Hemorrhagic Disease Virus, Iberian Peninsula

To the Editor: In this investigation, we found evidence for the apparent effects that a new variant of the rabbit hemorrhagic disease virus (RHDV) is having on native wild European rabbit (Oryctolagus cuniculus) populations on the Iberian Peninsula, and how this virus could threaten the conservation of endangered predators. Historically, European rabbits were extremely abundant on the Iberian Peninsula, which is in their native range. However, during the 20th century, the number of rabbits on the peninsula has declined >90%, mainly because of diseases (1). The first notable crisis among rabbits occurred during the 1950s concurrent with the arrival of myxomatosis among rabbit populations, which caused mortality rates of ≈90% (1), as registered in other regions. During the late 1980s, a calicivirus, RHDV, caused infections that made a strong impact on rabbit populations, causing initial mortality rates of 55%–75% in Iberia (1). Since their initial outbreaks, both diseases have become enzootic, and related mortality rates have decreased, in part because of increased host resistance, although the infections still play a major role in the dynamics of rabbit populations (2). In 2011, a new variant of RHDV, which appears to be closely related to an isolate originating in France that was described in 2010 (3), caused high mortality rates in some rabbit farms in Spain (4) and was also identified in an experimental wild rabbit plot in northern Spain (5). Since 2012, the new variant of RHDV has been detected in most rabbit farms in Spain (6), and in several wild populations distributed across Spain and Portugal (7), suggesting that it has rapidly spread throughout the Iberian Peninsula. This variant affects both of the wild rabbit subspecies (O. cuniculus cuniculus and O. c. algirus), and unlike the classical form of RHDV, it kills rabbits as young as 11 days of age and rabbits that have been vaccinated against classic RHDV (6,7). This scenario has raised concern for the survival of wild rabbit populations and its predators in this region. Data regarding rabbit trends seem to sustain this concern. For example, a long-term monitoring program in Aragon in northern Spain shows a notable decline in rabbit numbers during 2013 in populations that showed both long-term increasing and decreasing trends over the monitoring period (Figure, panels A, B, respectively). A similar trend has been observed in the main areas inhabited by the highly endangered Iberian lynx (Lynx pardinus). The lynx relies on rabbits for survival, because they represent >85% of the lynx’s diet (9). For instance, in Coto del Rey, the area within Donana National Park in southern Spain that traditionally held the highest rabbit densities and therefore represents the core of Iberian lynx populations in this national park, there was a decline in rabbits of >80% during 2012–2013 (Figure, panel C). Similar declines have been detected in low-density rabbit populations surveyed within Donana National Park (Figure, panel C). Rabbit numbers have also been progressively dropping in the proximity of the Yeguas River in Andujar and Cardena Natural Parks in southern Spain, where the largest Iberian lynx population currently lives: rabbit density was >3.5 rabbits/hectare in 2010 and <1 rabbit/hectare in 2013, a decline of ≈75% (10). In accordance with field surveys, hunters throughout Iberia claim that the number of rabbits harvested this season has decreased dramatically, pointing to a 70%–80% decline compared to the previous hunting season in some estates (A. Linares, pers. comm.). Figure Trends in rabbit abundance (number of rabbits/km) in Aragon and Donana National Park, northern and southern Spain, respectively, and in the number of Iberian lynx cubs born in the wild in Spain. A) Average rabbit abundance (+SD) of populations ... The European rabbit is a multifunctional keystone species of the Iberian Mediterranean ecosystem, where it serves as prey for >30 predatory animals, alters plant species composition and vegetation structure through grazing and seed dispersal, its excrement and urine have an effect on soil fertility and plant growth and provide feeding resources for invertebrates, and its burrows provide shelter for different species (9). Therefore, the decline in rabbit numbers could have potential cascading effects on ecosystem function. In fact, some of these effects may already be apparent on rabbit-reliant animals. On one hand, the sharp reduction in rabbit numbers observed in 2013 in the main lynx distribution area has been accompanied by a notable decrease in the number of lynx cubs born in the wild (Figure, panel D). On the other hand, the number of lynxes killed on roads doubled in 2013 (n = 14) in relation to 2012 (n = 7), and this has been linked to increased lynx displacements related to rabbit scarcity potentially associated with the impact of the new variant of RHDV (http://www.juntadeandalucia.es). The situation described exemplifies how emerging diseases can affect biodiversity conservation. It also highlights the importance of using wildlife monitoring schemes as detection tools for monitoring the impact of stochastic factors, such as the variant RHDV, on wildlife populations. Urgent management actions, designed within an Iberian rabbit conservation strategy that relies on a multidisciplinary framework, are needed to ensure the conservation of this keystone member of the Iberian Peninsula ecosystem and that of rabbit-reliant predators.

Influence of habitat management on the abundance and diet of wild rabbit (Oryctolagus cuniculus algirus) populations in Mediterranean ecosystems

During the last decades wild rabbit (Oryctolagus cuniculus) populations have been progressively declining in the Iberian Peninsula as a result of several factors, namely habitat deterioration. Hence, habitat management has become one of the most commonly used management techniques to restore wild rabbit populations. To test the efficacy of some of these measures (creation of pastures, opening firebreaks) in rabbit populations, two managed (M1 and M2) and two control areas (C1 and C2) were selected in the Portuguese Southwest (SW) Coast. In each study area, the influence of habitat management was tested assessing temporal changes in rabbit abundance obtained from pellet counts and in rabbits’ diet through microhistological analysis of fecal pellets. Rabbit densities were higher in managed than in control areas (mean annual values: M1–1.08 pellets/m2; M2–1.60 pellets/m2; C1–0.69 pellets/m2; C2–0.40 pellets/m2). In general, Gramineae was the most consumed plant group throughout the year and in all study areas. In control areas, consumption of alternative species with low nutritive value (e.g., Cistus ladanifer) was observed, especially in summer. Our data suggest a positive influence of habitat management on rabbit populations since in managed areas individuals presented an overall higher abundance and a more nutritive diet. In addition, there was no evidence that sown species were consumed in detriment to naturally occurring grasses, suggesting that in Mediterranean semi-arid regions clearing vegetation inside the scrubland might be sufficient to improve habitat conditions for rabbits.

The usefulness of field data and hunting statistics in the assessment of wild rabbit (Oryctolagus cuniculus) conservation status in Portugal

Context. The wild rabbit (Oryctolagus cuniculus) is a keystone species from the Iberian Peninsula that has suffered a strong decline in Spain during the past decades. Data on historical and current population trends in Portugal are virtually non-existent. Aims. To investigate changes in rabbit abundance at the national level so as to inform conservation status assessments, and to evaluate the usefulness of hunting bags as a rabbit abundance index. Methods. Field surveys based on latrine counts in linear transects were performed in two periods (1995 and 2002) to assess variation in population abundance. Hunting bags were also analysed for the same period to verify whether these data showed the same trends. General trends of rabbit abundance were estimated using TRIM software. Key results. Field data revealed that most of the sampling units across Portugal have low abundances, despite the observation of local high-density spots. A population reduction of 27% was estimated. Although some fluctuations were observed in hunting bags, global results obtained from these data suggest a slightly increasing trend in rabbit abundance. Conclusions. A discrepancy between field data and hunting statistics was observed. Because hunting bags may be influenced by sporadic management operations undertaken by hunters and the lack of systematic procedures in data collection, we believe that hunting statistics are not representative of real changes in rabbit populations. Thus, observed reduction in rabbit abundance estimated by field data, combined with the high initial morbidity due to rabbit haemorrhagic disease (RHD) after 1988 and the potential for continuing decline in population trends because of other factors, led to an inference of a reduction of >30% in rabbit abundance in Portugal during the past decade. Implications. Taking into account the estimated reduction, the species’ biology and socioeconomic implications, wild rabbit in Portugal was listed in 2005 in the Near Threatened category under IUCN criteria. Because of its ecological and economic importance, this classification prompted the definition of several conservation actions aimed at the recovery of the species in Portugal.

Field experimental vaccination campaigns against myxomatosis and their effectiveness in the wild.

We conducted a field experiment in SW Spain to test the efficacy of a myxomatosis vaccine, a viral disease strongly affecting wild rabbit populations, by assessing individual survival and antibody seroprevalence of monthly live-trapped, vaccinated (N=466) and unvaccinated (N=558) juvenile wild rabbits, between April and October 2007. Eight percent of all juveniles caught from April to June showed maternal antibodies against myxomatosis, whereas all animals were seropositive to the disease after the outbreak. Juveniles vaccinated before the outbreak showed 17% higher survival (31% vs. 14%) and an increased mortality probability of 8% after the outbreak. Results suggest that only a costly and systematic vaccination performed before the annual myxomatosis outbreak, would improve the survival of juvenile rabbits, a premise not always accomplished that compromises its efficacy in the field.

Proposal for a unified classification system and nomenclature of lagoviruses

Lagoviruses belong to the Caliciviridae family. They were first recognized as highly pathogenic viruses of the European rabbit (Oryctolagus cuniculus) and European brown hare (Lepus europaeus) that emerged in the 1970-1980s, namely, rabbit haemorrhagic disease virus (RHDV) and European brown hare syndrome virus (EBHSV), according to the host species from which they had been first detected. However, the diversity of lagoviruses has recently expanded to include new related viruses with varying pathogenicity, geographic distribution and host ranges. Together with the frequent recombination observed amongst circulating viruses, there is a clear need to establish precise guidelines for classifying and naming lagovirus strains. Therefore, here we propose a new nomenclature based on phylogenetic relationships. In this new nomenclature, a single species of lagovirus would be recognized and called Lagovirus europaeus. The species would be divided into two genogroups that correspond to RHDV- and EBHSV-related viruses, respectively. Genogroups could be subdivided into genotypes, which could themselves be subdivided into phylogenetically well-supported variants. Based on available sequences, pairwise distance cutoffs have been defined, but with the accumulation of new sequences these cutoffs may need to be revised. We propose that an international working group could coordinate the nomenclature of lagoviruses and any proposals for revision.

The evolution of peer review as a basis for scientific publication: directional selection towards a robust discipline?

Peer review is pivotal to science and academia, as it represents a widely accepted strategy for ensuring quality control in scientific research. Yet, the peer‐review system is poorly adapted to recent changes in the discipline and current societal needs. We provide historical context for the cultural lag that governs peer review that has eventually led to the systems current structural weaknesses (voluntary review, unstandardized review criteria, decentralized process). We argue that some current attempts to upgrade or otherwise modify the peer‐review system are merely sticking‐plaster solutions to these fundamental flaws, and therefore are unlikely to resolve them in the long term. We claim that for peer review to be relevant, effective, and contemporary with todays publishing demands across scientific disciplines, its main components need to be redesigned. We propose directional changes that are likely to improve the quality, rigour, and timeliness of peer review, and thereby ensure that this critical process serves the community it was created for.

European rabbit research in the Iberian Peninsula: state of the art and future perspectives

The European rabbit (Oryctolagus cuniculus) is a high-profile prey, native from the Iberian Peninsula, the only region in the world where the two rabbit subspecies (O. cuniculus algirus and O. cuniculus cuniculus) currently co-exist in natural conditions. In this area, this important prey represents a keystone species and ecosystem engineer of Mediterranean landscapes, being also the most harvested and one of the most managed small-game species. Additionally, the species can create damage to crops in some parts of the Iberian Peninsula where it is regarded as an agricultural pest. The scientific interest towards the species is becoming increasingly apparent most likely as a repercussion of declining population trends over the last decades. The latter has been the result of the impact of habitat deterioration, viral diseases, unsustainable hunting, and predation. In this paper, I present a review of the scientific literature currently available on the European rabbit in the Iberian Peninsula. I discuss knowledge gaps and highlight priority research guidelines to suppress them, in an attempt to provide a general perspective to target research efforts more effectively. This analysis is particularly relevant due to the current vulnerability of rabbit populations in Iberia and to the recent news of cuts in scientific funding in most Mediterranean countries.

Does ecophysiology mediate reptile responses to fire regimes? Evidence from Iberian lizards

Background. Reptiles are sensitive to habitat disturbance induced by wildfires but species frequently show opposing responses. Functional causes of such variability have been scarcely explored. In the northernmost limit of the Mediterranean bioregion, lizard species of Mediterranean affinity (Psammodromus algirus and Podarcis guadarramae) increase in abundance in burnt areas whereas Atlantic species (Lacerta schreiberi and Podarcis bocagei) decrease. Timon lepidus, the largest Mediterranean lizard in the region, shows mixed responses depending on the locality and fire history. We tested whether such interspecific differences are of a functional nature, namely, if ecophysiological traits may determine lizard response to fire. Based on the variation in habitat structure between burnt and unburnt sites, we hypothesise that Mediterranean species, which increase density in open habitats promoted by frequent fire regimes, should be more thermophile and suffer lower water losses than Atlantic species. Methods. We submitted 6–10 adult males of the five species to standard experiments for assessing preferred body temperatures (Tp) and evaporativewater loss rates (EWL), and examined the variation among species and along time by means of repeated-measures AN(C)OVAs. Results. Results only partially supported our initial expectations, since the medium-sized P. algirus clearly attained higher Tp and lower EWL. The two small wall lizards (P. bocagei and P. guadarramae) displayed low Tp and high EWL while the two large green lizards (T. lepidus and L. schreiberi) displayed intermediate values for both parameters. Discussion. The predicted differences according to the biogeographic affinities within each pair were not fully confirmed. We conclude that ecophysiology may help to understand functional reptile responses to fire but other biological traits are also to be considered.

Novel strategy to detect and locate periodontal pathogens: The PNA-FISH technique

PURPOSE We aim to develop peptic nucleic acid (PNA) probes for the identification and localization of Aggregatibacter actinomycetemcomintans and Porphyromonas gingivalis in sub-gingival plaque and gingival biopsies by Fluorescence in situ Hybridization (FISH). METHODS A PNA probe was designed for each microorganism. The PNA-FISH method was optimized to allow simultaneous hybridization of both microorganisms with their probe (PNA-FISH multiplex). After being tested on representative strains of P. gingivalis and A. actinomycetemcomitans, the PNA-FISH method was then adapted to detect microorganisms in the subgingival plaque and gingival samples, collected from patients with severe periodontitis. RESULTS The best hybridization conditions were found to be 59°C for 150min for both probes (PgPNA1007 and AaPNA235). The in silico sensitivity and specificity was both 100% for PgPNA1007 probe and 100% and 99.9% for AaPNA235 probe, respectively. Results on clinical samples showed that the PNA-FISH method was able to detect and discriminate target bacteria in the mixed microbial population of the subgingival plaque and within periodontal tissues. CONCLUSION This investigation presents a new highly accurate method for P. gingivalis and A. actinomycetemcomitans detection and co-location in clinical samples, in just few hours. With this technique we were able to observe spatial distribution of these species within polymicrobial communities in the periodontal pockets and, for the first time with the FISH method, in the organized gingival tissue.

Continental divide: Predicting climate-mediated fragmentation and biodiversity loss in the boreal forest

Climate change threatens natural landscapes through shifting distribution and abundance of species and attendant change in the structure and function of ecosystems. However, it remains unclear how climate-mediated variation in species’ environmental niche space may lead to large-scale fragmentation of species distributions, altered meta-population dynamics and gene flow, and disrupted ecosystem integrity. Such change may be especially relevant when species distributions are restricted either spatially or to a narrow environmental niche, or when environments are rapidly changing. Here, we use range-wide environmental niche models to posit that climate-mediated range fragmentation aggravates the direct effects of climate change on species in the boreal forest of North America. We show that climate change will directly alter environmental niche suitability for boreal-obligate species of trees, birds and mammals (n = 12), with most species ranges becoming smaller and shifting northward through time. Importantly, species distributions will become increasingly fragmented, as characterized by smaller mean size and greater isolation of environmentally-suitable landscape patches. This loss is especially pronounced along the Ontario-Québec border, where the boreal forest is narrowest and roughly 78% of suitable niche space could disappear by 2080. Despite the diversity of taxa surveyed, patterns of range fragmentation are remarkably consistent, with our models predicting that spruce grouse (Dendragapus canadensis), boreal chickadee (Poecile hudsonicus), moose (Alces americanus) and caribou (Rangifer tarandus) could have entirely disjunct east-west population segments in North America. These findings reveal potentially dire consequences of climate change on population continuity and species diversity in the boreal forest, highlighting the need to better understand: 1) extent and primary drivers of anticipated climate-mediated range loss and fragmentation; 2) diversity of species to be affected by such change; 3) potential for rapid adaptation in the most strongly-affected areas; and 4) potential for invasion by replacement species.