Use of camera trapping in determining Iberian lynx population parameters: The use area and its limitations

Below are the results of the survey of the Iberian lynx obtained with camera-trapping between 2000 and 2007 in Sierra Morena. Two very important aspects of camera-trapping concerning its efficiency are also analyzed. The first is the evolution along years according to the camera-trapping type used of two efficiency indicators. The results obtained demonstrate that the most efficient lure is rabbit, though it is the less proven (92 trap-nights), followed by camera-trapping in the most frequent marking places (latrines). And, we propose as a novel the concept of use area as a spatial reference unit for the camera-trapping monitoring of non radio-marked animals is proposed, and its validity discussed.

Favourable areas for expansion and reintroduction of Iberian lynx accounting for distribution trends and genetic diversity of the European rabbit

Although on a local scale Iberian lynx distribution is determined by the availability of prey rabbits, recent modelling analyses have uncovered broad-scale disagreements between these two species’ distribution trends. These analyses showed also that the lynx had become restricted to only a fraction of the rabbit’s genetic diversity, and that this could be jeopardising its survival in the face of environmental hazards and uncertainty. In the present paper, a follow-up was carried out through the building of lynx and rabbit distribution models based on the most recent Spanish mammal atlas. Environmental favourability values for lynx and rabbit were positively correlated within the lynx’s current distribution area, but they were negatively correlated within the total Spanish area where lynx used to occur in the 1980’s. Environmental favourability for rabbits was significantly higher where lynx maintains reproductive populations than where it recently disappeared, indicating that rabbit favourability plays an important role and can be a good predictor of lynx persistence. The lynx and rabbit models were extrapolated to predict favourable areas for both species in Spain as well as in Portugal, on the original scale of the distribution data (10x10 km) and on a 100 times finer spatial resolution (1x1 km). The lynx and rabbit models were also combined through fuzzy logic to forecast the potential for lynx occurrence incorporating information on favourable areas for its main prey. Several areas are proposed as favourable for lynx expansion or re-introduction,

Conservation biogeography of ecologically interacting species: The case of the Iberian lynx and the European rabbit

Aim To relate the recent Iberian lynx decline to changes in the distribution of the European rabbit after the haemorrhagic disease outbreak of 1989. As Iberian rabbits evolved in two geographically separated lineages, being the recent lynx range practically restricted to the southwestern lineage, we also test if differential range dynamics exists for these lineages, with the consequent implications for lynx conservation and reintroduction planning.

Worldwide occurrence of feline hemoplasma infections in wild felid species

While hemoplasma infections in domestic cats are well studied, almost no information is available on their occurrence in wild felids. The aims of the present study were to investigate wild felid species as possible reservoirs of feline hemoplasmas and the molecular characterization of the hemoplasma isolates. Blood samples from the following 257 wild felids were analyzed: 35 Iberian lynxes from Spain, 36 Eurasian lynxes from Switzerland, 31 European wildcats from France, 45 lions from Tanzania, and 110 Brazilian wild felids, including 12 wild felid species kept in zoos and one free-ranging ocelot. Using real-time PCR, feline hemoplasmas were detected in samples of the following species: Iberian lynx, Eurasian lynx, European wildcat, lion, puma, oncilla, Geoffroy's cat, margay, and ocelot. "Candidatus Mycoplasma haemominutum" was the most common feline hemoplasma in Iberian lynxes, Eurasian lynxes, Serengeti lions, and Brazilian wild felids, whereas "Candidatus Mycoplasma turicensis" was the most prevalent in European wildcats; hemoplasma coinfections were frequently observed. Hemoplasma infection was associated with species and free-ranging status of the felids in all animals and with feline leukemia virus provirus-positive status in European wildcats. Phylogenetic analyses of the 16S rRNA and the partial RNase P gene revealed that most hemoplasma isolates exhibit high sequence identities to domestic cat-derived isolates, although some isolates form different subclusters within the phylogenetic tree. In conclusion, 9 out of 15 wild felid species from three different continents were found to be infected with feline hemoplasmas. The effect of feline hemoplasma infections on wild felid populations needs to be further investigated.

Ingeniería de la conservación: Investigación aplicada para la conservación de la fauna mediterránea amenazada

El ser humano nunca ha tenido una capacidad semejante a la actual para alterar el medio en el que vive. A través fundamentalmente de cambios en el uso del hábitat, alteración de los ciclos biogeoquímicos, cambio climático y presencia de especies invasoras, la tasa de extinción de especies se ha acelerado enormemente. Al crecer más rápido la población humana dentro de las áreas en las que se concentra una mayor biodiversidad (biodiversity hotspots), las tasas de transformación son mayores, por lo que dicha biodiversidad se encuentra más amenazada. Entre los principales 25 biodiversity hotspots globales se encuentra la cuenca mediterránea. Las afecciones a la biodiversidad hacen por tanto que en dicha cuenca mediterránea sea necesario poner en práctica iniciativas innovadoras para su conservación. Pero además de una cuidadosa selección, es necesario el seguimiento y la evaluación de la eficacia y la eficienca de dichas medidas, para comprobar su idoneidad y mejorarlas cuando sea posible. Esta es la tarea de la ingeniería de la conservación. Esta Memoria busca analizar y proponer mejoras en cuatro acciones experimentales de conservación de la biodiversidad que tienen un marco común, la conservación de especies subrogadas del monte mediterráneo. En concreto de cinco especies amenazadas: conejo de monte (Oryctolagus cuniculus, especie llave), águila imperial ibérica (Aquila adalberti), águila perdicera (Aquila fasciata), cigüeña negra (Ciconia nigra) y lince ibérico (Lynx pardinus), todas ellas especies paraguas y bandera. Casi todas estas especies se enfrentan a amenazas comunes, como son la pérdida de la calidad del hábitat, la mortalidad de origen humano, la escasez de alimento o la falta de eficiencia en las técnicas de seguimiento. Las acciones destinadas a revertir o minimizar estas amenazas han tenido un marco geográfico y ecológico común, 49 fincas privadas de monte mediterráneo situadas en 9 espacios de la Red Natura 2000 del centro-occidental peninsular, en las que se ha podido trabajar merced a acuerdos de custodia del territorio. Dichas actividades han sido financiadas casi por completo con cargo a fondos LIFE Naturaleza de la Comisión Europea. El presente documento contribuye a aportar el conocimiento científico imprescindible para mejorar la eficacia y eficiencia de las medidas técnicas de gestión y conservación: la ingeniería de la conservación. Como resultados más relevantes se pueden citar que la selección del conejo de las zonas sembradas aumenta con la presencia tanto de isletas de matorral como de refugios y resulta inferior en las zonas de matorral más cerrado; que la electrocución es una de las principales causas de mortalidad de las rapaces amenazadas, así como que se ha detectado que la mortalidad se concentra en determinadas zonas que deben ser prioritarias para su corrección y que éstas deben pasar por las modificaciones estructurales; que la selección de zonas de alimentación por parte de la cigüeña negra se ve afectada por numerosos factores y que una adecuada ubicación y gestión de las charcas para ganadería y caza mayor puede favorecer no sólo la alimentación de esta especie, sino suponer un lugar de cría para diversas especies de anfibios y peces autóctonos, en franco declive; finalmente, hay que destacar que la mejora en el seguimiento de las poblaciones de lince ibérico pasa por la incorporación de métodos de seguimiento novedosos, como las cámaras infrarrojas en letrinas, dada la capacidad de aprendizaje de la especie. Abstract Nowadays the human being has reached its top ability to exchange its environment. Mainly through habitat change, altering biogeochemical cycles, climatic change and alien species, global extinction rate has increased dramatically. Population increases faster in biodiversity hotspots, thus change rates are higher. Mediterranean basin is included within the 25 most valuable biodiversity hotspots. Affections on biodiversity turns necessary to develop innovative actions to maintain the most threatened species in this hotspot. But further than a careful selection and implementarion, survey and evaluation of those practices is necessary to check its suitability. Those are actions for the conservation engineering. This Memory looks for to analyze and to put forward improvements in four experimental biodiversity conservation actions with a common framework: conservation of surrogate Mediterranean species. Those actions were specifically directed to five threatened species: the European wild rabbit (Oryctolagus cuniculus, key species), Spanish imperial eagle (Aquila adalberti) and Bonelli’s eagle (Aquila fasciata, both of the umbrella and flagship species), black stork (Ciconia nigra, umbrella and flagship species) and the Iberian lynx (Lynx pardinus, umbrella and flagship species). Those species have common threats: habitat loss, maninduced mortality, food shortening and lack of surveying efficiency. Actions aimed to minimize those threats also had a common geographical frame: 49 privately owned states within 9 Natura 2000 areas in Southwestern Spain. Actions were developed through lands tewardship agreements, and were even wholly undertaken through European Commision LIFE’s fund. This document contributes to develop cientific knowledge necessary for increasing efficacy and efficiency for implementing technical measures devoted to conservation, the conservation engineering. One of the most outstanding result might be the necessity of including bushy islets or rabbit shelter within sowings when enhacing rabbit populations is the goal. Electrocution is one of the commonest man-induced death causes for raptors, especially for the threatened ones. Areas of concentration of this mortality have been detected, and when mitigation measures have been evaluated, only structural modifications had results. The black stork’s selection of feeding areas is influenced by several factors. An adequate location and management of livestock’s ponds can favour not only this species, but also creating new breeding places for amphibians and indigenous fish species, most of them in a sharp decline. Finally, improving the survey of the Iberian lynx might be achieved through implementing newly developed surveying systems, such as the infrared cameras in latrines.

Faunal remains from an Almohad (Ad XII/XIII) silo at the Castle of Aljezur (Portugal)

The analysis of a faunal collection from a storage silo found in the castle of Aljezur, dating from the Almohad period (XII/XIIIth centuries AD), is presented. It appears that the community occupying the castle concentrated on hunting species such as the rabbit, wild boar, red deer and Iberian lynx, while evidences of stockbreeding were scarce and centered upon caprines with horses and chicken playing minor role. The presence of a large dog has been assumed to be an aid for hunting but possibly also in herd keeping. With the exception of the lynx, all large mammals evidenced traces of consumption. The domestic cat is taken to represent a pet whereas the lynx had probably a role as a fur provider. It should be noted that equids and the pond turtle were probably food items. Rodents are taken to represent commensals whereas the toad of the Genus Bufo probably represented an intrusive element.

A real time Taqman RT-PCR for the detection of rabbit hemorrhagic disease virus 2 (RHDV2)

As key prey, the wild rabbit downsize constitutes a major drawback on the endangered Iberian lynx (Lynx pardinus) re-introduction in the Iberia. Several captive breeding units mostly located in Alentejo, endeavour the wild rabbit repopulation of depleted areas assigned for the lynx re-introduction. Here we report an RHDV2 outbreak that occurred in early 2016 in a wild rabbit captive breeding unit located in Barrancos municipality. The estimated mortality rate between March and April 2016 was approximately 8.67%. Anatomopathologic examination was carried out for 13 victimized rabbits. Molecular characterization was based on the complete vp60 capsid gene. The 13 rabbit carcasses investigated showed typical macroscopic RHD lesions testing positive to RHDV2- RNA. Comparison of the vp60 nucleotide sequences obtained from two specimens with others publically available disclosed similarities below 98.22% with RHDV2 strains originated in the Iberia and Azores and revealed that the two identical strains from Barrancos-2016 contain six unique single synonymous nucleotide polymorphisms. In the phylogenetic analysis performed, the Barrancos-2016 strains clustered apart from other known strains, meaning they may represent new evolutionary RHDV2 lineages. No clear epidemiological link could be traced for this outbreak where the mortalities were lower compared with previous years. Yet, network analysis suggested a possible connection between the missing intermediates from which the strains from Barrancos 2013, 2014 and 2016 have derived. It is therefore possible that RHDV2 has circulated endemically in the region since 2012, with periodic epizootic occurrences. Still, six years after its emergence in wild rabbits, RHDV2 continues to pose difficulties to the establishment of natural wild rabbit populations that are crucial for the self-sustainability of the local ecosystems.

Tracking the Origin of a Rabbit Haemorrhagic Virus 2 Outbreak in a Wild Rabbit Breeding Centre in Portugal; Epidemiological and Genetic Investigation

As key prey, the wild rabbit downsize constitutes a major drawback on the endangered Iberian lynx (Lynx pardinus) re-introduction in the Iberia. Several captive breeding units mostly located in Alentejo, endeavour the wild rabbit repopulation of depleted areas assigned for the lynx re-introduction. Here we report an RHDV2 outbreak that occurred in early 2016 in a wild rabbit captive breeding unit located in Barrancos municipality. The estimated mortality rate between March and April 2016 was approximately 8.67%. Anatomopathologic examination was carried out for 13 victimized rabbits. Molecular characterization was based on the complete vp60 capsid gene. The 13 rabbit carcasses investigated showed typical macroscopic RHD lesions testing positive to RHDV2-RNA. Comparison of the vp60 nucleotide sequences obtained from two specimens with others publically available disclosed similarities below 98.22% with RHDV2 strains originated in the Iberia and Azores and revealed that the two identical strains from Barrancos-2016 contain six unique single synonymous nucleotide polymorphisms. In the phylogenetic analysis performed, the Barrancos-2016 strains clustered apart from other known strains,meaning they may represent new evolutionary RHDV2 lineages. No clear epidemiological link could be traced for this outbreak where the mortalities were lower compared with previous years. Yet, network analysis suggested a possible connection between the missing intermediates from which the strains from Barrancos 2013, 2014 and 2016 have derived. It is therefore possible that RHDV2 has circulated endemically in the region since 2012, with periodic epizootic occurrences. Still, six years after its emergence in wild rabbits, RHDV2 continues to pose difficulties to the establishment of natural wild rabbit populations that are crucial for the self-sustainability of the local ecosystems.

Tracking the Origin of a Rabbit Haemorrhagic Virus 2 Outbreak in a Wild Rabbit Breeding Centre in Portugal; Epidemiological and Genetic Investigation

As key prey, the wild rabbit downsize constitutes a major drawback on the endangered Iberian lynx (Lynx pardinus) re-introduction in the Iberia. Several captive breeding units mostly located in Alentejo, endeavour the wild rabbit repopulation of depleted areas assigned for the lynx re-introduction. Here we report an RHDV2 outbreak that occurred in early 2016 in a wild rabbit captive breeding unit located in Barrancos municipality. The estimated mortality rate between March and April 2016 was approximately 8.67%. Anatomopathologic examination was carried out for 13 victimized rabbits. Molecular characterization was based on the complete vp60 capsid gene. The 13 rabbit carcasses investigated showed typical macroscopic RHD lesions testing positive to RHDV2- RNA. Comparison of the vp60 nucleotide sequences obtained from two specimens with others publically available disclosed similarities below 98.22% with RHDV2 strains originated in the Iberia and Azores and revealed that the two identical strains from Barrancos-2016 contain six unique single synonymous nucleotide polymorphisms. In the phylogenetic analysis performed, the Barrancos-2016 strains clustered apart from other known strains, meaning they may represent new evolutionary RHDV2 lineages. No clear epidemiological link could be traced for this outbreak where the mortalities were lower compared with previous years. Yet, network analysis suggested a possible connection between the missing intermediates from which the strains from Barrancos 2013, 2014 and 2016 have derived. It is therefore possible that RHDV2 has circulated endemically in the region since 2012, with periodic epizootic occurrences. Still, six years after its emergence in wild rabbits, RHDV2 continues to pose difficulties to the establishment of natural wild rabbit populations that are crucial for the self-sustainability of the local ecosystems.

The "Shackleton Site" (IODP Site U1385) on the Iberian Margin

Nick Shackleton’s research on piston cores from the Iberian margin highlighted the importance of this region for providing high-fidelity records of millennial-scale climate variability, and for correlating climate events from the marine environment to polar ice cores and European terrestrial sequences. During the Integrated Ocean Drilling Program (IODP) Expedition 339, we sought to extend the Iberian margin sediment record by drilling with the D/V JOIDES Resolution. Five holes were cored at Site U1385 using the advanced piston corer (APC) system to a maximum depth of ∼ 155.9 m below sea floor (m b.s.f.). Immediately after the expedition, cores from all holes were analyzed by core scanning X-ray fluorescence (XRF) at 1 cm spatial resolution. Ca/Ti data were used to accurately correlate from hole-to-hole and construct a composite spliced section, containing no gaps or disturbed intervals to 166.5 m composite depth (mcd). A low-resolution (20 cm sample spacing) oxygen isotope record confirms that Site U1385 contains a continuous record of hemipelagic sedimentation from the Holocene to 1.43 Ma (Marine Isotope Stage 46). The sediment profile at Site U1385 extends across the middle Pleistocene transition (MPT) with sedimentation rates averaging ∼ 10 cm kyr−1. Strongprecession cycles in colour and elemental XRF signals provide a powerful tool for developing an orbitally tuned reference timescale. Site U1385 is likely to become an important type section for marine–ice–terrestrial core correlations and the study of orbital- and millennial-scale climate variability.

Phylogeography and demographic history of Lacerta lepida in the Iberian Peninsula

The Iberian Peninsula is recognized as an important refugial area for species survival and diversification during the climatic cycles of the Quaternary. Recent phylogeographic studies have revealed Iberia as a complex of multiple refugia. However, most of these studies have focused either on species with narrow distributions within the region or species groups that, although widely distributed, generally have a genetic structure that relates to pre-Quaternary cladogenetic events. In this study we undertake a detailed phylogeographic analysis of the lizard species, Lacerta lepida, whose distribution encompasses the entire Iberian Peninsula. We attempt to identify refugial areas, recolonization routes, zones of secondary contact and date demographic events within this species. Results support the existence of 6 evolutionary lineages (phylogroups) with a strong association between genetic variation and geography, suggesting a history of allopatric divergence in different refugia. Diversification within phylogroups is concordant with the onset of the Pleistocene climatic oscillations. The southern regions of several phylogroups show a high incidence of ancestral alleles in contrast with high incidence of recently derived alleles in northern regions. All phylogroups show signs of recent demographic and spatial expansions. We have further identified several zones of secondary contact, with divergent mitochondrial haplotypes occurring in narrow zones of sympatry. The concordant patterns of spatial and demographic expansions detected within phylogroups, together with the high incidence of ancestral haplotypes in southern regions of several phylogroups, suggests a pattern of contraction of populations into southern refugia during adverse climatic conditions from which subsequent northern expansions occurred. This study supports the emergent pattern of multiple refugia within Iberia but adds to it by identifying a pattern of refugia coincident with the southern distribution limits of individual evolutionary lineages. These areas are important in terms of long-term species persistence and therefore important areas for conservation.

Analysis of volatility transmissions in integrated and interconnected markets: The case of the Iberian and French markets

This paper models the mean and volatility spillovers of prices within the integrated Iberian and the interconnected Spanish and French electricity markets. Using the constant (CCC) and dynamic conditional correlation (DCC) bivariate models with three different specifications of the univariate variance processes, we study the extent to which increasing interconnection and harmonization in regulation have favoured price convergence. The data consist of daily prices calculated as the arithmetic mean of the hourly prices over a span from July 1st 2007 until February 29th 2012. The DCC model in which the variances of the univariate processes are specified with a VARMA(1,1) fits the data best for the integrated MIBEL whereas a CCC model with a GARCH(1,1) specification for the univariate variance processes is selected to model the price series in Spain and France. Results show that there are significant mean and volatility spillovers in the MIBEL, indicating strong interdependence between the two markets, while there is a weaker evidence of integration between the Spanish and French markets. We provide new evidence that the EU target of achieving a single electricity market largely depends on increasing trade between countries and homogeneous rules of market functioning.

Trace element concentrations in muscle tissue of the benthopelagic grenadier (Coryphaenoides armatus) from the Iberian deep-sea

11 specimens of Coryphaenoides armatus were collected at former dumping sites for radioactive material in the Iberian deep sea at a depth of 4700 m and their muscle tissue was analysed for four trace elements (copper, zinc, cadmium and lead) by differential pulse anodic stripping voltammetry (DPSAV). Concentrations of zinc were typical for fish muscle in general; copper content was somewhat higher than generally found in fish. The cadmium and lead contents were at a level found in fish from the open sea but the lead content of 2 specimens taken in area East-B was found to be higher.

Novel Papillomaviruses in Free-Ranging Iberian Bats: No Virus-Host Co-evolution, No Strict Host Specificity, and Hints for Recombination

Papillomaviruses (PVs) are widespread pathogens. However, the extent of PV infections in bats remains largely unknown. This work represents the first comprehensive study of PVs in Iberian bats. We identified four novel PVs in the mucosa of free-ranging Eptesicus serotinus (EserPV1, EserPV2, and EserPV3) and Rhinolophus ferrumequinum (RferPV1) individuals and analyzed their phylogenetic relationships within the viral family. We further assessed their prevalence in different populations of E. serotinus and its close relative E. isabellinus. Although it is frequent to read that PVs co-evolve with their host, that PVs are highly species-specific, and that PVs do not usually recombine, our results suggest otherwise. First, strict virus-host co-evolution is rejected by the existence of five, distantly related bat PV lineages and by the lack of congruence between bats and bat PVs phylogenies. Second, the ability of EserPV2 and EserPV3 to infect two different bat species (E. serotinus and E. isabellinus) argues against strict host specificity. Finally, the description of a second noncoding region in the RferPV1 genome reinforces the view of an increased susceptibility to recombination in the E2-L2 genomic region. These findings prompt the question of whether the prevailing paradigms regarding PVs evolution should be reconsidered.