João Queirós

Effect of microsatellite selection on individual and population genetic inferences: an empirical study using cross-specific and species-specific amplifications

Although whole‐genome sequencing is becoming more accessible and feasible for nonmodel organisms, microsatellites have remained the markers of choice for various population and conservation genetic studies. However, the criteria for choosing microsatellites are still controversial due to ascertainment bias that may be introduced into the genetic inference. An empirical study of red deer (Cervus elaphus) populations, in which cross‐specific and species‐specific microsatellites developed through pyrosequencing of enriched libraries, was performed for this study. Two different strategies were used to select the species‐specific panels: randomly vs. highly polymorphic markers. The results suggest that reliable and accurate estimations of genetic diversity can be obtained using random microsatellites distributed throughout the genome. In addition, the results reinforce previous evidence that selecting the most polymorphic markers leads to an ascertainment bias in estimates of genetic diversity, when compared with randomly selected microsatellites. Analyses of population differentiation and clustering seem less influenced by the approach of microsatellite selection, whereas assigning individuals to populations might be affected by a random selection of a small number of microsatellites. Individual multilocus heterozygosity measures produced various discordant results, which in turn had impacts on the heterozygosity‐fitness correlation test. Finally, we argue that picking the appropriate microsatellite set should primarily take into account the ecological and evolutionary questions studied. Selecting the most polymorphic markers will generally overestimate genetic diversity parameters, leading to misinterpretations of the real genetic diversity, which is particularly important in managed and threatened populations.

Host and Environmental Factors Modulate the Exposure of Free-Ranging and Farmed Red Deer (Cervus elaphus) to Coxiella burnetii

ABSTRACT The control of multihost pathogens, such as Coxiella burnetii, should rely on accurate information about the roles played by the main hosts. We aimed to determine the involvement of the red deer (Cervus elaphus) in the ecology of C. burnetii. We predicted that red deer populations from broad geographic areas within a European context would be exposed to C. burnetii, and therefore, we hypothesized that a series of factors would modulate the exposure of red deer to C. burnetii. To test this hypothesis, we designed a retrospective survey of 47 Iberian red deer populations from which 1,751 serum samples and 489 spleen samples were collected. Sera were analyzed by enzyme-linked immunosorbent assays (ELISA) in order to estimate exposure to C. burnetii, and spleen samples were analyzed by PCR in order to estimate the prevalence of systemic infections. Thereafter, we gathered 23 variables—within environmental, host, and management factors—potentially modulating the risk of exposure of deer to C. burnetii, and we performed multivariate statistical analyses to identify the main risk factors. Twenty-three populations were seropositive (48.9%), and C. burnetii DNA in the spleen was detected in 50% of the populations analyzed. The statistical analyses reflect the complexity of C. burnetii ecology and suggest that although red deer may maintain the circulation of C. burnetii without third species, the most frequent scenario probably includes other wild and domestic host species. These findings, taken together with previous evidence of C. burnetii shedding by naturally infected red deer, point at this wild ungulate as a true reservoir for C. burnetii and an important node in the life cycle of C. burnetii, at least in the Iberian Peninsula.

Tuberculosis-Associated Death among Adult Wild Boars, Spain, 2009–2014

We investigated adult Eurasian wild boar (Sus scrofa) survival and death in 2 tuberculosis-endemic populations with different harvest pressure in Spain. Overall, tuberculosis accounted for 30% of total deaths. Increased survival in protected areas has direct implications for wild boar management and tuberculosis control.

Comparative Proteomics Identifies Host Immune System Proteins Affected by Infection with Mycobacterium bovis

Mycobacteria of the Mycobacterium tuberculosis complex (MTBC) greatly impact human and animal health worldwide. The mycobacterial life cycle is complex, and the mechanisms resulting in pathogen infection and survival in host cells are not fully understood. Eurasian wild boar (Sus scrofa) are natural reservoir hosts for MTBC and a model for mycobacterial infection and tuberculosis (TB). In the wild boar TB model, mycobacterial infection affects the expression of innate and adaptive immune response genes in mandibular lymph nodes and oropharyngeal tonsils, and biomarkers have been proposed as correlates with resistance to natural infection. However, the mechanisms used by mycobacteria to manipulate host immune response are not fully characterized. Our hypothesis is that the immune system proteins under-represented in infected animals, when compared to uninfected controls, are used by mycobacteria to guarantee pathogen infection and transmission. To address this hypothesis, a comparative proteomics approach was used to compare host response between uninfected (TB-) and M. bovis-infected young (TB+) and adult animals with different infection status [TB lesions localized in the head (TB+) or affecting multiple organs (TB++)]. The results identified host immune system proteins that play an important role in host response to mycobacteria. Calcium binding protein A9, Heme peroxidase, Lactotransferrin, Cathelicidin and Peptidoglycan-recognition protein were under-represented in TB+ animals when compared to uninfected TB- controls, but protein levels were higher as infection progressed in TB++ animals when compared to TB- and/or TB+ adult wild boar. MHCI was the only protein over-represented in TB+ adult wild boar when compared to uninfected TB- controls. The results reported here suggest that M. bovis manipulates host immune response by reducing the production of immune system proteins. However, as infection progresses, wild boar immune response recovers to limit pathogen multiplication and promote survival, facilitating pathogen transmission.

Genome-wide associations identify novel candidate loci associated with genetic susceptibility to tuberculosis in wild boar

Tuberculosis (TB) affects a wide range of host species worldwide. Understanding host-pathogen co-evolution remains a global challenge owing to complex interactions among host genetic factors, pathogen traits and environmental conditions. We used an endemic wild boar population that had undergone a huge increase in Mycobacterium bovis infection prevalence, from 45% in 2002/06 to 83% in 2009/12, to understand the effects of host genetics on host TB outcomes and disease dynamics. Host genomic variation was characterized using a high-density single nucleotide polymorphism (SNP) array, while host TB phenotype was assessed using both gross pathology and mycobacterial culture. Two complementary genome-wide association (GWAS) analyses were conducted: (i) infected-uninfected; and (ii) 2002/06–2009/12. The SNPs with the highest allelic frequency differences between time-periods and TB outcomes were identified and validated in a large dataset. In addition, we quantified the expression levels of some of their closest genes. These analyses highlighted various SNPs (i.e. rs81465339, rs81394585, rs81423166) and some of the closest genes (i.e. LOC102164072, BDNF/NT-3, NTRK2, CDH8, IGSF21) as candidates for host genetic susceptibility. In addition to TB-driven selection, our findings outline the putative role of demographic events in shaping genomic variation in natural populations and how population crashes and drift may impact host genetic susceptibility to TB over time.

Long-Term Dynamics of Coxiella burnetii in Farmed Red Deer (Cervus elaphus).

Several aspects of the dynamics of Coxiella burnetii that are relevant for the implementation of control strategies in ruminant herds with endemic Q fever are unknown. We designed a longitudinal study to monitor the dynamics of exposure to C. burnetii in a red deer herd with endemic infection in order to allow the design of Q fever-specific control approaches. Other relevant aspects of the dynamics of C. burnetii – the effect of herd immune status, age, season, and early infection on exposure, the average half-life of antibodies, the presence and duration of maternal humoral immunity, and the age of first exposure – were analyzed. The dynamics of C. burnetii in deer herds seems to be modulated by host herd and host individual factors and by particular host life-history traits. Red deer females become exposed to C. burnetii at the beginning of their second year since maternal antibodies protect them after birth and during the main pathogen shedding season – at the end of spring-early summer. Infection pressure varies between years, probably associated with herd immunity effects, determining inter-annual variation in the risk of exposure. These results suggest that any strategy applied to control C. burnetii in deer herds should be designed to induce immunity in their first year of life immediately after losing maternal antibodies. The short average life of C. burnetii antibodies suggests that any protection based on humoral immunity would require re-vaccination every 6 months.

Voices in the revolution: Resisting territorial stigma and social relegation in Porto’s historic centre (1974–1976)

This article tries to broaden the research agenda on territorial stigmatisation. It reviews some theoretical arguments on the relevance of a relational sociological reading of the processes of territorial stigmatisation, and proposes a study of these processes during a period of political revolution and social instability, through discussion of the case presented by the city of Porto, Portugal, in the mid-1970s. Based on the study of institutional archives, ethnographic work in several neighbourhoods, and semi-structured interviews with social actors involved in these processes, the article describes the urban and housing conditions of inner city Porto’s working-class boroughs in the first three quarters of the 20th century and discusses the forms of political and social resistance taken up by residents from the most dilapidated neighbourhoods following the revolution of April 1974. The sociological analysis of the actions that gave origin to the voice of the residents in the historic centre of the city in this period reveals significant interaction with the processes of territorial stigmatisation, via organised collective resistance.

Quantificação de glucocorticóides fecais e avaliação dos níveis de stress fisiológico em veados selvagens

Este estudio fue financiado por el Ministerio de Agricultura y Medio Ambiente (Proyecto OAPN 755/2012), CSIC (Intramural 201330E041), FEDENCA (Real Federacion Espanola de Caza) y la Oficina Nacional de la Caza con la colaboracion de la Fundacion Biodiversidad.8 Pags.- 5 Figs. Trabajo originalmente presentado en la XIV Reunion Nacional de Geomorfologia (Malaga. 22-25 junio 2016)Trabajo presentado al IV Encontro Nacional Pos-Graduacao Ciencias Bilogicas (IV ENPGCB), celebrado en Aveiro (Portugal) del 30 de marzo al 2 de abril de 2015.El “Diseno de una metodologia para la aplicacion de indicadores del estado de conservacion de los tipos de habitat de interes comunitario en Espana” es parte del proyecto Bases ecologicas para la gestion de los tipos de habitat de interes comunitario en Espana promovido y financiado por el Ministerio de Agricultura, Alimentacion y Medio Ambiente.14 paginas, con graficos e imagenes.-- Duracion del proyecto: noviembre de 2011 - diciembre de 2015.6 paginas, 3 tablas, 16 referencias.-- V International Symposium on Olive Growing, celebrado del 27 de septiembre-2 de octubre 2004, en Izmir, Turquia.Trabajo presentado en la European Geosciences Union General Assembly (EGU), celebrado en Viena (Austria), del 8 al 13 de abril de 2018