Outlier SNP markers reveal fine-scale genetic structuring across European hake populations (Merluccius merluccius)

Shallow population structure is generally reported for most marine fish and explained as a consequence of high dispersal, connectivity and large population size. Targeted gene analyses and more recently genome-wide studies have challenged such view, suggesting that adaptive divergence might occur even when neutral markers provide genetic homogeneity across populations. Here, 381 SNPs located in transcribed regions were used to assess large- and fine-scale population structure in the European hake (Merluccius merluccius), a widely distributed demersal species of high priority for the European fishery. Analysis of 850 individuals from 19 locations across the entire distribution range showed evidence for several outlier loci, with significantly higher resolving power. While 299 putatively neutral SNPs confirmed the genetic break between basins (F(CT) = 0.016) and weak differentiation within basins, outlier loci revealed a dramatic divergence between Atlantic and Mediterranean populations (F(CT) range 0.275-0.705) and fine-scale significant population structure. Outlier loci separated North Sea and Northern Portugal populations from all other Atlantic samples and revealed a strong differentiation among Western, Central and Eastern Mediterranean geographical samples. Significant correlation of allele frequencies at outlier loci with seawater surface temperature and salinity supported the hypothesis that populations might be adapted to local conditions. Such evidence highlights the importance of integrating information from neutral and adaptive evolutionary patterns towards a better assessment of genetic diversity. Accordingly, the generated outlier SNP data could be used for tackling illegal practices in hake fishing and commercialization as well as to develop explicit spatial models for defining management units and stock boundaries.

The dynamics of murid gammaherpesvirus 4 within wild, sympatric populations of bank voles and wood mice

Murid gammaherpesvirus 4 (MuHV-4) is widely used as a small animal model for understanding gammaherpesvirus infections in man. However, there have been no epidemiological studies of the virus in wild populations of small mammals. As MuHV-4 both infects cells associated with the respiratory and immune systems and attempts to evade immune control via various molecular mechanisms, infection may reduce immunocompetence with potentially serious fitness consequences for individuals. Here we report a longitudinal study of antibody to MuHV-4 in a mixed assemblage of bank voles (Clethrionomys glareolus) and wood mice (Apodemus sylvaticus) in the UK. The study was conducted between April 2001 and March 2004. Seroprevalence was higher in wood mice than bank voles, supporting earlier work that suggested wood mice were the major host even though the virus was originally isolated from a bank vole. Analyses of both the probability of having antibodies and the probability of initial seroconversion indicated no clear seasonal pattern or relationship with host density. Instead, infection risk was most closely associated with individual characteristics, with heavier males having the highest risk. This may reflect individual variation in susceptibility, potentially related to variability in the ability to mount an effective immune response.

ANRIL Variants and Aggressive Periodontitis in European and African Populations

Introduction: The chromosome 9p21 locus has been identified as a marker of coronary artery disease. In this locus studies have focused on variations in the ANRIL gene that has also been identified as a strong candidate for association with aggressive periodontitis (AgP).
Objective: To investigate possible associations between gene variants of ANRIL and AgP in European and African populations.
Methods: European AgP cases (n= 213) and age-matched periodontally healthy controls (n= 81) were recruited from centres in the United Kingdom (Belfast, Glasgow, Newcastle and London). African AgP cases (n= 95) and controls (n= 105) were recruited in Khartoum, Sudan. Five single nucleotide polymorphisms (SNPs) in ANRIL were genotyped using Sequenom and analysed using Haploview with permutation testing to correct for multiple candidates. Odds ratios (OR) and 95% confidence intervals (95%CI) were calculated.
Results: In the European subjects there was a significant association between rs518394 (p=0.0013; OR = 1.81, 95%CI 1.26-2.61) and rs1333049 (p=0.0028; OR = 1.75, 95%CI 1.21-2.52) and AgP. These associations remained significant after permutation testing. In addition there was an association between rs 1360590 (p=0.035) and AgP in females. In the African subjects there was a significant association between only one SNP rs1537415 and AgP (p=0.036; OR = 1.59, 95%CI 1.04-2.43), however, this was not significant following permutation testing. There were no significant associations with rs3217992 in either population.
Conclusions: SNP variants in the ANRIL locus were shown to be significantly associated with AgP in a European population and for the first time in an African population confirming this as the best replicated locus for aggressive periodontitis.

Biometry and primary angle-closure glaucoma among Chinese, white, and black populations

PURPOSE: Primary angle-closure glaucoma (PACG) is more prevalent among Chinese than whites. The authors tested the hypothesis that Chinese have shallower anterior chambers than do whites, a factor that may be related to PACG prevalence. METHODS: The authors compared anterior chamber depth, axial length, radius of corneal curvature, and refractive error among 531 Chinese, 170 whites, and 188 blacks older than 40 years of age using the same model of instruments and identical technique. RESULTS: Mean anterior chamber depth and axial length did not differ significantly for the three groups. Whites had a significantly higher prevalence of hyperopia > 2 diopters than did Chinese. Radius of corneal curvature was significantly smaller among Chinese than whites or blacks. CONCLUSIONS: These results suggest that Chinese do not differ on a population basis from other ethnic groups in many of the biometric risk factors known to be of importance for PACG. It will be necessary to identify other ocular biometric parameters to explain the excess burden of PACG among Chinese, which may improve the effectiveness of screening for this disease in all populations.

Potentially inappropriate prescribing in two populations with differing socio-economic profiles: a cross-sectional database study using the PROMPT criteria

PURPOSE: The purpose of this study is to establish the prevalence of potentially inappropriate prescribing (PIP) in middle-aged adults (45-64 years) in two populations with differing socio-economic profiles, and to investigate factors associated with PIP, using the PROMPT (PRescribing Optimally in Middle-aged People's Treatments) criteria.METHODS: A retrospective cross-sectional study was conducted using 2012 data from the Enhanced Prescribing Database (EPD), covering the full population in Northern Ireland and the Health Services Executive Primary Care Reimbursement Service (HSE-PCRS) database, covering the most socio-economically deprived third of the population in this age group in the Republic of Ireland. The prevalence for each PROMPT criterion and overall prevalence of PIP were calculated. Logistic regression was used to investigate the association between PIP and gender, age group and polypharmacy.RESULTS: This study included 441,925 patients from the EPD and 309,748 patients from the HSE-PCRS database. Polypharmacy was common in both datasets (46.7 % in the HSE-PCRS and 20.3 % in the EPD). The prevalence of PIP was 42.9 % (95%CI 42.7, 43.1) in the HSE-PCRS and 21.1 % (95%CI 21.0, 21.2) in the EPD. Age group, female gender and polypharmacy were significantly associated with PIP in both populations (p < 0.05) and polypharmacy had the strongest association.CONCLUSIONS: PIP is common amongst middle-aged people with the risk of PIP increasing with polypharmacy. Differences in the prevalence of polypharmacy and PIP between the two populations may relate to heterogeneity in healthcare services and different socio-economic profiles, with higher rates of multimorbidity and associated polypharmacy in more deprived groups.

Ecological interactions in populations facing environmental stress

O zooplâncton, particularmente os cladóceros, são organismos de água doce importantes na regulação da produção primária dos ecossistemas de água doce. No entanto, também podem adaptar-se a condições salobras. Tendo em conta as previsões no âmbito das alterações climáticas, a intrusão salina pode ocorrer a par com a subida de temperatura. As populações de água doce podem ficar vulneráveis aos efeitos interativos da salinidade e da temperatura, de acordo com os seus limites de tolerância e capacidade de adaptação ao stress ambiental. Assim, a presente tese analisou as interações resultantes das alterações destes agentes de stress em populações de cladóceros de água doce. Primeiro, comparou-se a halotolerância de diferentes genótipos de Simocephalus vetulus provenientes de populações de água doce e de água salobra de modo a avaliar a existência de uma componente genética de resistência à salinidade. A sensibilidade aguda dos genótipos variou na mesma gama de concentrações; todavia, todos os genótipos da população salobra, exceto um, foram mais tolerantes do que os de água doce, em termos de tempo à imobilização. Contudo, não foi possível estabelecer uma relação entre a performance reprodutiva em condições salobras e o contexto ambiental de origem destes genótipos. Mais, estes ensaios mostraram que as populações de água doce têm potencial para tolerar incrementos de salinidade. Como tal, pode-se concluir que a seleção a que os genótipos estão sujeitos no seu local de origem foi mais fraca do que o esperado. Segundo, investigou-se a capacidade de aclimatação de Daphnia galeata à salinidade e temperatura, de modo a avaliar a halotolerância de Daphnia a duas temperaturas num cenário de aclimatação multigeracional. O objetivo foi compreender se a pré-adaptação ao stress ambiental (20ºC e 25ºC versus 0 g/L e 1 g/L de NaCl) influenciou posteriormente as respostas a estes agentes de stress. Verificou-se uma tendência para um aumento de sensibilidade ao NaCl, a temperaturas mais elevadas. No entanto, este efeito foi anulado após nove gerações, mas apenas quando os organismos foram aclimatados aos dois agentes de stress em simultâneo (salinidade e temperatura elevada). Terceiro, demonstrou-se experimentalmente que a salinidade interferiu com a competição interespecífica, alterando a composição das comunidades zooplanctónicas. Este conjunto de evidências permitiu-nos refletir nos múltiplos impactos de agentes de stress, particularmente os relacionados com as previsões de alterações climáticas. Em paralelo aos estudos de natureza experimental, e numa perspetiva de Educação para o Desenvolvimento Sustentável (EDS), importa também promover o desenvolvimento de competências necessárias à compreensão de mudanças ambientais globais (e.g., o impacto da salinidade e da temperatura) para implementar estratégias de mitigação e adaptação. Neste contexto, foi realizada uma atividade com estudantes do ensino secundário, que se tornou uma boa oportunidade para a sua aprendizagem e aquisição de competências de interpretação de dados experimentais, assim como de sensibilização para as questões ambientais.

Genetic structure at range edge: Low diversity and high inbreeding in Southeast Asian mangrove (Avicennia marina) populations

Understanding the genetic composition and mating systems of edge populations provides important insights into the environmental and demographic factors shaping species’ distribution ranges. We analysed samples of the mangrove Avicennia marina from Vietnam, northern Philippines and Australia, with microsatellite markers. We compared genetic diversity and structure in edge (Southeast Asia, and Southern Australia) and core (North and Eastern Australia) populations, and also compared our results with previously published data from core and southern edge populations. Comparisons highlighted significantly reduced gene diversity and higher genetic structure in both margins compared to core populations, which can be attributed to very low effective population size, pollinator scarcity and high environmental pressure at distribution margins. The estimated level of inbreeding was significantly higher in northeastern populations compared to core and southern populations. This suggests that despite the high genetic load usually associated with inbreeding, inbreeding or even selfing may be advantageous in margin habitats due to the possible advantages of reproductive assurance, or local adaptation. The very high level of genetic structure and inbreeding show that populations of A. marina are functioning as independent evolutionary units more than as components of a metapopulation system connected by gene flow. The combinations of those characteristics make these peripheral populations likely to develop local adaptations and therefore to be of particular interest for conservation strategies as well as for adaptation to possible future environmental changes.

Trawling and creeling for nephrops: impacts on biodiversity and populations structure

Dissertação de mestrado, Aquacultura e Pescas, Faculdade de Ciências e Tecnologia, Universidade do Algarve, 2015

Argyrosomus regius (Asso, 1801) fishery and ecology in portuguese waters, with reference to its relationships to other european and african populations

Tese de doutoramento, Biologia (Biologia Marinha e Aquacultura), Universidade de Lisboa, Faculdade de Ciências, 2014

Diallelic analysis to obtain cowpea (Vigna unguiculata L. Walp.) populations tolerant to water deficit.

The purpose of this study was to identify parents and obtain segregating populations of cowpea (Vigna unguiculata L. Walp.) with the potential for tolerance to water deficit. A full diallel was performed with six cowpea genotypes, and two experiments were conducted in Teresina, PI, Brazil in 2011 to evaluate 30 F2 populations and their parents, one under water deficit and the other under full irrigation.

Variation in protein expression levels in cell populations

Dissertation presented to obtain the Ph.D degree in Systems Biology

Constraint-based modelling of mixed microbial populations: Application to polyhydroxyalkanoates production

Dissertação para obtenção do Grau de Doutor em Engenharia Química e Bioquímica

Mediterranean populations of the lesser white-toothed shrew (Crocidura suaveolens group): an unexpected puzzle of Pleistocene survivors and prehistoric introductions.

An earlier study revealed the strong phylogeographical structure of the lesser white-toothed shrew (Crocidura suaveolens group) within the northern Palaearctic. Here, we aim to reconstruct the colonization history of Mediterranean islands and to clarify the biogeography and phylogeographical relationships of the poorly documented Middle East region with the northern Palaearctic. We performed analyses on 998-bp-long haplotypes of the mitochondrial cytochrome b gene of 143 samples collected around the Mediterranean basin, including islands and the Middle East. The analyses suggest that the Cypriot shrew belongs to the rare group of relict insular Pleistocene mammal taxa that have survived to the present day. In contrast, the Cretan, Corsican and Menorcan populations were independently introduced from the Middle East during the Holocene. The phylogeographical structure of this temperate Palaearctic species within the Middle East appears to be complex and rich in diversity, probably reflecting fragmentation of the area by numerous mountain chains. Four deeply divergent clades of the C. suaveolens group occur in the area, meaning that a hypothetical contact zone remains to be located in central western Iran.

Analyse des risques d'extinction des populations naturelles

A review of extinction risk analysis and viability methods is presented. The importance of environmental, demographic and genetic uncertainties, as well as the role of catastrophes are successively considered, and different approaches aiming at the integration of these risk factors in predictive population dynamic models are discussed.