O processo de construção da cidadania: a Associação Olho Vivo como estudo de caso

Tese de mestrado, Cultura e Comunicação, Universidade de Lisboa, Faculdade de Letras, 2012A presente dissertação foi redigida com o objetivo de criar, na Parte I, uma ligação entre três conceitos e o seu respetivo modelo de funcionamento: cidadania, direitos humanos e terceiro sector. Os conceitos serão definidos e relacionados entre si, demonstrando que funcionam em estreita relação e são importantes motores para o funcionamento da vida em comunidade e da construção da cidadania. A parte II é dedicada ao estudo da Associação Olho vivo para a defesa do Património, ambiente e Direitos Humanos. Este estudo abrange o trabalho que a associação desenvolveu desde o ano da sua criação até aos dias de hoje; uma reflexão das dificuldades que sente no desempenho das suas funções e uma proposta de criação de um modelo de comunicação mais eficiente e atual. Para estudar o trabalho desenvolvido pela Organização Não Governamental Associação Olho Vivo temos de ter em conta três circunstâncias. A primeira é entender o terceiro sector como referência na prestação de apoio social. A segunda é compreender os direitos humanos à luz dos dias de hoje, em termos de uma estrutura social que centraliza o emprego como veículo para a integração social. Por último, há que ter em conta as consequências da centralidade do desemprego nas políticas de inserçãoABSTRACT: This dissertation aims at building, in Part I, a connection between three concepts and their respective operating model: citizenship, human rights and third sector. The concepts are explained and connected in order to prove that they exist and work together on a strict relationship and as important factors for both social life and the construction of citizenship. Part II focus on the study of Associação Olho Vivo para a Defesa do Património, Ambiente e Direitos Humanos. The study has three major concerns, namely 4 the work developed by Associação Olho Vivo since its creation, a reflection on the problems it has to deal with, and the proposal for the creation of a more effective and updated communication model. In order to study the work developed by the NGO Associação Olho Vivo para a Defesa do Património, Ambiente e Direitos Humanos three conditions have been accounted for in this research. The first one is the consideration of the third sector as a reference in social welfare. The second is the understanding of human rights in our own contemporary context in terms of a social structure that centralizes employment as the key towards social integration. Finally, this research focuses on unemployment related issues and on their relevance in policies of inclusion

Mountain hare transcriptome and diagnostic markers as resources to monitor hybridization with European hares

We report the first mountain hare (Lepus timidus) transcriptome, produced by de novo assembly of RNA-sequencing reads. Data were obtained from eight specimens sampled in two localities, Alps and Ireland. The mountain hare tends to be replaced by the invading European hare (Lepus europaeus) in their numerous contact zones where the species hybridize, which affects their gene pool to a yet unquantified degree. We characterize and annotate the mountain hare transcriptome, detect polymorphism in the two analysed populations and use previously published data on the European hare (three specimens, representing the European lineage of the species) to identify 4 672 putative diagnostic sites between the species. A subset of 85 random independent SNPs was successfully validated using PCR and Sanger sequencing. These valuable genomic resources can be used to design tools to assess population status and monitor hybridization between species

Transcriptomic regulation of seasonal coat color change in hares

Color molts from summer brown to winter white coats have evolved in several species to maintain camouflage year-round in environments with seasonal snow. Despite the eco-evolutionary relevance of this key phenological adaptation, its molecular regulation has only recently begun to be addressed. Here, we analyze skin transcription changes during the autumn molt of the mountain hare (Lepus timidus) and integrate the results with an established model of gene regulation across the spring molt of the closely related snowshoe hare (L. americanus). We quantified differences in gene expression among three stages of molt progression-"brown" (early molt), "intermediate," and "white" (late molt). We found 632 differentially expressed genes, with a major pulse of expression early in the molt, followed by a milder one in late molt. The functional makeup of differentially expressed genes anchored the sampled molt stages to the developmental timeline of the hair growth cycle, associating anagen to early molt and the transition to catagen to late molt. The progression of color change was characterized by differential expression of genes involved in pigmentation, circadian, and behavioral regulation. We found significant overlap between differentially expressed genes across the seasonal molts of mountain and snowshoe hares, particularly at molt onset, suggesting conservatism of gene regulation across species and seasons. However, some discrepancies suggest seasonal differences in melanocyte differentiation and the integration of nutritional cues. Our established regulatory model of seasonal coat color molt provides an important mechanistic context to study the functional architecture and evolution of this crucial seasonal adaptation

Museomics Dissects the Genetic Basis for Adaptive Seasonal Coloration in the Least Weasel

Dissecting the link between genetic variation and adaptive phenotypes provides outstanding opportunities to understand fundamental evolutionary processes. Here, we use a museomics approach to investigate the genetic basis and evolution of winter coat coloration morphs in least weasels (Mustela nivalis), a repeated adaptation for camouflage in mammals with seasonal pelage color moults across regions with varying winter snow. Whole-genome sequence data were obtained from biological collections and mapped onto a newly assembled reference genome for the species. Sampling represented two replicate transition zones between nivalis and vulgaris coloration morphs in Europe, which typically develop white or brown winter coats, respectively. Population analyses showed that the morph distribution across transition zones is not a by-product of historical structure. Association scans linked a 200-kb genomic region to coloration morph, which was validated by genotyping museum specimens from intermorph experimental crosses. Genotyping the wild populations narrowed down the association to pigmentation gene MC1R and pinpointed a candidate amino acid change cosegregating with coloration morph. This polymorphism replaces an ancestral leucine residue by lysine at the start of the first extracellular loop of the protein in the vulgaris morph. A selective sweep signature overlapped the association region in vulgaris, suggesting that past adaptation favored winter-brown morphs and can anchor future adaptive responses to decreasing winter snow. Using biological collections as valuable resources to study natural adaptations, our study showed a new evolutionary route generating winter color variation in mammals and that seasonal camouflage can be modulated by changes at single key genes

Building a Portuguese Coalition for Biodiversity Genomics

The diverse physiography of the Portuguese land and marine territory, spanning from continental Europe to the Atlantic archipelagos, has made it an important repository of biodiversity throughout the Pleistocene glacial cycles, leading to a remarkable diversity of species and ecosystems. This rich biodiversity is under threat from anthropogenic drivers, such as climate change, invasive species, land use changes, overexploitation or pathogen (re)emergence. The inventory, characterization and study of biodiversity at inter- and intra-specific levels using genomics is crucial to promote its preservation and recovery by informing biodiversity conservation policies, management measures and research. The participation of researchers from Portuguese institutions in the European Reference Genome Atlas (ERGA) initiative, and its pilot effort to generate reference genomes for European biodiversity, has reinforced the establishment of Biogenome Portugal. This nascent institutional network will connect the national community of researchers in genomics. Here, we describe the Portuguese contribution to ERGA’s pilot effort, which will generate high-quality reference genomes of six species from Portugal that are endemic, iconic and/or endangered, and include plants, insects and vertebrates (fish, birds and mammals) from mainland Portugal or the Azores islands. In addition, we outline the objectives of Biogenome Portugal, which aims to (i) promote scientific collaboration, (ii) contribute to advanced training, (iii) stimulate the participation of institutions and researchers based in Portugal in international biodiversity genomics initiatives, and (iv) contribute to the transfer of knowledge to stakeholders and engaging the public to preserve biodiversity. This initiative will strengthen biodiversity genomics research in Portugal and fuel the genomic inventory of Portuguese eukaryotic species. Such efforts will be critical to the conservation of the country’s rich biodiversity and will contribute to ERGA’s goal of generating reference genomes for European species.info:eu-repo/semantics/publishedVersio

Range dynamics driven by Quaternary climate oscillations explain the distribution of introgressed mtDNA of Lepus timidus origin in hares from the Iberian Peninsula

[Aim]: A striking case of mitochondrial DNA (mtDNA) introgression occurs in the Iberian Peninsula: the mtDNA of Lepus timidus, a species that inhabited this territory during the Last Glacial Maximum (LGM), is almost fixed in the Iberian range of Lepus europaeus, is very frequent in the northern half of Iberia within Lepus granatensis, and is fixed in Lepus castroviejoi. Here, we used a transdisciplinary approach to understand the ecological drivers of the distribution of this introgressed mtDNA in the Iberian hare species. [Location]: Europe, with an emphasis on the Iberian Peninsula. [Methods]: First, we modelled the climatic niche of L. timidus to predict the favourability for the species during the LGM. Second, we gathered data regarding L. timidus mtDNA introgression for 1137 individuals (139 populations) from the Iberian Peninsula. We tested whether the climatic favourability for L. timidus during the LGM reflects the frequency of the introgressed mtDNA in the carrier hare populations. [Results]: The climatic favourability for the LGM is positively related to the presence of individuals with L. timidus mtDNA, and discriminates better than by chance between individuals with and without this lineage. At the population level, the favourability values relate to the observed frequencies of mtDNA introgression and discriminate between populations with and without L. timidus mtDNA. [Main conclusions]: The results suggest that the geographical distribution of L. timidus mtDNA introgression is linked to L. timidus distribution in Iberia during the LGM. Our study helps to improve our understanding of the role of climate in the reticulated evolutionary history of hares, and is a first step towards understanding the ecological impact of mtDNA introgression on Iberian hares.P.A. is currently supported by the Spanish Ministerio de Economía y Competitividad (MINECO) and Universidad de Castilla-La Mancha (UCLM) through a ‘Ramón y Cajal’ contract (RYC-2012-11970). J.M.-F. and R.C. hold FCT Investigator and postdoctoral grants, respectively, from the Fundaçao para a Ciência e a Tecnologia (FCT), funded by Programa Operacional Potencial Humano (POPH) – Quadro de Referencia Estrategico Nacional (QREN) from the European Social Fund and by the Portuguese Ministerio da Educacao e Ciencia (IF/00033/2014 and SFRH/BPD/64365/2009, respectively). This work is funded by FEDER funds through the Operational Programme for Competitiveness Factors – COMPETE and by National Funds through FCT – Foundation for Science and Technology under the EXPL/AAG-MAA/1082/2013 and FCOMP-01-0124-FEDER-041082. Partial funding was also obtained from FCT-ANR/BIA-EVF/0250/2012 and by the Spanish Ministry of Agriculture, Food and Environment, Spanish National Park’s Network (project 1098/2014).Peer Reviewe

Postglacial range revolutions in South European hares (Lepus spp.): insights from ancient DNA and ecological niche modelling

[Aim]: The distribution of hares (Lepus spp.) in southern Europe was markedly different at the Last Glacial Maximum. Historical hybridization during range replacements led to high frequencies of mtDNA introgression from Lepus timidus into populations of three other species in northern Iberian Peninsula, even though L. timidus subsequently disappeared from the region. We use palaeontological records to provide new insights on the biogeographic history of these range replacements, combining ancient DNA and ecological niche modelling. [Location]: Southern France. [Taxon]: Hares (genus Lepus). [Methods]: DNA was extracted from hare bones collected at Neolithic sites in southern France (5.5–7.5 thousand years before present; kyr bp) with uncertain species assignment. One mtDNA fragment was sequenced and 27 SNPs from 11 nuclear genes with species-diagnostic information were genotyped. Distributions of L. granatensis, L. europaeus, and L. timidus were modelled using spatial and bioclimatic predictors, and the favourability function. Each model was transferred to 6 kyr bp and favourabilities were combined to determine the species with the highest environmental favourability in each sampled locality. [Results]: Ancient DNA analysis showed that the screened specimens belong to L. granatensis, a species presently confined to the Iberian Peninsula, but carried mtDNA haplotypes from L. timidus. Niche models show that L. granatensis achieved highest favourability in southern France 6 kyr bp reinforcing the molecular evidences. [Main conclusions]: L. granatensis replaced L. timidus populations from Iberia to southern France, being present in this region 5.5 kyr bp. Subsequent westwards invasion of L. europaeus likely replaced these L. granatensis populations towards northern Iberia, establishing current ranges. Despite successive species replacements, introgressed mtDNA haplotypes from L. timidus mark the distribution of the species in northern Iberian Peninsula before it disappeared in the region. Characterizing complex biogeographic histories of interacting species is a key to understand processes that led to current distributions of genetic diversity.This work was supported by Fundação para a Ciência e a Tecnologia, project “CHANGE”PTDC/BIA‐EVF/1624/2014 (Portuguese national funds) and Investigador FCT IF/00033/2014/CP1256/CT0005 to JMF(POPH‐QREN funds from the European Social Fund and Portuguese MCTES‐FCT). Further support was obtained from project NORTE‐01‐0145‐FEDER‐000007 supported by the Norte Portugal Regional Operational Programme (NORTE2020), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (ERDF). LD acknowledges funding from the Swedish Research Council. PA is supported by the Spanish Ministerio de Economía y Competitividad (MINECO) and Universidad de Castilla‐La Mancha (UCLM) through a Ramón y Cajal contract (RYC‐2012‐11970). Instrumentation and laboratory support was provided by CIBIO NEW‐GEN sequencing platform, supported by European Union's Seventh Framework Programme for research, technological development and demonstration under grant agreement no. 286431.Peer Reviewe

Recurrent Introgression of Mitochondrial DNA Among Hares (Lepus spp.) Revealed by Species-Tree Inference and Coalescent Simulations

International audienceUnderstanding recent speciation history requires merging phylogenetic and population genetics approaches, taking into account the persistence of ancestral polymorphism and possible introgression. The emergence of a clear phylogeny of hares (genus Lepus) has been hampered by poor genomic sampling and possible occurrence of mitochondrial DNA (mtDNA) introgression from the arctic/boreal Lepus timidus into several European temperate and possibly American boreal species. However, no formal test of introgression, taking also incomplete lineage sorting into account, has been done. Here, to clarify the yet poorly resolved species phylogeny of hares and test hypotheses of mtDNA introgression, we sequenced 14 nuclear DNA and 2 mtDNA fragments (8205 and 1113 bp, respectively) in 50 specimens from 11 hare species from Eurasia, North America, and Africa. By applying an isolation-with-migration model to the nuclear data on subsets of species, we find evidence for very limited gene flow from L. timidus into most temperate European species, and not into the American boreal ones. Using a multilocus coalescent-based method, we infer the species phylogeny, which we find highly incongruent with mtDNA phylogeny using parametric bootstrap. Simulations of mtDNA evolution under the speciation history inferred from nuclear genes did not support the hypothesis of mtDNA introgression from L. timidus into the American L. townsendii but did suggest introgression from L. timidus into 4 temperate European species. One such event likely resulted in the complete replacement of the aboriginal mtDNA of L. castroviejoi and of its sister species L. corsicanus. It is remarkable that mtDNA introgression in hares is frequent, extensive, and always from the same donor arctic species. We discuss possible explanations for the phenomenon in relation to the dynamics of range expansions and species replacements during the climatic oscillations of the Pleistocene. [Coalescent simulations; discordant phylogenies; introgression; Lepus; rapid radiation; species-tree inference.

Data from: Home loving boreal hare mitochondria survived several invasions in Iberia: the relative roles of recurrent hybridisation and allele surfing

Genetic introgression from a resident species into an invading close relative can result from repeated hybridisation along the invasion front and/or allele surfing on the expansion wave. Cases where the phenomenon is massive and systematic, such as for hares (genus Lepus) in Iberia, would be best explained by recurrent hybridisation but this is difficult to prove since the donor populations are generally extinct. In the Pyrenean foothills, Lepus europaeus presumably replaced Lepus granatensis recently and the present species border is parallel to the direction of invasion, so that populations of L. granatensis in the contact zone represent proxies of existing variation before the invasion. Among three pairs of populations sampled across this border, we find less differentiation of mtDNA across than along it, as predicted under recurrent hybridisation at the invasion front. Using autosomal microsatellite loci and X and Y-linked diagnostic loci, we show that admixture across the border is quasi-absent, making it unlikely that lack of interspecific mtDNA differentiation result from ongoing gene flow. Furthermore, we find that the local species ranges are climatically contrasted, making it also unlikely that ongoing ecology-driven movement of the contact account for mtDNA introgression. The lack of mtDNA differentiation across the boundary is mostly due to sharing of mtDNA from a boreal species currently extinct in Iberia (Lepus timidus) whose mitochondria have thus remained in place since the last deglaciation despite successive invasions by two other species. Home loving mitochondria thus witness past species distribution rather than ongoing exchanges across stabilised contact zones