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Mapping Knowledge Gaps of Mozambique’s Terrestrial Mammals
Publication . Neves, Isabel Queirós; Mathias, Maria da Luz; Bastos-Silveira, Cristiane
A valuable strategy to support conservation planning is to assess knowledge gaps regarding primary species occurrence data to identify and select areas for future biodiversity surveys. Currently, increasing accessibility to these data allows a cost-effective method for boosting knowledge about a country's biodiversity. For understudied countries where the lack of resources for conservation is more pronounced to resort to primary biodiversity data can be especially beneficial. Here, using a primary species occurrence dataset, we assessed and mapped Mozambique's knowledge gaps regarding terrestrial mammal species by identifying areas that are geographically distant and environmentally different from well-known sites. By comparing gaps from old and recent primary species occurrence data, we identified: (i) gaps of knowledge over time, (ii) the lesser-known taxa, and (iii) areas with potential for spatiotemporal studies. Our results show that the inventory of Mozambique's mammal fauna is near-complete in less than 5% of the territory, with broad areas of the country poorly sampled or not sampled at all. The knowledge gap areas are mostly associated with two ecoregions. The provinces lacking documentation coincide with areas over-explored for natural resources, and many such sites may never be documented. It is our understanding that by prioritising the survey of the knowledge-gap areas will likely produce new records for the country and, continuing the study of the well-known regions will guarantee their potential use for spatiotemporal studies. The implemented approach to assess the knowledge gaps from primary species occurrence data proved to be a powerful strategy to generate information that is essential to species conservation and management plan. However, we are aware that the impact of digital and openly available data depends mostly on its completeness and accuracy, and thus we encourage action from the scientific community and government authorities to support and promote data mobilisation.
Evolutionary history of philaenus spumarius (hemiptera, aphrophoridae) and the adaptive significance and genetic basis of its dorsal colour polymorphism
Publication . Rodrigues, Ana S. B.; Paulo, Octávio, 1963-; Jiggins, Chris
Understanding the genetic basis of adaptive traits and how natural populations adapt to their environment, are fundamental problems in evolutionary biology. Colour polymorphisms are good systems in which these issues can be addressed. This work exploits the adaptive significance of the dorsal colour polymorphism in Philaenus spumarius and describes the efforts to identify genomic region(s) linked to the dorsal colour variation in this species. It also involves the investigation of the evolutionary pattern of P. spumarius. The phylogeographic results showed that main demographic and evolutionary events for the European populations seem to have occurred during Pleistocene, probably as a consequence of the main climatic oscillations that characterised this period. Evidence of recent gene-flow among Mediterranean peninsulas, as well as a close relationship between Iberia and North Africa, a probable British origin for the populations of the Azores and New Zealand, and indication that both western and north-eastern Europe colonised North America, were also found. Captivity experiments, testing the adaptive function of P. spumarius' dorsal colour polymorphism, indicated a higher longevity, a higher number of oviposition events, and a higher number of eggs laid for trilineatus than for marginellus and typicus. A total of 1,837 genomic markers (SNPs) and 928 loci were obtained through RAD sequencing for 33 individuals of three colour phenotypes (trilineatus, marginellus and typicus), and a genome wide association study performed to identify regions related to dorsal colour variation. Single and multi-association analyses identified a total of 60 SNPs associated with dorsal colour phenotypes but none of these SNPs showed homology with colour genes described in other insect species. A stronger differentiation of the trilineatus colour phenotype was also found with these markers. New genomic and transcriptomic resources were developed, constituting important tools and a basis for future research in this species. The resources correspond to a genome draft (25% of the total estimated genome (5.3 Gb)) and to an 81.4 Mb transcriptome assembly. The analysis of the candidate gene yellow found no association with dorsal colour phenotypes. Although suggesting that yellow is not involved in colour variation in P. spumarius, a possible effect of this gene can not be totally excluded without, further analyses. Phylogenetic analyses found contrasting patterns between yellow and the neutral ITS2, indicating that, contrary to ITS2, yellow is conserved within the genus. A higher haplotype and nucleotide diversity was observed for P. spumarius. This could be related to a higher sample size or to the different ecology of the species. The present thesis showed that P. spumarius constitutes a potential good model system to study adaptation and the evolutionary mechanisms involved in the maintenance of polymorphisms.
Genomic signatures of introgression between commercial and native bumblebees, Bombus terrestris, in Western Iberian Peninsula - implications for conservation and trade regulation
Publication . Seabra, Sofia G.; Silva, Sara E.; Nunes, Vera L.; Sousa, Vitor C.; Martins, Joana; Marabuto, Eduardo; Rodrigues, Ana S.B.; Pina-Martins, Francisco; Laurentino, Telma G.; Rebelo, Maria Teresa; Figueiredo, Elisabete; Paulo, Octávio S.
Human‐mediated introductions of species may have profound impacts on native ecosystems.
One potential impact with largely unforeseen consequences is the potential
admixture of introduced with autochthonous species through hybridization.
Throughout the world, bumblebees have been deliberately introduced for crop pollination
with known negative impacts on native pollinators. Given the likely allochthonous
origin of commercial bumblebees used in Portugal (subspecies Bombus
terrestris terrestris and B. t. dalmatinus), our aim was to assess their putative introgression
with the native Iberian subspecies B. terrestris lusitanicus. We analysed one mitochondrial
gene, cytochrome c oxidase subunit I (COX1) and genomic data involving
thousands of genome‐wide restriction‐site‐associated DNA markers (RAD‐seq). In
the mitochondrial COX1 analyses, we detected one relatively common haplotype in
commercial bumblebees, also present in wild samples collected nearby the greenhouses
where the commercial hives are used. In the RAD‐seq analysis, we found a
clear genetic differentiation between native and commercial lineages. Furthermore,
we detected candidate hybrids in the wild, as well as putatively escaped commercial
bumblebees, some of which being potentially fertile males. Although we cannot assess
directly the fitness effects of introgressed alleles, there is a risk of maladaptive
allele introgression to the local bumblebee subspecies, which can negatively impact
autochthon populations. One immediate recommendation to farmers is for the
proper disposal of hive boxes, after their use in greenhouses, so as to minimize the
risk of escapees contaminating native populations. On the other hand, the feasibility
of using local subspecies B. t. lusitanicus, preferably with local production, should be
evaluated
Allele-specific expression variation at different ploidy levels in Squalius alburnoides
Publication . Matos, Isa; Machado, Miguel P.; Schartl, Manfred; Coelho, Maria Manuela
Allopolyploid plants are long known to be subject to a homoeolog expression bias of varying degree. The same phenomenon was only much later suspected to occur also in animals based on studies of single selected genes in an allopolyploid vertebrate, the Iberian fish Squalius alburnoides. Consequently, this species became a good model for understanding the evolution of gene expression regulation in polyploid vertebrates. Here, we analyzed for the first time genome-wide allele-specific expression data from diploid and triploid hybrids of S. alburnoides and compared homoeolog expression profiles of adult livers and of juveniles. Co-expression of alleles from both parental genomic types was observed for the majority of genes, but with marked homoeolog expression bias, suggesting homoeolog specific reshaping of expression level patterns in hybrids. Complete silencing of one allele was also observed irrespective of ploidy level, but not transcriptome wide as previously speculated. Instead, it was found only in a restricted number of genes, particularly ones with functions related to mitochondria and ribosomes. This leads us to hypothesize that allelic silencing may be a way to overcome intergenomic gene expression interaction conflicts, and that homoeolog expression bias may be an important mechanism in the achievement of sustainable genomic interactions, mandatory to the success of allopolyploid systems, as in S. alburnoides.
New insights into the genetic composition and phylogenetic relationship of wolves and dogs in the Iberian Peninsula
Publication . Pires, Ana Elisabete; Amorim, Isabel R.; Borges, Carla; Simões, Fernanda; Teixeira, Tatiana; Quaresma, Andreia; Petrucci-Fonseca, Francisco; Matos, José
This study investigates the gene pool of Portuguese autochthonous dog breeds and their wild counterpart, the Iberian wolf subspecies (Canis lupus signatus), using standard molecular markers. A combination of paternal and maternal molecular markers was used to investigate the genetic composition, genetic differentiation and genetic relationship of native Portuguese dogs and the Iberian wolf. A total of 196 unrelated dogs, including breed and village dogs from Portugal, and other dogs from Spain and North Africa, and 56 Iberian wolves (wild and captive) were analyzed for nuclear markers, namely Y chromosome SNPs, Y chromosome STR loci, autosomal STR loci, and a mitochondrial fragment of the control region I. Our data reveal new variants for the molecular markers and confirm significant genetic differentiation between Iberian wolf and native domestic dogs from Portugal. Based on our sampling, no signs of recent introgression between the two subspecies were detected. Y chromosome data do not reveal genetic differentiation among the analyzed dog breeds, suggesting they share the same patrilineal origin. Moreover, the genetic distinctiveness of the Iberian wolf from other wolf populations is further confirmed with the description of new mtDNA variants for this endemism. Our research also discloses new molecular markers for wolf and dog subspecies assignment, which might become particularly relevant in the case of forensic or noninvasive genetic studies. The Iberian wolf represents a relic of the once widespread wolf population in Europe and our study reveals that it is a reservoir of unique genetic diversity of the grey wolf, Canis lupus. These results stress the need for conservation plans that will guarantee the sustainability of this threatened top predator in Iberia.
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Fundação para a Ciência e a Tecnologia
Programa de financiamento
5876
Número da atribuição
UID/BIA/00329/2013