Estudo da influência de parâmetros ambientais no desenvolvimento larvar de Pelophylax perezi

Tese de mestrado. Biologia (Biologia Evolutiva e do Desenvolvimento). Universidade de Lisboa, Faculdade de Ciências, 2009Os anfíbios apresentam variações geográficas em vários aspectos das histórias de vida. Investigaram-se as causas das variações num gradiente de altitudes, no estádio larvar de Pelophylax perezi, de modo a perceber se eram provocadas por adaptação local ou plasticidade fenotípica. Utilizaram-se características das histórias de vida, de forma a tentar destrinçar a componente genética da ambiental. Os tamanhos e a diferenciação dos girinos foram medidos, mensalmente, em charcos naturais e em experiências de common garden no laboratório, em que se usaram dois níveis de temperatura. Na maioria dos casos, observou-se uma resposta semelhante das características consoante a origem e a temperatura, tendo-se apenas prolongado o período larvar na temperatura mais elevada. Não parecem existir diferenças genéticas entre as populações, mas observou-se um efeito ambiental, em que diferentes temperaturas da água influenciam o desenvolvimento dos girinos.Amphibians have geographic variations in many aspects of life history. The causes of variation in an altitudinal gradient in the larval stage of Pelophylax perezi have been investigated in order to see whether they were caused by local adaptation or phenotypic plasticity. We used life history traits in order to try to disentangle the genetic component from the environment component. Size and differentiation of tadpoles were measured monthly in natural ponds and in common garden experiments in the laboratory, where were used two levels of temperature. In most cases, traits responded similarly according to the origin and temperature and only the larval period at higher temperature was prolonged. There seem to be no genetic differences between populations, but an environmental effect, where different water temperatures influence the development of tadpoles

The genetic structure of a mouse lemur living in a fragmented habitat in Northern Madagascar

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Two Different High Throughput Sequencing Approaches Identify Thousands of <em>De Novo</em> Genomic Markers for the Genetically Depleted Bornean Elephant

<div><p>High throughput sequencing technologies are being applied to an increasing number of model species with a high-quality reference genome. The application and analyses of whole-genome sequence data in non-model species with no prior genomic information are currently under way. Recent sequencing technologies provide new opportunities for gathering genomic data in natural populations, laying the empirical foundation for future research in the field of conservation and population genomics. Here we present the case study of the Bornean elephant, which is the most endangered subspecies of Asian elephant and exhibits very low genetic diversity. We used two different sequencing platforms, the Roche 454 FLX (shotgun) and Illumina, GAIIx (Restriction site associated DNA, RAD) to evaluate the feasibility of the two methodologies for the discovery of <em>de novo</em> markers (single nucleotide polymorphism, SNPs and microsatellites) using low coverage data. Approximately, 6,683 (shotgun) and 14,724 (RAD) SNPs were detected within our elephant sequence dataset. Genotyping of a representative sample of 194 SNPs resulted in a SNP validation rate of ∼ 83 to 94% and 17% of the loci were polymorphic with a low diversity (<em>H</em>_o = 0.057). Different numbers of microsatellites were identified through shotgun (27,226) and RAD (868) techniques. Out of all di-, tri-, and tetra-microsatellite loci, 1,706 loci had sufficient flanking regions (shotgun) while only 7 were found with RAD. All microsatellites were monomorphic in the Bornean but polymorphic in another elephant subspecies. Despite using different sample sizes, and the well known differences in the two platforms used regarding sequence length and throughput, the two approaches showed high validation rate. The approaches used here for marker development in a threatened species demonstrate the utility of high throughput sequencing technologies as a starting point for the development of genomic tools in a non-model species and in particular for a species with low genetic diversity.</p> </div

Genetic Differentiation and Demographic History of the Northern Rufous Mouse Lemur (Microcebus tavaratra) Across a Fragmented Landscape in Northern Madagascar

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Summary statistics of data obtained using two different sequencing approaches: Illumina (RAD-seq) and 454 (shotgun).

<p>Note that the eight elephant samples (1 to 8) used in Illumina RAD-sequencing are different from the two.</p><p>samples (A and B) used in 454 shotgun sequencing.</p>*<p>weighted median statistic such that 50% of the entire assembly is contained in the number of contigs equal.</p><p>to or greater than this value.</p>#<p>>q20: 0.01% chance that a base was wrongly called.</p>$<p>identified in elephant sample 4.</p

Histogram of contig size distribution.

<p>Length distribution of contigs assembled from 454 shotgun sequencing (A) and RAD-sequencing (B) using Illumina platform. The average contig length in the 454 dataset (<i>n</i> = 2) was 328.13 bp and ranged from 100 to 6,407 bp. The average contig length in the RAD-sequencing dataset (<i>n</i> = 8) was between 259 (sample 4) and 288 bp (sample 2). The RAD contig lengths ranged from 150 to 560 bp.</p