Publicação
Genomics of adaptation to cadmium on a spatially heterogeneous environment
| datacite.subject.fos | Departamento de Biologia Animal | pt_PT |
| dc.contributor.advisor | Fragata, Inês Regina Lopes de Mendonça, 1985- | |
| dc.contributor.advisor | Sousa, Vítor Martins Conde e, 1981- | |
| dc.contributor.author | Ferreira, Marta Cardoso | |
| dc.date.accessioned | 2023-07-11T09:54:46Z | |
| dc.date.available | 2025-04-30T00:31:00Z | |
| dc.date.issued | 2023 | |
| dc.date.submitted | 2023 | |
| dc.description | Tese de mestrado, Biologia Evolutiva e do Desenvolvimento, 2023, Universidade de Lisboa, Faculdade de Ciências | pt_PT |
| dc.description.abstract | Many species are shifting their ranges due to climate change, hence understanding how adaptation occurs in spatially heterogeneous environments is important. Yet, little is known about adaptation in heterogeneous environments, in particular at the genomic level. To tackle this question, experimental evolution under controlled laboratory conditions, combined with population genomics is a powerful approach. Such “Evolve-and-Reseq” studies allow uncovering the genetic basis of adaptive traits in different organisms. A caveat of experimental evolution is that the potentially reduced genetic diversity of laboratory populations might influence both the speed and end point of adaptation. In this thesis, we address these issues using experimental populations of two closely related species (Tetranychus urticae and T. evansi) of spider mites, which are arrhenotokous haplodiploid herbivorous species, considered worldwide pests. Both species can feed on tomato plants, which are known to accumulate heavy metals. These metals can be used as a defence against herbivory, and it is known that cadmium accumulation can decrease spider mites’ fitness. Taking advantage of this setup, we addressed two important gaps in knowledge by using population genomic data of outbred and inbred lines and experimental populations. Namely (1) quantify the genetic variability of the outbred populations and inbred lines, and (2) understand how spatial heterogeneity affects the adaptation to new environments, namely on environments with cadmium. Using Illumina sequencing of pools of >200 mites (Pool-seq), we estimated expected heterozygosity as a proxy for the genetic diversity of outbred T. evansi and T. urticae and nine inbred lines of T. evansi. We expected inbred lines would present lower genetic diversity compared to the outbred populations, as a result of the inbreeding process. However, we found that the nine inbred lines had similar expected heterozygosity to the outbred population, leading us to conclude they are not inbred isogenic lines. These results might be explained by gene flow between lines and/or outbred population, but we also found an effect of the choice of reference genome. To identify genomic regions of adaptation to cadmium on T. urticae and/or to spatially heterogeneous environments, we analysed Pool-seq data from experimental evolution selection regimes of T. urticae, evolving with low (control) or high cadmium concentrations (homogeneous environment) or both (heterogeneous environments). We used consistent changes in allele frequencies across five replicates as evidence for positive selection, assuming that the control regime represented the initial allele frequency. We found many SNPs with significant changes in allele frequencies, both in homogeneous and heterogeneous environments, indicating a polygenic basis of adaptation. We found that only 10.9% of the candidate genes are shared between homogeneous and heterogeneous environments, suggesting that adaptation in heterogeneous environments may select for alleles different from those favoured in the different homogeneous environments. Furthermore, metallothioneins did not show significative changes in allele frequencies in environments with cadmium, although they are the best-known stress response system to heavy metals, but we found a voltage-gated T-type calcium channel (CACNA2D3) with several SNPs with allele frequency changes consistent with adaptation in homogeneous and heterogeneous environments. | pt_PT |
| dc.identifier.tid | Tese de mestrado em Biologia Evolutiva e do Desenvolvimento | pt_PT |
| dc.identifier.tid | 203486170 | |
| dc.identifier.uri | http://hdl.handle.net/10451/58538 | |
| dc.language.iso | eng | pt_PT |
| dc.subject | Tetranychus urticae | pt_PT |
| dc.subject | Tetranychus evansi | pt_PT |
| dc.subject | Populações exogâmicas | pt_PT |
| dc.subject | Populações endogâmicas | pt_PT |
| dc.subject | CACNA2D3 | pt_PT |
| dc.subject | Teses de mestrado - 2023 | pt_PT |
| dc.title | Genomics of adaptation to cadmium on a spatially heterogeneous environment | pt_PT |
| dc.type | master thesis | |
| dspace.entity.type | Publication | |
| rcaap.rights | openAccess | pt_PT |
| rcaap.type | masterThesis | pt_PT |