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Authors
Abstract(s)
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.
Description
Tese de mestrado, Biologia Evolutiva e do Desenvolvimento, 2023, Universidade de Lisboa, Faculdade de Ciências
Keywords
Tetranychus urticae Tetranychus evansi Populações exogâmicas Populações endogâmicas CACNA2D3 Teses de mestrado - 2023