... R e s e a r c h
The rapid environmental changes accelerated by human activities have facilitated the introduction of invasive species worldwide. In this process, many of these species have become extinct, while others have managed to survive but are not considered invasive. However, there are a few that have thrived, gained reproductive success, and spread extensively, thereby altering the local eco-evolutionary dynamics.
For instance, a case in Switzerland demonstrates the rapid and sudden expansion of the range of a native species of wall lizards, Podarcis muralis, within just two decades. Interestingly, the spreading population of lizards does not exhibit the phenotypic characteristics of the native lizards. These phenotypic differences suggest the possibility that the expanding lizards may not representing the native lizards, but rather introduced subspecies or possibly the result of genetic hybridisation between the native lizards and other subspecies whose ranges overlap, such as the Italian lineage and the southern Alps lineages.
While hybridisation often carries a negative connotation due to its homogenising effect on gene pools, recent shifts in understanding have revealed that in certain cases, hybridisation can enrich genetic variation, potentially facilitating rapid routes to adaptation and speciation. As a visiting MSc student of the MEME program at the Sanger Institute, I am utilising these organisms to study the genetic mechanisms that explain why and how a species spreads rapidly.
Moreover, invasive introduced species also have the potential to create new ecological niches for native organisms. During the era of European exploration to the East, Europeans brought numerous seeds and introduced high-value economically and aesthetically significant species beyond their native ranges. Many neotropical plants now thrive in Southeast Asia, primarily due to similar microclimatic conditions. These species present new and challenging obstacles to overcome, but they also have the potential to open up new ecological opportunities for local herbivores.
One example is a phytophagous ladybird beetle species in Southeast Asia that has repeatedly colonised an introduced invasive plant within a relatively short period. Similar colonisation patterns have been observed in other ladybird beetle species within the same tribe. Interestingly, in one case, adaptation to the new habitat has the potential to act as a critical driving force in population divergence or speciation due to host plants specialisation, while in some cases, it leads to generalisation.
Now, I'm starting my PhD at the Sanger Institute. I am interested in characterising the evolutionary agents that drive genetic changes in cases of specialisation and generalisation to host plants. I aim to study the genomic features that facilitate these changes during the host plant colonisation process, and trace the origin of genetic variants responsible for the behavioural preferences and adaptations of these beetles to new host plants. More information will be provided soon!
In recent years, I have also been involved in several projects related to the genetic basis of speciation in popular model systems. With Matteo Rossi and Richard Merrill, we have functionally validated the genetic basis of visual mate preference in Heliconius butterflies. Using gene editing, we have knocked out one of the five candidate genes recently found to be strongly associated with preference behaviours across the broader Heliconius clade. In another opportunity, with Marjolaine Rousselle and Carole Smadja, we are investigating the presence, link, and causes of fast-X and large-X effects, exploring the role of sex chromosome evolution in the development of reproductive isolation across the continuum of divergence using various pea aphid, Acyrthosiphon pisum, host-specialised biotypes.
Past projects
Chromosomal evolution in Coleoptera
Coleoptera is widely recognised as one of the most diverse and species-rich taxa among insects. Having emerged from a super-radiation in deep evolutionary time, beetles present a unique opportunity to unravel the macroevolutionary processes underlying this remarkable diversity. Surprisingly, despite their immense species richness, relatively few studies have delved into the chromosomal scale of coleopteran genomes. In my PhD rotation project with Sam Ebdon and Kamil Jaron, we conducted an analysis of 151 chromosomally complete coleopteran genomes to reconstruct their ancestral linkage groups and explore the dynamics of chromosomal rearrangements across major lineages of coleopteran taxa.
Hyper-divergent haplotypes across the tree of life
Recent research has revealed hyper-divergent haplotypes in diverse taxa, including free-living nematodes, parasitic nematodes, molluscs, and spiders. These regions are often associated with ecologically and survival-related traits. Despite this, there is no consensus on the prevalence of these regions across the tree of life and their biological functions. In my PhD rotation project with Lewis Stevens and Mark Blaxter, we utilised 859 reference genomes from the Darwin Tree of Life Programme to investigate the presence of hyper-divergent haplotypes and explore whether these regions are enriched with protein-coding genes that play significant biological roles.
Genetics of rapid expansion
Dispersal of an organism sometimes occurs rapidly and often facilitated by the evolution of adaptive phenotypes. However, while cases of rapid range expansion are plentiful and we know a lot about the ecological drivers, little is known about the evolutionary drivers, especially the genetic basis of the underlying phenotypes. In my MSc project with Joana Meier and Anna Orteu, using large-scale whole genome sequencing data from hundred of individuals, we test whether hybridisation between lineages fuel the rapid expansion of wall lizards (Podarcis muralis) in Switzerland. We also investigated, via GWAS, the genetics of several traits thought to be associated with the rapid spread of this species within just two decades, including brown-green dorsal colouration, ventral melanism pattern, UV-reflective blue spots, and head size.
Sex chromosome evolution throughout speciation continuum
Sex chromosomes are expected to play a disproportionate role both in adaptation and in reproductive isolation due to the large-X and fast-X effects expected to promote accelerated genetic differentiation and molecular evolution in species with XY or X0 sex chromosome systems. Both the fast-X and the large-X hypotheses have been empirically demonstrated in a number of species, including insects, but debate is still active about their importance in driving the evolution of reproductive isolation. In my MSc project with Carole Smadja and Marjolaine Rousselle, we test the presence, the link, and causes of fast-X and large-X effects and compare those effects along this continuum of divergence using pool-seq whole genome resequencing data representing various pea aphid (Acyrthosiphon pisum) biotypes.
Genetics of assortative mating
Speciation can be facilitated when the trait under divergent selection also contributes to assortative mating, creating effective barriers to interbreeding. However, while we know a lot about the genetic basis of its ecological component, little is known about the genetic mechanisms underlying changes in mate preference behaviour. In my MSc mini-project with Richard Merrill and Matteo Rossi, we functionally validate the genetic basis of visual mate preference in Heliconius butterflies. Using genome editing, we knockout one of the five candidate genes recently found to be strongly associated with preference behaviours across the broader Heliconius clade.
Reproductive isolation beyond the first barriers
Recent work has contributed much to our understanding of how reproductive barriers begin to evolve, and how they are maintained in the face of gene flow. In herbivorous insects, host plant specialisation often results in complete habitat isolation and automatic assortative mating, generate strong barriers to gene flow, and thus very critical driving force in early stage of speciation. However, little is known about the transition from partial to strong reproductive isolation (RI) and the completion of speciation. In my BSc with Sih Kahono and Tri Atmowidi, we use lab and field experimental manipulation to quantify multiple potential isolating barriers beyond the first barriers using Southeast Asian ladybird beetle H. diekei populations at the later phases of divergence.
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