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Speciation and hybridization: a sex chromosome perspective

Periodic Reporting for period 1 - Hybrid Conflicts (Speciation and hybridization: a sex chromosome perspective)

Período documentado: 2018-03-01 hasta 2020-02-29

Speciation is frequent and ongoing, and has resulted in millions of species. Nevertheless, the speciation process has proven difficult to disentangle because several evolutionary processes—including genetic drift, selection and admixture—may co-occur during divergence, leaving similar genomic footprints. Here, we address what happens genetically when a pair of closely related sister species of damselflies meet in secondary contact. We are particularly interested in whether genes located on the sex chromosome play a key role for evolution of reproductive isolation during hybridization and speciation.

The central theme of this project—the origin of species boundaries in two hybridizing sister insect species—is a hot topic of discussion in the scientific as well as the non-scientific society. Evolution happening on an ecological timescale is not well understood by the community, yet speaks to the imagination. Also the origin of species is a classic theme in biology, which can be associated with the founding father of evolutionary biology, Charles Darwin. Therefore, our research and its possible outcomes will captivate a broad interest.

The overall objective of this research is to determine the factors that lead to heterogeneity in genomic divergence between species and the characterisation of loci that are associated with pre- and postzygotic barriers to gene exchange. Specifically, we seek to clarify the role of sexual selection and the X-chromosome in the origin of reproductive barriers across the recently established hybrid zone of a pair of damselfly sister species (Ischnura elegans and I. graellsii). Closely related hybridizing species offer the possibility unique insights into the role of ecology and gene flow in the speciation process.
We firstly assembled and annotated the genome of the damselfy Ischnura elegans and for the first time identified X-linked loci within odonates. Our results revealed orthologous relationships between X-linked genes of I. elegans, which is an extant representative of an ancestral insect lineage, and (X-) chromosome regions of more derived insect lineages (manuscript under review). Secondly, we performed a genome-wide genotype (RADseq) analysis using individuals from both allopatric and sympatric populations in Spain to estimate degree of hybridization and overall introgression patterns. This showed that some I. graellsii individuals originate from an admixed population presumably subjected to introgression from I. elegans into I. graellsii (in contrast to the previously recorded introgression from I. graellsii into I. elegans). Using resequencing we are able to assess – for the first time – introgression into I. graellsii across the whole genome (in preparation). Using mating experiments we show, however, that reproductive barriers are stronger in I. graellsii than in I. elegans. Overall, premating isolation was higher than other barriers (in preparation).

Multiple sympatric zones in Spain have been sampled for subsequent genomic analyses using RADseq. These results suggest the presence of hybrids from different crosses (F1, F2 and backcrosses) in all sympatry regions. Introgression levels were detected to be low in Central Spain and relatively high in the western part of Spain. No difference was detected between autosomal and X-linked genomic windows. This data has been supplemented with a RADseq dataset of 120 extra individuals from Spain comprising extra geographical hybrid zones and allopatric I. elegans populations from Europe (in preparation). Using a RADseq dataset comprising temporal samples from the oldest hybrid zone in western Spain, we also plan to assess the introgression dynamics and temporal progression of introgression at autosomal and sex-chromosome loci (in preparation).

In parallel, a pedigree has been constructed to identify genes of sexually and naturally selected traits in a hybrid pedigree. Offspring will be genotyped for genome-wide distributed SNPs, using RADseq genotyping to perform a QTL analysis (in preparation). Ultimately, we will screen the panel of mapped candidate genes across populations of the hybrid zone (with already available RADseq genomic data), which will enable us to compare population genetic structure at these characterised genes with the genome-wide population structure. This will allow us to test the hypothesis whether “speciation genes” can be more often found on the X chromosome and determine the factors leading to heterogeneity in genomic divergence between species.
This is one of the first projects to use ecological and genomic tools to tease apart the many forces that direct the evolution of reproductive barriers. The project is innovative in its use of varied experimental approaches, which we expect will significantly advance our understanding of the processes leading to species mixing and the origin of species.

Expected results include understanding the role of sexual selection, sexual conflict and X-linkage in the heterogeneity in genomic divergence, i.e. something that is rather unexplored. Moreover, we expect to disentangling the forces involved in the evolution of reproductive barriers. These forces are generally only examined in isolation and often in allopatric parental species instead of hybrid zones. This work takes an important step towards untangling multiple effects by taking selection and ecological effects into account and by examining a hybrid zone with populations that vary in their timing of sympatry.

Additional impact of this work includes contribution to the foundation of a new genetic model system to study speciation in nature. Although hybridisation dynamics of I. elegans and I. graellsii has been investigated previously, new genomic resources that have been developed will open the path for future in-depth studies of speciation and pinpoint the roles of individual genes. A new system is much needed because most of the work has focused on model organisms such as Drosophila where we have little knowledge about ecology.

The project also provides crucial information for applied science related to the preservation of biodiversity in Europe. Because anthropogenic forces cause rapid environmental changes, it is essential to understand how hybridization between introduced and native species progresses as this can cause problems in conservation. Finally, we hope that our work will contribute to Europe’s excellence in ecological genomics by employing a multidisciplinary research approach that draws upon techniques used in both ecology and genomics.
Distribution range and population genetic structure in Ischnura elegans and I. gaellsii
Comparative genomics of X-linked genes in insects
Genome assembly of Ischnura elegans