ESR1: Polyploid phylogenetics under the multispecies coalescent

In short

We have all stopped in front of a garden to admire different flowers, their different colours, and sometimes their amazing shapes. It is the diversity of species that makes them particularly appealing and interesting. But what is a species exactly? Can we just trust the morphology to define a species? The emergence of genetic and multilocus approaches have shown that species delimitation is not as straightforward as it looks.
My project is about a fundamental question in biology and evolution: how can we reach a better understanding of species evolutionary history and species delimitation? Indeed, for many years scientists have been debating about the concept of species and species trees uncertainties. During my PhD, I will use a mathematical model, the multispecies coalescent (MSC), to address this major issue. However, I will explore another important aspect of biology by applying the MSC to polyploid species, polyploidy being the inheritable condition of having more than two complete sets of chromosomes. This trait has arisen in all angiosperms history and seems to be underestimated in animals: regarding the high frequency of polyploidization events in so many species, it is essential to include this phenomena in the debate about species delimitation and phylogenetic inferences.
To reach these very exciting goals, I will focus on the section Physolychnis within the very species-rich genus Silene, spread all across the globe: Physolychnis is a good study model because it counts many polyploids and some preliminary studies have already been published on this group.

Project description

Polyploidy is an important process in plants, accounting for a large proportion of speciation events. Many important crops are polyploid. We have previously contributed to the methodology where multi-locus sequence data can be used to infer the phylogenetic networks, while gene tree variation due to multispecies coalescent (MSC) stochasticity is taken into account. In the MSC model, species have a precise mathematical definition, which is fundamentally different from species as a taxonomic rank. For diploids, we have used the MSC model to account for uncertainties in species delimitation. In this project, we will merge these two models in order to reconstruct the phylogenetic history of Silene sect. Physolychnis. Previous work has revealed the general pattern by which the polyploids have formed, and in this project we will identify the number of polyploid hybridizations between MSC lineages, as well as the extant MSC lineages.

Objective: A phylogenetic network depicting the speciation events in arctic members of Silene sect. Physolychnis. This will provide underlying information for an updated taxonomy of the group. A database of DNA sequences that can be used for identification of DNA extracted from for example ice/soil samples will be produced, enabling reliable taxon identification and dating of polyploidization events.

Research output

Presentations

Quatela Anne-Sophie.Exploring the utility and limits of target enrichment methods to study polyploidy and reticulate evolution. At: Botany 2020 (Virtual). Hosted by the American Botanical Society. 27-31 July 2020.

Quatela A-S, Oxelman B, Bacon C, de Boer H, 2019. Long read sequencing unravels polyploids evolution. At: Systematic Days. Gothenburg, Sweden. 18-19 November 2019.

Cangren P, Jafari F, Moiloa N, Quatela A-S, Bacon C, Oxelman B, 2019. How long reads sequencing technologies enable reaching a double challenge in polyploid complexes: species delimitation by target capture from old herbarium specimens. At: Botany 2019. Tucson, Arizona, USA. 27-31 July 2019.

Oxelman B, 2019. Species delimitation under the multi-species coalescent and its assumptions. At: 45th Annual Congress of the South African Association of Botanists. Johannesburg, South Africa. 8-11 January 2019.

Quatela A-S, 2018. Species delimitation in polyploids under the multi-species coalescent. At: PhD day. University of Gothenburg, Gothenburg, Sweden. 12 December 2018.

Quatela, Anne-Sophie. Polyploid species, the Achilles’ heel ​ of molecular taxonomy?​ ​​ A study case of (sub)arctic Silene sect. Physolychnis. Given at the Plant ID Seminar Series Molecular identification of plants for science and society, Series 2:  Modern tools and old methods: Descriptive taxonomy and phylogeny (hosted by NHM, UiO, Oslo, Norway). 25 March 2021. 

Posters

Quatela A-S, 2018. Species delimitation and polyploidy. At: Poster conference. Faculty of Science, University of Gothenburg, Gothenburg, Sweden. 19 October 2018.