Abstract Detail

Phylogenomics

Gagnon, Edeline [1], Hilgenhof, Rebecca [2], Orejuela, Andrés [2], Sablok, Gaurav [3], Aubriot, Xavier [4], Giacomin, Leandro [5], Gouvêa, Yuri [6], Bohs, Lynn [7], Dodsworth, Steven [8], Maurin, Olivier [9], Forest, Félix [10], Poczai, Péter [11], Knapp, Sandra [12], Särkinen, Tiina [2].

Phylogenomic data reveals hard polytomies in the large genus Solanum (Solanaceae).

The increasing availability of phylogenomic data is revealing incongruent topologies in gene trees between and even within genomes. Some of these incongruences indicate hard polytomies that are due to underlying biological processes may remain impossible to fully resolve. The incongruent topologies and hard polytomies will mean that multiple, alternative topologies will have to be used to explore macro-evolutionary patterns. Here we focus on the large and economically important genus Solanum which with 1,230 accepted species, is one of the ten largest flowering plant genera. To provide an evolutionary framework for the large research community working on the genus, we build a new supermatrix phylogeny comprising 61% of all accepted species (750 spp.), based on two nuclear (ITS and WAXY) and seven plastid markers. To assess whether the recovered topology is robust, we explore phylogenomic analyses of a full plastome alignment of 141 species and nuclear genome dataset, composed of a target-capture dataset of 14 species based on the Angiosperm353 probes and supplemented from data extracted from published genomes and transcriptomes (c. eight species). Both datasets contain species from all the major recognized lineages within the genus, and we explore how various taxon sampling, missing data, phylogenetic analyses, and data partitions influence the topology of the recovered species tree. A single strongly supported topology is recovered from the different plastome phylogenomic analyses, which is incongruent with the topology recovered from the supermatrix phylogeny. Phylogenomic analyses of the Angiosperm353 target capture data will allow us to determine the potential reasons for the incongruence. We measure the distribution of phylogenetic signal from different genes and sites supporting these alternative topologies and discuss the biological significance of these various hypotheses. This highlights how such topological uncertainty should be incorporated in downstream macro-evolutionary and ecological analyses because it potentially reflects non-bifurcating evolution.

1 - Royal Botanic Garden of Edinburgh, Tropical Science , 20A Inverleith Row, Edinburgh, Eh5 2AB, UK
2 - Royal Botanic Garden of Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5LR, Royaume-Uni
3 - University of Helsinki, Helsinki, PO Box 7 FI-00014 , Finland
4 - Université Paris-Saclay, CNRS, AgroParisTech, Ecologie Systématique et Evolution, Orsay, 91405, France
5 - Instituto de Ciências e Tecnologia das Águas & Herbário HSTM, Unive, Av. Mendonça Furtado, 2946, Santarém, PA, CEP 68040-050, , Brazil
6 - Instituto de Ciências Biológicas, Universidade Federal de Minas Gera, Departamento de Botânica,, Av. Antônio Carlos, 6627, Pampulha, Belo Horizonte, MG, CEP 31270-901, Brazil
7 - University Of Utah, Department Of Biology, 257 South 1400 East Room 201, Salt Lake City, UT, 84112.0, United States
8 - University of Bedfordshire, School of Life Sciences, University Square, Luton , LU1 3JU, UK
9 - Kew Royal Botanic Gardens, Richmond, Surrey, TW9 3AE, UK
10 - Royal Botanic Gardens, Kew, Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
11 - Finnish Museum of Natural History, University of Helsinki, Botany Unit, Helsinki, PO Box 7 FI-00014 , Finland
12 - Natural History Museum, Plants Division, Life Sciences, Cromwell Road, London, SW7 5BD, United Kingdom

Keywords:
Solanaceae
PAFTOL
Solanales.

Presentation Type: Oral Paper
Session: PHYL1, Phylogenomics I
Location: Virtual/Virtual
Date: Monday, July 27th, 2020
Time: 1:30 PM
Number: PHYL1005
Abstract ID:216
Candidate for Awards:None