Does hybridisation promote tree species diversification in the Amazon?

Lead Research Organisation: UNIVERSITY OF EXETER
Department Name: Geography

Abstract

The Amazon rain forest holds the highest diversity of plant species on Earth, but the mechanisms which gave rise to this superlative diversity remain enigmatic. A long-held view, first proposed by Alfred Russell Wallace, was that this diversity reflected gradual accumulation of species over long geological periods due to minimal extinction. However, more recent studies point to a large contribution of rapid and recent formation of new species of some groups of trees. Inga, the focus of this proposal, is an exemplar for these recent evolutionary radiations, having evolved at least 300 species in the last 6 million years in the Amazon and other Latin American rain forests. Moreover, in Amazonia hundreds of tree species can coexist in a single hectare (up to 300), and this extremely high local diversity is largely accounted for by a few species-rich genera such as Inga. The high overall and local diversity of Amazonian forests suggests parallels with other species-rich systems where evolutionary radiation - the rapid rise of many species from one ancestor population - produced many new lineages. Here, we aim to develop Inga as a model for plant species radiation in Amazonia, building global examples beyond animals (e.g. Darwin's finches, rift lake cichlid fishes) and a few plant groups that are geographically restricted (e.g. Hawaiian silverswords), or non-tropical (e.g. Andean lupins).

In particular, we will investigate the role of hybridization, the interbreeding between groups of species, as recent work shows it is a major cause of evolutionary radiations. Hybridization's effect on evolutionary radiation has not yet been studied within tropical trees, despite being widely acknowledged as a powerful creative force in plant evolution. Hybridization generates morphological and genetic novelty, impacting the rate of speciation in many groups and is evident in all major adaptive radiation events for which multiple sequenced genomes exist. In plants, one mechanism of speciation, polyploidy or the doubling of genome size, which is often linked with hybridisation, is known to be particularly important. While the prevailing view has been that hybridization between tropical tree species is exceptionally rare, this view is challenged by recent DNA sequence data. In Inga, hybridization has been recently demonstrated to occur, despite prior reports of species intersterility, and a few chromosome counts have demonstrated that unrelated species are polyploid.

Here, using new genomic techniques for the first time in Amazonian trees, we aim to test the significance of hybridization and polyploidy in Inga diversification. We will use DNA sequences for 810 genes generated by the target capture technique to find signatures of hybridisation and polyploidy across all 300 Inga species. Because insect herbivore pressure demonstrably structures local Inga communities at fine spatial scales, we suspect that a powerful selective factor driving divergence among Inga species may be chemical defences. We will therefore search for signatures of selection among 113 chemical defence gene regions in our target capture gene set. We will then generate whole-genome data for multiple populations of a select number of widespread Inga species to determine whether groups of chemical defence genes are transferred together during hybridization in 'linkage blocks', thereby facilitating the movement of adaptive variation between species. Finally, we will use our target capture data to identify possible polyploid Inga species and use genome sequencing to discover if they are the result of hybridisation and genome doubling (allopolyploidy) or genome doubling without hybridisation (autopolyploidy).

This project will improve our understanding of the evolution of a large portion of Amazonian tree diversity, because Inga is an exemplar for other species-rich tree genera that have high local species diversity and underwent similar recent evolution.

Publications

10 25 50
 
Description We have so far discovered genomic evidence of hybridisation (i.e. interbreeding between species) across multiple Inga species. This is interesting because hybridisation was previously assumed to be negligible in tropical trees, but evidence is emerging that it is fairly common.
Exploitation Route We aim to more deeply investigate whether chemical defence loci are passed between species leading to speciation, or whether they remain divergent between species and act as barriers between them. Characterising the genomic underpinnings of chemical defence against herbivores could also be of significant interest to those using Inga, which is the most commonly used Neotropical tree for agroforestry and ecological restoration.
Sectors Agriculture

Food and Drink

Environment

 
Title Chromosomally contguous genome for Inga oerstediana 
Description Genome generated by Project Partner Wellcome Sanger Institute for Inga oerstediana 
Type Of Material Database/Collection of data 
Year Produced 2024 
Provided To Others? Yes  
Impact none yet 
URL https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_963210345.1/
 
Title Chromosomally contguous genome for species in the genus Inga 
Description Genome generated by project partners at the Sanger Centre from living plants held to Royal Botanic Garden Edinburgh, for Inga leiocalycina 
Type Of Material Database/Collection of data 
Year Produced 2024 
Provided To Others? Yes  
Impact None yet as genomes just published 
URL https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_963242795.1/
 
Description Collaboration with Dr Maria-Jose Endara and Dr Dale Forrister 
Organisation Smithsonian Institution
Department Smithsonian Tropical Research Institute
Country Panama 
Sector Academic/University 
PI Contribution We have generated whole-genome resequencing data for >530 trees from >40 Inga species. This interdigitates well with the decades of ecological and metabolomic data utilised and produced by Dr Endara and Dr Forrister, as well as by their forebears Prof. Phyllis Coley and Prof. Thomas Kursar.
Collaborator Contribution Dr Endara and Dr Forrister, as well as by their forebears Prof. Phyllis Coley and Prof. Thomas Kursar, produced large volumes of metabolomic data in many of the same populations (and often for the same individuals) for which we have produced whole-genome data. This allows us to perform analyses in unequalled depth of how genomes, defence chemistry and ecological interactions bring about the superlative species-richness of Neotropical tree communities. In addition, Dr Endara was instrumental in teaching co-I Schley how to identify Inga species in the field.
Impact Co-I Schley is writing a NERC IR fellowship application with Dr Endara as a collaborator.
Start Year 2021
 
Description Collaboration with Dr Maria-Jose Endara and Dr Dale Forrister 
Organisation Universidad de Las Américas
Country Ecuador 
Sector Academic/University 
PI Contribution We have generated whole-genome resequencing data for >530 trees from >40 Inga species. This interdigitates well with the decades of ecological and metabolomic data utilised and produced by Dr Endara and Dr Forrister, as well as by their forebears Prof. Phyllis Coley and Prof. Thomas Kursar.
Collaborator Contribution Dr Endara and Dr Forrister, as well as by their forebears Prof. Phyllis Coley and Prof. Thomas Kursar, produced large volumes of metabolomic data in many of the same populations (and often for the same individuals) for which we have produced whole-genome data. This allows us to perform analyses in unequalled depth of how genomes, defence chemistry and ecological interactions bring about the superlative species-richness of Neotropical tree communities. In addition, Dr Endara was instrumental in teaching co-I Schley how to identify Inga species in the field.
Impact Co-I Schley is writing a NERC IR fellowship application with Dr Endara as a collaborator.
Start Year 2021
 
Description 8th International Legume conference, Pirenopolis, Brazil, invited presentation: "Inga as a model for the evolutionary radiation in tropical rain forest trees" 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Invited conference talk, which brought many questions from the audience, especically from Brazilian scientists who wish to adopt some of the analytical approaches suggested
Year(s) Of Engagement Activity 2023
 
Description Invited conference talk, Association of Tropical Biology and Conservation, Cartgena, Colombia "Continuous colonisation of the Atlantic Coastal Rain Forests of South America from Amazonia" 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Invited conference talk with considerable discussion afterwards
Year(s) Of Engagement Activity 2022
 
Description Invited presentation, 8th International Legume conference, Pirenopolis, Brazil: "The potential of silvopastoral systems incorporating legume trees in the Brazilian Amazon's 'arc of deforestation'" 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Invited conference talk that stimulated debate and questions. Being given in Brazil but to an international audience was a great venue to communicate the significance and impact of our work
Year(s) Of Engagement Activity 2023
 
Description Invited seminar, Rio de Janeiro Botanical Gardn: "Inga as a model for the evolutionary radiation in tropical rain forest trees" 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Postgraduate students
Results and Impact Invited seminar in the graduate school at Rio de Janeiro Botanical Garden. The venue and format allowed extensive discussion. Students reported great interest in following some of the analytical approaches suggested
Year(s) Of Engagement Activity 2023
 
Description Invited speaker. Association for Tropical Biology and Conservation, Cartagena, Colombia. "The potential of silvopastoral systems in the Brazilian Amazon's 'arc of deforestation" 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Invited conference talk. Resulted in invitations for further collaborative activity in this area
Year(s) Of Engagement Activity 2022