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Biodiversity and genetic impacts of low impact logging in Peru

Supervisor: Prof. Chris Jiggins

Project summary:

The project has two main goals, to study the impacts of sustainable logging on individual species abundances and phylogenetic diversity. The project will involve setting up a butterfly monitoring programme using trapping and transect methods to investigate the impact of logging activities on butterfly diversity in one of the most species-rich areas of the world. We have detailed records of the past logging activities in the concession and can therefore measure the forest biodiversity recovery throughout time and with varying levels of logging intensity. The project will investigate phylogenetic diversity changes after logging using genomic approaches, by whole genome sequencing and population sampling.

As tropical forests are increasingly impacted by human activities, it is important to identify sustainable approaches to exploiting the remaining forests, while protecting biodiversity. To do so it is crucial to understand how different species groups respond to disturbance, and identify which are at most risk of going extinct. This project will work with a logging company, GreenGold Forestry in Peru that runs a large logging concession with low levels of timber extraction and is intended to be 'sustainable’. An important part of their logging approach, and essential for obtaining sustainability certificates, is to ensure that their practices will minimise long-lasting impacts on biodiversity, such as local extinction of phylogenetically distinct and charismatic groups. The project has two main goals, to study the impacts of sustainable logging on individual species abundances and phylogenetic diversity, and to build on from this knowledge and published studies to design logging management strategies that minimise these impacts.

What the student will be doing:

The student will work extensively in Peru at the Iquitos logging concession. They will work with local people to help establish the butterfly monitoring scheme. This will be coordinated with an existing project in Ecuador where long term butterfly monitoring is already underway in the Yasuni National Park. We have detailed records of the past logging activities in the concession and can therefore measure the impact of different ages and levels of logging ondiversity. This will allow plots to be established in logged regions of different ages, and potentially also before and after logging. 

The student will then use genomic approaches to study the butterfly populations. Reference genomes will be sequenced for a few selected taxa and resequenced data obtained for population samples from Peru and Ecuador. Data will be mapped to the reference genomes to relate extinction probability to genomic characteristics and genetic variability within populations. We will also search for signatures of hybridisation and introgression between species to characterise genetic variation in different lineages. Overall there is scope for this project to go in different directions depending on interests.

The student will learn methods for sampling butterflies in the rainforest in South America, coordinated with a consortium also based in Ecuador. The student will learn project management skills to coordinate the project in challenging conditions. The student will also learn genomics techniques for studying the genetic variation in natural populations. This will include bioinformatic methods for de novo assembly of genome sequences and coding skills for analysis of large data sets. The host group has considerable expertise in genomics and analysis of large genome data sets.

References:

Montejo-Kovacevich G, Hethcoat MG, Lim FKS, et al. 2018. Impacts of selective logging management on butterflies in the Amazon. Biological Conservation 225: 1–9.

The Heliconius Genome Consortium. 2012. Butterfly genome reveals promiscuous exchange of mimicry adaptations among species. Nature 487: 94–98.