Group projects are planned to run throughout the entire workshop, from Tuesday, September 29th to Wednesday, October 7th. These mostly involve re-analyzing previously published data to address new, unanswered questions and apply techniques and concepts covered throughout the workshop. Each group will consist of three participants of mixed town and university origins. Each group will choose a subject from the list of projects detailed below. They will first form questions and/or hypotheses from the project description and the literature. Second, they will develop and implement a structured population genomic analytical approach to answer the raised question(s). Finally, they will write a very short report and prepare a final presentation with visual support to defend their work on Wednesday, October 7th, the last day of the workshop. Each group will be supervised/mentored by at least one member of the teaching team and of the guest professors.

Project 1 - Revisiting Varecia variegata landscape genetics!

The effects of landscape features on the genetic diversity and differentiation of Varecia variegata have been studied at several scales using resistanceGA. This project aims to revisit these effects using new modeling and surface optimization approaches, as well as including new/other/additional landscape variables.

Project 2 - What influenced the demographic history of bottlenose dolphins?

In contrast to the Mediterranean, which humans have occupied for tens of thousands of years, the Azores archipelago was colonized by humans very recently. Since human colonization of the Atlantic islands, marine mammals have been severely impacted by whaling and fishery activities. The project will evaluate the relative role of climate, hunter-gatherer settlements, the first large civilization, early medieval settlers (700–850 CE), and Portuguese Colonization (15th Century Onward) on the demographic fluctuations of the Mediterranean and Azorean bottlenose dolphin populations.

Project 3 - Have north-eastern lemurs been affected by deforestation?

Van Elst et al. (2025, Mol Ecol) have studied the landscape genetics of north-eastern lemurs extensively. However, van Elst did not assess the effect of recent documented deforestation (i.e., 1950-2026, e.g., Vieilledent et al., 2018) on the lemur populations of northeastern Madagascar. The project intends to reuse the RAD data from van Elst et al., 2025 to assess the forest loss and fragmentation effect on the genetic diversity and differentiation of northeastern lemurs.

Project 4 - Are Indian Ocean white-eyes subject to inbreeding?

White-eyes (Zosterops) are widespread birds found in Africa, Asia, Australasia, and many islands of the Indian and Pacific Oceans. Islands can be particularly interesting systems for studying genetic diversity and inbreeding because geographic isolation and small population sizes may increase genetic drift and reduce genetic diversity. On Réunion Island, the Réunion grey white-eye (Zosterops borbonicus) is divided into four geographically differentiated forms. Although their population structure and demographic history have been studied, less is known about their genomic inbreeding and genetic load.

Project 5 - Are Réunion Island white-eyes influenced by landscape features?

White-eyes (Zosterops) are common birds on Réunion Island. The Réunion grey white-eye (Zosterops borbonicus) is divided into four geographically differentiated forms, whose population structure and demographic history have been extensively studied. However, less is known about how the landscape of Réunion Island influences gene flow and genetic differentiation among populations. The volcanic landscape of Réunion is characterized by strong variation in elevation, vegetation, and habitat, which may affect the movement and connectivity of birds. This project will investigate whether genetic differentiation among Z. borbonicus populations is related to geographic distance and/or to specific landscape features.

Project 6 - Are blue sharks affected by seascape components?

The blue shark Prionace glauca is a top predator with one of the widest geographical distributions of any shark species. It is classified as Critically Endangered in the Mediterranean Sea and Near Threatened globally. Several genetic studies did not detect population structure. Nikolic et al., using blue shark samples from its global range, identified two main groups, with Mediterranean Sea and northern Atlantic samples (Northern population) differentiated significantly from the Indo-West Pacific samples (Southern population). Here we will evaluate which seascape features affect connectivity and influence the genetic population structure of the blue shark.

Project 7 - Are invasive Rattus populations of Haida Gwaii archipelago inbred?

Invasive species suffer from founder effects that limit their diversity. Here we will use data from rats that sequentially invaded subsequent islands in the Haida Gwaii archipelago, further away from the continent. We will study this stepping-stone repeated founder effect to assess whether the last immigrating populations accumulated higher levels of long runs of homozygosity (ROH).

Project 8 - Are Aristida similis and Aristida rufescens separate species or one species with high morphological variation associated with environmental variation?

The grasses and grasslands of Madagascar are sometimes controversial. Determining which grasslands are natural and which are Anthropogenic can have practical consequences on the management of protected areas and species. The evolution of endemic fire-adapted grass species would be more in favor of a natural origin hypothesis. Two common C4 tussock-forming grasses with fire-adaptions are the closely-related Aristida similis Steud. and Aristida rufescens Steud. While both species are accepted, an alternative hypothesis is that the taxonomy reflects morphology associated with environmental variation rather than true species boundaries. Basic analyses of population structure for a sample of these two named species would be insightful as to whether one species should be synonymized, and further demographic analyses on the species could be helpful for understanding the extent of grassy ecosystems through time.

  • Data: Unpublished target-enrichment data from a few hundred probes designed to work across angiosperms.
  • Data paper: Breinholt et al. 2021 provide an overview of the type of data.
  • Method papers: Tiley et al. 2023 show that the type of target-enrichment data used here, while limiting for some types of demographic modeling, can be useful for basic assessments of population structure and potentially species delimitation analyses.
  • Case study papers: Tiley et al. 2023 show the basic analyses that should be feasible for this project, which align well with the practical activities. Additional background reading on the organism can be found in Besnard et al. 2014 and Cerros-Tlatipla et al. 2011.
  • Link to the drive folder
  • Path in the cluster: /work/projects/madagene/mwcgls/data/mini_projects/Project_8_Aristida

Project 9 - Are there undescribed Dalbergia species in Madagascar or are they relicts from fragmentation?

Dalbergia spp. (Fabaceae) are highly desirable rosewoods, with many species threatened or endangered due to unsustainable logging, habitat loss, and poaching. Like many endemic radiations within Madagascar, species diversity may be underdescribed and an understanding of genetic diversity within and between species is important for the conservation and management of natural resources. Crameri et al. (2022) found genetic substructure within D. monticola and D. orientalis. General analyses of genetic variation/heterozygosities were not done and may be insightful regarding species hypotheses and identifying if such structure was due to fragmentation of historically more contiguous populations, and if fragmentation is more attributed to anthropogenic activities or paleoclimate.

  • Data: Target enrichment data from a set of approximately 2400 Dalbergia-specific probes. The data in the supplied VCF has 51 individuals from at least two named species.
  • Data paper: Crameri et al. 2022
  • Method papers: The population genetic components of this paper only did some basic analyses of population structure. Questions about the effects of fragmentation on genetic variation and sustainability of populations remain. Because the individual GPS points are obscured, this creates some challenges to analysis and interpretation, but analysis by region or ecoregion should be possible.

  • Case study papers: Additional examples of conservation genetic analyses with target-enrichment data for tree species includes Dauphin et al. 2020. Related to the mini-project data, detecting signatures of selection or demographic processes affecting the efficacy of selection could be options.

  • Link to the drive folder
  • Path in the cluster: /work/projects/madagene/mwcgls/data/mini_projects/Project_9_Dalbergia

Record your group’s composition and 2-3 prefered subject per group in the following document: