MADGRASS

Population Dynamics of Polyploids: Testing the Mechanisms of grassland expansion in Madagascar (MADGRASS) is the fellowship awarded by the Marie Sklodowska-Curie Actions (MSCA-IF-EF-ST 101026923) to investigate the origins and extend of Madagascar’s grasslands. This funding also supports development of bioinformatic tools for the analysis of polyploids with phylogenetic networks and population genomic demographic modeling. The project started 10 January 2022 and ended 10 January 2024.

Understanding Grassland Expansions through Population Genetics and Distribution Models

Some of the first products of MADGRASS are getting published:

1. The first is a pilot investigation of genetic variation within Loudetia simplex. We show how some analyses of population genetic structure are robust to ploidy level variation and provide bioinformatic tools for correctly accounting for dosage variation in polyploids. We also touch on the prospects of target-enrichment data for polyploids. While I would not generally recommend it, the truth is that there is now a lot of target-enrichment data available and it should be useful in some limited cases, especially over older data types such a microsatellites. The paper is open-access and available here.
   
   
2. A rigorous investigation of morphology and distribution models for Loudetia simplex across Africa, led by a Malagasy MSc student. She predicts regions of Madagascar where L. simplex is expected based on other occurrences in relevant botanical regions in mainland Africa. There is strong agreement on the Central Highlands of Madagascar as suitable habitat, but maps can also serve as a resource to land managers to understand where grasslands may expand, raising the need for communication between grassland and forest managers. A preprint is available online.
   

MADGRASS attracts more funding

The prospects of developing genotyping and phasing resources for polyploids has helped secure funding for the sequencing and assembly of a Loudetia simplex reference genome from the NERC Environmental Omics Facility (NEOF1435). The MADGRASS team looks forward to seeing Loudetia simplex contribute to other large-scale genomic investigations in addition to fulfilling our immediate population genomic goals. An additional round of funding from the from the NERC Environmental Omics Facility (NEOF1506) has increased our capacity to generate ddRADseq data for more populations and extend inferences to continental African grasslands in addition to Madagascar.

The 2022 Field Season

Field work commenced on 11 March 2022 and ended 2 April 2022. Researchers representing both the Kew Madagascar Conservation Center and the Parc Botanique et Zoologique de Tsimbazaza and I traveled west from Antananarivo towards Morondava. Sampling occurred in unprotected areas and in the protected Kirindy and Andranomena national parks where open habitats could be found. Collections resulted in 219 vouchered specimens along with their silica-dried DNA samples. Some vouchers are tied to population-level silica samples, including 7 populations of Loudetia simplex. Ecological data was also collected to quantify species abundance and diversity at 13 sites.

Field site near Miandrivazo, Madagascar.

Phylogenomics Workshop at the University of Antananarivo

From 7 March to 9 March 2022, I led a phylogenomics workshop hosted by the department of plant biology and ecology. We introduced the theoretical background of basic maximum likelihood and multispecies coalescent analyses, along with real-time labs to build computational skills. Participants included MSc and PhD students as well as some curious postdocs and faculty.

Deriving transition probabilities at the DBEV phylogenomics workshop.

Abstract

As a consequence of anthropogenic climate change, it has been hypothesized that human-mediated deforestation degraded closed-canopy forest into grasslands dominated by fire- and grazing-resistant grasses. There is accumulating evidence, however, that tropical grasslands are natural biomes with origins that predate human activities. The extent to which grasslands have expanded and contracted in response to natural climate cycles versus more recent agricultural practices remains an open question and is the motivation for the proposed research. MADGRASS focuses on the grasslands of central Madagascar, because identifying ancient grasslands and protecting them is of urgent conservation interest. Population genomic methods and novel bioinformatic approaches will be used to test demographic hypotheses that will identify the timing of grassland expansions and contractions, population structure, and gene flow between populations. Research goals are made possible by recent advances in the analysis of polyploid species, which will be implemented through MADGRASS. There are direct conservation policy outcomes expected from MADGRASS. Currently, tree-planting programs are attempting to re-forest the grasslands of central Madagascar. These programs often include invasive tree species that grow quickly and require more water than is available, which can unintentionally lead to increased frequency and intensity of fires and overall detrimental outcomes. We will identify the range of Madagascar’s natural grasslands that should be protected. Results will also be used to identify which grasslands should be released from protected status for community and commercial use, building respect and trust with local Malagasy people. All aspects of the proposed research will be conducted in close collaboration with Malagasy colleagues and include specific outreach activities for both local communities in Madagascar and broader scientific and lay groups.