Phylogenomics of endangered and threatened species of grasses reveal close phylogenetic relationships

Blog written by P. H. Pischl, S.V. Burke, E. M. Bach, and M. R. Duvall.  Read the full paper here.

Biodiversity is the variety of life forms on Earth, and includes the variation seen in animals, plants, fungi, and microorganisms.  A major cause for a decrease in biodiversity is loss of a species’ home or habitat.  Habitats are being lost by the conversion of natural areas to urban and agricultural lands by humans.  As habitats are lost, species and ecosystems (the community of living organisms and the place where they live) become threatened or endangered as their numbers and area decrease.

At The Nature Conservancy’s Nachusa Grasslands, grazing bison are partly obscured in the September tallgrass prairie.  Photo by P. H. Pischl.

One of the most endangered ecosystems in North America is the tallgrass prairie.  Illinois is nicknamed the “Prairie State” because it was once covered in tallgrass prairies.  However, since 1830 when European settlement began, 99.9% of Illinois’ original tallgrass prairies have been lost to agriculture, industry, and urbanization (Ellis, 2017).  The removal of the tallgrass prairie habitat has caused seventeen species of grasses to be listed as endangered and one species to be listed as threatened by the Illinois Environmental Species Protection Board.  Grasses provide many ecosystem services, such as erosion control, soil formation, habitat for wildlife and carbon storage.  Loss of these endangered and threatened species would result in a loss of ecosystem services as well as a loss of biodiversity.

Ecologists and conservation biologists work to preserve biodiversity by conserving the various species in a region or an ecosystem.  They not only look at the number of species, but also consider the phylogenetic diversity between the species in the ecosystem.  The phylogenetic diversity compares the DNA of the species in the ecosystem to better understand the variation in genetic background of the species.  This genetic variation is seen in the traits the species have or do not have in common.  Plant communities with greater genetic variation are considered to have higher phylogenetic diversity.  Plant communities with higher phylogenetic diversity have been shown to be more productive and resistant to invasion by nonnative species (Barak, 2017).  Plant communities that are more closely related and exhibit less phylogenetic diversity may share traits that make them more vulnerable to the same threat.  These species are considered to be at a higher risk of extirpation from the ecosystem by habitat loss or changes in environmental conditions.

Leaf tissue was obtained from preserved herbarium specimens for DNA extraction.  Photo by M. R. Duvall.

In our article in Ecology and Evolution, we study the phylogenetic diversity of the endangered and threatened species of grasses from Illinois.  However, in order to study phylogenetic diversity, it is necessary to extract DNA from the species of interest.  Since these species are endangered and threatened, we were able to refine our methods to use preserved grass tissue from herbarium specimens.  The use of herbarium specimens avoided the disturbance of living populations of the endangered or threatened grasses.  From the extracted DNA, we were able to use Next Generation Sequencing techniques to sequence the complete plastid genomes for the endangered and threatened species of grass.  Our use of the complete plastid genome in our analysis leads to phylogenetic trees with greater support than studies using gene coding sequences alone.  We then analyzed these phylogenetic trees with three phylogenetic diversity metrics to relate the evolutionary history of the species to their ecological characteristics.  All of these phylogenetic diversity metric values show that the endangered and threatened species are phylogenetically clustered at evolutionary points in both past and more recent events.  Phylogenetic clustering means that these species may be more closely related than expected by chance and share traits that make them vulnerable to the same threats.  Phylogenetic clustering is indicative of phylogenetic niche conservatism.  Should these species be lost from the landscape, several small groups of native grass diversity would be lost. 

In our study, we have shown how herbarium material is useful for ecological research, allowing the study of endangered and threatened species without disturbing the few remaining populations.  DNA extracted from the herbarium material was used to produce complete plastid genome sequences using Next Generation Sequencing techniques.  The complete plastomes from species of grasses known to grow in Illinois provided a robust and strongly supported phylogeny.  Communities of grasses in Illinois were evaluated using three phylogenetic diversity metrics.  The three phylogenetic diversity metrics all led to the same result; the endangered and threatened species are phylogenetically clustered, which can be interpreted as phylogenetic niche conservatism of these grasses.  The loss of the endangered and threatened species and the genetic biodiversity they supply would also lead to changes in ecosystem services and protection from invasive species.  The niches occupied by the endangered and threatened grasses should be considered as priority conservation sites to protect these species, the biodiversity, and ecosystem services they provide.  Maintaining healthy native plant communities is essential.  Not only for organisms that share these habitats and rely on these plants for shelter and forage, but for humans and the ecosystem services that are provided to maintain a healthy environment.

Barak, R. S., Williams, E. W., Hipp, A. L., Bowles, M. L., Carr, G. M., Sherman, R., & Larkin, D. J. (2017). Restored tallgrass prairies have reduced phylogenetic diversity compared with remnants. Journal of Applied Ecology, 54(4), 1080-1090.

Ellis, J. L. (2017). Ecosystem Conservation and Management in an Era of Global Climate Change. Science & Ecological Policy Paper. Retrieved January 7, 2018, from

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