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A multilocus approach to the phylogenetic inference of an island and continental plant radiations

Final Report Summary - PLANT SPECIATION (A multilocus approach to the phylogenetic inference of an island and continental plant radiations)

The tropical region harbors the world’s richest plant biodiversity, yet it is the most poorly known ecologically and genetically. Through the reconstruction of evolutionary trees we can understand the time and manner this biodiversity arose. Understanding the evolution of economically important plant species and their wild relatives is of importance to human society because it will inform decisions on sustainable use and conservation of our plant resources. Coffea and Astrocaryum are two large tropical plant genera that include economically important species such as coffee and non-timber forest products, thus they constitute good case studies of tropical evolution. The general goal of this project was to conduct a comparative analysis of two plant radiations, one occurring in continental south America (the palm genus Astrocaryum), and the other occurring in the island of Madagascar (wild coffee trees in the genus Coffea). Phylogenetic trees based on DNA evidence were constructed to achieve this goal.

For the continental palm case, we have carefully selected and sequenced a set of five nuclear and five chloroplast genes not commonly used toward species tree reconstructions. Selection criteria were mainly the low copy number of the gene within the whole genome and the adequate mutation rate needed at this taxonomic scale. The Astrocaryum phylogeny consisted of a total of 51 species (30 species in Astrocaryum and 21 in related palm genera). Cloning was performed when necessary to achieve good-quality sequences. This tree was then dated using the fossil record to obtain the divergence time (ca. 6 million years) of a subgroup of 13 Astrocaryum species growing mostly in the western Amazon. We used novel methods on biogeographical analysis to show that colonization of the western Amazon occurred after the disappearance of a big aquatic system called Pebas that existed until the middle Miocene, 11 million years ago. Our results also suggested a role for the Guiana Shield as an area that harbored the ancestral populations of plants in South America. We found an increased speciation rate of palms at a time that coincided with a period of climatic change and the elevation of the Andean mountains (13 million years ago). These results have been presented at a major International Botanical Congress in Australia in 2011 and published as part of a special issue in the Botanical Journal of the Linnean Society.

Once we revealed the divergence time of the western Amazonian palm subgroup (section Huicungo), we carried out a phylogeographic analysis to unravel the geographic distribution of genetic units (haplotypes) that could provide insight on the speciation pattern of lowland Amazonian plant species. Our sampling consisted of 87 individuals from 13 Huicungo species and six other Astrocaryum species. We inferred the divergence times and phylogeny of these haplotypes using a Bayesian-based modeling approach. Huicungo species had unique mutation events with respect to other palms. The ancestral population of this radiation likely originated south of the Western Andean Portal (a south American marine incursion localized at 3-5°S) as revealed by the wide geographic distribution of the ancestral haplotype south of this formation. A speciation pattern of populations from the central to the northern Andes was thus found reflecting the Andean elevation history. This central (or south) to north Andean speciation pattern has also been proposed for other plant and animal groups.

An extensive molecular phylogenetic study of the genus Coffea was developed as part of a PhD thesis at the host institution. This phylogeny allowed selection of a recent radiation of Malagasy species, which includes the C. millotii species complex, a mostly humid forest group of around six species in active diversification. Through the availability of the entire commercial coffee genome, the host institution is characterizing a set of 1700 “virus-like” DNA fragments called retrotransposons. Using these genomic resources we have characterized a set of 10 putatively active retrotransposons in C. millotii. We optimized a fingerprinting technique, which detects the “copy and paste” activity of retrotransposons. The insertion of the same DNA fragment in the same genomic region is inherited from ancestors to descendents and thus can be a useful tool to track the evolutionary history of plants. We analyzed the “copy and paste” activity of four of the ten characterized retrotransposons in a sampling scheme of 136 coffee individuals distributed in humid and dry forests of Madagascar. Using a distance tree we found well to moderately supported clusters corresponding to different species and populations. These results support the morphological evidence for species boundaries, and the synonymy of previously recognized species. However, the evolutionary relationships among species were not clear in the tree. We mapped habitat type and geographic region for each individual in the tree. No interesting pattern emerged from the habitat types, however individuals grouped by geographic regions separating the northwest from the east and southeast of Madagascar. These results support the hypothesis of a north to south speciation pattern as suggested by an increased genome size of Coffea in the south.

Ecosystems and the biodiversity harbored within them provide human society the fundamental goods and services required for life on earth. These natural products are currently threatened by climate change and shifts in land-use. It is therefore imperative that biodiversity is integrated in mitigation and conservation efforts. Research on speciation patterns like the one we have conducted is fundamental for biodiversity conservation because the environmental and genetic factors that promote speciation must be considered in the design and management of protected natural areas and in restoration actions. Through a better understanding of how species evolve, conservation scientists and practitioners can strive to preserve an environment that will sustain current and potentially new species.

Relevant contact details:
Julissa Roncal
Department of Biology, Memorial University of Newfoundland
232 Elizabeth Avenue, St. John’s NL, A1B 3X9, Canada

Jean Christophe Pintaud
Institut de Recherche pour le Developpement (IRD), UMR DIADE
911 Av. Agropolis, BP 64501, 34394 Montpellier, Cedex 5, France
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