Faculty of Science of the Nelson Mandela Metropolitan University
Department of Botany
South Campus, Building 12, Room 008
Port Elizabeth, 6031
Abstracts (first author)
Comparative phylogeography of three tree species from the Albany Subtropical Thicket of South Africa: testing cornerstone hypotheses of a large-scale conservation network
An ambitious large-scale network of conservation areas and corridors has been designed with the aim of preserving the evolutionary patterns and processes of the Albany Subtropical Thicket biome of South Africa. Two main hypotheses, largely based on expert opinion, formed the foundation for this conservation plan: 1) drainage basins are discrete biogeographical, and thus evolutionarily-distinct, units, and 2) long-distance movement of the primary agents of disturbance in this landscape, African elephants (Loxodonta africana), is critical for ecosystem functioning. Here we test these hypotheses using chloroplast phylogeography of three tree species with similar ecologies but different seed dispersal syndromes, specifically Nymania capensis (Meliaceae; inflated wind-dispersed seeds), Pappea capensis (Sapindaceae; small bird-dispersed seeds) and Schotia afra (Fabaceae, large seed-pods dispersed by elephants and other large mammals). Each drainage basin was found to have isolated populations of the wind- and bird-dispersed species, whereas the elephant-dispersed species has a single regional meta-population that extends across all the drainage basins. These results suggest that the deeply-incised drainage basins along the coastal lowlands of South Africa are unique phylogeographic, as well as biogeographic, units for species that that lack long-distance dispersal mechanisms over such a topographically-complex landscape. At present, elephants and many other large herbivores are restricted to an extremely reduced and fragmented proportion of their historical distribution along the coastal lowlands. The phylogeographic patterns of S. afra highlight the importance of re-establishing the free movement of megaherbivores across the regional landscape for this and other elephant-dispersed plants. These phylogeographic patterns offer pivotal support for the proposed network of conservation corridors for this biome.
Phylogeny reconstruction in the presence of intra-individual site polymorphisms: getting your support backPDF
Intra-individual site polymorphisms (2ISPs, e.g. Y or R) in DNA sequences can arise from sequencing errors, or the presence of numerous variants within a multi-copy gene region such as the internal transcribed spacers (ITS) from the nuclear-encoded 35S rDNA cistron. If 2ISPs are due to the latter, and arose from a lack of concerted evolution (and not hybridisation), these sites still offer phylogenetic information. At present, the majority of tree inference algorithms either remove 2ISPs or treat them as ambiguities. This reduces the information content of the dataset and/or creates site uncertainty which in turn can reduce support. Here we propose 2ISP-informative implementations for distance-based, maximum parsimony and maximum likelihood algorithms. These implementations are compared against the standard methods (with 2ISP-ambiguous treatments) using simulated datasets, a meta-analysis from over 20 published datasets, and two case studies. We show that the 2ISP-informative approach offers improved phylogenetic resolution and support as the 2ISP content increases in the dataset. Importantly, hybrid samples with 2ISPs do not result in falsely inflated branch supports under the informative approach. We envisage that this informative approach will greatly aid phylogenetic inference using any nuclear DNA regions that contain 2ISPs (including consensus sequences generated from next generation sequencing), especially at the intra-generic or intra-specific level.