Abstract
BackgroundDelimiting species boundaries and reconstructing the evolutionary relationships of late Tertiary and Quaternary species radiations is difficult. One recent approach emphasizes the use of genome-wide molecular markers, such as amplified fragment length polymorphisms (AFLPs) and single nucleotide polymorphisms (SNPs), to identify distinct metapopulation lineages as taxonomic species. Here we investigate the properties of AFLP data, and the usefulness of tree-based and non-tree-based clustering methods to delimit species and reconstruct evolutionary relationships among high-elevation Ourisia species (Plantaginaceae) in the New Zealand archipelago.ResultsNew Zealand Ourisia are shown to comprise a geologically recent species radiation based on molecular dating analyses of ITS sequences (0.4–1.3 MY). Supernetwork analyses indicate that separate tree-based clustering analyses of four independent AFLP primer combinations and 193 individuals of Ourisia produced similar trees. When combined and analysed using tree building methods, 15 distinct metapopulations could be identified. These clusters corresponded very closely to species and subspecies identified on the basis of diagnostic morphological characters. In contrast, Structure and PCO-MC analyses of the same data identified a maximum of 12 and 8 metapopulations, respectively. All approaches resolved a large-leaved group and a small-leaved group, as well as a lineage of three alpine species within the small-leaved group. We were unable to further resolve relationships within these groups as corrected and uncorrected distances derived from AFLP profiles had limited tree-like properties.ConclusionOurisia radiated into a range of alpine and subalpine habitats in New Zealand during the Pleistocene, resulting in 13 morphologically and ecologically distinct species, including one reinstated from subspecies rank. Analyses of AFLP identified distinct metapopulations consistent with morphological characters allowing species boundaries to be delimited in Ourisia. Importantly, Structure analyses suggest some degree of admixture with most species, which may also explain why the AFLP data do not exhibit sufficient tree-like properties necessary for reconstructing some species relationships. We discuss this feature and highlight the importance of improving models for phylogenetic analyses of species radiations using AFLP and SNP data.
Highlights
Delimiting species boundaries and reconstructing the evolutionary relationships of late Tertiary and Quaternary species radiations is difficult
We investigate the potential of amplified fragment length polymorphism (AFLP) analyses for delimiting New Zealand Ourisia species and reconstructing their evolutionary relationships
Comparison of nuclear DNA sequence distances and AFLP distances AFLP profiles of New Zealand Ourisia did not diverge as a simple function of increasing DNA sequence divergence
Summary
Delimiting species boundaries and reconstructing the evolutionary relationships of late Tertiary and Quaternary species radiations is difficult. We investigate the properties of AFLP data, and the usefulness of treebased and non-tree-based clustering methods to delimit species and reconstruct evolutionary relationships among high-elevation Ourisia species (Plantaginaceae) in the New Zealand archipelago Volcanic island archipelagos, such as Hawai'i, Macaronesia, and Juan Fernández have long been the focus of studies investigating patterns and processes of species diversification (e.g., [1,2,3,4,5,6,7,8]). Endemism is greatest in the high-elevation habitats of its North and South Islands, where many genera have diversified following late Tertiary transoceanic dispersal of a single founder species to New Zealand [12,13,18,19,20,21] These radiations have produced ecologically and morphologically distinct taxa, many of which have highly restricted distributions. This is because the criteria for recognizing species continue to be debated and because the phylogenetic relationships of species, as well as the genetic characteristics that distinguish them, are poorly understood [14,24,25]
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