Genome evolution and systematics of the Paenungulata (Afrotheria, Mammalia)

[摘要] ENGLISH ABSTRACT: Increases in taxonomic sampling and the numbers and types of markers used inphylogenetic studies have resulted in a marked improvement in the interpretation ofsystematic relationships within Eutheria. However, relationships within several clades,including Paenungulata (Hyracoidea, Sirenia, Proboscidea), remain unresolved. Here thecombination of i) a rapid radiation and ii) a deep divergence have resulted in limitedphylogenetic signal available for analysis. Specifically i) a short internode separatingsuccessive branching events reduces the time available for changes to occur, while ii) thelonger the time since divergence, the greater the opportunity for signal to be negativelyaffected by homoplasy. This is evident in both molecular and morphological data wherean overall consensus on paenungulate relationships is lacking. Morphological analysis ofanatomical and fossil evidence favours the association of Sirenia (S) and Proboscidea (P)(Tethytheria) to the exclusion of Hyracoidea (H); further, support for uniting these threetaxa as Paenungulata is contentious. In contrast, molecular data provide strong supportfor Paenungulata but intra-ordinal relationships are ambiguous. Although results frommitochondrial DNA sequence data favour Tethytheria, there is no consensus of supportfor this clade from nuclear DNA. Nuclear DNA is typified by node instability but favoursH+P in the largest concatenation of sequences. Due to the expected increased effect fromhomoplasy and consequently the increased likelihood for misleading signal, it is unclearwhich result is most likely to represent the 'true tree.An analysis of available and added intron sequences to characterise signal heterogeneityamong nuclear DNA and mitochondrial DNA partitions indicated that the phylogeneticutility of partitions varies considerably. Subpartitioning of the data according to similarevolutionary processes/characteristics (e. g., mtDNA vs. nDNA and codon position)revealed new insights into the signal structure of the data set; specifically i) that nuclearDNA first codon positions, and to a lesser degree second codon sites, provide convincingsupport for H+P, and ii) that support for S+P by faster evolving sites within mtDNAsuggests that this may be the result of misleading signal. If H+P represents the 'truetree, then support for this clade indicates that phylogenetic signal has been reduced over time as a result of multiple hits, which explains the presence of (hidden) support inslower evolving sites where homoplasy is less likely to occur, in contrast to fasterevolving sites where no support for H+P was observed.In an attempt to provide further resolution from an alternative perspective to that possiblewith DNA sequence data, chromosomal rearrangements were identified among the threepaenungulate lineages. Using comparative chromosome painting, unique changes withineach order and specific to Paenungulata were characterised, however, intra-ordinalsynapomorphies were not recovered. Although this may suggest a hard polytomy, theslow to moderate rate of evolution estimated from the data is likely not sufficient relativeto the rapid radiation associated with the paenungulate node. Further examination ofchromosomal rearrangements at a higher level of resolution may yet reveal informativechanges.

[发布机构] Stellenbosch University