Dissertation (PhD)--University of Stellenbosch, 2006. / ENGLISH ABSTRACT: Increases in taxonomic sampling and the numbers and types of markers used in
phylogenetic studies have resulted in a marked improvement in the interpretation of
systematic relationships within Eutheria. However, relationships within several clades,
including Paenungulata (Hyracoidea, Sirenia, Proboscidea), remain unresolved. Here the
combination of i) a rapid radiation and ii) a deep divergence have resulted in limited
phylogenetic signal available for analysis. Specifically i) a short internode separating
successive branching events reduces the time available for changes to occur, while ii) the
longer the time since divergence, the greater the opportunity for signal to be negatively
affected by homoplasy. This is evident in both molecular and morphological data where
an overall consensus on paenungulate relationships is lacking. Morphological analysis of
anatomical and fossil evidence favours the association of Sirenia (S) and Proboscidea (P)
(Tethytheria) to the exclusion of Hyracoidea (H); further, support for uniting these three
taxa as Paenungulata is contentious. In contrast, molecular data provide strong support
for Paenungulata but intra-ordinal relationships are ambiguous. Although results from
mitochondrial DNA sequence data favour Tethytheria, there is no consensus of support
for this clade from nuclear DNA. Nuclear DNA is typified by node instability but favours
H+P in the largest concatenation of sequences. Due to the expected increased effect from
homoplasy and consequently the increased likelihood for misleading signal, it is unclear
which result is most likely to represent the “true” tree.
An analysis of available and added intron sequences to characterise signal heterogeneity
among nuclear DNA and mitochondrial DNA partitions indicated that the phylogenetic
utility of partitions varies considerably. Subpartitioning of the data according to similar
evolutionary processes/characteristics (e. g., mtDNA vs. nDNA and codon position)
revealed new insights into the signal structure of the data set; specifically i) that nuclear
DNA first codon positions, and to a lesser degree second codon sites, provide convincing
support for H+P, and ii) that support for S+P by faster evolving sites within mtDNA
suggests that this may be the result of misleading signal. If H+P represents the “true
tree”, 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 in
slower evolving sites where homoplasy is less likely to occur, in contrast to faster
evolving sites where no support for H+P was observed.
In an attempt to provide further resolution from an alternative perspective to that possible
with DNA sequence data, chromosomal rearrangements were identified among the three
paenungulate lineages. Using comparative chromosome painting, unique changes within
each order and specific to Paenungulata were characterised, however, intra-ordinal
synapomorphies were not recovered. Although this may suggest a hard polytomy, the
slow to moderate rate of evolution estimated from the data is likely not sufficient relative
to the rapid radiation associated with the paenungulate node. Further examination of
chromosomal rearrangements at a higher level of resolution may yet reveal informative
changes. / AFRIKAANSE OPSOMMING: ‘n Toename in die aantal taksonomiese monsters sowel as die aantal en soort merkers wat
in filogenetiese studies gebruik word, het tot ‘n merkbare verbetering in die vertolking
van sistematiese verwantskappe binne die Eutheria gelei. Desondanks bly ‘n aantal klades
(stamlyne), met inbegrip van Paenungulata (Hyracoidea, Sirenia, Proboscidea), steeds
onopgelos. By laasgenoemde het die kombinasie van i) ‘n vinnige radiasie en ii) ‘n diep
divergensie die filogenetiese sein wat vir analise beskikbaar is, beperk. Meer spesifiek sal
i) opeenvolgende vertakkings wat deur kort internodusse geskei word die beskikbare tyd
waartydens veranderings kan intree, verminder, terwyl ii) ‘n toename in tydsverloop
sedert divergensie die kans dat die sein deur homoplasie nadelig beïnvloed sal word,
vergroot. Dit word in sowel molekulêre en morfologiese data, waar ‘n oorhoofse
konsensus t.o.v. verwantskappe van Paenungulata ontbreek, waargeneem. Morfologiese
analise van anatomiese en fossielbewyse ondersteun die samevoeging van Sirenia (S) en
Proboscidea (P) (Tethytheria) ten koste van Hyracoidea (H). Ondersteuning vir die
samevoeging van dié drie taksa as Paenungulata is egter aanvegbaar. In teenstelling
hiermee word Paenungulata sterk deur molekulêre data ondersteun, al bly die
verwantstkappe op intra-orde vlak, steeds onduidelik. Alhoewel die resultate van
mitochondriale DNA op Tethytheria dui, word die klade nie deur data van kern-DNA
ondersteun nie. Kern-DNA word gekarakteriseer deur node instabiliteit maar verkies H+P
in die grootste samevoeging van geen volgordes. Na aanleiding van die verwagte
toename in die effek van homoplasie en die gevolglik groter kans op ‘n misleidende sein,
is dit nie duidelik watter van die resultate die meer korrekte filogenetiese stamboom
verteenwoordig nie.
Analise van beskikbare en nuut toegevoegde intron-volgordes om sein-heterogeniteit
tussen kern- en mitochondriale DNA verdelings te karakteriseer, toon dat die
filogenetiese nut van verdelings beduidend verskil. Onderverdeling van die data op grond
van soortgelyke evolusionêre prosesse/karaktereienskappe (bv. mtDNA vs. nDNA, en
kodonposisie) het na nuwe insigte in die seinstruktuur van die datastel gelei. Meer
spesifiek dat i) kern-DNA se eerste kodonposisies, en tot ‘n mindere mate die tweede kodonposisies, H+P oortuigend ondersteun en ii) dat ondersteuning vir S+P deur posisies
binne mtDNA wat vinnig verander, op ‘n misleidende sein mag dui. As H+P die korrekte
stamboom verteenwoordig dui ondersteuning vir die klade op ‘n filogenetiese sein wat
met verloop van tyd as gevolg van veelvuldige seinvoorkomste verklein het. Dit verklaar
die aanwesigheid van versluierde ondersteuning in stadig-veranderende posisies waar die
neiging tot homoplasie klein is, in teenstelling met posisies wat vinniger verander en
waar ondersteuning vir H+P nie waargeneem is nie.
Op soek na verhoogde resolusie vanuit ‘n ander perspektief as DNA-volgordebepaling, is
chromosomale herrangskikkings in die drie stamlyne van Paenungulata nagevors. Met
behulp van vergelykende chromosoomkleuring is unieke veranderings binne elke orde en
spesifiek binne Paenungulata gekarakteriseer, maar geen sinapomorfe kenmerke is op die
intra-orde vlak gevind nie. Alhoewel dit op ‘n onopgeloste politomie mag dui, is die
stadige tot matige evolusietempo wat van die data afgelei word, relatief tot die vinnige
radiasie wat met die Paenungulata-nodus geassosieer word, waarskynlik onvoldoende vir
‘n oplossing. Verdere navorsing oor chromosomale herrangskikkings met ‘n hoër
resolusievlak mag addisionele insiggewende veranderings aantoon.
| Identifer | oai:union.ndltd.org:netd.ac.za/oai:union.ndltd.org:sun/oai:scholar.sun.ac.za:10019.1/21697 |
| Date | 12 1900 |
| Creators | Pardini, Amanda T. |
| Contributors | Robinson, T.J., Stellenbosch University. Faculty of Science. Dept. of Botany and Zoology. |
| Publisher | Stellenbosch : Stellenbosch University |
| Source Sets | South African National ETD Portal |
| Language | en_ZA |
| Detected Language | English |
| Type | Thesis |
| Format | xiii, 163 leaves : ill. |
| Rights | Stellenbosch University |
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