<p>The fern family Cystopteridaceae has been a thorn in the side of fern phylogeneticists, on many levels. Until this thesis, its basic existence (as a deeply isolated clade) and composition were unrecognized, hypotheses as to the relationships of its constituents within the broader fern tree-of-life were wildly inconsistent, the relationships of its genera to each other were contested, the species limits within those genera weakly understood, and the relationships among those species unknown. This thesis first establishes the broad evolutionary context for the family, which is that it is the first-diverging branch in Eupolypods II (it is sister to the rest of the eupolypod II clade). Eupolypods II is a large clade, containing nearly a third of extant fern species, making the Cystopteridaceae's position pivotal to a full understanding of fern evolution. </p><p>The evolution of the Eupolypods II is marked by an "ancient, rapid radiation" at the base of the clade, which helps to explain the difficulty that this broad group has historically posed to evolutionary biologists. Molecular data from five plastid loci show that Eupolypods II is comprised of 10 deeply divergent lineages, each worthy of recognition at the rank of family: Cystopteridaceae, Rhachidosoraceae, Diplaziopsidaceae, Hemidictyaceae, Aspleniaceae, Thelypteridaceae, Woodsiaceae, Onocleaceae, Blechnaceae, and Athyriaceae. The ancestors of Cystopteridaceae diverged from those of the rest of the clade approximately 100 million years ago, and the family is now comprised of five extant genera: Acystopteris, Cystoathyrium (the only genus for which we lack molecular data--it may be extinct), Cystopteris, Gymnocarpium, and ×Cystocarpium.</p><p>Within the family, the relationships of Cystoathyrium are unknown. Acystopteris is sister to Cystopteris, and those two genera, together, are sister to Gymnocarpium. Gymnocarpium is the maternal parent of ×Cystocarpium, so that genus falls within Gymnocarpium in phylogenetic trees based on maternally transmitted loci (i.e., plastid or mitochondrial loci). Plastid data resolve a basal trichotomy in Gymnocarpium, among the G. disjunctum clade, the G. robertianum clade, and core Gymnocarpium. The earliest diverging branch of core Gymnocarpium is the morphologically anomalous G. oyamense, followed by a split that separates G. appalachianum and G. jessoense parvulum (on one side) from G. remotepinnatum and G. jessoense jessoense, on the other. In Acystopteris, the first division surprisingly separates A. taiwaniana (which is frequently treated as a variety of A. japonica) from A. japonica + A. tenuisecta (which are morphologically very distinct from each other).</p><p>The evolution of Cystopteris is, as expected, more complex. The first lineage to diverge from the rest of the genus is the one that gave rise to C. montana. The next division, however, is unclear; molecular data infer a trichotomy among the sudetica clade (containing C. sudetica, C. moupinensis, and C. pellucida), the bulbifera clade (containing C. bulbifera and its related allopolyploids C. tennesseensis and C. utahensis), and the C. fragilis complex. Within the C. fragilis complex relationships (and species limits) get particular messy. The diploid species of eastern North America--C. protrusa--is sister to the rest of the complex, but after that point the major named species (including C. fragilis and C. tenuis) cease to be monophyletic, being found on both sides of a major split, alongside such taxa as the Australian/New Zealand C. tasmanica, the Hawaiian C. douglasii, and the Mexican C. membranifolia and C. millefolia.</p><p>In the context of the deep divergence of Gymnocarpium from Cystopteris, and the complicated species-level patterns of relationship within each genus, it is particularly surprising that molecular data confirm that ×Cystocarpium is a hybrid between Gymnocarpium dryopteris and a European tetraploid member of the Cystopteris fragilis complex. The ancestors of Cystopteris diverged from those of Gymnocarpium approximately 58 million years ago, meaning that the ×Cystocarpium hybridization event (which happened very recently) united genomes that contain, between them, over 100 million years of independent evolution. This breadth of divergence makes ×Cystocarpium the most extreme example of wide hybridization currently documented, with important implications for the pace of evolution of reproductive isolation, and thus for species formation.</p><p>This thesis ends with a tentative synopsis of the Cystopteridaceae (Appendix E). The family, as construed here, contains five genera and approximately 36 species (three in Acystopteris, one in Cystoathyrium, ~25 in Cystopteris, seven in Gymnocarpium, and one in ×Cystocarpium), plus two named subspecies (one each in Cystopteris and Gymnocarpium), and eight named sterile hybrids (three in Cystopteris and five in Gymnocarpium). Each of these tallies is highly subjective--much further research, with an emphasis on cytological and low-copy nuclear data, is necessary before we can hope to have any confidence in the species limits and finer-scale evolutionary patterns in this family.</p> / Dissertation

In this thesis, I investigate the phylogeny and evolution of Lerista, a clade of more than 75 species of scincid lizards, distributed in arid, semi-arid, and seasonally dry habitats throughout Australia. Among extant tetrapods, Lerista is exceptional in comprising a large number of closely-related species displaying prodigious variability of body form; several species possessing well-developed, pentadactyl limbs resemble typical non-fossorial scincids in body proportions, while many other species exhibit varying degrees of limb reduction and body elongation, including two that are highly elongate and entirely limbless. The extensive variation in limb morphology observed among species, incorporating at least 20 distinct phalangeal configurations, has prompted some authors to identify Lerista as the best available model for studying limb reduction in squamates. Nonetheless, lack of a well-resolved phylogeny has impeded investigation of the pattern and mode of limb reduction and loss within the clade. The primary goal of my research was to furnish a comprehensive phylogenetic hypothesis for Lerista, enabling more sophisticated study of the evolution of limb morphology and body form in this clade than has previously been possible. A recent phylogenetic analysis of mitochondrial DNA sequences for a series of Australian Sphenomorphus group scincids (including two species of Lerista) recovered several well-supported, major clades, although these were generally separated by relatively short branches associated with low support values. Applying a recently described methodology for inferring lineage-level polytomies, I use ATP synthetase-β subunit intron sequences and the existing mitochondrial DNA data set (with sequences for additional taxa) to assess the hypothesis that the poorly resolved basal relationships within the Australian Sphenomorphus group are a consequence of the major clades having originated essentially simultaneously. Phylogenetic analyses of the separate mitochondrial DNA and intron sequence data reveal a number of congruent clades, however, the relationships among these clades indicated by the two data sets are generally incongruent. Although this may be partly ascribed in to error in estimating phylogenetic relationships due to insufficient data, some incongruence is evident when uncertainty in inferred relationships is allowed for. Moreover, the congruent clades are typically separated by very short branches, several having a length insignificantly different from zero. These results suggest that initial diversification of Australian Sphenomorphus group scincids was rapid relative to the substitution rates of the mitochondrial DNA and intron fragments considered, if not essentially simultaneous. The pattern and rate of limb reduction in Lerista are investigated, employing a nearly complete phylogeny inferred from nucleotide sequences for a nuclear intron and six mitochondrial genes. Ancestral digit configurations reconstructed assuming this phylogeny indicate at least ten independent reductions in the number of digits from a pentadactyl condition, including four independent losses of all digits, three from pentadactyl or tetradactyl conditions. At the highest rate, complete loss of digits from a pentadactyl condition is estimated to have occurred within no more than 3.6 million years. Patterns of digit loss for the manus and pes are consistent with selection for preserving hindlimb utility as the limbs are reduced, and suggest that intermediate digit configurations exhibited by extant species do not represent transitory stages in a continuing process of limb reduction. An increase in the relative length of the body is demonstrated to precede digit loss in lineages experiencing substantial reduction of the limbs, supporting the hypothesis that limb reduction and loss is a consequence of the adoption of lateral undulation as a significant locomotory mode. However, less extensive limb reduction may proceed in the absence of body elongation, perhaps due to a decrease in absolute body size. The exceptionally high frequency and rate of limb reduction in Lerista emphasise the potential for rapid and dramatic evolutionary transformation of body form in squamates. The substantial divergence of relative limb and body length evident within Lerista is more readily explained by the correlated progression model of phenotypic transformation than the independent blocks model. At each step in the attainment of a limb-reduced, elongate body form, alterations to the relative length of the limbs are accompanied by changes in relative snout-vent length (or vice versa) enabling the maintenance of locomotory ability. Nonetheless, some dissociation of hindlimb reduction and body elongation is possible, emphasising the potentially variable intensity of functional constraints and, accordingly, that the independent blocks model and correlated progression are extremes of a continuum of models (each invoking a different degree of functional integration) and do not describe discrete categories of phenotypic change. An increase in the extent of seasonally dry and arid habitats coincident with the origination of Lerista would have facilitated limb reduction and body elongation by furnishing an environment conducive to the adoption of fossorial habits, however, trends toward a limbless, highly elongate body form may be attributed primarily to the very low probability of re-elaborating reduced limbs. Such asymmetry in the probabilities of possible phenotypic changes may be a significant cause of evolutionary trends resulting in the emergence of higher taxa. / Thesis (Ph.D.) -- University of Adelaide, School of Earth and Environmental Sciences, 2008

In this thesis, I investigate the phylogeny and evolution of Lerista, a clade of more than 75 species of scincid lizards, distributed in arid, semi-arid, and seasonally dry habitats throughout Australia. Among extant tetrapods, Lerista is exceptional in comprising a large number of closely-related species displaying prodigious variability of body form; several species possessing well-developed, pentadactyl limbs resemble typical non-fossorial scincids in body proportions, while many other species exhibit varying degrees of limb reduction and body elongation, including two that are highly elongate and entirely limbless. The extensive variation in limb morphology observed among species, incorporating at least 20 distinct phalangeal configurations, has prompted some authors to identify Lerista as the best available model for studying limb reduction in squamates. Nonetheless, lack of a well-resolved phylogeny has impeded investigation of the pattern and mode of limb reduction and loss within the clade. The primary goal of my research was to furnish a comprehensive phylogenetic hypothesis for Lerista, enabling more sophisticated study of the evolution of limb morphology and body form in this clade than has previously been possible. A recent phylogenetic analysis of mitochondrial DNA sequences for a series of Australian Sphenomorphus group scincids (including two species of Lerista) recovered several well-supported, major clades, although these were generally separated by relatively short branches associated with low support values. Applying a recently described methodology for inferring lineage-level polytomies, I use ATP synthetase-β subunit intron sequences and the existing mitochondrial DNA data set (with sequences for additional taxa) to assess the hypothesis that the poorly resolved basal relationships within the Australian Sphenomorphus group are a consequence of the major clades having originated essentially simultaneously. Phylogenetic analyses of the separate mitochondrial DNA and intron sequence data reveal a number of congruent clades, however, the relationships among these clades indicated by the two data sets are generally incongruent. Although this may be partly ascribed in to error in estimating phylogenetic relationships due to insufficient data, some incongruence is evident when uncertainty in inferred relationships is allowed for. Moreover, the congruent clades are typically separated by very short branches, several having a length insignificantly different from zero. These results suggest that initial diversification of Australian Sphenomorphus group scincids was rapid relative to the substitution rates of the mitochondrial DNA and intron fragments considered, if not essentially simultaneous. The pattern and rate of limb reduction in Lerista are investigated, employing a nearly complete phylogeny inferred from nucleotide sequences for a nuclear intron and six mitochondrial genes. Ancestral digit configurations reconstructed assuming this phylogeny indicate at least ten independent reductions in the number of digits from a pentadactyl condition, including four independent losses of all digits, three from pentadactyl or tetradactyl conditions. At the highest rate, complete loss of digits from a pentadactyl condition is estimated to have occurred within no more than 3.6 million years. Patterns of digit loss for the manus and pes are consistent with selection for preserving hindlimb utility as the limbs are reduced, and suggest that intermediate digit configurations exhibited by extant species do not represent transitory stages in a continuing process of limb reduction. An increase in the relative length of the body is demonstrated to precede digit loss in lineages experiencing substantial reduction of the limbs, supporting the hypothesis that limb reduction and loss is a consequence of the adoption of lateral undulation as a significant locomotory mode. However, less extensive limb reduction may proceed in the absence of body elongation, perhaps due to a decrease in absolute body size. The exceptionally high frequency and rate of limb reduction in Lerista emphasise the potential for rapid and dramatic evolutionary transformation of body form in squamates. The substantial divergence of relative limb and body length evident within Lerista is more readily explained by the correlated progression model of phenotypic transformation than the independent blocks model. At each step in the attainment of a limb-reduced, elongate body form, alterations to the relative length of the limbs are accompanied by changes in relative snout-vent length (or vice versa) enabling the maintenance of locomotory ability. Nonetheless, some dissociation of hindlimb reduction and body elongation is possible, emphasising the potentially variable intensity of functional constraints and, accordingly, that the independent blocks model and correlated progression are extremes of a continuum of models (each invoking a different degree of functional integration) and do not describe discrete categories of phenotypic change. An increase in the extent of seasonally dry and arid habitats coincident with the origination of Lerista would have facilitated limb reduction and body elongation by furnishing an environment conducive to the adoption of fossorial habits, however, trends toward a limbless, highly elongate body form may be attributed primarily to the very low probability of re-elaborating reduced limbs. Such asymmetry in the probabilities of possible phenotypic changes may be a significant cause of evolutionary trends resulting in the emergence of higher taxa. / Thesis (Ph.D.) -- University of Adelaide, School of Earth and Environmental Sciences, 2008

Thesis (MSc)--Stellenbosch University, 2003. / ENGLISH ABSTRACT: The phylogenetic relationships and taxonomic status of South African Oxalis L. species are highly unresolved, both regionally and with regard to precise placement within the genus as a whole. Studies based exclusively on morphological and palynological characteristics have hitherto proved only partially successful in resolving natural groupings among the indigenous taxa of the region. Recent studies involving a few native taxa have indicated the plastid trnL-trnF non-coding DNA region as useful for the purposes of reconstructing phylogenetic relationships within the genus. The present study addressed the taxonomic monophyly and relationships of the highly unresolved section Angustatae subsection Lineares, using DNA sequence data. The phylogenetic reconstruction of southern African Oxalis species renders five of the subsections of section Angustatae sensu Salter (1944) polyphyletic, three of them conclusively so. The members of subsection Lineares are split between three clades, two of them with strong bootstrap support. None of these three clades consists exclusively of species of subsection Lineares. Likewise four of the seven assemblages of related taxa within subsection Lineares sensu Salter (1944) are not retrieved as monophyletic. Pollen data sensu Dreyer (1996) supports the clades retrieved in this study, whereas very few morphological characters could be plotted as potential synapomorphies for these clades. The resultant phylogenetic reconstruction thus supports palynological data of this subsection, and indicates the urgent need for a revision of the current morphological classification of Salter (1944). / AFRIKAANSE OPSOMMING: Die filogenetiese verwantskappe en taksonomiese klassifikasie van Suid Afrikaanse Oxalis L. spesies is nog baie onduidelik, beide binne die gebied en ten opsigte van die presiese plasing binne die genus as 'n geheel. Vorige werk, uitsluitlik gebaseer op morfologiese en palinologiese kenmerke, was tot dusver nog net gedeeltelik suksesvol in die identifikasie van natuurlike groepe binne die inheemse taksa van die gebied. Onlangse studies op 'n paar inheemse spesies het die nut van die plastied trnL-trnF nie-koderende DNA area bevestig vir die rekonstruksie van filogenetiese verwantskappe in die genus. Hierdie studie is gerig op die taksonomiese monofilie en verwantskappe van die onnatuurlike seksie Angustatae subseksie Lineares, deur gebruik te maak van DNA basis-volgorde data. Die filogenetiese rekonstruksie van Suid Afrikaanse Oxalis spesies dui aan dat vyf van die subseksies van seksie Angustatae sensu Salter (1944) polifileties is, met sterk steun daarvoor dat drie van hulle onnatuurlik is. Die lede van subseksie Lineares is tussen drie verskillende groepe versprei; twee van dié groepe het sterk ondersteuning. Nie een van die drie groepe bestaan uitsluitlik uit spesies van subseksie Lineares nie. So ook is vier van die sewe groepe van verwante spesies binne subseksie Lineares sensu Salter (1944) polifileties. Stuifmeel data volgens Dreyer (1996) ondersteun die groepe wat deur die DNA volgordes uitgewys is, terwyl baie min morfologiese kenmerke gebruik kan word as potensiële sinapomorfe/kenmerke. Die filogenetiese rekonstruksie ondersteun dus die palinologiese data van die subseksie, en dui op die dringende behoefte aan 'n hersiening van die huidige morfologiese klassifikasie van Salter (1944).

Thesis (PhD)--University of Stellenbosch, 2003. / ENGLISH ABSTRACT: The geographic genetic population structure and evolutionary history of the African four-striped mouse, Rhabdomys pumilio, was investigated using mitochondrial (mtDNA) cytochrome b gene (1140 bp) and control region (994 bp) sequences and a combination of cytogenetic banding techniques (G- and C-banding), and fluorescence in situ hybridization. Two cytotypes (2n = 46 and 2n = 48) were identified by cytogenetic analysis. No evidence of diploid number variation within populations was found nor were there differences in gross chromosome morphology, or subtle interchromosomal rearrangements at levels detected by ZOO-FISH. The comparative painting data (using the complete suite, N = 20, of Mus musculus chromosome specific painting probes) show that 10 mouse chromosomes have been retained as chromosomal arms, or intact chromosome blocks within the R. pumilio genome, six produced double signals, while the remaining four hybridized to three or more R. pumilio chromosomes. In total, the 20 mouse chromosome paints detected 40 segments of conserved synteny. Their analysis revealed eight R. pumilio specific contiguous segment associations, a further two that were shared by R. pumilio and other rodents for which comparable data are available, the Black (Rattus rattus) and Norwegian (Rattus nONegicus) rats, but not by the Chinese hamster, Cricetulus grise us. The results suggest that mouse chromosomes 1, 10, and 17 have undergone extensive rearrangements during genome evolution in the murids and may be useful markers for enhancing our understanding of the mode and tempo of chromosome evolution in rodents. Following initial studies using control region sequences, the phylogeographic appraisal of R. pumilio was done using cytochrome b gene sequences. Analyses based on a variety of analytical procedures resulted in the detection of two major mtDNA lineages that correspond roughly to the xeric and mesic biotic zones of southern Africa. One clade comprises specimens with 2n = 48, and the other representatives of two cytotypes (2n = 48 and 2n = 46). The mean sequence divergence (12.0%, range 8.3% -15.6%) separating the two mtDNA clades is comparable to among-species variation within murid genera suggesting their recognition as distinct species, the prior names for which would be R. dilecfus and R. pumilio. Low sequence divergences and the diploid number dichotomy within the mesic lineage support the recognition of two subspecies corresponding to R. d. dilecfus (2n = 46) and R. d. chakae (2n = 48). The data do not support subspecific division within the nominate, R. pumilio. Molecular dating places cladogenesis of the two putative species at less than 5 million years, a period characterised by extensive climatic oscillations which are thought to have resulted in habitat fragmentation throughout much of the species' range. / AFRIKAANSE OPSOMMING: Die geografiesebevolkingsstruktuur en evolusionêre verwantskappe binne die Afrika streepmuis, Rhabdoys pumilio, is ondersoek deur middel van mitochondriale ONS volgordebepaling van die geenfragment sitochroom b (1140 basispare) en die reguleerstreek (994 bp) in kombinasie met sitogenetiese tegnieke (G- en Cbandkleuring en f1uoreseerende in situ hibridisasie). Twee sitotipes (2n = 46 en 2n = 48) is geidentifiseer deur sitogenetiese analasie. Geen bewys van variasie in die 2n chromosoomgetal binne bevolkings is gevind nie. Verder is daar ook geen verskil in die morfologies struktuur van chromosome aanwesig binne bevolkings nie. Vergelykende data (verkry met behulp van die N = 20 Mus musculus chromosoomspesifiekepeilers) dui daarop dat 10 muis chromosome behoud gebly het as chromosoomarms of chromosoomblokke binne die R. pumilio genoom. Ses peilers het dubbel seine gelewer terwyl die oorblywende vier peilers gehibridiseer het aan drie of meer R. pumilio chromosome. In totaal het die 20 muischromosoomverwe 40 konserwatiewe segmente geidentifiseer. Die analise dui agt R. pumilio spesifieke aaneenlopende segmentassosiasies aan, met 'n addisionele twee wat deur R. pumilio en ander muisagtiges vir wie vergelykende data beskikbaar is, byvoorbeeld die swart (Rattus rattus) en Noorweegse (R. norvegicus) rot maar nie die Chinese hamster, Cricetulus grise us, gedeel word. Die resultate stel voor dat muischromosoom 1, 10 en 17 ekstensiewe herrangskikkings ondergaan het gedurende die genoom evolusie binne die Muridae en dat hulle waarskynlik waardevolle merkers kan wees om beide die patroon en tempo van chromosome evolusie in muisagtiges verder te kan verstaan. Die filogeografiese verwantskappe binne R. pumilio is ondersoek deur middel van ONS volgordebepalings van die reguleerstreek asook sitochroom b. Die resultate van hierdie studie het twee divergente mitochondriale ONS eenhede ontdek wat gekorreleer kan word met xeriese en mesiese klimaatsones binne suidelike Afrika. Een groep bestaan uit diere met 2n = 48, terwyl die ander genetiese groep twee sitotipes (2n = 46 en 2n= 48) insluit. 'n Gemiddelde genetiese divergensie van 12.0% (varieer tussen 8.3% - 15.5%) verdeel die twee mtDNS-groepe en is vergelykbaar met tussenspesievariasie binne ander muisagtige genera, wat moontlik daarop dui dat twee verskillende spesies teenwoordig is; die voorgestelde name is R. di/ectus en R. pumilio. Lae genetiese divergensie binne die mesiese groep versterk die moontlike teenwoordigheid van twee subspesies, R. d. di/ectus (2n = 46) en R. d. chakae (2n = 48). Die data verleen egter nie steun aan die divisie binne R. pumilio nie. Molekulêre datering van die twee spesies dui daarop dat die divergensie ten minste 5 miljoen jaar gelede plaasgevind het. Die periode was gekarakteriseer deur ekstensiewe klimaatsossilasies, wat gely het tot habitat fragmentasie in die spesie se verspreidingsgebied.

published_or_final_version / Ecology and Biodiversity / Doctoral / Doctor of Philosophy

published_or_final_version / abstract / Ecology and Biodiversity / Doctoral / Doctor of Philosophy

published_or_final_version / abstract / Biological Sciences / Doctoral / Doctor of Philosophy

published_or_final_version / abstract / Biological Sciences / Doctoral / Doctor of Philosophy

One statistical approach with a long history in the social sciences is a multivariate method called Structural Equation Modeling (SEM). The development of SEM followed the evolution of factor and path analyses, multiple regression analysis and MACOVA. One of the key innovations of factor analysis and SEM is that they group a set of multivariate statistical approaches that condense variability among a set of variables in fewer latent (unobserved) factors. Most biological systems are multivariate, which are not easily dissected into their component parts. However, most biologists use only univariate statistical methods, which have definitive limitations in accounting for more than a few variables simultaneously. Therefore, the implementation of methodologies like SEM into biological research is necessary. However, SEM cannot be applied directly to most biological datasets or generalized across species because of the hierarchical pattern of evolutionary history (i.e., phylogenetic non-independence or signal). This report includes the theoretical grounds for the development of Phylogenetic SEM in preparation of the development of utilitarian algorithms. I have divided this report in six parts: (1) a brief introduction to factor analysis and SEM from historical perspective and a brief description of its utility; (2) a summary of the implications of using biological data and the underlying hierarchical structure due to shared common ancestry or phylogeny; (3) a summary of the two most common comparative methods to incorporate the phylogeny in univariate analyses (i.e., phylogenetic independent contrasts and phylogenetic generalized least squares); (4) I describe how some intermediate output from both comparative methods can be used to estimate the variance–covariance matrix that has been corrected for phylogenetic signal; (5) I describe how to perform a exploratory factor analysis, specifically principal component analysis, with the corrected variance–covariance matrix; and (6) I describe the development of the phylogenetic confirmatory factor analysis and phylogenetic SEM. I hope that this report encourages other researchers to develop adequate multivariate analysis that incorporate the evolutionary principles in its analyses. / text