Dissertations / Theses on the topic 'Mammal evolution'

Understanding the maintenance of the variation that is typically observed in natural populations has been a central aim of evolutionary biology. In a feral population of Soay sheep on the island of Hirta, St. Kilda there is a phenotypic polymorphism for horns with males growing either normal or reduced (scurred) horns, and females growing either normal, scurred or no (polled) horns, with further variation in horn size within each of the horn types. This thesis examines the potential factors which maintain these polymorphisms. I first present an overview of the literature relating to the factors that potentially maintain variance in traits in natural populations. In chapter two I present an analysis that suggests that polymorphisms in both horn type and horn size may be maintained by trade-offs between allocation to reproductive success and survival in males, and by sexually antagonistic selection between males and females. In chapter three I test the hypothesis that female weaponry may convey an advantage in intrasexual conflicts over resources, rather than just being expressed as a consequence of genetic associations with the male phenotype. Chapter four examines the environmental factors which create variation between individuals in their horn length, revealing that individuals vary in response to the environment. In chapter five I investigate whether the temporally fluctuating environmental conditions of St. Kilda generate fluctuating selection on the horn length of normal-horned males, revealing that this mechanism constrains the evolution of horn length potentially maintaining variance. In chapter six I examine the genetic relationships between morphological traits, revealing that these relationships are dependent upon the environmental conditions experienced during the first year of life. Finally, I discuss the wider implications of these findings for our understanding of the maintenance of trait variation in the wild.

Female mammals play a central role in determination of social structure and are thus central to understanding the overall fission-fusion grouping pattern characteristic of many delphinid societies. Focusing specifically on female-female relatedness and association patterns, I have analysed more than 17 years of group composition, behavioural data, and genetic information to investigate complex interactions between behavioural ecology and relatedness and to also examine the common social evolutionary theory, that variation in mammalian social systems is typically attributed to five main factors: inclusive fitness, predation pressure, sexual conflict and male harassment, inbreeding avoidance, and resource competition. Overall, I found that female bottlenose dolphin association patterns depend upon the interplay between matrilineal kinship, biparental relatedness and home range overlap, and that female bottlenose dolphins seem to adapt their social strategies to seasonal variation in levels of predation and male harassment. The presence of both high sexual conflict and bisexual philopatry lead me to investigate the extent of inbreeding avoidance. I found that more than 14% of the calves were most likely the product of mating between close relatives, and identified female fitness costs to inbreeding. We were able to show that the effect of inbreeding on females??? fitness occurs via two independent mechanisms: being inbred and having at least one inbred calf. Inbred calves are on average weaned later than non-inbred calves, and a female???s first calf has a higher probability to be an inbred than subsequent calves. Last, I examined whether sociality provides inclusive fitness to female bottlenose dolphins through an investigation of both the additive genetic and social variance components of female calving success using a pedigree-free animal model. I found that variance in calving success of female bottlenose dolphins is best explained by complex genetic and social interactions. Females with high calving success showed both high genetic and social merit; they not only have good genes but also prefer to associate with others of high fitness. This study reveals that both social and heritable genetic variance contribute to fitness trait variance in the wild.

Morphological data are crucial in evolutionary analyses for merging fossils into the tree of life, calibrating dating analyses and for enhancing inference of biological patterns and processes. Morphological phylogenetics is dominated by homoplastic characters, functional and developmental correlations, and also by highly subjective definitions of characters and their states, which in turn can mislead phylogeny reconstruction. A first study assessed the implications of biases among characters in Mesozoic mammals. Then, geometric morphometrics and molecular data were combined to study the systematics of kangaroos and wallabies. Finally, new methodologies using 3D morphometrics and multivariate statistical analyses were developed for phylogenetic inference.

Cette thèse porte sur la convergence morphologique du crâne des mammifères placentaires myrmécophages qui se nourrissent principalement de fourmis et de termites. Les objectifs ici sont de caractériser la réduction dentaire, les patrons de covariance et la variation morphologique du crâne, et d'explorer leur lien avec les pressions sélectives associées à la myrmécophagie.Le premier chapitre se concentre sur les variations évolutives, ontogénétiques et statiques du crâne des pangolins, un groupe d'animaux myrmécophages qui comprend les espèces de mammifères les plus menacées sur Terre. La délimitation morphologique entre sept des huit espèces de pangolins est démontrée. Leurs trajectoires allométriques ontogénétiques sont décrites et l’influence des variations de taille sur la systématique du groupe sont discutées. De plus, la variation intraspécifique était en partie associée au caractère distinctif moléculaire d'espèces cryptiques récemment divergentes au sein du pangolin à petites écailles. Ces résultats ont été obtenus à l'aide de méthodes morphométriques géométriques tridimensionnelles.Le deuxième chapitre était consacré à l'anatomie comparée de la mandibule et de l'appareil masticateur. Tout d'abord, l'anatomie interne de la mandibule a été étudiée sur un échantillon comparatif de mammifères placentaires par microtomographie et histologie. Les structures supposément associées à l'innervation des dents (canalicules dorsaux) sont présents chez les fourmiliers édentés, alors qu'elles sont absentes chez les pangolins également édentés. L'anatomie comparative intra- et interspécifique permet de : i) montrer que les canalicules dorsaux sont invariablement présents chez les fourmiliers ; ii) confirmer la relation entre les canalicules dorsaux et le développement dentaire précoce ; iii) montrer l'évolution indépendante des canalicules dorsaux chez les fourmiliers et les baleines à fanons. Les canalicules dorsaux sont vascularisés et innervés chez le fourmilier à collier, malgré la perte de ses dents. Ceci suggère, qu'en dépit de la perte des dents, l'innervation de la pulpe dentaire a probablement gardé un rôle sensoriel sur la partie dorsale de la mandibule des fourmiliers. La deuxième partie du chapitre 2 est consacrée à l'anatomie comparée de la musculature de la tête des trois genres de fourmiliers actuels. Les dissections classiques et numériques ont confirmé la réduction de l'appareil masticateur des fourmiliers. L'appareil masticateur du fourmilier pygmée est très différent de celui des deux autres genres. Une comparaison avec les musculatures crânienne des pangolins et des oryctéropes a été faite, uniquement basée sur des études publiées précédemment. Bien que myrmécophages, la musculature de la tête des oryctéropes et des pangolins présente quelques différences importantes avec celle des fourmiliers. Cela suggère que l'appareil masticateur des mammifères placentaires myrmécophages varie au niveau fonctionnel.Le dernier chapitre de cette thèse couvre les modèles de covariance phénotypique du crâne de 15 espèces myrmécophages. Une approche de morphométrie géométrique est utilisée afin d'explorer et de confirmer les hypothèses de modularité. Les résultats montrent que les patrons de modularité chez les mammifères myrmécophages ressemblent à ceux des autres mammifères placentaires. Aucun changement commun dans la parcellisation du crâne n'a été détecté, autre que celui attendu de l'hypothèse nulle. Les résultats suggèrent plutôt que l'allongement du crâne a pu entraîner un léger remodelage des patrons de modularité dans la région du rostre des fourmiliers myrmécophagidés. Une analyse préliminaire des trajectoires ontogénétiques des matrices de covariance phénotypique chez deux espèces myrmécophages montre que les patrons de covariance changent significativement pendant l'ontogenèse. Cela indique que les interprétations fonctionnelles de la modularité statique et de l'intégration doivent être effectuées avec prudence<br>The subject of this thesis is the morphological convergence in the skull of ant- and termite-eating placentals. Its goals are to characterize tooth reduction, covariance patterns, and morphological variation of the skull, and explore their link to the selective pressures associated to myrmecophagy.The first chapter focuses on the evolutionary, ontogenetic, and static variations of the skull in pangolins, a group of myrmecophagous animals that include the most threatened mammalian species on Earth. The morphological delimitation between seven of the eight species is demonstrated. Their ontogenetic allometric trajectories are described and the implications of the size variation on systematics are discussed. Additionally, intraspecific variation was partly associated to molecular distinctiveness of recently diverged cryptic species within the white-bellied pangolin. These results were obtained with the use of three-dimensional geometric morphometric methods.The second chapter was dedicated to the comparative anatomy of the mandible and masticatory apparatus. First, I investigate the internal mandibular anatomy on a comparative sample of placental mammals using µ-CT tomography and histology. Structures putatively associated to tooth innervation (dorsal canaliculi) are present in toothless anteaters, while they are absent in pangolins, which are equally toothless. Comparative anatomy performed intra- and interspecifically allowed to: i) show that dorsal canaliculi are invariably present in anteaters; ii) confirm the relationship between dorsal canaliculi and early tooth development; iii) show the independent evolution of dorsal canaliculi in anteaters and toothless whales. Dorsal canaliculi are vascularized and innervated in the collared anteater, despite its tooth loss. This suggests that despite tooth loss, tooth pulp innervation likely maintained its sensorial role on the dorsal part of the mandible of anteaters. The second part of chapter 2 is devoted to the comparative anatomy of the head musculature of the three extant anteater genera. Classical and digital dissections confirmed the reduction of the masticatory apparatus in anteaters. The masticatory apparatus of the pygmy anteater is found to significantly differ from that the other two genera. A comparison with the head musculatures of pangolins and aardvarks was done, based on previously published studies. Despite being myrmecophagous, the head musculature of aardvarks and pangolins shows some key differences from that of anteaters. This suggests that the feeding apparatus of ant- and termite-eating placentals varies at the functional level.The last chapter of this thesis covers the patterns of phenotypic covariance of the skull of 15 myrmecophagous species. A geometric morphometrics approach is used in order to explore and confirm hypotheses of modularity. Results show that patterns of modularity in myrmecophagous mammals resemble those of other placentals mammals. No common shift in the parcellation was found, other than that expected from the null hypothesis. Results suggest instead that skull elongation might have resulted on a slight remodeling of modularity patterns on the rostrum region in myrmecophagid anteaters. A preliminary analysis of ontogenetic trajectories of phenotypic covariance matrices in two myrmecophagous species shows that covariance patterns significantly change during ontogeny. This indicates that functional interpretations of static modularity and integration must be taken with caution

Thesis: Ph. D., Massachusetts Institute of Technology, Department of Biology, 2014.<br>Title as it appears in MIT commencement exercises program, June 6, 2014: The evolution of mRNA splicing in mammalian tissues Cataloged from PDF version of thesis.<br>Includes bibliographical references (pages 167-172).<br>In this thesis, I describe investigations into the evolution of splicing in mammals. I first investigate a small class of alternative splicing events, tandem splice sites, and show how they are used to introduce and remove coding sequence in a species-specific manner. I then describe the generation and analysis of a large RNA-seq dataset from 9 matched tissues in 5 species, with the aim to investigate the evolution of splicing in mammals. I first investigate the evolution of exons that predate the most ancient divergence of species studied, finding that their splicing is frequently poorly conserved. For a subset of these exons, I identify unique regulatory properties and provide evidence linking alternative splicing to phosphorylation potential of proteins. I then consider sources of novel exons, in these species. I use these and other published data to identify one way in which splicing of novel exons impacts the biology of the cell. I also present evidence implicating genomic indels in exon creation and splicing variation.<br>by Jason Jay Merkin.<br>Ph. D.

Although tremendous progress has been made in many other groups, the forces and factors which affect synonymous codon use in mammals remain something of a mystery. At least some of the differences in codon usage between mammalian genes can be summarised in terms of composition: within any one species some genes have very low G+ C contents (< 30%) and others very high G+ C content (> 90&37), with the majority lying somewhere in between. The very simplicity of this trend and the fact that this composition is correlated to that of introns and isochores suggests that the differences in synoymous codon use may be the result of variation in the pattern of mutation across the genome. This hypothesis is examined by considering the three most likely ways in which the mutation pattern might vary across the genome: (1) temporal changes in the performance of the replicative machinery; (2) variation in the efficiency of DNA repair; and (3) variation in the frequency of gene conversion across the genome. Evidence is found against all these hypotheses. Principally none of them predict the silent substitution rate to be related to G+ C content in the manner which is observed. Furthermore the lack of any discernible difference between the silent site G+ C contents of early and late replicating genes, and the very small parameter range over which DNA repair can generate large differences in synonymous codon use, support the conclusions that replication and repair, respectively, are not responsible for the codon use of mammalian genes. It is therefore suggested that selection might act upon synonymous codon use. However an analysis of codon usage within genes suggests that selection of the type commonly found in other groups, selection upon tRNA interaction, is not operative in mammals. It is tentatively suggested that selection upon mRNA secondary structure might be the responsible agent. Some of the results obtained also have implications for the maintenance of isochores. Since the G+ C contents of isochores and silent sites are correlated, the lack of any distinction with respect to composition between early and late replicating genes suggests that the differences in isochore G+ C content are not cuasd by DNA replication. However it is hypothesised that variation in the frequency of recombination can provide a very elegant explanation of the differences in isochore G+ C contents, and the relationship between gene density and isochore G+ C content.

Males care for offspring across a diverse range of taxa. Why males give up mating opportunities and spend time and energy caring for offspring is unclear, especially when females already provide parental care. The evolutionary drivers for biparental care are currently uncertain, as are the evolutionary consequences of male care on female and offspring fitness. Using modern phylogenetic comparative methods, I test hypotheses on the evolution of biparental care in a sample of over 500 mammalian species while considering the diversity in parental care behaviours. Both male care and monogamy occur in species where levels of paternity are high, but only monogamy associates with reduced investment in sperm competition traits. Male care also has energetic benefits for females and offspring; females have higher fecundity and offspring faster growth in species with biparental care, in support of the ‘load-lightening’ hypothesis. I find strong support for the hypothesis that monogamy drives the evolution of male care but only for behaviours that provide fecundity benefits, while behaviours unrelated to female fecundity may either precede or follow monogamy. However, I find no support for the hypothesis that infanticide by males promotes the evolution of male care. Lastly, I investigate whether care by non-parental helpers exhibit similar associations with life history traits as male care and find that care by helpers associates with increased fecundity, but by influencing different times of the female reproductive cycle. Overall I identify a two-step process of evolution between male care and social monogamy, with care behaviours which do not confer fecundity benefits facilitating the evolution of social monogamy and higher paternity levels, which subsequently promote the evolution of further care behaviours with higher energetic benefits. Thus, this research demonstrates the importance of considering the care behaviour performed, the time of female reproduction at which it is performed, and the identity of the carer, in studies investigating the evolution of parental care.

This thesis comprises comparative genomics analyses primarily focussing on the evolution of mammalian proteins. We concentrate on three species of direct relevance as model organisms, for which high quality genome sequences are available, and human. Having previously investigated protein evolution in terms of substitution rates, here we explored less well studied insertions and deletions (indels). We show that indel and substitution frequencies are correlated at the level of protein sequence, and that indels, and in particular insertions, are elevated in regions of low-complexity and repetitive sequence. Furthermore we observe that selection acts more strongly against the incorporation of insertions than deletions in coding sequence. We also look examine in detail the process of evolution following gene duplication in rodents. We show that in general there is a marked increase in evolutionary rate following duplication, which is restricted to the new copy. We find evidence that this increase is sometimes driven by positive selection, and often accompanied by changes in tissue expression profile. These results lead support to the role of neofuntionalisation following gene duplication.<br>Aquesta tesi consta d’anàlisis de genòmica comparada centrades principalment en l'evolució de les proteïnes de mamífers. Les anàlisis se centren en humans i en tres espècies de gran rellevància com a organismes model, per les quals les seqüències genòmiques són d’alta qualitat. Després d'haver investigat prèviament l'evolució de proteïnes considerant les taxes de substitució, en aquesta tesi hem explorat les insercions i delecions (indels), menys estudiades. Demostrem que existeix una correlació entre la freqüència d’indels i substitucions en la seqüència proteica, i que els indels, i en particular, les insercions, són habituals en les regions de baixa complexitat i seqüències repetitives. A més, observem que la selecció actua més fortament en contra de la incorporació d'insercions que de delecions en la seqüència codificant. D’altra banda, també pretenem analitzar detalladament el procés evolutiu després d’una duplicació gènica en rosegadors. Demostrem que, en general, hi ha un marcat augment en la taxa d'evolució després de la duplicació, que es limita a la nova còpia. I trobem evidències que aquest augment és, de vegades, impulsat per la selecció positiva, i, sovint acompanyada de canvis en el perfil d'expressió de teixits. Aquests resultats recolzen el procés de neofuncionalització després de la duplicació gènica.

Thesis (Ph. D.)--Harvard-MIT Division of Health Sciences and Technology, 2011.<br>Cataloged from PDF version of thesis.<br>Includes bibliographical references.<br>This thesis explores two aspects of small regulatory RNAs in mammals: (1) the genomic origin of mammalian piwi-interacting RNAs (piRNAs), (2) the evolutionary and functional implication of the seed-based target recognition mechanism of microRNAs (miRNAs). First, we participated in the discovery of mammalian piRNAs from adult rat testes. Our initial characterization of mammalian piRNAs by high-throughput sequencing revealed the peculiar features of their genomic origin: they predominantly derive from long singlestranded RNA precursors that are encoded at ~100 loci with no preferential association to repeat elements. Second, we measured the efficacy of polymorphic miRNA target sites in mammals. A large part of the miRNA-target recognition is determined by the 7-8-nt match between the seed region of miRNAs and the 3'UTR of mRNAs. Because of the small informational complexity of the specificity, spontaneous point mutations in 3'UTRs often create or disrupt miRNA target sites. The resulting polymorphisms in the target sites may contribute to gene expression diversity. By experimentally measuring the efficacy of such polymorphic target sites, we were able to conclude that between two unrelated mammalian individuals of the same species more than 100 genes are likely differentially regulated due to the target-site polymorphisms. Some of the expression diversity might translate into phenotypic diversity, providing substrates for the natural selection to act upon. We also constructed a miRNA library covering nearly all ~-16,000 theoretically possible seed sequences. Under the assumption that the functionality of a miRNA is approximately defined by the identity of the seed, the library is a resource that may enable the systematic exploration of the phenotypic consequences of nearly all possible functionally distinct miRNA species.<br>by Jinkuk Kim.<br>Ph.D.

Auf der Basis von Fossilien wird angenommen, dass die ersten Säugetiere nachtaktiv waren. Diese Arbeit untersucht diese Hypothese mit bioinformatischen und molekularbiologischen Techniken. Der Fokus liegt auf dem Rhodopsin, ein Sehpigment im Wirbeltierauge, das für Sehen unter schlechten Lichtverhältnissen verantwortlich ist. Zunächst wurde das Rhodopsin der monotrematen Echidna, einem basalen Säugetier, sequenziert und mit zwei Mutanten mit Mutationen an Positionen 158 und 169 in vitro exprimiert. Die biochemische und funktionelle Charakterisierung ergab, dass das Echidna-Rhodopsin farbpigment-typische Charakteristika aufweist, was auf eine Expression auch in Zapfen hindeutet. Dies ist die erste Charakterisierung eines Rhodopsins eines nachtaktiven Tieres. Dann wurden anzestrale Rhodopsinsequenzen für die Knotenpunkte Amniota, Mammalia und Theria mithilfe der Maximum-Likelihood-Methode berechnet. Die in vitro Expression und biochemische und funktionelle Charakterisierung zeigt funktionale und rhodopsin-typische Sehpigmente. Das Mammalia- und Theria-Rhodopsin zeigen eine hohe Meta II Halbwertszeit. Dieses Ergebnis wird als eventuelle Anpassung an Sehen unter schlechten Lichtverhältnissen interpretiert, wobei, aufgrund von Unstimmigkeiten in der Literatur, Schlussfolgerungen auf ökologisch-bedingte Anpassungen basierend auf einzelnen Funktionstests problematisch sind, da die visuelle Signalkaskade ein sehr komplexes und durch viele Proteine vernetztes System darstellt. Zuletzt zeigen Selektionsanalysen, dass das Rhodopsin entlang der Theria-Linie positive Selektion auf nicht-synonyme Substitutionen erfahren hat, was zu Anpassungen in einem Protein führt. Der Fossilbericht belegt entlang dieser Linie mehrere Einnischungsevents in neue Lebensräume. Entlang der Mammalia-Linie wurde positive Selektion auf synonyme Substitutionen gemessen, was zu einer Zunahme an Rhodopsin-Molekülen führt und damit eine Anpassung an Sehen unter schlechten Lichtverhältnissen darstellt.<br>Based on information from the fossil record, the first mammals are thought to have been nocturnal. This thesis investigates this popular hypothesis using bioinformatic and molecular techniques, focusing on the rhodopsin, a visual pigment in the vertebrate eye that is responsible for vision at low-light levels. First, the rhodopsin gene of the monotreme echidna, a basal mammal, was sequenced and successfully expressed in vitro, together with two mutants with substitutions at sites 158 and 169. Biochemical and functional analyses revealed that the echidna rhodopsin displays cone-like characteristics, likely due to being also expressed in cones. With the echidna being nocturnal, this thesis comprises the first characterisation of a rhodopsin of a nocturnal animal. Second, ancestral rhodopsin sequences for the tetrapod nodes Amniota, Mammalia, and Theria were inferred using Maximum likelihood estimates. All expressed pigments were successfully expressed in vitro, functional and rod-like. Mammalia and Theria rhodopsins display a high meta II half life time, a pattern that is usually interpreted to facilitate better vision at low-light levels. However, due to inconsistency in the available data, the result also suggests that, with the visual signaling cascade being a complex and interconnected system, erecting ecological interpretations based on single biochemical and functional reactions is problematic. Third, selective constraint analyses performed on a set of tetrapod rhodopsin sequences indicate that positive selection on non-synonymous sites, was acting along the branch leading to Theria. This result reflects the rapid diversification into modern ecological habitats during the Triassic and Jurassic, as indicated by the fossil record. In addition, positive selection on synonymous sites, leading to an increase of rhodopsin molecules, was found along the branch leading to Mammalia and suggests adaptations to vision at low-light levels.

<p>Here I look at three stages in the evolutionary development of mammalian brains. Chapter one addresses how connectivity in neocortex scales with brain size. This is of evolutionary interest because it helps define the basic mammalian condition. Neocortical white matter increases disproportionately in large brains. This might reflect increases in the number of connections per neuron. It might also reflect scaling in axon diameter. I compare these hypotheses by examining white matter-gray matter scaling in cerebellum. Because the white matter of cerebellum lacks cortico-cortical connections, the connectivity theory predicts that cerebellar white matter should not hyperscale relative to gray matter. I have measured white matter and gray matter volume in a large sample of mammals and I find that cerebellar white matter does not hyperscale. This supports the proposition that neocortical hyperscaling reflects an increase in the number of connections per neuron in large brains.</p> <p>In chapter two I use independent contrasts analysis to examine the scaling of frontal cortex in a large sample of mammals. I find significant differences in scaling between primates and carnivores. Primate frontal cortex hyperscales relative to the rest of neocortex and the rest of the brain, and the primate slope is significantly greater than that for carnivores. This suggests that there are substantial differences in frontal cortex structure and development between the two groups. Combined with with anatomical differences, it suggests that primates have evolved a number of unique adaptations in frontal cortex.</p> <p>Chapter three examines the evolution of brain size in anthropoid primates. Living anthropoids have larger brains than strepsirrhines. What about early anthropoid fossils? I measure brain size in the early anthropoid Parapithecus grangeri using computed tomography. I find that relative to the living anthropoids, Parapithecus had a small brain for its body size. Thus large brains did not develop at the same time as a number of other anthropoid adaptations.</p>

Dissertation (PhD)--University of Stellenbosch, 2006.<br>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.<br>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.

The aim of this project was to study the nature and relative proportion of the volatile components in the sternal-gland secretions obtained from a wide range of Australian marsupials.The results obtained were then used to investigate the evolution of semiochemicals in Australian marsupials by using the current phylogenetic tree as a template.The initial part of the study was dedicated to the investigation of some of the techniques available for the sampling and analysis of gland secretions. Individuals from 8 families within the Marsupialia and 1 family from the Monotremata were sampled over an 18 month period.The obtained results were then subjected to multivariate statistical analysis followed by cladistic analysis.In several species the secretion composition was found to be affected by the breeding status of individuals for both genders.Many other factors such as animal-age, hierarchical status, diet,and lifestyle were also observed to affect the secretion composition. Finally, cladistic analysis demonstrated the differences in the levels of divergence at the species, familial and ordinal levels and highlighted secretion components that could be used to differentiate between super families, species and even sexual status of individuals.<br>Master of Science (Hons)

<p> Aposematic prey animals use conspicuous, high contrast color patterns to warn potential predators that they possess a defense mechanism. Avian predators show an innate phobia of bold, contrasting color patterns, and can readily learn to avoid a prey item displaying bold warning coloration. Signal uniformity is important to promote predator learning and memory retention; however, there is documented variation in the aposematic pattern of many species, including the striped skunk (<i>Mephitis mephitis</i>). Most of the literature on aposematism refers to studies using avian predators and insect prey &ndash; we know relatively little about how mammalian predators learn about and interact with aposematic prey, despite the recognized influence of predation on the evolution of aposematism in mammals. This study examined the behavior of coyote (<i>Canis latrans</i>) subjects during interactions with baited black-and-white models that were able to spray a dilute skunk oil solution. Coyotes are the most common mammalian predator of striped skunks. To test their ability to generalize, after being sprayed coyotes were introduced to a variant model design based on natural documented variation in striped skunk pelage. The results demonstrate that coyotes show innate wariness of a black-and-white striped model, and most can effectively learn to avoid the model after being sprayed. Variants with proportionately more white incited more avoidance behaviors than darker patterns, although they did not allow for greater signaling power than the diagnostic black-and-white striped pattern. </p>

This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.<br>Thesis: Ph. D., Massachusetts Institute of Technology, Department of Biology, 2019<br>Cataloged from student-submitted PDF version of thesis. "June 2019."<br>Includes bibliographical references.<br>Sex differences are widespread in mammalian health, development, and disease. Ultimately, sex differences derive from the sex chromosomes; males are XY and females are XX, but the mammalian X and Y chromosomes evolved from an ancestral pair of ordinary autosomes. These genetic sex differences, through a variety of regulatory mechanisms, give rise to sex differences in gene expression across the genome, which in turn result in the observed phenotypic differences between males and females. In this thesis, I take an evolutionary perspective on this pathway, using computational analysis of both publically available and newly generated data to provide insight into the molecular basis of mammalian sex differences.<br>First, to better understand the selective forces underlying the evolution of the amniote sex chromosomes from ordinary autosomes, we reconstructed gene-by-gene dosage sensitivities on the ancestral autosomes through phylogenetic analysis of microRNA target sites, finding that preexisting heterogeneities in dosage sensitivity shaped the evolution of both the mammalian XY and avian ZW sex chromosomes. Second, to understand the extent to which genome-wide sex differences are conserved across both tissues and species, we conducted a five-species, twelve tissue survey of sex differences in gene expression, finding that most sex bias in gene expression has arisen during since the last common ancestor of boroeutherian mammals, and that evolutionary gains or losses of regulation by sex-biased transcription factors likely drove a significant fraction of lineage-specific changes in sex bias.<br>Third, we used the results of this survey to show that conserved sex bias in gene expression contributes to the male bias in height and body size observed in a range of mammalian species, including humans. Together, these studies suggest that dosage sensitivity played a key role in both the evolution of mammalian sex chromosomes and their contribution to phenotypic sex differences, as well revealing the widespread nature and phenotypic impact of sex differences in gene expression across the genome.<br>by Sahin Naqvi.<br>Ph. D.<br>Ph.D. Massachusetts Institute of Technology, Department of Biology

Characterising and understanding factors that affect the rate of molecular evolution in proteins has played a major part in the development of evolutionary theory. The early analyses of amino acid substitutions stimulated the development of the neutral theory of molecular evolution, which later evolved into the nearly neutral theory. More recent work has lead to a better understanding of the role selection plays at the molecular level, but there is still limited understanding of how higher levels of protein organisation affect the way natural selection acts. The investigation of this question is the central aim of this thesis, which is addressed via the analysis of selective pressures in secondary protein structures in insects, mammals and fungi. The analyses for the first two groups were conducted using publically available datasets. To conduct the analyses in fungi, genome sequence data from the fungal genus Microbotryum (sequenced in our laboratory) was assembled and annotated, resulting in the development of a number of bioinformatics tools which are described here. The fungal, insect and mammalian datasets were interrogated with regard to a number of structural features, such as protein secondary structure, position of a site with regard to adaptively evolving sites, hydropathy and solvent-accessibility. These features were correlated with the signals of positive and purifying selection detected using phylogenetic maximum likelihood and Bayesian approaches. I conclude that all of the factors examined can have an effect on the rate of molecular evolution. In particular, disordered and hydrophilic regions of the protein are found to experience fewer physiochemical constraints and contain a higher proportion of adaptively evolving sites. It is also revealed that positively selected residues are ‘clustered’ together spatially, and these trends persist in the three taxa. Finally, I show that this variation in adaptive evolution is a result of both selective events and physiochemical constraint.

The main objectives of this work are:<br/>a) To test the predictions of suppressed-recombination chromosomal speciation models on two different lineages of mammals: rodents and rimates. Suppressed-recombination chromosomal speciation is still quite elusive as a mode of speciation in mammals. Experimental results are scarce and the first objective of this work is to analyze whole-genome data looking for traces of events of chromosomal speciation. Rodent and primate lineages were chosen for this search, not just because of their particular biological and cytological characteristics, which make them good candidates to have speciated by this mechanism, but also because they were the first mammalian organisms to be fully sequenced. b) To study the effects of chromosomal rearrangements on genic evolutionary rates. As have been seen in the introduction, there are many of potential interactions among chromosomal rearrangements and evolutionary rates, so the second goal of this work was to try to understand the impact of chromosomal rearrangements over substitution rates by means of other mechanisms not related with speciation. c) To distinguish individual contributions of different genomic factors in the potential association among chromosomal rearrangements and evolutionary rates.The third main goal of this thesis was to discern among the different factors that could be explaining the many associations between chromosomal and genic evolution that were detected in different studies.

Genomic imprinting is responsible for monoallelic gene expression that depends on the sex of the parent from which the alleles (one active, one silent) were inherited. X-chromosome inactivation is also a form of monoallelic gene expression. One of the two X chromosomes is transcriptionally silenced in the somatic cells of females, effectively equalising gene dosage with males who have only one X chromosome that is not complemented by a gene poor Y chromosome. X chromosome inactivation is random in eutherian mammals, but imprinted in marsupials, and in the extraembryonic membranes of some placentals. Imprinting and X inactivation have been studied in great detail in placental mammals (particularly humans and mice), and appear to occur also in marsupial mammals. However, both phenomena appear to have evolved specifically in mammals, since there is no evidence of imprinting or X inactivation in non-mammalian vertebrates, which do not show parent of origin effects and possess different sex chromosomes and dosage compensation mechanisms to mammals.¶ In order to understand how imprinting and X inactivation evolved, I have focused on the mammals most distantly related to human and mouse. I compared the sequence, location and expression of genes from major imprinted domains, and genes that regulate genomic imprinting and X-chromosome inactivation in the three extant mammalian groups and other vertebrates. Specifically, I studied the evolution of an autosomal region that is imprinted in humans and mouse, the evolution of the X-linked region thought to control X inactivation, and the evolution of the genes thought to establish and control differential expression of various imprinted loci. This thesis is presented as a collection of research papers that examines each of these topics, and a review and discussion that synthesizes my findings.¶ The first paper reports a study of the imprinted locus responsible for the human Prader-Willi and Angelman syndromes (PWS and AS). A search for kangaroo and platypus orthologues of PWS-AS genes identified only the putative AS gene UBE3A, and showed it was in a completely different genomic context to that of humans and mice. The only PWS gene found in marsupials (SNRPN) was located in tandem with its ancient paralogue SNRPB, on a different chromosome to UBE3A. Monotremes apparently have no orthologue of SNRPN. The several intronless genes of the PWS-AS domain also have no orthologues in marsupials or monotremes or non-mammal vertebrates, but all have close paralogues scattered about the genome from which they evidently retrotransposed. UBE3A in marsupials and monotremes, and SNRPN in marsupials were found to be expressed from both alleles, so are not imprinted. Thus, the PWA-AS imprinted domain was assembled from many non-imprinted components relatively recently, demonstrating that the evolution of imprinting has been an ongoing process during mammalian radiation.¶ In the second paper, I examine the evolution of the X-inactivation centre, the key regulatory region responsible for X-chromosome inactivation in humans and mice, which is imprinted in mouse extraembryonic membranes. By sequencing and aligning flanking regions across the three mammal groups and non-mammal vertebrates, I discovered that the region homologous to the X-inactivation centre, though intact in birds and frogs, was disrupted independently in marsupial and monotreme mammals. I showed that the key regulatory RNA of this locus (X-inactive specific transcript or XIST) is absent, explaining why a decade-long search for marsupial XIST was unsuccessful. Thus, XIST is eutherian-specific and is therefore not a basic requirement for X-chromosome inactivation in all mammals.¶ The broader significance of the findings reported in these two papers is explored with respect to other current work regarding the evolution and construction of imprinted loci in mammals in the form of a review. This comparison enabled me to conclude that like the PWS-AS domain and the X-inactivation centre, many domains show unexpected construction from disparate genomic elements that correlate with their acquisition of imprinting.¶ The fourth and last paper examines the evolution of CCCTC-binding Factor (CTCF) and its parologue Brother Of Regulator of Imprinted Sites (BORIS) which contribute to the establishment and interpretation of genomic imprinting at the Insulin-Like Growth Factor 2/H19 locus. In this paper I show that the duplication of CTCF giving rise to BORIS occurred much earlier than previously recognised, and demonstrate that a major change in BORIS expression (restriction to the germline) occurred in concert with the evolution of genomic imprinting. The papers that form the bulk of this thesis show that the evolution of epigenetic traits such as genomic imprinting and X-chromosome inactivation is labile and has apparently responded rapidly to different selective pressures during the independent evolution of the three mammal groups. I have introduced these papers, and discussed them generally in terms of current theories of how and why these forms of monoallelic expression have evolved in mammals.

Remarkable feats of breath-hold endurance are observed in diving mammals, with some species routinely diving for an hour. During most mammalian dives metabolism remains aerobic in nature, which is accomplished by restricting the blood flow to parts of the body through peripheral vaso-constriction and bradycardia. This mechanism preserves essential oxygen (02) for heart and brain function, but also means some parts of the body, including locomotory muscles, become isolated and have to rely on O2 stored within the tissues. Due to the isolation of skeletal muscles, mammalian divers must be able to buffer large quantities of H+ ions due to the production of CO2 during aerobic metabolism and acidic end products of anaerobic metabolism once muscle O2 stores have been consumed. The protein responsible for storing molecular 02 is myoglobin (Mb), a small 17 kDa monomeric globular haemoprotein with the primary function of reversible O2 binding and facilitated diffusion of O2 to the mitochondria. A hallmark of mammalian divers is increased Mb concentrations ([Mb]. with divers exhibiting concentrations up to thirty times those seen in non-diving species. Previous research has found that proteins at high concentrations are prone to form aggregations leading to non-functioning protein. This raises the question of Mb solubility at such high concentrations as observed in mammalian divers. The central hypothesis of this thesis is that mammalian myoglobin has undergone previously unrecognised, parallel and adaptive evolution in several lineages of mammalian divers that has profoundly increased their maximal physiological diving capacity. To test the hypothesis, Mb amino acid sequences of 124 mammals, including 24 newly determined sequences, are analysed for the content and individual buffering properties of their ionisable amino acids. This is used to calculate the specific Mb buffer value (~Mb) for each species, which is experimentally verified by acid-base titration of purified Mb. Together with known [Mb], the contribution of Mb to whole muscle buffer capacity WmuscleMb) is then quantified. Amino acid sequences are assessed for substitutions that increase modelled net Mb charge in mammalian divers compared to terrestrial species and predictions are confirmed by measuring electrophoretic mobility of purified Mb. Observed changes in Mb buffer properties and net surface charge are mapped on a composite mammalian phylogeny to test whether they are significantly linked to the evolution of diving behaviour. Observed molecular changes in Mb amino acid sequence are integrated with diving capacity, producing a model that allows prediction of maximal dive duration from Mb amino acid sequence and body mass. Using ancestral Mb sequence reconstructions and body mass estimates, the model is applied to infer the evolution of maximal diving capacity in the cetacean lineage. Results suggest a general trend towards increasing ~Mb due to increased Mb histidine content in mammalian divers.βmuscleMb is significantly higher in divers compared to terrestrial species, and can account for up to 45%, of the increase in whole muscle buffering observed in diving mammals. This study shows a remarkable trend in all diving species to significantly increase the net charge of the Mb protein, which would convey increased Mb solubility. This is supported by a significant correlation between Mb net charge and maximal [Mb]. Evolutionary analysis shows that high Mb net charge is significantly linked to the occurrence of diving. Contrary to previous findings, the model developed here finds that increases in [Mb] convey greater increases in dive duration than similar increases in body mass. This study provides novel in sights into how cumulative substitutions on the molecular surface of Mb can have profound adaptive effects on the physiological properties conveyed to the whole animal. It suggests that adaptation to diving in multiple lineages of mammals involved not only evolution of increased expression levels of Mb, but also substantial qualitative changes to the protein to avoid aggregation and increase solubility and buffering.

MHC genes encode proteins that are responsible for the recognition of foreign antigens and the triggering of a subsequent, adequate immune response of the organism. Thus they hold a key position in the immune system of vertebrates. It is believed that the extraordinary genetic diversity of MHC genes is shaped by adaptive selectional processes in response to the reoccurring adaptations of parasites and pathogens. A large number of MHC studies were performed in a wide range of wildlife species aiming to understand the role of immune gene diversity in parasite resistance under natural selection conditions. Methodically, most of this work with very few exceptions has focussed only upon the structural, i.e. sequence diversity of regions responsible for antigen binding and presentation. Most of these studies found evidence that MHC gene variation did indeed underlie adaptive processes and that an individual’s allelic diversity explains parasite and pathogen resistance to a large extent. Nevertheless, our understanding of the effective mechanisms is incomplete. A neglected, but potentially highly relevant component concerns the transcriptional differences of MHC alleles. Indeed, differences in the expression levels MHC alleles and their potential functional importance have remained unstudied. The idea that also transcriptional differences might play an important role relies on the fact that lower MHC gene expression is tantamount with reduced induction of CD4+ T helper cells and thus with a reduced immune response. Hence, I studied the expression of MHC genes and of immune regulative cytokines as additional factors to reveal the functional importance of MHC diversity in two free-ranging rodent species (Delomys sublineatus, Apodemus flavicollis) in association with their gastrointestinal helminths under natural selection conditions. I established the method of relative quantification of mRNA on liver and spleen samples of both species in our laboratory. As there was no available information on nucleic sequences of potential reference genes in both species, PCR primer systems that were established in laboratory mice have to be tested and adapted for both non-model organisms. In the due course, sets of stable reference genes for both species were found and thus the preconditions for reliable measurements of mRNA levels established. For D. sublineatus it could be demonstrated that helminth infection elicits aspects of a typical Th2 immune response. Whereas mRNA levels of the cytokine interleukin Il4 increased with infection intensity by strongyle nematodes neither MHC nor cytokine expression played a significant role in D. sublineatus. For A. flavicollis I found a negative association between the parasitic nematode Heligmosomoides polygyrus and hepatic MHC mRNA levels. As a lower MHC expression entails a lower immune response, this could be evidence for an immune evasive strategy of the nematode, as it has been suggested for many micro-parasites. This implies that H. polygyrus is capable to interfere actively with the MHC transcription. Indeed, this parasite species has long been suspected to be immunosuppressive, e.g. by induction of regulatory T-helper cells that respond with a higher interleukin Il10 and tumor necrosis factor Tgfb production. Both cytokines in turn cause an abated MHC expression. By disabling recognition by the MHC molecule H. polygyrus might be able to prevent an activation of the immune system. Indeed, I found a strong tendency in animals carrying the allele Apfl-DRB*23 to have an increased infection intensity with H. polygyrus. Furthermore, I found positive and negative associations between specific MHC alleles and other helminth species, as well as typical signs of positive selection acting on the nucleic sequences of the MHC. The latter was evident by an elevated rate of non-synonymous to synonymous substitutions in the MHC sequences of exon 2 encoding the functionally important antigen binding sites whereas the first and third exons of the MHC DRB gene were highly conserved. In conclusion, the studies in this thesis demonstrate that valid procedures to quantify expression of immune relevant genes are also feasible in non-model wildlife organisms. In addition to structural MHC diversity, also MHC gene expression should be considered to obtain a more complete picture on host-pathogen coevolutionary selection processes. This is especially true if parasites are able to interfere with systemic MHC expression. In this case advantageous or disadvantageous effects of allelic binding motifs are abated. The studies could not define the role of MHC gene expression in antagonistic coevolution as such but the results suggest that it depends strongly on the specific parasite species that is involved.<br>Die Hauptaufgabe von MHC-kodierten Proteinen ist die Erkennung von körperfremden Molekülen sowie das Einleiten einer adäquaten Immunantwort, womit sie eine Schlüsselrolle im Immunsystem der Wirbeltiere einnehmen. Man nimmt an, dass ihre außergewöhnliche Vielfalt eine Antwort auf die sich ständig anpassenden Parasiten und Krankheitserreger ist, durch adaptive Selektion erhalten wird und dass die individuelle Allelausstattung einen Großteil der Parasitenbelastung erklärt, wofür bereits zahlreiche MHC-Studien Hinweise gefunden haben. Trotzdem ist unser Verständnis über die wirkenden Mechanismen teilweise noch lückenhaft. Ein stark vernachlässigter Aspekt hierbei sind z.B. eventuelle Unterschiede in der Genexpression der MHC-Allele und eine geringere Expression wäre gleichbedeutend mit einer geringeren Aktivierung des Immunsystems. Ich habe hierzu zwei frei lebende Kleinsäugerarten (Delomys sublineatus, Apodemus flavicollis) unter natürlichen Selektionsbedingungen untersucht. Dabei habe ich neben der genotypischen Diversität von MHC-Genen auch deren Expression, sowie die Genexpression immunregulativer Zytokine mit in Betracht gezogen und in Relation zur individuellen Belastung mit gastrointestinalen Helminthen gesetzt. Anhand von Leber und Milzproben beider Arten habe ich die Methode der ‚real-time PCR‘ zur relativen Quantifizierung von mRNA im Labor etabliert. Bereits für die Labormaus etablierte PCR-Primersysteme wurden an beiden Arten getestet und so konnten stabile Referenzgene gefunden werden, die Grundvoraussetzung für zuverlässige Genexpressionsmessungen. Für D. sublineatus konnte gezeigt werden, dass Helminthenbefall eine typische Th2 Immunantwort induziert, und dass der Zytokin Il4 Gehalt mit Befallsintensität strongyler Nematoden zunimmt. Es wurde für D. sublineatus kein signifikanter Zusammenhang zwischen MHC Expression oder anderen Zytokinen mit Helminthenbefall gefunden. In A. flavicollis wurde ein negativer Zusammenhang zwischen haptischer MHC-Expression und dem parasitären Nematoden Heligmosomoides polygyrus festgestellt, was auf eine Immunvermeidungsstrategie des Nematoden hindeutet. Ich fand typische positive und negative Assoziationen zwischen MHC-Allelen und anderen Helminthenarten, sowie Zeichen eines positiven Selektionsdruckes auf den MHC-Sequenzen, was sich durch eine erhöhte Rate aminosäureverändernder Mutationen zeigte. Diese nicht-synonymen Veränderungen waren auf Positionen innerhalb des zweiten Exons des DRB-Genes beschränkt, wohingegen die untersuchten Bereiche des ersten und dritten Exons stark konserviert vorlagen. Diese variablen Positionen kodieren Schlüsselstellen im Bereich der Antigenbindungsstelle im MHC Molekül. Zusammenfassend zeigt diese Arbeit, dass Genexpressionsstudien auch an Wildtieren durchgeführt und verlässliche Daten erzeugt werden können. Zusätzlich zur strukturellen Vielfalt sollten zukünftig auch mögliche Genexpressionsunterschiede bei MHC-Studien berücksichtigt werden, um ein kompletteres Bild der koevolutiven Wirt-Parasiten-Beziehungen zeichnen zu können. Dies ist vor allem dann von evolutiver Bedeutung, wenn die Parasiten in der Lage sind die MHC Expression aktiv zu beeinflussen. Die Studien konnten nicht die exakte Bedeutung von MHC-Genexpression in der antagonistischen Koevolution definieren, aber sie konnten zeigen dass diese Bedeutung stark von den jeweils beteiligten Partnern abzuhängen vermag.

<p>In this thesis, the shape of the distal humerus trochlea is analysed using landmark-based morphometrics and multivariate methods, with the aim of exploring locomotor evolution in carnivorans. Elbow joint morphology is used together with body size and craniodental morphology to characterize past and present carnivorans. Evolutionary implications are studied at the ordinal, familial, and species levels, testing specific hypotheses about scaling, morphological constraints, evolutionary trajectories, and potential for social pack-hunting behaviour. The circumference of the distal humerus trochlea is found to be highly correlated with body mass, and appears to scale similarly throughout the order Carnivora. A general predictive model for carnivoran bodymass is presented (a=0.601; b= 2.552; r2=0.952, SEE=0.136, p<0001, n=92), which removes the need for the investigator to actively choose between the diverging estimates that different predictors and their equations often produce. At the elbow joint, manual manipulation and locomotion appear to be conflicting functions, thus suggesting mutually exclusive lifestyles involving either forelimb grappling or pursuit. At large body sizes, carnivorans are distributed over a strongly dichotomised pattern (grappling or locomotion), a pattern coinciding with the postulated threshold in predator-prey size ratio at 21.5-25 kg. This pattern is compared to that of two carnivoran faunas from the Tertiary. In the Oligocene (33.7-23.8 Myr BP), the overall pattern is remarkably similar to that observed for extant Carnivora. In the Miocene (23.8-11.2 Myr BP) carnivores show a similarly dichotomised pattern as the Oligocene and Recent, although the whole pattern is shifted towards larger body sizes. This difference is suggested to be a reflection of the extraordinary species richness of browsing ungulates in the early Miocene of North America. Such an increase in prey spectrum would create a unique situation, in which large carnivores need not commit to a cursorial habitus in order to fill their nutritional requirements. Finally, the elbow joints and craniodental morphology (14 measurements) of fossil canids were examined with the aim of assessing the potential for pack-hunting in fossil canids. It is clear that small and large members of the Recent Caninae share similar craniodental morphologies. However, this pattern is not present in Borophaginae and Hesperocyoninae. In the latter, large representatives are characterized by being short-faced, with reduced anterior premolars and enlarged posterior premolars, thus approaching a “pantherine-like” craniodental configuration. These traits are interpreted as an adaptation for killing prey with canine bites. It is similarly determined that, unlike recent Caninae, all analyzed species of borophagines and hesperocyonines have retained the ability to supinate their forearms. It is therefore likely that manual manipulation was part of their hunting behaviour, thus removing an essential part of the argument for social pack-hunting in these forms, as the benefits of such a strategy become less obvious.</p>

La mida corporal (o el seu proxy: pes corporal) té una posició central en la immensa web de variables biològiques interdependents d’un organisme. Mostra correlació amb moltes característiques fisiològiques, morfològiques, comportamentals, ecològiques i de life history, i, per tant, afecta a l’aptitud biològica dels individuals i, en última instància, a la biologia i evolució de les espècies. Els canvis de mida (o massa) des d’un punt de vista evolutiu són indicatius d’adaptacions als ecosistemes per selecció natural. Una de les tendències eco-geogràfiques més atractiva en variació de mida és la coneguda Regla d’Illes. Es descriure que en ecosistemes insulars els mamífers de talla petita evolucionen cap a formes gegants (en relació als seus ancestres continentals), mentre que els mamífers grans cap a formes nanes. Associat amb els canvis de mida, les biotes insulars també mostres adaptacions característiques en quan a morfologia, demografia, comportament i life history com a conseqüència dels diferents règims selectius de les illes (Síndrome d’Illes). Les possibles causes de la Regla d’Illes han estat sempre estudiades en biotes actuals, les quals manquen d’espècies nadiues veritablement endèmiques i han estat altament modificades per l’arribada de l’home i les espècies invasores. Les biotes extintes són les úniques que ens poden proporcionar una visió verdadera i donar-nos respostes genuïnes per explicar aquest fenomen. Els ecòlegs de comunitats han proposat diverses teories per explicar com les pressions ecològiques desencadenen el gegantisme operant directament sobre la mida de l’individu (hipòtesis de depredació, de viabilitat de recursos i socio-sexual). No obstant, recentment, altres autors han interpretat el gegantisme com a conseqüència de canvis en la life history dels individus als quals la mida corporal es sensitiva. L’objectiu principal de la present tesis doctoral és fer inferència en les pressions selectives que estan darrera la Regla d’Illes tenint en compte la massa corporal d’espècies extintes i els ecosistemes insulars (Illes Mediterrànies). Degut a la gran quantitat d’ordres de mamífers, la tesi doctoral es troba centrada en els micromamífers perquè la seva investigació ha estat més descuidada. Per conèixer el pes de les espècies fòssils, s’han mesurat dents, cranis i ossos postcranials de 1340 individus (170 espècies) de parents actuals (rosegadors, lagomorfs i sorícids). Amb aquestes dades, diversos models predictius han estat desenvolupats amb resultats satisfactoris. Analitzant la fiabilitat d’aquests models, s’ha observat que les mesures dels estilopodis (principalment diàmetres de fèmurs i húmers) són millors indicadors del pes corporal que altres elements esquelètics. Utilitzant aquests nous models, els pesos corporals de 22 espècies fòssils (2250 individus), incloent espècies insulars i els seus ancestres o parents continents, han estat estimats. Els resultats obtinguts contrasten amb prèvies aproximacions, on els autors van utilitzar models dentals no adequats. Quan comparem el pes corporal de les espècies insulars amb els dels seus ancestres continentals o parents actuals o extints, s’observa que la majoria d’ells mostra un morfotip gegant (amb l’excepció de les musaranyes de Creta i Sicília). Els resultats d’aquesta tesi evidencien que en petits mamífers l’absència de depredadors és un dels principals impulsors del canvi de mida corporal en règims insulars. Per això en illes petites i més aïllades és on es produeixen els màxims exponents de gegantisme. L’estudi també evidencia que en absència de depredació, la disponibilitat de recursos podria regular l’augment de mida. L’estudi sobre la life history d’aquestes espècies revela que aquests vivien molt més del que s’esperaria pel seu pes. Per tant, es mourien cap una life history lenta, implicant una major longevitat i una reproducció retardada. Els resultats d’aquesta tesi donarien suport al model proposat on el pes canviaria degut a la sensibilitat amb la life history.<br>El tamaño corporal (o su proxy: peso corporal) tiene una posición central en la inmensa web de variables biológicas interdependientes de un organismo. Muestra correlación con muchas características fisiológicas, morfológicas, ecológicas y de life history, y, por lo tanto, afecta a la aptitud biológica de los individuos y, en última instancia, a la biología y evolución de las especies. Los cambios de tamaño (o masa) des de un punto de vista evolutivo son indicativos de adaptaciones a los ecosistemas por selección natural. Una de las tendencias eco-geográficas más atractiva en variación de tamaño es la conocida Regla de Islas. Se describe que en ecosistemas insulares los mamíferos de tamaño pequeño evolucionan hacia formas gigantes (en relación a sus ancestros continentales), mientras que los mamíferos grandes hacia formas enanas. Asociado con los cambios de tamaño, las biotas insulares también muestran adaptaciones en referencia a su morfología, demografía, comportamiento y life history como consecuencia de los distintos regímenes selectivos de las islas (Síndrome de Islas). Las posibles causes de la Regla de Islas han estado siempre estudiadas en biotas actuales, las cuales carecen de especies nativas endémicas y han estado altamente modificadas por la llegada del hombre y las especies invasoras. Las biotas extintas son las únicas que nos pueden dar respuestas genuinas para explicar este fenómeno. Los ecólogos de comunidades han propuesto distintas teorías para explicar cómo las presiones ecológicas originar el gigantismo operando directamente sobre el tamaño del individuo (hipótesis de depredación, de viabilidad de reservas y socio-sexual). No obstante, recientemente, otros autores han interpretado el gigantismo como consecuencia de cambio en la life history de los individuos a los cuales el tamaño es sensitivo. El objetivo principal de la tesis es hacer inferencia en las presiones selectivas que están detrás de la Regla de Islas teniendo en cuenta la masa corporal de las especies extintas y los ecosistemas insulares (Islas Mediterráneas). Debido a la gran cantidad de órdenes de mamíferos, la tesis se centra en los micromamíferos. Para conocer el peso de las especies fósiles, se han medido dientes, cráneos y huesos postcraneales de 1340 individuos (170 especies) de parientes actuales (roedores, lagomorfos y sorícidos). Con estos datos, distintos modelos predictivos han estado desarrollados con resultados satisfactorios. Analizando la fiabilidad de estos modelos, se ha observado que las medidas de los estilopodios (principalmente diámetros de fémures y húmeros) son mejores indicadores de peso corporal que otros elementos esqueléticos. Utilizando estos nuevos modelos, los pesos corporales de 22 especies fósiles (2250 individuos) han sido predichos. Los resultados obtenidos contrastan con estimaciones previas, donde los autores usaron modelos dentales no adecuados. Cuando comparamos el peso corporal de las especies insulares con los de sus ancestros contientales o parientes actuales o extintos, se observa que la mayoría de ellos muestra un morfotipo gigantes (con la excepción de las musarañas de Creta y Sicilia). Los resultados de esta tesis evidencian que en pequeños mamíferos la ausencia de depredadores es uno de los principales impulsores de cambio de tamaño en regímenes insulares. Por esto en las islas pequeñas y más aisladas es donde se producen los máximos exponentes de gigantismo. El estudio también evidencia que en ausencia de depredación, la disponibilidad de reservas podría regular el aumento de tamaño. El estudio sobre la life history de estas especias revela que éstas viven mucho más de lo que esperaríamos por su peso. Por lo tanto, se moverían hacia una life history lenta, implicando una mayor longevidad y una reproducción retardada. Los resultados de esta tesis darían soporte al modelo propuesto donde el peso cambiaría debido a la sensibilidad con la life history.<br>Body size (or its proxy: body mass) has a central position in the colossal web of interdependent biological variables of an organism. It shows correlation with lots of physiological, morphological, behavioral, ecological and life history features, and, thus, it affects the fitness of individuals and, ultimately, the biology and evolution of species. The shifts in size (or mass) from an evolutionary point of view are indicative of adaptations to ecosystems through natural selection. One of the most attractive and awesome ecogeographical trends in variation of body size is the well-known Island Rule. It is described that in island ecosystems small mammals evolve towards giants (relative to their mainland ancestors), while large mammals towards dwarf morphotypes. Associated with these size shifts, the insular biotas also show characteristic morphological, demographic, behavioral, and life history adaptations consequence of the different selective regimens of island (Island Syndrome). The possible causes of Island Rule have always been studied in extant biotas, which lack true endemic native species and have been highly modified by the arrival of humans and invasive species. The extinct biotas are the only ones that can provide a true view and genuine answers for explaining this phenomenon. Community ecologists have proposed several hypotheses to explain how ecological pressures trigger gigantism operating directly on the size of individual (predation hypothesis, food availability hypothesis or social-sexual hypothesis). However, recently other authors have interpreted the gigantism as a consequence of changes in the life history of individuals to which the body size is sensitive. The main objective of the present PhD Thesis is to make inference on the selection pressures behind the Island Rule taking into account the body mass of the extinct species and the island ecosystem (Mediterranean Islands). Due to the large amount of mammalian orders, the PhD Thesis is centered in micromammals because the knowledge of gigantism remains widely neglected. For knowing the weight of fossil species, it has been measured teeth, skulls and postcranial bones of 1340 individuals (170 species) of current relatives (rodents, lagomorphs and soricids). With this data, several predictive models have been developed with satisfactory results. Assessing the reliability of these models, it has been observed that the measurements of stylopods (principally diameters of femora and humeri) are better proxies of BM than other skeletal elements. Using these new models, the body masses of 22 fossil species (2250 individuals), including insular species and their mainland ancestor or relatives, were estimated. The results obtained contrast with previous approximations, where the authors used not suitable teeth predictive models. When the BM of insular species was compare with their mainland ancestor or extinct and extant relatives, it is observed that the most of them show a giant morph (with the exception of shrews from Crete and Sicily). The results of this PhD Thesis evidence that in small mammals the absence of predators is a primary driver in the body size shift in insular regimes. Thus, in small and more isolated islands is where the most incredible gigantism cases are observed. The study also evidences than in a total absence of predators, the resource availability can regulate the size increase. The study of the life history of these species reveals that they lived more than expected from their size. Thus, they move towards a slow life history, implying a longer lifespan and delayed reproduction. The results of this PhD Thesis give support to the model proposed where the mass changes due to their sensitive with life history changes.

This thesis began as an investigation into evolution of the platypus family (Ornithorhynchidae, Monotremata), now known from both Australia and South America. The thesis broadened its scope with inclusion of non-ornithorhynchid Mesozoic monotremes from Lightning Ridge, NSW. This change in direction brought an unexpected result: a fossil mammal from Lightning Ridge investigated for this thesis (presumed to be monotreme: Flannery et al., 1995) appears to be a new and unique type of mammal. Specimens were procured through Queensland Museum (Riversleigh material); Australian Museum (Lightning Ridge material); and Museum of Victoria and the South Australian Museum (fossil ornithorhynchids). Specimens were examined under a light microscope and scanning electron microscope; specimens were photographed using light photography and a scanning electron microscope; and illustrations and reconstructions were done with a camera lucida microscope attachment and photographic references. Parsimony analysis utilised the computer programs PAUP and MacClade. Major conclusions: 1) analysis and reconstruction of the skull of the Miocene platypus Obdurodon dicksoni suggest this robust, large-billed platypus was a derived northern offshoot off the main line of ornithorhynchid evolution; 2) the well-preserved skull of Obdurodon dicksoni shows aspects of soft anatomy previously unknown for fossil ornithorhynchids; 3) two upper molars from Mammalon Hill (Etadunna Formation, late Oligocene, central Australia) represent a third species of Obdurodon; 4) the South American ornithorhynchid Monotrematum sudamericanum from the Paleocene of Argentina is very close in form to the Oligocene-Miocene Obdurodon species from Australia and should be considered congeneric; 5) a revised diagnosis of the lower jaw of the Early Cretaceous monotreme Steropodon galmani includes the presence of two previously undescribed archaic features: the probable presence of postdentary bones and a meckelian groove; 6) morphological evidence is presented supporting a separate family Steropodontidae; and 7) analysis of new fossil material for Kollikodon ritchiei suggests that this taxon is not a monotreme mammal as originally identified but is a basal mammal with close relationships to allotherian mammals (Morganucodonta; Haramiyida). Kollikodon is provisionally placed as basal allotherian mammal (Allotheria sensu Butler 2000) and is unique at the ordinal level, being neither haramiyid nor multituberculate. A new allotherian order ??? Kollikodonta ??? is proposed.

Microsatellites are strings of short DNA motifs (≤6 bp) repeated in tandem across genomes of both prokaryotes and eukaryotes. In 20 years, they became popular genetic markers, successfully employed in the field of genetic mapping and gene hunting, as well as to address various biological questions at the individual, family, population and species level. However, evolutionary and demographic inferences from microsatellite polymorphism are hampered by controversy and ambiguity in the mutational processes of microsatellite sequences. Drawing on new data from genome projects, I review in Chapter 1 the concept of a microsatellite life cycle, which hypothesizes that microsatellites follow a life cycle from birth, through expansion, contraction, death and potentially resurrection. To document and understand this integrative concept of evolution, which could help improve current models of microsatellite evolution, there is an implicit need to study the evolution of microsatellites above the species level. A prerequisite of such comparative studies is therefore to find microsatellite loci that are conserved between different species. The near or full completion of many vertebrate genomes and their alignment against one another offer the ultimate approach to find genomic elements conserved over a large evolutionary scale. In Chapter 2, I present a new comprehensive method to find conserved microsatellites in whole genomes. Using the multiple-alignment of the human genome against those of 11 mammalian and five non-mammalian vertebrates, I examine the genomewide conservation of microsatellites, and challenge the general assumption that microsatellites are too labile to be maintained in distant species. In Chapter 3, I present similar results using the alignment of the newly sequenced platypus genome against those of three mammals, the chicken and the lizard, and incorporate these data into the framework created by the 17-genome analysis. This enlarged dataset was ground for attempting to reconstruct a vertebrate phylogeny from the presence/absence of microsatellites in the different genomes. Maximum parsimony analyses resulted in a tree much similar to that of the current view of the vertebrate phylogeny, while Bayesian analyses showed some discrepancies. This work opens a way for novel theoretical developments regarding the inference of ancestral states of microsatellites. In Chapter 4, I show how knowledge on conserved microsatellite sites can help for the development of a set of comparative primers useful across the Mammalia; implementing a similar protocol, nine conserved dinucleotide repeats were genotyped in 20 unrelated individuals of 18 species (nine sister species) encompassing the mammalian phylogeny, including marsupials and monotremes, and four microsatellites were sequenced in 4 individuals per species. My results emphasize conserved microsatellites as a new resource for genetic mapping and population studies. Finally, in Chapter 5, I recount the unexpected extent of structural change among mammalian orthologous microsatellites, including change of complexity, motif replacement and overall length variability. Altogether, these findings provide a comprehensive framework that may help in many areas of research, including molecular ecology, genome mapping, population genetics, and genome and microsatellite evolution.

The latitudinal diversity gradient in which species diversity is highest near the equator and declines toward the poles is well characterized in most higher level taxonomic groups and is strongest in the New World. However, the underlying causes of this gradient are poorly understood. By sampling New World birds and mammals, we found that the distribution of the evolutionary ages of sister species adheres to a latitudinal gradient. The time to divergence for sister species is shortest at high latitudes and longer in the tropics. Birth-death models fitting these data estimate that the highest recent speciation and extinction rates occur at high latitudes and decline toward the tropics suggesting that rates of species turnover are greatest where diversity is lowest. A pattern of endemism in boreal superspecies plausibly links the recent divergence of high latitude species to the fragmentation of the North American boreal forest by climatic oscillations during the Pleistocene ice ages. While all boreal superspecies tested date to the Pleistocene, only 56% of sub-boreal superspecies members date to this period. Similarly, montane tropical faunas, which were also directly impacted by buildup of glaciers during ice age cycles, were composed of younger species than low elevation faunas. Together these results suggest that faunas directly fragmented by expanding and retracting ice sheets experienced rapid rates of species turnover contributing to the lower species diversity of these regions. In contrast, the older ages of faunas at lower latitudes and altitudes suggest that long-term climatic stability promoted the gradual accumulation of high species diversity in these regions. Faunal interchange between continents may also have contributed to the exceptionally high species diversity of the New World tropics. Molecular dating suggests interchange rates between the distinctive avifaunas of North and South America were significantly faster after completion of the Central American landbridge three million years ago. Composition of tropical bird faunas were directly impacted by a relatively recent burst of faunal mixing which had the potential to elevate Neotropical species diversity over other tropical regions.<br>Science, Faculty of<br>Zoology, Department of<br>Graduate

Pulmonary surfactant is a complex mixture of lipids and proteins that lowers surface tension, increases lung compliance, and prevents the adhesion of respiratory surfaces and pulmonary oedema. Pressure can have an enormous impact on respiratory function, by mechanically compressing tissues, increasing gas tension resulting in increased gas absorption and by increasing dissolved gas tensions during diving, resulting in the formation of bubbles in the blood and tissues. The lungs of diving mammals have a huge range of morphological adaptations to enable them to endure the extremely high pressures associated with deep diving. Here, I hypothesise that surfactant will also be modified, to complement the morphological changes and enable more efficient lung function during diving. Molecular adaptations to diving were examined in surfactant protein C (SP-C) using phylogenetic analyses. The composition and function of pulmonary surfactant from several species of diving mammals was examined using biochemical assays, mass spectrometry and captive bubble surfactometry. The development of surfactant in one species of diving mammal (California sea lion), and the control of surfactant secretion using chemical and mechanical stimuli were also determined. Diving mammals showed modifications to SP-C, which are likely to lead to stronger binding to the monolayer, thereby increasing its fluidity. Phospholipid molecular species concentrations were altered to increase the concentration of more fluid species. There was also an increase in the percentage of alkyl molecular species, which may increase the stability of the monolayer during compression and facilitate rapid respreading. Levels of SP-B were much lower in the diving species, and cholesterol was inversely proportional to the maximum dive depth of the three species. Surface activity of surfactant from diving mammals was very poor compared to surfactant from terrestrial mammals. The newborn California sea lion surfactant was similar to terrestrial mammal surfactant, suggesting that these animals develop the diving-type of surfactant after they first enter the water. The isolated cells of California sea lions also showed a similar response to neuro-hormonal stimulation as terrestrial mammals, but were insensitive to pressure. These findings showed diving mammal surfactant to have a primarily anti-adhesive function that develops after the first entry into the water, with a surfactant monolayer, which would be better suited to repeated collapse and respreading.<br>Thesis (Ph.D.)--School of Earth and Environmental Sciences, 2005.

Among mammals, primates are exceptional for their large brain size relative to body size. Relative brain size, or encephalization, is particularly striking among humans and their direct ancestors. Since the human-chimp split 5 to 7 million years ago, brain size has tripled in the human lineage (Wood &amp;amp; Collard 1999). The focus of this doctoral work is to investigate some of the cell biological mechanisms responsible for this increase in relative brain size. In particular, the processes that regulate symmetric cell division (ultimately generating more progenitors), the constraints on progenitor proliferation, and how neural progenitors have overcome these constraints in the process of primate encephalization are the primary questions of interest. Both functionally analyses in the mouse model system and comparative neurobiology of rodents and primates are used here to address these questions. Using the mouse model system, the cell biological role of the Aspm (abnormal spindle-like microcephaly associated) protein in regulating brain size was investigated. Specifically, Aspm function in symmetric, proliferative divisions of neuroepithelial (NE) cells was analyzed. It was found that Aspm expression in the mouse neuroepithelium correlates in time and space with symmetric, proliferating divisions. The Aspm protein localizes to NE cell spindle poles during all phases of mitosis, and is down-regulated in cells that undergo asymmetric (neurogenic) cell divisions. Aspm RNAi alters the division plane in NE cells, increasing the likelihood of premature asymmetric division resulting in an increase in non-NE progeny. At least some of the non-NE progeny generated by Aspm RNAi migrate to the neuronal layer and express neuronal markers. Importantly, whatever the fate of the non-NE progeny, their generation comes at the expense of the expansion of the proliferative pool of NE progenitor cells. These data have contributed to the generation of an hypothesis regarding evolutionary changes in the regulation of spindle orientation in vertebrate and mammalian neural progenitors and their impact on brain size. Specifically, in contrast to invertebrates that regulate the switch from symmetric to asymmetric division through a rotation of the spindle (horizontal versus vertical cleavage), asymmetric NE cell division in vertebrates is accomplished by only a slight deviation in the cleavage plane away from the vertical, apical-basal axis. The requirement for the precise alignment of the spindle along the apical-basal axis in symmetric cell divisions may have contributed to selection on spindle “precision” proteins, thus increasing the number of symmetric NE cell division, and contributing to brain size increases during mammalian evolution. Previous comparative neurobiological analyses have revealed an increase in basally dividing NE cells in the brain regions of highest proliferation and in species with the largest brains (Smart 1972a,b; Martinez-Cerdeno et al. 2006). The cell biological characteristics of these basally dividing cells are still largely unknown. We found that primate basal progenitors, similar to rodent apical progenitors, are Pax6+. This suggests that primate basal progenitors may share other properties with rodent apical progenitors, such as maintenance of apical contact. Our previous finding that artificial alteration of cleavage plane in NE cells affects their ability to continue proliferating supports the hypothesis that the apical membrane and junctional complexes are cell fate determinants (Huttner &amp;amp; Kosodo 2005). As such, the need to maintain apical membrane contact appears to be a constraint on proliferation (Smart 1972a,b; Smart et al. 2002). Together, these data favor the hypothesis that primate basally dividing cells maintain apical contact and are epithelial in nature.

Thesis (MSc)--Stellenbosch University, 2003.<br>ENGLISH ABSTRACT: The evolutionary history of the African tribe Tragelaphini (spiral-horn antelope) is controversial. Past phylogenetic relationships among species were based on morphology or limited fossil evidence and are in conflict with mitochondrial DNA sequencing studies that have been conducted more recently. Although the group is distinguished from other African ungulates by the presence of spirally-twisted horns, the nine recognized extant species differ considerably in morphology, feeding habits and their habitat preference. The present study aims to resolve the phylogenetic uncertainties of the Tragelaphini using nuclear DNA sequence data derived from four independent DNA loci (MGF, PRKCl, SPTBN and THY). These data were combined with all previously published DNA sequences to produce a molecular supermatrix comprising approximately 6000 characters. Both parsimony and model based phylogenetic analyses of the nuclear DNA support the associations resulting from the analysis of mitochondrial genes. These findings suggest that the morphological characters previously used to delimit species within the group are subject to convergent evolution. The molecular phylogeny presented herein suggests that early members of Tragelaphini diverged from the other bovids during the mid-Miocene approximately 15.7 million years before present (MYBP). The common nyala (Tragelaphus enqest; and lesser kudu (Tragelaphus imberbis) representing the most basal species, separated from the other tragelaphids approximately 7.1 MYBP. This was subsequently followed by the radiation of those species adapted to a more tropical environment and they include the mountain nyala (Tragelaphus buxtom), bongo (Tragelaphus euryceros), sitatunga (Tragelaphus spekel) and bushbuck (Tragelaphus scriptus), and the arid adapted clade comprising the giant eland (Taurotragus derbianus), common eland (Taurotragus oryx) and greater kudu (Tragelaphus strepsiceros). It is thought that this split occurred at the Miocene-Pliocene boundary approximately 5.4 MYBP. The timing of evolutionary events within the tribe suggests climatic oscillations and subsequent biotic shifts as the major driving forces underpinning speciation in the tribe Tragalaphini.<br>AFRIKAANSE OPSOMMING; Die evolusionêre geskiedenis van die ras Tragelaphini (spiraalhoringwildsbokke) is kontroversieël. Vorige filogenetiese verwantskappe tussen die spesies is gebaseer op morfologie of beperkte fossiel bewyse. Meer onlangse studies, gebaseer op mitochondriale ONS nukleotieddata, is in teenstryding met baie van die evolusionêre hypotese afkomstig van morfologiese studies. Alhoewel die groep van die ander hoefdiere uitgeken kan word deur die aanwesigheid van spiraalvormige horings, verskil die nege hedendaagse spesies grootliks ten opsigte van morfologie, voedingswyse en habitat. Die hoof doelwit van hierdie studie was om die filogenetise verwantskappe tussen die Tragelaphini spesies te ontleed deur gebruik te maak van nukluêre ONS nukleotieddata afkomstig van vier onafhanklike ONS merkers (MGF, PRKCl, SPTBN en THY). Die data verkry is saamgevoeg by vorige gepubliseerde ONS nukleotidedata om 'n "supermatris" van sowat 6000 karakters te produseer. Parsimonie en modelgebaseerde filogenetise analise van die nukluêre ONS nukleotieddata het ooreengestem met die resultate van vorige mitochondriale studies. Hierdie bevindings dui daarop dat die morfologiese karakters wat voorheen gebruik is om die evolusionêre verwantskappe tussen die Tragelaphini spesies te ontleed onderhewig is aan konvergente evolusie. Die molekulêre filogenie wat hierin beskryf word stel voor dat die ras Tragelaphini gedurende die mid- Miocene, omtrent 15.7 miljoen jaar (MJ) gelede van die ander lede van die subfamilie Bovinae geskei het. Tragelaphus angasi en Tragelaphus imberbis, die mees basale spesies in die filogenie, het omtrent 7.1 MJ gelede van die ander lede van die Tragelaphini geskei. Hierdie skeiding is gevolg deur 'n split tussen die spesies aangepas vir 'n meer tropiese habitat (Tragelaphus buxtoni, Tragelaphus euryceros, Tragelaphus spekei en Tragelaphus scriptus) en die spesies aangepas vir 'n droë habitat (Taurotragus derbianus, Taurotragus oryx en Tragelaphus strepsiceros) Hierdie finale skeiding het gedurende die Miocene-Pliocene oorgang plaasgevind. Die tydsberekening van die evolusionêre gebeurtenisse wat binne die Tragelaphini ras plaasgevind het, gekoppel aan paleoklimaatdata, dui aan dat veranderinge in klimaat en die geassosieerde habitatveranderinge verantwoordelik was vir die spesiasie patroon wat ons vandag in die Tragelaphini ras waarneem.

La radiation adaptative des Equoidea est encore mal comprise en raison notamment de la méconnaissance de la phylogénie de cette super-famille. La principale irrésolution de ces relations de parenté porte sur les pachynolophes, Equoidea européens rapprochés des Equidae ou des Palaeotheriidae. Pendant une grande part de l'Éocène, l'Europe est isolée et subit à la fin de cette période de profonds changements climatiques. Lors de la Grande Coupure son isolement s'achève, tandis que l'aridité du climat s'installe, et des faunes migrantes provoquent l'extinction de nombreux groupes endémiques. Un Equoidea européen basal, richement représenté par un matériel bien préservé permet d'appuyer une des hypothèses phylogénétiques les plus récentes. Cependant, les caractères couramment utilisés pour débattre de cette question n'apportent pas de réponse claire et définitive. Aussi, cette étude se propose de mener des investigations sur des régions encore peu explorées de ces animaux comme le neurocrâne, grâce à la microtomographie (CT scan), qui permet un accès non destructif aux structures (encéphale, pétreux, labyrinthe osseux, sinus). Outre l'intérêt phylogénétique, ces organes peuvent, de par leurs fonctions, receler un intérêt paléoécologique. Jusqu'à présent, peu d'études à large échelle ont porté sur ces structures chez les Perissodactyla, s'agissant pour la plupart de mentions anecdotiques. Comme préalable indispensable, une étude modèle a été réalisée sur un Equidae sauvage actuel afin de mieux appréhender la variabilité de ces structures méconnues. Pour la première fois, un large échantillon d'Equoidea européens a été scanné et leurs structures neurocrâniennes reconstruites en trois dimensions virtuelles. Ce sont au total 20 espèces qui ont été échantillonnées, couvrant l'évolution de ces animaux de leur origine à leur extinction, pendant plus de 20 millions d'années. Leurs crânes ont été scannés, leurs structures internes reconstruites, comparées et analysées au moyen de la cladistique. Une nouvelle hypothèse phylogénétique propose des relations de parenté intra-Equoidea et montre la pertinence des caractères neurocrâniens, tout en conduisant à envisager une étude plus vaste. Les Palaeotheriidae apparaissent comme un groupe très diversifié, notamment au regard des Equidae éocènes d'Amérique du Nord, et caractérisé par une évolution en mosaïque. Ils connaissent une évolution cérébrale précoce par rapport aux faunes contemporaines (Equidae, Cetartiodactyla, Carnivora), ce qui, via le développement de nouvelles stratégies adaptatives, pourrait expliquer partiellement cette grande diversification familiale. Un parallèle est envisagé avec l'évolution endémique des Notoungulata, qui semblent eux aussi montrer une complexification cérébrale précoce. Cependant, face à un environnement biotique et abiotique bouleversé (fin de l'Éocène et lors de la Grande Coupure), ces structures complexes impliquant un coût métabolique important et une trop grande spécialisation, avec en conséquence, moins de potentiel adaptatif, auraient pu les désavantager et les conduire à l'extinction<br>The Equoidea adaptive radiation still remains badly known, especially due to the ignorance of their phylogeny. The main indecision of these relationships concerns the pachynolophs, European Equoidea either approached to the Equidae or to the Palaeotheriidae. During a great part of the Eocene times, Europe was isolated, and, at the end of this period, has undergone strong climatic changes. That isolation ended at the « Grande Coupure » event, whereas an arid climate moved, and migrant faunas caused the extinction of many endemic groups. A basal European Equoidea, richly represented by well-preserved material, can support one of the latest phylogenetic hypotheses. However, commonly used characters to discuss this issue do not provide a clear and definitive answer.Therefore, this study aims to investigate on unexplored regions of these animals as the neurocranium through microtomography (CT), which allows access to non-destructive structures (brain, petrosal, bony labyrinth, and sinus).Furthermore phylogenetic interest these bodies may, through their functions, harbor paleoecological interest. Until now, few large-scale studies have focused on those structures in the Perissodactyla, with regard to most were anecdotal reports. As a prerequisite, a model study was performed on a wild current Equidae to better understand the variability of these unknown structures. For the first time, a large sample of European Equoidea has been scanned and their neurocranium structures virtually reconstructed in three-dimensions. A total of 20 species were sampled, covering the evolution of these animals from their origin to their extinction, for over 20 million years. Their skulls were scanned; their internal structures reconstructed compared and analyzed using cladistics. A new phylogenetic hypothesis provides intra Equoidea relationships and shows the relevance of neurocranium characters, while driving to consider a larger study. The Palaeotheriidae appears as a highly diverse group, particularly with regard to Eocene Equidae in North America, and characterized by a mosaic evolution. Their brain evolved earlier than that of contemporary faunas (Equidae, Cetartiodactyla, Carnivora); which may partially explain the strong diversification of that family, through the development of new adaptive strategies

The theory of “punctuated equilibrium” suggests that species evolve rapidly during or immediately upon speciation, “punctuating” long periods of little or no morphological evolution. Here I confirm that body size differences within clades of birds and mammals are best explained using a model of punctuated evolution. This allows me to suggest that rates of speciation and extinction are responsible for why there are more small mammals than large, as large mammals likely speciate and go extinct at a higher rate than small mammals, and hence undergo cladogenetic change more often. Likewise, mammals appear to evolve at a higher rate than birds, because mammals, as a whole, speciate and go extinct at a higher rate than birds. Furthermore I show that mass extinctions and competition, i.e. forms of natural selection, do not seem to explain differences in body size between species on a macroevolutionary scale. Taken together, these findings not only contradict the idea that apparently different rates of evolution are due to differential selection intensities, and emphasize the importance of the speciation process in evolution, but raise the intriguing question as to what limits evolution in established species. Here I suggest that phenotypic traits, dependent on one another for development and/or function may constrain evolution by exerting stabilizing selection from within the organism, as opposed to external environmental selection, which has been the main focus of evolutionary studies thus far.<br>Teorin om "punkterad jämvikt" säger att arter utvecklas snabbt under och omedelbart efter artbildning, vilket "punkterar" långa perioder med lite eller ingen morfologisk föränding. I den här avhandlingen visar jag att skillnader i kroppsstorlek inom klader (grupp med gemensam förfader) hos fåglar och däggdjur förklaras bäst när man använder en modell med punkterad evolution. Detta gör i sin tur att jag kan föreslå att hastigheten var med artbildning och utdöende sker, förklarar varför det finns fler små däggdjur än stora, eftersom stora däggdjur sannolikt bildar nya arter och dör ut med en högre hastighet än små däggdjur. Likaså förefaller däggdjur i sin helhet att evolvera med en högre hastighet än fåglar, detta eftersom däggdjur bildar nya arter och dör ut med en högre hastighet än fåglar. Dessutom visar jag att massutdöenden och konkurrens (naturlig selektion) inte verkar förklara skillnader mellan arter över makroevolutionära skalor (över geologisk tid). Sammantaget motsäger dessa resultat inte bara idén om att skenbart olika hastighet på evolution främst beror på skillnader i selektionstryck utan understryker också vikten av artbildningsprocessen som en viktig faktor som styr evolutionens hastighet. Dessutom leder dessa resultat till frågan om vad som begränsar evolutionen hos redan etablerade arter. Här föreslår jag att fenotypiska karaktärsdrag som är beroende av varandra för sin funktion och utveckling kan begränsa evolutionen genom att utöva stabiliserande selektion inifrån organismen, i motsats till selektion från den omgivande miljön vilket har varit fokus för de flesta evolutionära studier hittills.

Caviomorph rodents arrived from Africa as sweepstakes colonists to the South American island continent between 54 and 37 Ma, and subsequently underwent a rapid and widespread adaptive radiation beginning in the middle Eocene. The geographic isolation of South America gave rise to a number of endemic mammal species that filled a wide variety of ecological niches. The resulting size of caviomorph rodents spanned over three orders of magnitude, making them an intriguing lineage to explore the morphological and ecological implications of size evolution. Here, I explore the morphological cranial patterns of extinct and extant caviomorph taxa using 2D landmark-based geometric morphometric analysis. Results are key to advancing our understanding of the effects phylogeny and body size have on cranial morphology of caviomorphs (and more broadly, mammals). This study indicates a deviation from the mammalian modular patterns determined a priori, suggesting unique evolutionary processes at play during the caviomorph adaptive radiation.

Made available in DSpace on 2014-06-11T19:26:07Z (GMT). No. of bitstreams: 0 Previous issue date: 2008-10-07Bitstream added on 2014-06-13T19:53:59Z : No. of bitstreams: 1 gualberto_af_me_jabo.pdf: 464930 bytes, checksum: 799ea2a9f048c84fac80100f93c28e4f (MD5)<br>Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)<br>O veado-mateiro (Mazama americana) é a maior espécie do Gênero Mazama, e encontra distribuído geograficamente por quase toda a região neotropical. Animais originários do Estado de Rondônia têm apresentado importantes diferenças citogenéticas em relação ao padrão de outras populações, o que suscita necessidade de estudos mais aprofundados para definição da sua posição filogenética. O presente estudo objetivou identificar as diferentes populações de veado-mateiro desta região, verificando a existência de mais de uma espécie no local. Para tanto, foram obtidos 51 fragmentos de tecido de animais caçados por indígenas e pela população local em todas as regiões do Estado dos quais 33 tiveram seu DNA extraídos, amplificados (região de 480pb do citocromo b) e seqüenciados de forma satisfatória. Estas seqüências foram alinhadas e comparadas, gerando 21 haplótipos que se encontram distribuídos de forma aleatória pelas diversas regiões de coleta. Estes haplótipos serviram de base para a elaboração de redes de distância e árvores filogenéticas que quando analisadas sugeriram a existência de espécies crípticas dentro do que hoje se denomina Mazama americana no Estado de Rondônia.<br>The red brocket deer is the largest species of Mazama genus and it is distributed in almost all Neotropical regions. Individuals originated from Rondônia state in Brazil have been presented important cytogenetic differences when compared with populations of other regions of country; however more studies are necessary to define correct phylogenetic position of species. The objective of present study was performed the identification of different populations of red brocket deer from Rondônia state by verification of occurrence of more than one species on mentioned region. For this, 51 fragments of tissues from hunted animals were obtained with Indians and local people of all regions of Rondônia state. In 31 fragments of tissues the DNA was successful extract, amplified (480 bp region of cytochrome b) and sequenced. These sequences were aligned and compared creating 21 haplotypes, which are distributed in a randomly way thru the different regions of sampling. The haplotypes were used to elaborate distance nets and phylogenetic trees, which when analyzed suggested the existence of cryptic species on Mazama americana species that occurs in Rondônia state.

The impact of large-scale volcanic eruptions on landscapes can affect many processes ranging from interrupting or redirecting regional soil forming processes and hydrological systems to generating temporary changes in global climate. Though more studies exist every year, less is known of the direct impact of large-scale volcanic eruptions on ecosystems and extinction, while even less is known of their impact on speciation. In deposits throughout the Pacific Northwest a special combination and association of volcanic magnitude with palaeoecological yield frequently presents unique prospects for inquiry. In this study, particular attention is given to large, late Miocene ash-flow tuffs of central and eastern Oregon, the Rattlesnake Tuff among them. Additionally, a scenario is tested whereby populations become isolated from one another across the expanse of ash-flow tuff and enclosed by nearby physical barriers. Exploration into this scenario and the effects of ecological recovery on speciation in mammals are made through a cellular automaton created here and speciation modeling by H.A. Orr. The cellular automaton is validated by a small data set from New Zealand with results of all models compared to studies in ecology, the fossil record, genetics, and island evolution. Results suggest ecosystem recovery is much faster than mammalian species origination rates. Though evolution in mammals is known to occur over relatively short intervals of time (10 - 10 yrs), based on model comparisons, primary productivity generally returns to its carrying capacity two orders of magnitude (10 - 10 vs. ≥ 10 yrs) faster than mammalian speciation.

Thesis (PhD (Botany and Zoology)) -- University of Stellenbosch, 2008.<br>Afrosoricida is a 65 million years old (my) eutherian order that together with the Tubulidentata (aardvark) and Macroscelidea (elephant shrews) form the Afroinsectiphillia, a subclade of Afrotheria. It includes two families – Chrysochloridae (nine genera of golden moles) and Tenrecidae (11 genera of tenrecs) – that collectively represent ~59% of the afrotherian generic diversity. This study presents the first comprehensive cytogenetic comparison between members of these two families (seven genera and 11 species/subspecies of golden moles, and two genera and 11 species of tenrecs) using G- and C-banding and chromosome painting. All detected rearrangements are interpreted in a strict cladistic framework. In the case of Chrysochloridae, this provides evidence for a sister relationship between Chrysochloris and Cryptochloris, the monophyly of the Amblysomus genus, and for the elevation of A. hottentotus meesteri to specific rank. The detection of telomeric-like repeats in the centromeres of all chromosomes of the Amblysomus species/subspecies but not in those of A. h. meesteri further strengthens its recognition as a distinct species. Parsimony analysis of chromosomal rearrangements within Tenrecidae, the second Afrotheria assemblage studied, showed that rearrangements which could be interpreted as Whole Arm Reciprocal Translocations (WARTs) were more likely to be the result of Robertsonian translocations. Four interspecific associations are recovered within Microgale that are consistent with morphological and molecular characters. It was also possible to infer ancestral karyotypes for the Chrysochloridae, Oryzorictinae and the two tenrecid genera, Oryzorictes and Microgale. Given the relatively high karyotypic diversity observed among some Microgale species and the prevailing debates on chromosomal evolution and regional palaeoenvironmental fluctuations, it is suggested that Microgale be added to the list of taxa where structural rearrangements are likely to have played a role in speciation. Using Genbank sequences and a relaxed Bayesian clock method, we estimate the age of the family Chrysochloridae at ~28.5 my and that of the genus Microgale at ~9.9 my. Based on these dates, it can be shown that most of the evolutionary branches are characterized by a slow rate of chromosomal change, but that markedly high rates are observed in some Microgale species and to a lesser extent in the lineage leading to A. robustus. The rates of chromosomal evolution and other cytogenetic features highlighted in this study are discussed in light of recent advances in understanding the molecular mechanims that underpin changes to genomic architecture.

Etude consacree a la connaissance generale de l'anatomie osseuse comparee de la famille des gerbillidae et a l'etude de l'evolution de la sous-famille des gerbillinae au cours du plio-pleistocene au maghreb. Proposition de nouvelles relations phylogeniques basees sur les caracteres morphologiques et leur evolution qui peuvent etre comparees avec celles etablies sur la base des chromosomes et des enzymes. Precisions sur l'age de certains gisements maghrebins

Made available in DSpace on 2014-06-11T19:32:15Z (GMT). No. of bitstreams: 0 Previous issue date: 2009-07-24Bitstream added on 2014-06-13T20:43:06Z : No. of bitstreams: 1 abril_vv_dr_jabo.pdf: 1648950 bytes, checksum: a989c1942e3dd9ac9da5d7078193a943 (MD5)<br>Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)<br>Estudos com veado-mateiro (Mazama americana) mostram que há muitas controvérsias quanto ao número de subespécies ou até quanto ao desdobramento destas em espécies. Em estudo citotaxonômico foram encontradas variações cromossômicas intra e interpopulacionais em populações de M. americana geograficamente distantes, com número diplóide de 48 a 53 e número fundamental de 46 a 57. Com base nisto, o presente estudo visou compreender como ocorreu a reorganização cromossômica dentro das variantes encontradas durante a evolução do grupo. Para isto, estrutura e organização dos cromossomos de M. americana foram analisadas para identificar os rearranjos que originaram a variação intraespecífica através das técnicas de bandamento cromossômico (bandas G, C, Ag-NOR), hibridação in situ (FISH) com sondas teloméricas e pintura cromossômica com o uso de sondas cromossômicas da espécie Mazama gouazoubira. Foram identificados seis citótipos distribrídos em 12 cariótipos diferentes: Rondônia (2n=42 ou 43 e NF=46; 2n=42 e NF=49), Juína (2n= 43, 44 ou 45 e NF=48; 2n=44 e NF=46), Jarí (2n=49; NF=56, Carajás (2n=50 e NF=54), Santarém (2n=51 e NF=56) e Paraná (2n=51,52 ou 53 e NF=56). O cariótipo básico do citótipo Paraná foi utilizado como base comparativa para os demais. Os rearranjos que originaram essas diferenças foram fusões cêntricas, em tandem e inversões pericêntricas. A análise de complexo sinaptonêmico confirmou a existência de um sistema sexual múltiplo do tipo XX/XY1Y2 através da detecção de uma trivalente sexual. Sítios teloméricos intersticiais evidenciam que a ocorrência de eventos de fusões em tandem foi essencial para a evolução cariotípica desta espécie e a homologia de sondas cromossomo-específicas de M. gouazoubira corroboram que o caminho da reorganização cromossômica entre estas espécies foi principalmente através de fusões.<br>Studies with the red brocket deer (Mazama americana) shown that there are a lot of controversies about the number of subspecies or about the unfolding of these in new species. Citotaxonomic studies found intra and interpopulational chromosomal variations, with diploid number varing from 48 to 53 and fundamental number from 46 to 57. Based on these studies, the aim of the present study was understood how the chromosomal reorganization occurred between this variants during the evolution process. For that, we analyzed the chromosomal structure and organization of M. americana, identifying the rearrangements responsible for the intraspecific variation through chromosome banding (G and C-banding, Ag-NOR), in situ hybridization of telomeric probes and chromosome painting using probes of M. gouazoubira species. It were found six different variants: Rondônia (2n=42 or 43 and FN=46; 2n=42 and FN=49), Juína (2n= 43, 44 or 45 and FN=48; 2n=44 and FN=46), Jarí (2n=49 and FN=56), Carajás (2n=50 and FN=54), Santarém (2n=51 and FN=56) and Paraná (2n=51,52 or 53 and FN=56). The basic karyotype of Paraná variant was choosing for comparative analysis. The rearrangements responsible for these chromosomal differences were centric and tandem fusions and pericentric inversions. The synaptonemal analysis sustained the existence of a multiple sexual system (XX/XY1Y2) with detection of a sexual trivalent. Intersticial telomeric sites shown the occurrence of tandem fusions was essential for the karyotype evolution of this species and the homology with the probes of M. gouazoubira corroborated that the way of chromosomal reorganization between these species was mainly through chromosome fusions.

Orientador: José Maurício Barbanti Duarte<br>Banca: Fausto Foresti<br>Banca: Cláudio de Oliveira<br>Banca: Orlando Moreira Filho<br>Banca: Vera Fernanda Martins Hossepian de Lima<br>Resumo: Estudos com veado-mateiro (Mazama americana) mostram que há muitas controvérsias quanto ao número de subespécies ou até quanto ao desdobramento destas em espécies. Em estudo citotaxonômico foram encontradas variações cromossômicas intra e interpopulacionais em populações de M. americana geograficamente distantes, com número diplóide de 48 a 53 e número fundamental de 46 a 57. Com base nisto, o presente estudo visou compreender como ocorreu a reorganização cromossômica dentro das variantes encontradas durante a evolução do grupo. Para isto, estrutura e organização dos cromossomos de M. americana foram analisadas para identificar os rearranjos que originaram a variação intraespecífica através das técnicas de bandamento cromossômico (bandas G, C, Ag-NOR), hibridação in situ (FISH) com sondas teloméricas e pintura cromossômica com o uso de sondas cromossômicas da espécie Mazama gouazoubira. Foram identificados seis citótipos distribrídos em 12 cariótipos diferentes: Rondônia (2n=42 ou 43 e NF=46; 2n=42 e NF=49), Juína (2n= 43, 44 ou 45 e NF=48; 2n=44 e NF=46), Jarí (2n=49; NF=56, Carajás (2n=50 e NF=54), Santarém (2n=51 e NF=56) e Paraná (2n=51,52 ou 53 e NF=56). O cariótipo básico do citótipo Paraná foi utilizado como base comparativa para os demais. Os rearranjos que originaram essas diferenças foram fusões cêntricas, em tandem e inversões pericêntricas. A análise de complexo sinaptonêmico confirmou a existência de um sistema sexual múltiplo do tipo XX/XY1Y2 através da detecção de uma trivalente sexual. Sítios teloméricos intersticiais evidenciam que a ocorrência de eventos de fusões em tandem foi essencial para a evolução cariotípica desta espécie e a homologia de sondas cromossomo-específicas de M. gouazoubira corroboram que o caminho da reorganização cromossômica entre estas espécies foi principalmente através de fusões.<br>Abstract: Studies with the red brocket deer (Mazama americana) shown that there are a lot of controversies about the number of subspecies or about the unfolding of these in new species. Citotaxonomic studies found intra and interpopulational chromosomal variations, with diploid number varing from 48 to 53 and fundamental number from 46 to 57. Based on these studies, the aim of the present study was understood how the chromosomal reorganization occurred between this variants during the evolution process. For that, we analyzed the chromosomal structure and organization of M. americana, identifying the rearrangements responsible for the intraspecific variation through chromosome banding (G and C-banding, Ag-NOR), in situ hybridization of telomeric probes and chromosome painting using probes of M. gouazoubira species. It were found six different variants: Rondônia (2n=42 or 43 and FN=46; 2n=42 and FN=49), Juína (2n= 43, 44 or 45 and FN=48; 2n=44 and FN=46), Jarí (2n=49 and FN=56), Carajás (2n=50 and FN=54), Santarém (2n=51 and FN=56) and Paraná (2n=51,52 or 53 and FN=56). The basic karyotype of Paraná variant was choosing for comparative analysis. The rearrangements responsible for these chromosomal differences were centric and tandem fusions and pericentric inversions. The synaptonemal analysis sustained the existence of a multiple sexual system (XX/XY1Y2) with detection of a sexual trivalent. Intersticial telomeric sites shown the occurrence of tandem fusions was essential for the karyotype evolution of this species and the homology with the probes of M. gouazoubira corroborated that the way of chromosomal reorganization between these species was mainly through chromosome fusions.<br>Doutor