In the past few decades, an area of skeletal research focusing on shape analyses has gained popularity in the field of physical anthropology, and subsequently forensic anthropology. Known as geometric morphometrics, this type of analysis allows the researcher to place the morphological shape of bones into a statistical framework to answer questions on a variety of topics, including sexual dimorphism. Sex assessment from the long bones has been traditionally conducted using traditional morphometric methods (Iscan and Miller-Shaivitz 1984; Steyn and Iscan 1997), and as a result, relies mainly on size differences and has not considered how joint morphology and shape affect sex. For this project, a geometric morphometric analysis of the proximal tibia in a modern Caucasian American population was conducted using a sample of 100 male and 100 female tibiae from the William M. Bass Donated Skeletal Collection at the University of Tennessee at Knoxville. The proximal tibia's effectiveness as an indicator of sex in a modern American population was evaluated via generalized Procrustes, principal components, and discriminant function analyses. Principal components revealed a lack of separation between males and females in terms of proximal tibia shape. The discriminant function analysis was successful at discriminating males from females, but cross-validation yielded a low total accuracy rate of 58%. The shape of the proximal tibia contributes to sexual dimorphism in a Caucasian American population, but is only slightly useful in a discriminant function. Further research should be conducted on different populations and using different skeletal landmarks.

The use of geometric morphometrics (GM) in physical anthropology has increased markedly over the recent years. In current studies of secular change, anthropologists have more frequently turned to this technique as it provides scientists with a powerful tool for shape analysis. Secular change is defined as changes in the skeletal biology, usually seen in a population, resulting from shifts in living standards or exposure to a new environmental factor over a short timeframe (Jantz and Meadows Jantz 2000; Weisensee and Jantz 2011). Studies conducted in Europe, Asia, and the United States have shown significant signs of secular change in craniofacial morphology. This thesis will utilize GM analyses of 57 craniofacial landmarks from 313 individuals to determine secular change in the European male populations of the Raymond A. Dart and Pretoria Skeletal Collections located in Johannesburg and Pretoria, South Africa, respectively, with birth years ranging from 1850 to 1956. Craniofacial data points were collected using a 3D Microscribe digitizer, upon which the Generalized Procrustes Analysis (GPA) was used to align all landmarks into one coordinate reference plane. In order to determine the presence of shape change, a Principal Components Analysis (PCA) was run on the Procrustes coordinates of all individuals. Then, a multivariate regression of shape score on year of birth was conducted to determine the magnitude of change as explained over time. Following the multivariate regression, various Canonical Variates Analyses (CVA) were performed to determine whether secular change was occurring. In addition to collecting metric data, ultimate and proximate causes are explored to provide a more holistic understanding of the potential reasons for the changing or unchanging nature of the crania in the ancestrally European South African population. This study hypothesizes these collections will exhibit craniofacial secular change resulting from greater exposure to increased nutrition over time, greater access to healthcare, and socioeconomic and political stability. Additionally, genetic factors could be affecting the development of the crania through time. As many studies use the Dart and Pretoria collections in tandem to understand population-specific traits of modern South Africans, the presence of secular change will greatly affect the way researchers utilize samples for their studies. Forensic anthropologists study collections to create better estimations for elements of the biological profile such as stature, age, and sex. However, failure to take into account secular change would provide erroneous results. This study provides answers regarding the need to account for secular change if necessary. This research indicates that there are some changes occurring in the craniofacial morphology as see by the PCA, but the results of the CVA indicate that this is not necessarily due to secular change. The results do not clearly indicate the presence of secular change. There are many possibilities dictating potentially why. The first possibility is that there are small changes occurring in the craniofacial morphology; however, this is not caused by secular change. There are other variables, potentially genetic, that are influencing these slight changes that we see. Despite other nations with similar economic development trajectories experiencing a definite presence of secular change, the unique history and population structure of European South Africans could be contributing to the lack of secular change present. Another possible reason is the lack of passage of time from the industrialization of the nation. Furthermore, there is potentially not enough data tested to warrant a reliable conclusion that secular change is or is not occurring. With the cranium, the possibility exists that a minimum threshold of specimens is needed in order to have a reliable conclusion.

This project analyzes the sexual dimorphism of the femur and tibia using geometric morphometrics. The study sample includes 250 individuals of known sex and age at death with complete, non-damaged, non-pathological skeletal remains from the William M. Bass Donated Skeletal Collection at the University of Tennessee, Knoxville. Ages range from 19-96 for males (mean=56.92 years) and 29-97 for females (mean=59.48 years). A combination of landmarks and semi-landmarks were collected on the proximal and distal epiphyses of each bone using a Microscribe, which helps capture the overall size and shape variation present in the sample. Only individuals from one population, White, where analyzed in order to eliminate population variation bias. Classification rates for males and females for the proximal femur were 80.8% and 78.4% respectively, for the distal femur 92.6% and 89.6% respectively, for the proximal tibia 80.8% and 83.2% respectively, and the distal tibia 81.6% and 80.8% respectively, all with a p<0.0001. These rates created a classification model for which epiphysis gave the most accurate assessment of sex: the distal femur, followed by the proximal tibia, then the distal tibia, and lastly the proximal femur. This study indicates the knee joint is the most dimorphic, followed by the ankle and then the hip. The results fall in line with another study indicating the knee is more sexually dimorphic in a modern White population (Spradley and Jantz 2011), though in contrast to their results this study found the distal femur was more dimorphic than the proximal tibia. This method indicates that in comparison to standard measurements, geometric morphometrics may provide a more reliable method for sex estimation when used, specifically on the knee. Certain landmarks were then selected based on the standard taphonomic process of coffin wear and postmortem damage (Pokines and Baker 2014) for exclusion to determine the usability of the method on fragmented or damaged skeletal remains. When combinations of landmarks were removed, the distal femur still possessed the highest classification rates with over 80% accuracy.

The results of evolution can be inferred from comparative studies of related organisms. In this doctoral thesis, I use phylogenetic comparative methods along side geometric morphometrics to analyse shape variation in order to infer evolution of the caecilian skull. Caecilians are elongate, limbless amphibians that superficially resemble snakes or earthworms, and use their head as a locomotory organ. I characterise large-scale patterns of cranial morphological diversity and quantify variation across the main family-level clades by describing patterns relating to phylogeny, disparity and ecology. Then I examine the origins and evolution of morphological variation in the skull by describing patterns relating to morphological integration and modularity. This thesis demonstrates a variety of existing statistical techniques that can be used to infer processes from large-scale evolutionary patterns in morphological data using non model organisms. Throughout the thesis, I show that the evolution of the caecilian skull to be multifaceted. On the patterns of diversity, the most striking is a "starburst" arrangement in shape space, which suggests that early in caecilian evolution ancestral lineages traversed greater expanses of the shape space, while subsequent phylogenetic divergence within the main clades entailed less morphological diversification. This may be related to early diversification into different ecological-niches, yet more data are needed to test this. The clades differ considerably in their cranial disparity, but there appears to be no unified pattern across the whole order that indicates disparity is coupled with clade age or speciation events. I show that aquatic species are more diverse than their terrestrial relatives, and that there is convergence of cranial shape among dedicated burrowers with eyes covered by bone. On the patterns of morphological integration and modularity, another remarkable finding is the caecilian cranium is modular with respect to two functional regions, the snout and the back of the cranium. Modularity is important for understanding the evolution of this structure. The main elements of the caecilian anterior skeleton, the cranium, mandible and atlas vertebra, reveal different patterns of morphological integration, suggesting different developmental and evolutionary processes are involved in sorting and maintaining new variation of each structure. Allometry is an important component of integration in each of the structures. Covariation of the cranium-mandible after size correction is significant and follows the same direction of shape change across all levels and as shown for allometry. In contrast, covariation of the cranium-atlas follows different directions at each level. These results suggest the two main joint of the caecilian skull differ substantially in their origin and evolution. I discuss the contribution made in this thesis to caecilian and evolutionary biology and offer an outlook of how theses findings can be used to initiate future studies to better understand of the evolution of the caecilian skull.

This thesis is focused on the biosystematic study of the Central-European endemic Spergularia echinosperma. With the combined use of morphometric analyses, genome size measurements and molecular tools, the taxonomic issues associated with this species have been clarified. The existence of S. kurkae, a stable allotetraploid hybrid between diploid S. echinosperma and tetraploid S. rubra, has been proven. Based on several lines of evidence, including distinct morphological separation and frequent occurrence in the absence of the parental species, treating S. kurkae as a separate species is proposed. In addition, two infraspecific taxa within S. echinospermaS. echinosperma subsp. echinosperma and S. echinosperma subsp. albensisdiffering in distributions and ecology have been described. A complete revision of the localities of S. echinosperma, S. kurkae and S. rubra in the Czech Republic is also presented. Furthermore, the development of 16 polymorphic microsatellite loci for S. echinosperma is reported.

Orientador: Ricardo Cardoso Benine / Resumo: Atualmente, os reservatórios artificiais de água causam grandes impactos e representam uma grande ameaça à biodiversidade de todo o mundo. Moenkhausia costae é uma espécie de peixe da Família Characidae, amplamente distribuída nos diversos ambientes da bacia do rio São Francisco, sendo presente no reservatório da UHE Três Marias. Observando populações coletadas na lagoa da represa e fora da mesma foram identificadas variações morfológicas notáveis. Trabalhos prévios com peixes demonstraram que populações alocadas em ambientes alterados por barramento de rios apresentavam variações morfológicas com relação à populações que permaneciam em ambiente natural. Neste trabalho avaliou-se a variação morfológica presente entre populações de M. costae que estão sob influência direta da lagoa da UHE Três Marias e populações sob condições naturais, fora da influência do reservatório. Para avaliar a variação morfológica existente entre populações de M. costae de ambos os ambientes, foram levantados caracteres morfológicos através das morfometrias linear e geométrica, sendo estas testadas posteriormente através de análises multivariadas. A morfometria linear demonstrou um padrão morfológico com formas mais limitadas nas populações da represa, concordando com os resultados exibidos pela morfometria geométrica, que também demonstrou formas corporais limitadas para as populações da represa. / Abstract: Currently, artificial water reservoirs are causing impacts and represent a major threat to biodiversity around the world. Moenkhausia costae is a fish species of the Characidae, and is widely distributed in the different environments of the rio São Francisco basin, being present in UHE Três Marias dam. Examining populations collected in and out of the dam influence area, remarkable morphological variations were identified. Previous works with fish showed that populations allocated in environments altered by dam’s construction presented morphological variations in relation to populations that remained in a natural environment. This work evaluated the morphological variation present among populations of M. costae that are under direct influence of UHE Três Marias lagoon and populations that are outside the influence of the dam. For this, morphological characters were collected through linear and geometric morphometry methodologies, which were later tested through multivariate analyzes. Linear morphometry demonstrated a morphological pattern with more limited patterns in dam populations, agreeing with the results exhibited by geometric morphometry, which also demonstrated limited body shapes for dam populations. / Mestre

Master of Science / Biology / Michael Tobler / Environmental variation can shape phenotypic variation in organisms. Most evidence for trait differentiation along environmental gradients comes from analyses of dichotomous habitat types that differ in only one or few environmental factors. In reality, however, environmental variation is often more subtle, gradual, and multifarious. I investigated geographic variation in body shape, trophic resource use, and individual diet specialization in two species of darters (Etheostoma spectabile and E. flabellare; Percidae) that occur along river gradients. I explicitly tested how abiotic and biotic environmental factors shape trait variation within and between species. Results indicated significant among population variation in the body shape of both species. Population differences in body shape were correlated with variation in substrate composition. Although body shape analyses revealed a small but significant signal of convergent evolution of body shape when both species occur in sympatry, E. spectabile and E. flabellare mostly exhibited unique responses to shared sources of selection. The analyses of darter trophic resource use uncovered significant resource partitioning between the two species and geographic variation in diets that is likely driven by differences in resource availability. Furthermore, the majority of populations exhibited significant individual specialization. Variation in individual specialization in populations of E. flabellare was related to invertebrate density and competitor richness, and in E. spectabile to the combined effects of invertebrate density and invertebrate diversity. My results indicate substantial variation in trophic resource use among individuals, populations, and species of small-bodied fishes that are typically assumed to be generalist insectivores. Variation in diet specialization may be more widespread than previously considered, and ecological opportunity is an important factor in shaping trophic resource use of individuals and populations. Overall, the results indicate that even subtle and gradual environmental variation can induce substantial variation in phenotypes on a relatively small spatial scale.

Les processus d’hybridation et d’introgression occupent une place importante dans l’étude du mécanisme de spéciation, car ils permettent d’analyser les conséquences évolutives des échanges génétiques entre espèces partiellement isolées. Ici, nous nous sommes intéressés à la zone d’hybridation entre les soles S. senegalensis et S. aegyptiaca au niveau des côtes nord-tunisiennes, pour comprendre l’origine de leur diversification. Nous avons premièrement caractérisé les conséquences phénotypiques de l’hybridation sur la variabilité morphologique. Nos résultats montrent que si l’introgression provoque la convergence de certains caractères morphologiques, elle est en revanche à l’origine de transgressions et de distorsions morphologiques sur d’autres traits, pouvant refléter une condition plus faible des génotypes recombinants. Les phénomènes d’incompatibilité génétique associés à une éventuelle contre-sélection des hybrides sont supposés créer une perméabilité différentielle du génome face au flux génique entre espèces. Pour étudier cette semi-perméabilité à l’échelle du génome, nous avons établi un jeu de données de polymorphisme par la méthode RAD-seq. Ceci nous a permis de génotyper 200 individus pour 10 756 marqueurs SNP, qui nous ont permis de caractériser les flux géniques entre ces deux espèces à travers trois approches complémentaires. La première est basée sur une reconstitution démographique de l’histoire des échanges génétiques qui intègre les effets de la semi-perméabilité des génomes. La seconde approche se focalise sur l’évolution spatiale des fréquences alléliques à travers la zone d’hybridation. La dernière méthode, dite des clines génomiques, compare le comportement de chaque locus au patron d’introgression moyen attendu sous l’hypothèse de neutralité. Nos résultats indiquent que S. senegalensis et S. aegyptiaca ont subi une divergence ancienne en allopatrie suivie d’un contact secondaire récent. Seule une faible proportion du génome parvient à introgresser de manière asymétrique dans la zone hybride qui en résulte, selon une grande diversité de patrons d’introgression dont nous discutons les origines possibles. / Hybridisation and introgression processes have an important place in the study of speciation as they allow to analyse the evolutionary consequences of genetic exchanges between partially isolated species. Here we are interested in the hybrid zone resulting from the contact between the soles S. aegyptiaca and S. senegalensis along the North Tunisian coast. First, we studied the consequences of hybridisation on phenotypic variation. This allowed us to evidence that phenotypic convergence in hybrids was accompanied by phenotypic transgression and morphological distortions for certain traits that seem to reflect a reduced condition of hybrids. Possible genetic incompatibilities between species should be responsible for the differential permeability of the genome to gene flow, thereby creating a semi-permeable barrier. To study this barrier at the genome scale, we have produced a polymorphism dataset using the RAD-seq method. This allowed us to genotype 200 individuals at 10,756 SNP markers and to characterise genomic patterns of gene flow between the two species through three complementary approaches. The first is based on a reconstruction of the demographic history of the genetic and exchanges that incorporates the effects of the semi-permeability to gene flow. The second approach focuses on the spatial evolution of allele frequencies across the hybrid zone. The last method, called genomic clines, compares the behaviour of each locus to the average introgression pattern expected under the hypothesis of neutrality. Our results indicate that S. aegyptiaca and S. senegalensis underwent ancient divergence in allopatry followed by a recent secondary contact. Only a small proportion of the genome can asymmetrically introgress across the hybrid zone, resulting in a variety of introgression patterns of which we discuss the possible origins.

Le premier objectif de ce travail de thèse était de développer la méthodologie d’étude des postures basée sur la morphométrie géométrique. Cela nécessitait un perfectionnement de la méthodologie déjà existante sur la ligne du dos du cheval afin d’obtenir une méthode précise, quantifiable, objective et reproductible, permettant de discriminer des populations. Pour cela, plusieurs améliorations méthodologiques (ajout de marqueurs pour dessiner le contour de laligne du dos du cheval, analyse de contour, annulation de la rotation de l’encolure) ont été testées sur un important jeu de données et finalement retenues. Cette méthodologie retenue a ensuite été utilisée afin de valider sa pertinence, et de rechercher des postures associées à des états de mal-être et à des conditions de travail différentes. Nos résultats ont tout d’abord mis en évidence l’existence d’une posture atypique, dans l’ensemble plate, voire creuse, associée à des marqueurs de mal-être parmi les chevaux de centre équestre. D’une part des chevaux issus de différentes disciplines équestres, et d’autre part des individus entrainés pour les courses de galop par plusieurs entraineurs, aux pratiques distinctes, ont permis d’observer un effet du type de travail sur la ligne du dessus notamment sur la forme de la croupe, del’encolure et du garrot. La méthodologie ainsi validée, il était possible de proposer un protocole de mesure de la posture par morphométrie géométrique chez l’humain, pour une application à l’étude de la communication non verbale, à la constitution d’un répertoire de postures « normales », ou encore pour le diagnostic de pathologies physiques (e.g. contextesportif) ou psychologiques. / The first goal of this thesis work was to develop the study methodology of the posture based on geometric morphometrics. This required an upgrading of the already existing methodology using the upper line of the horse in order to obtain a precise, quantifiable, unbiased and reproducible method which allows to discriminate populations. To achieve this, manymethodological improvements (addition of markers for the modelling of the contour of horse upper line, contour analyses, cancellation of the neck rotation) has been tested on a very large dataset and retained. Then this adopted methodology has been used to validate its relevance, and searching for postures associated with poor welfare and different working conditions. Our results has first brought to light the existence of an atypical posture, globally flat, even hollow, related to poor welfare indicators among the population of riding school horses. On one side horses from different equestrian disciplines, and on the other side individuals trained for horseracing by several trainers with distinct practices, has allowed to observe an impact of the type of work on the upper line, notably on the shape of the croup, neck and withers. This methodology thereby validated, it was possible to propose a protocol for the measure of the posture through geometric morphometrics on humans, for an application in the non-verbal communication research, the creation of a repertoire of « normal » postures, or for the diagnosis of psychological or physical pathologies (e.g. in the sport context).

Current patterns of faunal diversity, geographic distribution, phylogenetic relationships and biogeography constitute a tool for understanding the evolutionary history of taxa. The boundaries of these taxa and their phylogenetic relationships reveal speciation events and therefore allow us to raise general hypotheses about the diversification of a particular group. Into the Oryzomyini, one of the most diverse tribe of Sigmodontinae subfamily, we can found the genus Hylaeamys. Currently seven species were described to that genus: H. acritus, H. seuanezi, H. megacephalus, H. oniscus, H. perenensis, H. tatei and H. yunganus. These species are distributed throughout the tropical and subtropical evergreen cis-andinean forests, from sea level to an altitude of 1500 meters, from Venezuela and Guyana, through the Amazon and the Atlantic Forest, to the north of Paraguay. The distribution of taxa within the genus were confusing and phylogenetic relationships among these species have been little explored, as well as the positioning of the genus within the clade B of Oryzomyini tribe and consequently his sister group. So my proposal was to reassess the species currently described through morphometric and molecular data to better explore the diversity within the genus, and the relations within the genus Hylaeamys and clade where it is inserted. My results showed a greater diversity than the currently described. Morphometric analysis could be helpful in the delimitation of taxa, however did not translate all the phylogenetic diversity found within the genus, witch may present cryptic species. The genus is monophiletic and a new species of Hylaeamys related to H. yunganus populations, from eastern South America was recognized. The results, also highlighted a geographical structure present within H. megacephalus, so, samples from north of the Rio Amazonas showed to be genetically distinct to those samples in southern of Rio Amazon. But this pattern was not observed in morphometric analysis. The species of the Atlantic Forest were closer to the western amazonian species. Hylaeamys showed as a sister group of a clade containing Cis and Trans Andean genera: Oecomys, Euryoryzomys and Transandinomys, indicating that the dispersion for trans-Andean areas occurred after the diversification of the Forest clade in South America. / Padrões faunísticos atuais de diversidade, distribuição geográfica, relações filogenéticas e biogeográficas constituem uma ferramenta para a compreensão da história evolutiva dos táxons. As delimitações destes táxons e suas respectivas relações filogenéticas nos revelam eventos de especiação e consequentemente nos permitem levantar hipóteses gerais de diversificação de um determinado grupo. O gênero Hylaeamys está inserido na tribo Oryzomyini, a mais diversa da subfamília Sigmodontinae. Possui atualmente sete espécies descritas: H. acritus, H. laticeps, H. megacephalus, H. oniscus, H. perenensis, H. tatei, e H. yunganus. Estas espécies se distribuem pelas florestas tropicais e subtropicais sempre verdes cisandinas, do nível do mar até uma altitude de 1500 metros, desde a Venezuela e as Guianas, passando pela Amazônia e pela Floresta Atlântica, até o norte do Paraguai. A distribuição dos táxons dentro do gênero eram confusas e as relações filogenéticas entre estas espécies, também, foram pouco exploradas, assim como o posicionamento do gênero dentro do clado B da tribo Oryzomyini e consequentemente seu grupo irmão. Portanto, minha proposta foi reavaliar as espécies atualmente descritas abordando de forma integrativa os dados morfométricos e moleculares para melhor explorar a diversidade dentro do gênero, assim como as relações de parentesco dentro do gênero Hylaeamys e do clado onde este se encontra inserido. Como resultado, obtive uma diversidade maior do que a descrita atualmente. Análises morfométricas puderam auxiliar na delimitação dos taxa, porem não traduziu toda a diversidade filogenética encontrada dentro do gênero, podendo o gênero apresentar espécies cripticas. O gênero se mostrou monofilético e uma nova espécie de Hylaeamys, relacionada às populações de H. yunganus do leste da América do Sul foi reconhecida, assim como, ficou evidente a estruturação geográfica presente dentro da espécie H. megacephalus, onde as amostras ao norte do Rio Amazonas se mostraram geneticamente distintas das amostras ao sol do Rio Amazonas. Porém nas análises morfométricas não foi observado esse padrão. As espécies da Floresta Atlântica se mostraram filogeneticamente mais próximas das espécies do oeste Amazônico. Hylaeamys se mostrou groupo irmão de um clado contendo gêneros Cis e Trans- Andinos, sendo eles, Oecomys, Euryoryzomys e Transandinomys, indicando que a dispersão para áreas trans-andinas se deu após a diversificação do gênero na América do Sul.