Submitted by Alison Vanceto (alison-vanceto@hotmail.com) on 2017-01-26T10:20:58Z No. of bitstreams: 1 TeseDTR.pdf: 5686221 bytes, checksum: b836c587b2a3a8ef73d83716fc17704e (MD5) / Approved for entry into archive by Camila Passos (camilapassos@ufscar.br) on 2017-02-07T15:39:53Z (GMT) No. of bitstreams: 1 TeseDTR.pdf: 5686221 bytes, checksum: b836c587b2a3a8ef73d83716fc17704e (MD5) / Approved for entry into archive by Camila Passos (camilapassos@ufscar.br) on 2017-02-07T15:42:54Z (GMT) No. of bitstreams: 1 TeseDTR.pdf: 5686221 bytes, checksum: b836c587b2a3a8ef73d83716fc17704e (MD5) / Made available in DSpace on 2017-02-07T15:43:01Z (GMT). No. of bitstreams: 1 TeseDTR.pdf: 5686221 bytes, checksum: b836c587b2a3a8ef73d83716fc17704e (MD5) Previous issue date: 2013-10-09 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / The network of South American rivers network has experienced deep changes during Late Miocene through Pleistocene, including major marine transgressions, Andean uplift driving drainage changes, and changes in eustatic level. After a marine transgression during Late Miocene in northwest South America, the ancestor of freshwater stingrays (Potamotrygonidae) adapted to the freshwater environment. Since then, the group has diversified while colonizing new drainage networks, given rise to new phenotypes and diet preferences. There are currently 24 species described, a number that will certainly rise once new species already known are described and new geographical regions are sampled. In the present work, I present a phylogeny for the Potamotrygonidae family based on molecular markers, with estimates of age and statistical tests of changes in rates of diversification while also testing for the occurrence of hybridization among some species of the family. The pattern of diversification in time and space was interpreted in light of major paleogeographical events that shaped drainage networks in South America during the Neogene, Mitochondrial and nuclear data corroborate the hypothesis of family origin in northwest South America around 25 Million years ago (MYA), after a major marine transgression, in a time when the Andes was not a topographic barrier between the Caribbean Sea and coastal regions. After those hydrographic basins were differentially colonized, whereas lineages that given rise to the genera Heliotrygon and Plesiotrygon possibly originated in the Pebas System, the lineage that gave rise to Potamotrygon probably was restricted to the region that is now the upper Negro river/Orinoco/Essequibo. After the inversion of the proto-Amazonas direction from East-West to West-East and reorganization of drainages, the Potamotrygon stingrays colonized both West portions of the Amazon Basin, previously occupied by Pebas megawetlands, and an Eastern portion, previously isolated by the Purus Arch. Contrary to the more accepted hypothesis, the estimated speciation ages suggest that this reorganization occurred around 3 MYA. Alternatively, the inversion of proto- Amazonas may have occurred earlier but the Negro river basin was kept isolated from the Amazon Basin at least as long to prevent stingrays dispersion. Following the reorganization of the drainages, a group of Potamotrygon named spotocellated underwent an increase in speciation rate – a radiation – as new regions were colonized. Upstream colonization of Crystalline Shields probably occurred in periods of higher eustatic level at the end of Pliocene, followed by vicariance after reduction of water levels.The Paraguai-lower Paraná basin was probably colonized at this same time, after headwater capture between Paraguai and Amazon Basins driven by foredeep formation. During the radiation, extensive hybridization took place among species of the spot-ocellated group. / As redes de drenagem da América do Sul passaram por profundas transformações do Mioceno Tardio ao Pleistoceno, incluindo grandes transgressões marinhas, soerguimento dos Andes com consequente mudança nas redes de drenagem, e oscilações no nível eustático. Após transgressão marinha no final do Mioceno no noroeste da América do Sul, os ancestrais das arraias da família Potamotrygonidae adaptaram-se a água doce. Desde então o grupo vem se diversificando à medida que coloniza novas redes de drenagem, com o surgimento de novos fenótipos e adaptações a diferentes ambientes e dieta. Dado o conhecimento taxonômico atual, existem cerca de 24 espécies na família, número esse que certamente será elevado à medida que novas espécies já conhecidas forem descritas, e novas regiões geográficas forem amostradas. Neste trabalho, apresento hipótese filogenética baseada em marcadores moleculares para a família Potamotrygonidae, com estimativa de idade dos eventos cladogenéticos e testes de mudança das taxas de especiação. A ocorrência de hibridação entre algumas espécies da família também foi testada. O padrão geográfico e tempo de diversificação das arraias da família Potamotrygonidae foram interpretados à luz dos principais eventos paleogeográficos que influíram nas mudanças das redes de drenagem da América do Sul durante o Neógeno, eventos esses revisados aqui. Os dados corroboram a hipótese de origem da família no noroeste da América do Sul há aproximadamente 25 milhões de anos atrás, após grande transgressão marinha, época em que os Andes ainda não serviam de barreira topográfica entre o Mar do Caribe e as regiões costeiras dessa região. A partir daí as bacias hidrográficas foram diferencialmente colonizadas, sendo que as linhagens que deram origem aos gêneros Heliotrygon e Plesiotrygon possivelmente se originaram no sistema Pebas, enquanto que a linhagem que deu origem ao gênero Potamotrygon provavelmente ficou restrito à região compreendida hoje pelo alto Rio Negro/Oricono/Essequibo. Após a inversão do sentido do proto-Amazonas de Leste-Oeste para o sentido moderno Oeste-Leste e reorganização das bacias de drenagem que atingiram conformação próxima a atual, as arraias do gênero Potamotrygon colonizaram tanto a região a Oeste da Bacia Amazônica, anteriormente ocupada pelas megawetlands do Sistema Pebas, quanto a região Leste, anteriormente isolada pelo Arco do Purus. Diferentemente da hipótese mais difundida, as idades de especiação estimadas sugerem que essa reorganização ocorreu há aproximadamente 3 milhões de anos atrás. Alternativamente, a inversão do proto-Amazonas pode ter ocorrido antes, mas a bacia do rio Negro teria se mantido isolada da bacia do rio Amazonas, ao menos a ponto de evitar a dispersão das arraias. Seguindo essa reorganização das drenagens, um grupo do gênero Potamotrygon denominado roseta-ocelado sofreu um aumento na taxa de especiação – radiação – à medida que novas regiões foram colonizadas. A colonização sentido rio acima das drenagens dos Escudos Cristalinos provavelmente ocorreu em período de águas mais altas no final do Plioceno, com posterior vicariância devido ao rebaixamento das águas. A Bacia do Paraguai-baixo Paraná provavelmente foi colonizada nessa mesma época, possibilitada pela conexão entre as cabeçeiras do rio Paraguai e Bacia Amazônica, após subsidência do tipo foredeep desencadeada por soerguimento dos Andes. Durante o processo de radiação do grupo roseta-ocelado houve extensiva hibridação entre as espécies do grupo.

The main objectives of this work are: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.