Broad whitefish, Coregonus nasus, is an important subsistence fish species in Arctic North America, yet virtually nothing is known regarding the genetic population structure of Nearctic populations of this species. In this thesis, microsatellite DNA variation was assayed among 1213 broad whitefish from 47 localities throughout North America, with emphasis on the Mackenzie River system, Northwest Territories. Specifically, I examined geographic variation in allele frequencies to assess how historical factors (Pleistocene glaciations) have shaped the current structuring of genetic variability and population differentiation. Microsatellite data was also used to resolve the relative contributions of broad whitefish populations to subsistence fisheries in the Mackenzie River system. Overall, broad whitefish exhibit relatively high intrapopulation microsatellite variation (average 12.29 alleles/locus, average HE = 0.58) and there were declines in these measures of genetic diversity with distance from putative refugia suggesting historical factors, namely post-glacial dispersal, have influenced current microsatellite variation. Interpopulation divergence was low (overall FST = 0.07), but the main regions assayed in this study (Russia, Alaska, Mackenzie River and Travaillant Lake systems) are genetically differentiated. Strong isolation-by-distance among samples was resolved when including only those populations occupying former Beringia, but not when assaying those at the periphery of the range in the Mackenzie River system, suggesting that broad whitefish in the Mackenzie system have not occupied the region long enough since their invasion post-glacially to have approached equilibrium between gene flow and drift. Mixture analysis indicated that most fish from the lower Mackenzie River subsistence fishery originated from the Peel River, highlighting the importance of this tributary. Additionally the mixture analysis provides evidence for a putative riverine life history form in the Mackenzie River. My results indicate that glaciation and post-glacial colonization have been important in shaping the current genetic population structure of North American broad whitefish. They also illustrate the utility of microsatellite DNA to delineate population structure and patterns of genetic diversity in recently founded populations in addition to resolving contributions to fisheries. My data also support the hypothesis that there are several designatable units of conservation among broad whitefish populations and that management strategies should be implemented accordingly. / Science, Faculty of / Zoology, Department of / Graduate

Acacia mangium Willd. est une légumineuse ligneuse introduite dans de nombreux pays tropicaux à partir de son aire d'origine (Australie), avec ou sans inoculations volontaires par des rhizobiums sélectionnés. Des campagnes d'échantillonnage des bactéries symbiotiques fixatrices d'azote ont été réalisées dans sa zone d'origine à différentes époques (1986, 2007 et 2009) et dans trois zones d'introduction (Brésil, Sénégal et Malaisie). Après isolement et test de nodulation homologue, la diversité de plus de 500 souches a été analysée sur un gène de ménage (recA) et un gène symbiotique (nodA). Nous avons confirmé qu'A. mangium était essentiellement nodulé par des Bradyrhizobium. La comparaison des communautés symbiotiques issues de la zone d'origine et des zones d'introduction montre une importante diversité dans la région d'origine et une diversité plus réduite dans les zones d'introduction. En Australie, quelques génotypes sont majoritaires et persistent durant 20 ans. Une structuration phylogéographique et un isolement par la distance à une échelle mondiale ont été mis en évidence pour le gène symbiotique nodA. Enfin, lorsque A. mangium a été introduit conjointement avec une souche sélectionnée, le devenir de cet inoculum est variable en fonction des essais d'introduction. De plus, nous mettons en évidence des phénomènes de transfert du gène symbiotique nodA entre une souche introduite et les bactéries autochtones. Les résultats acquis nous permettent d'émettre des recommandations en termes de sauvegarde de la biodiversité microbienne symbiotique en zone naturelle, et sur la pertinence de procéder à des inoculations lors de la mise en place de plantations d'A. mangium. / From Australia, its native area and since three decades, the legume tree Acacia mangium Willd. has been introduced in many tropical countries, sometimes with selected rhizobium strains. A. mangium symbiotic nodule bacteria have been sampled in Australia at different times (1986, 2007, 2009), as well as in countries where it was introduced for inoculation trials (Brazil, Senegal and Malaysia). More than 500 isolates were obtained and checked for homologous nodulation. They were then characterized on the housekeeping recA and symbiotic nodA genes. We demonstrated through this study that A. mangium was almost always nodulated by Bradyrhizobium. Phylogenies of the obtained sequences were made, showing a high level of bacterial diversity in the native area, and a much more reduced diversity in introduced areas. In Australia, some genotypes were predominant and persist over 20 years. A phylogeographic structuration and isolation by distance at a global scale were demonstrated for the nodA symbiotic gene. Among introduced areas, the main result was the unsystematic occurrence of inoculated strains. We highlighted horizontal nodA symbiotic gene transfer between inoculated and indigenous bacterial strains. These data allow to make recommendations in terms of microbial diversity conservation in natural areas and on the need for inoculation of A. mangium in forestry practices.

Au travers d'une approche de génétique des populations et de phylogéographie, basée sur la comparaison des patrons de diversité chloroplastiques et nucléaires, cette étude s'attache à retracer les processus qui ont façonné la diversité de la patate douce depuis sa domestication en Amérique tropicale jusqu'à son introduction et sa diffusion en Océanie. Dans un premier temps, cette étude s'intéresse à l'histoire de la domestication et à l'identification de l'origine botanique et géographique de la patate douce dans son aire d'origine - l'Amérique tropicale. La patate douce est un taxon hexaploïde pour lequel les différents contributeurs sauvages n'ont pas encore été clairement identifiés. Deux hypothèses sont classiquement invoquées: 1) une origine autopolyploide à partir d'un taxon sauvage diploide I. tridida et 2) une origine allopolyploide ayant impliqué l'hybridation de deux espèces distinctes I. trifida et I. triloba. Nos résultats génétiques viennent corroborer le scénario auto-polyploïde. Néanmoins, contrairement à ce qui était avancé auparavant, I. trifida ne peut être considérée comme l'ancêtre sauvage de la patate douce. Des formes sauvages de I. batatas existent, populations à partir desquelles les formes cultivées ont été domestiquées. Par ailleurs, nous révélons l'existence de deux lignées chloroplastiques distinctes au sein des cultivars de patate douce, ce qui laisse penser que plusieurs parents sauvages, différenciés génétiquement mais probablement conspécifiques, sont impliqués dans la formation du génome de I. batatas. Deux scénarios (non exclusifs) peuvent alors être envisagés: i) I. batatas résulte de l'hybridation de plusieurs lignées distinctes (conspécifiques ou proches); ii) I. batatas est un complexe autopolyploïde avec une origine multiple. La caractérisation génétique des cultivars de patate douce met en lumière l'existence de deux groupes génétiques différenciés et géographiquement structurés: l'un correspond aux variétés d'Amérique centrale et caribéenne et l'autre aux variétés de la région du Pérou et de l'Equateur. Ce patron de diversité suggère fortement une domestication multi-locale - en Amérique centrale et en Amérique du Sud - et renforce l'hypothèse d'une origine autopolyploïde multiple dans ces deux régions. Dans un deuxième temps, notre étude nous conduit en Océanie, une aire d'introduction de la patate douce. La distribution de la patate douce dans le Pacifique s'explique par une (des) introduction(s) pré-historique(s) en Polynésie en provenance d'Amérique du Sud (par les polynésiens eux-mêmes) et des introductions historiques dans le Pacifique Ouest, en provenance du Mexique et des Caraïbes. Il s'agit là d'une hypothèse élaborée par des linguistes, ethnobotanistes et archéologues, mais qui à ce jour manquait de preuves génétiques. En combinant un échantillonnage de variétés traditionnelles contemporaines et des spécimens d'herbiers datant du 18ième au début du 20ième siècle, nous avons pu retracer l'évolution temporelle et spatiale de la diversité dans le Pacifique. Nous montrons que les variétés de patate douce présentes jusqu'au début du 20ième siècle en Polynésie ont clairement une signature génétique sud-américaine, c'est-à-dire qu'elles dérivent directement des variétés de la région Pérou-Equateur. Ainsi nos données génétiques apportent une preuve supplémentaire à l'existence d'au moins une connexion préhistorique entre la Polynésie et l'Amérique du Sud. A l'Ouest du Pacifique, les cultivars de patate douce ont une origine principalement centraméricaine. Nous montrons également qu'il y a eu un remaniement de la base génétique au fil des nouvelles introductions, effaçant progressivement la signature des introductions d'origine. En revanche, les phénotypes reconnus par les cultivateurs et les noms associés - c'est-à-dire les déterminants « culturels » des variétés - ont probablement été maintenus. La patate douce est essentiellement propagée par voie clonale par les cultivateurs. / Following a population genetics and phylogeography approach, based on the comparison of chloroplastic and nuclear diversity patterns, this study aims at describing the processes which built sweet potato diversity from its domestication in tropical America to its introduction and diffusion into Oceania. We first studied the history of sweet potato domestication and identified its botanic and geographic origin in the area from which it originates - tropical America. Sweet potato is a hexaploid taxa of which the wild parents still remain to be identified. Two hypothesis are classically refered to: 1) an autopolyploid origin deriving from a wild diploid I. tridida and 2) an allopolyploid origin implying the hybridization between I. trifida et I. triloba. Our genetic results corroborate the autopolyploid scenario. However, in contrast to what was previously anticipated, I. trifida cannot be considered the wild ancestor of sweet potato. Wild forms of I. batatas do exist, these are populations from which cultivated forms were domesticated. In addition, we highlighted the existence of two distinct chloroplastic lineages within sweet potato cultivars, suggesting that several wild parents, genetically differenciated but probably conspecifics are involved in the formation of the I. batatas genome.Two scenari (non exclusive) are to be envisaged: i) I. batatas would result from the hybridization of several independent lines (conspecific or near); ii) I. batatas is an autoploid complex with multiple origin. The genetic characterization of sweet potato cultivars highlight the existence of two genetically differentiated and geographically structured groups: one includes central american and caribbean varieties while the other is made of varieties from Peru and Equador region. This diversity pattern is strongly suggestive of multilocal domestication events - in Central America and in South America - and strengthens the hypothesis of a multiple autopolyloid origin in these two regions.Next, we investigated Oceania as area of introduction of sweet potato. The sweet potato distribution in the Pacific can be explained by pre-historic introductions in Polynesia originating from South America (brought by Polynesians), and historical introductions in West-Pacific originating from Mexico and the Caribbean islands.This is a hypothesis originally proposed by linguists, ethnobotanists and archeologists, but which was lacking until now of genetic proves. Combining the sampling of contemporary traditional varieties and herbarium specimens dating from the 18th to the early 20st century, we were able to refine the temporal and spatial evolution of sweet potato diversity in the Pacific. We demonstrate that sweet potato varieties present until the early 20th century in Polynesia clearly harbor a south-american genetic signature, indicating that they directly derive from varieties found in the Peru-Ecuador area. Thus our genetic data provide an additional prove to the existence of at least one prehistoric connection between Polynesia and South America. On the west side of Pacific, sweet potato cultivars mainly display a central-american origin. We also demonstrate that a reshuffling of the genetic base happened in line with the occurrence of new introductions, progressively erasing the signature of original introductions. In contrast, phenotypes and associated names known by farmers, i.e. cultural determinants of these varieties - were probably maintained over time. Sweet potato is essentially propagated clonally by farmers. However, it also maintained active sexual reproduction. Our genetic data demonstrate that the impressive numbers of cultivars found nowadays in Oceania mainly derive from independent recombination events and from the local selection of true-seed plants. In some regions, this diversification process even lead to the emergence of secondary diversity centers, as exemplified by New Guinea highlands.

Scarabaeus (Pachysoma) consists of 13 flightless dung beetle species endemic to the arid west coast of southern Africa. Scarabaeus (Pachysoma) are unique in their feeding and foraging habits, in that they randomly search for dry dung/detritus which, when found, is dragged forwards, and buried in a pre-constructed holding chamber, as opposed to the convention of rolling it backwards. This action is repeated to provision the chamber after which the nest is expanded to below the moisture line to allow the stored food to re-hydrate. Poor vagility, taxonomic contention - seen in Scarabaeus taxonomy - and conservation concern, made Scarabaeus (Pachysoma) an ideal group of beetles to study both the phylogenetics and potential influences that anthropogenic and environmental changes have had on structuring the species and populations thereof. Both molecular and morphological data were used as individual datasets and combined in a total evidence approach. Biogeographic inferences were made based on recent detailed Namib biogeography and the ages of the species were estimated using the molecular clock method. A phylogeographic study was done on three of the species of Scarabaeus (Pachysoma) – S. (P.) hippocrates, S. (P.) gariepinus and S. (P.) denticollis - that had previously shown south-north morphological clinal variation. Lastly, an attempt was made to isolate microsatellite loci for Scarabaeus, in the hope of characterising genetic diversity within and between populations of the same species. Scarabaeus (Pachysoma) was found to be monophyletic within Scarabaeus and was therefore classified as a derived subgenus thereof. Morphologically Scarabaeus (Pachysoma) was shown to have 13 species while at a molecular level strong resolution for 11 of the 13 was obtained. S. (P.) hippocrates and S. (P.) glentoni formed a species complex the hippocrates/glentoni complex. The combined phylogenetic tree showed good overall support for all 13 species. Both the morphological and molecular data partition phylogenies show congruence with the combined phylogeny, lending support for combining datasets. Scarabaeus (Pachysoma) appears to have arisen 2.9 million years ago. The formation of advective fog is a consistent water source for Desert dwelling organisms and appears to be associated with Scarabaeus (Pachysoma) radiation into inhospitable areas. Analysis of gene flow revealed large amounts of south-north movement, lending support for movement of psammophilous taxa with their substratum, the barchan dune. Population demographics of the three species, S. (P.) hippocrates, S. (P.) gariepinus and S. (P.) denticollis, chosen for this study differed greatly except in areas of geographic similarity. Major rivers appear to have acted as gene barriers, allowing for distinct genetic entities to be identified within the three species. Phylogeographic partitioning was supported by an AMOVA analysis. All three species were shown to have undergone historical population expansion dating back to the Pleistocene era. Nested Clade Analysis indicated that allopatric speciation; isolation by distance and continuous range expansion could be the factors having affected overall population structure. Recent events show that human induced factors, environmental barriers and reduced vagility have influenced the species population structure. Four potentially polymorphic loci were isolated for Scarabaeus using the FIASCO protocol. Identification of at least one additional locus is needed in order to obtain statistical significance for future studies directed at uncovering recent population dynamics. / Thesis (PhD (Entomology))--University of Pretoria, 2007. / Zoology and Entomology / unrestricted

Orientadores: Clarice Weis Arns, Márcia Bianchi dos Santos / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-27T11:13:27Z (GMT). No. of bitstreams: 1 Carvalho_RicardoDuraesde_D.pdf: 3518273 bytes, checksum: 7b6f8b159eb057429823e23f6852c29b (MD5) Previous issue date: 2015 / Resumo: A evolução e a dinâmica populacional dos Coronavírus (CoVs) ainda permanecem pouco exploradas. No presente estudo, análises filogenéticas e de filogeografia foram conduzidas para investigar a dinâmica evolutiva dos CoVs detectados em aves silvestres e sinantrópicas. Um total de 500 amostras, que inclui os suabes traqueais e cloacais coletados de 312 aves silvestres pertencentes a 42 espécies, foram analisadas através da RT-qPCR. Sessenta e cinco amostras (13%) provenientes de 23 espécies foram positivas para o Coronavírus aviário (AvCoV). Trezentos e duas amostras foram investigadas para a pesquisa do Pan-Coronavírus (Pan-CoV) através do nPCR, destas, 17 (5,6%) foram positivas, sendo que 11 foram detectadas em espécies diferentes. Análises filogenéticas dos AvCoVs revelaram que as sequências de DNA das amostras coletadas no Brasil não agruparam com nenhuma das sequências do gene Spike (S1) dos AvCoVs depositados no banco de dados GenBank. Análise Bayesiana estimou uma variante do AvCoV proveniente da Suécia (1999) como o ancestral comum mais recente dos AvCoVs detectados neste estudo. Além disso, as análises realizadas através do "Bayesian Skyline Plot" (BSP) inferiram um aumento na dinâmica da população demográfica do AvCoV em diferentes espécies de aves silvestres e sinantrópicas. As análises filogenéticas do Pan-CoV mostrou que a maioria das amostras se agruparam com o Vírus da Hepatite Murina A59 (MHV A59), CoV pertencente ao grupo dos Beta-CoVs. Uma amostra [CoV detectado em Amazona vinacea(Papagaio-de-peito-roxo)] se agrupou com um CoV de Suínos, o PCoV HKU15, que pertence ao gênero Delta-CoV, ainda não relatado na América do Sul. Nossos achados sugerem que as aves podem ser novos potenciais hospedeiros responsáveis pela propagação e disseminação de diferentes CoVs para diferentes espécies de animais / Abstract: The evolution and population dynamics of Coronaviruses (CoVs) still remain underexplored. In the present study, phylogenetic and phylogeographic analyseswere conducted to investigate the evolutionary dynamics of CoV detected in wild and synanthropic birds. A total of 500 samples, including tracheal and cloacal swabs collected from 312 wild birds belonging to 42species, were analysed by RT-qPCR. A total of 65 samples from 23bird species were positive for Avian Coronaviruses (AvCoVs).Three hundred and two samples were screened for the Pan-Coronavirus (Pan-CoV) through the nPCR, 17 (5.6%) were positive, being that 11 were detected in different species. AvCoVs phylogenetic analyses revealed that the DNA sequences from samples collected in Brazil did not cluster with any of the AvCoV S1 gene sequences deposited in the GenBank database. Bayesian framework analysis estimated an AvCoV strain from Sweden (1999) as the most recent common ancestor of the AvCoVs detected in this study. Furthermore, Bayesian Skyline Plot (BSP) analysis inferred an increase in the AvCoV dynamic demographic population in different wild and synanthropic bird species. Phylogenetic analysis of the Pan-CoV showed that most of the samples clustered with the Murine Hepatitis Virus A59 strain (MHV A59) belong to the BetaCoV group. Besides, one of our samples [CoV detected in Amazona vinacea (parrot-breasted-purple)] clustered with a CoV isolated from pigs, PCoV HKU15, belonging to the DeltaCoV genus, still not reported in South America. Our findings suggest that birds may be potential new hosts responsible for spreading of different CoVs for different species of animals / Doutorado / Microbiologia / Doutor em Genetica e Biologia Molecular

Este presente estudo apresenta dados sobre duas análises complementares: a filogenia do gênero Scaura (Capítulo 2) e a filogeografia da espécie Scaura latitarsis (Capítulo 3). O estudo filogenético do gênero Scaura utilizou como fonte de dados sequências do ND2 (1095 pb), COI (1560 pb), COII (310 pb), Cyt B (746 pb), 16S (547 pb) e 12S (437 pb), obtidas a partir de indivíduos das quatro espécies desse gênero (S. atlantica, S. latitarsis, S. longula e S. tenuis) e quatro espécies como grupos externos (Schwarzula timida, Schwarziana quadripunctata, Plebeia remota, Plebeia droryanna). As reconstruções filogenéticas obtidas indicam que: 1) táxons do atual gênero formam um grupo monofilético; 2) dentre as espécies do grupo externo, a Schwarzula timida é a mais próxima ao gênero Scaura. Para análise filogeográfica foram utilizados 743 pb referente a parte do gene COI do DNA mitocondrial e a análise de sete locos polimórficos de microssatélites para 36 indivíduos de S. latitarsis provenientes de 9 localidades diferentes. Com os dados do gene COI foram identificados 26 haplótipos, com alta diversidade haplotípica e baixa diversidade nucleotídica. Os dados moleculares de morfometria de asa e os dados moleculares mostram grandes similaridades e indicam a existência de uma nova espécie dentro do grupo latitarsis. Portanto, a taxonomia atual do Gênero Scaura deve ser revista. / This present study presents data on two complementary analysis: the phylogeny of the genus Scaura (Chapter 2) and phylogeography of the species S. latitarsis (Chapter 3). The phylogenetic analysis of genus of Scaura used as a data source of ND2 sequences (1095 bp), COI (1560 bp), COII (310 bp), Cyt B (746 bp), 16S (547 bp) and 12S (437 bp) obtained from individuals of four species of the genus (S. atlantica, S. latitarsis, S. longula and S. tenuis) and four species as outgroups (Schwarzula timida, Schwarziana quadripunctata, Plebeia remota and Plebeia droryanna). The phylogenetic reconstructions obtained indicate that: 1) taxa of the genus form a monophyletic group, 2) among the species of the outgroup, the species Schwarzula timida is closest to the genus Scaura. Phylogeographic analyses were used to 743 bp relative to part of the COI gene and mitochondrial DNA analysis of seven polymorphic microsatellite loci for 36 individuals of S. latitarsis from nine different locations. Using data from the COI gene were identified 26 haplotypes, high haplotype diversity and low nucleotide diversity. The molecular data of morfomentria wing and molecular data show great similarities and indicate the existence of a new species within the group latitarsis. Therefore, the current taxonomy of the genus Scaura should be reviewed.

Gymnotus pantherinus é uma espécie de peixe endêmica das drenagens costeiras brasileiras com distribuição desde o sul da Bahia até o Rio Grande do Sul, embora evidências morfológicas sugiram que esse táxon constitua um complexo de espécies. No presente trabalho, foram conduzidas análises filogenéticas com base em marcadores moleculares, mitocondriais e nucleares, com o objetivo de avaliar o status taxonômico do grupo. Padrões demográficos foram também inferidos para as populações de Gymnotus pantherinus (senso estrito). As análises filogenéticas sob o critério de Parcimônia, bem como as inferências bayesianas, mostraram que o grupo é composto por cinco linhagens geográficas estatisticamente bem suportadas. Das cinco linhagens identificadas, aquela composta por espécimes da Bahia e Espírito Santo é também suportada por evidências morfológicas, a qual propomos que seja reconhecida como uma nova espécie. As demais linhagens, das quais a mais recente é a de Gymnotus pantherinus senso estrito, foram consideradas como espécies incipientes. As análises populacionais revelaram que as populações de Gymnotus pantherinus (senso estrito) se apresentam altamente estruturadas, exibindo um alto índice de fixação e baixo compartilhamento de haplótipos, sendo reconhecidas três linhagens principais com alta associação geográfica. A maior diversidade genética foi encontrada na região do Vale do Ribeira e o clado SP/Sul é o que apresenta a divergência mais recente, a qual pode ter ocorrido após o Último Máximo Glacial. Populações localizadas a oeste da Serra do Mar (Paraíba do Sul, Alto Tietê e Alto Iguaçu) demonstram maior similaridade com drenagens adjacentes a leste, o que reforça a hipótese de captura de cabeceiras entre drenagens previamente postulada a partir do compartilhamento de fauna. Finalmente, os resultados apontam a existência de pelo menos cinco Unidades Evolutivas Significativas para a espécie, tendo implicações importantes na conservação dos riachos de Mata Atlântica. / Gymnotus pantherinus is an endemic fish species found in the Brazilian coastal drainages occurring from Bahia to Rio Grande do Sul states. Morphological evidence has suggested that Gymnotus pantherinus might constitute a species complex. In the present study, the taxonomic status of Gymnotus species group has been evaluated using both mitochondrial and nuclear markers. Demographic patterns have also been inferred for the Gymnotus pantherinus populations (stricto sensus). Parsimony and Bayesian phylogenetic inferences showed that the group is composed of five well supported geographic lineages. From those, a well supported lineage constituted by the specimens from Bahia and Espírito Santo states is also corroborated by morphological data. Thus, it is suggested that this lineage be recognized as a new species within Gymnotus. The other lineages, from which the most recent representative is the Gymnotus pantherinus lineage itself, have been considered as incipient species. The population analysis showed highly structured populations with low number of shared haplotypes and three main phylogenetic lineages with high geographic association. The higher genetic diversity was found in the Ribeira Valley region, while the clade SP/South was the most recently diverged, which may have occurred after the Last Glacial Maximum. Populations occurring west of the Serra do Mar were more closely related to the adjacent east drainages, which strengthens the hypothesis of headwaters stream capture. Finally, at least five evolutionary significant units can be recognized, with important implications for the conservation of Atlantic Forest streams.

Dendrocolaptes platyrostris é uma espécie de ave florestal associada às matas de galeria do corredor de vegetação aberta da América do sul (D. p. intermedius) e à Floresta Atlântica (D. p. platyrostris). Em um trabalho anterior, foi observada estrutura genética populacional associada às subespécies, além de dois clados dentro da Floresta Atlântica e evidências de expansão na população do sul, o que é compatível com o modelo Carnaval-Moritz. Utilizando approximate Bayesian computation, o presente trabalho avaliou a diversidade genética de dois marcadores nucleares e um marcador mitocondrial dessa espécie com o objetivo de comparar os resultados obtidos anteriormente com os obtidos utilizando uma estratégia multi-locus e considerando variação coalescente. Os resultados obtidos sugerem uma relação de politomia entre as populações que se separaram durante o último período interglacial, mas expandiram após o último máximo glacial. Este resultado é consistente com o modelo de Carnaval-Moritz, o qual sugere que as populações sofreram alterações demográficas devido às alterações climáticas ocorridas nestes períodos. Trabalhos futuros incluindo outros marcadores e modelos que incluam estabilidade em algumas populações e expansão em outras são necessários para avaliar o presente resultado / Dendrocolaptes platyrostris is a forest specialist bird associated to gallery forests of the open vegetation corridor of South America (D. p. intermedius) and to the Atlantic forest (D. p. platyrostris). A previous study showed a population genetic structure associated with the subspecies, two clades within the Atlantic forest, and evidence of population expansion in the south, which is compatible with Carnaval- Moritz\'s model. The present study evaluated the genetic diversity of two nuclear and one mitochondrial markers of this species using approximate Bayesian computation, in order to compare the results previously obtained with those based on a multi-locus strategy and considering the coalescent variation. The results suggest a polytomic relationship among the populations that split during the last interglacial period and expanded after the last glacial maximum. This result is consistent with the model of Carnaval-Moritz, which suggests that populations have undergone demographic changes due to climatic changes that occurred in these periods. Future studies including other markers and models that include stability in some populations and expansion in others are needed to evaluate the present result

O gênero Hypostomus (Siluriformes: Loricariidae) com cerca de 130 espécies nominais, se destaca como um dos mais diversos e amplamente distribuídos gêneros de peixes de água doce neotropical. Devido a sua ampla distribuição e alta diversidade, os conhecimentos taxonômicos, filogenéticos e biogeográficos para as espécies do gênero são ainda consideravelmente incompletos. Consequentemente, pouco se sabe sobre processos naturais envolvidos em diversificação e variação morfológica para o gênero. Hypostomus ancistroides é uma espécie descrita para a bacia do Alto Paraná, uma eco-região hidrográfica tradicionalmente reconhecida por seu endemismo ictiofaunístico, ocorrendo também na bacia costeira do rio Ribeira de Iguape. Esta espécie apresenta considerável variação morfológica, cariotípica e isoenzimática em suas diferentes populações, sugerindo a existência de um complexo de espécies. Sua ampla área de distribuição, somada aos novos conhecimentos sobre padrões biogeográficos para diversas espécies de peixes do Alto Paraná, reforça essa possibilidade. Entretanto, a variação encontrada na morfologia das populações de H. ancistroides é ampla e contínua, impedindo que se defina diferentes espécies através das abordagens taxonômicas clássicas em ictiologia. Assim, este trabalho se propõe a utilizar ferramentas da sistemática molecular, genética de populações e filogeografia para responder questões fundamentais sobre a evolução desse potencial complexo de espécies. Sequências nucleotídicas completas do marcador mitocondrial ATP sintase (subunidades 6 e 8; 842 pb) foram obtidas para diversas espécies de Hypostomus, incluindo 162 exemplares de H. ancistroides provenientes de doze localidades abrangendo toda a sua área de ocorrência, além de outros gêneros da família Loricariidae, utilizados como grupos externos. Análises filogenéticas de Máxima Verossimilhança, Máxima Parcimônia e Neighbor Joining resultaram em topologias essencialmente semelhantes, sustentando a monofiletismo da espécie, e apontando como seus parentes mais próximos espécies de bacias hidrográficas adjacentes ao Alto Paraná. Esses resultados mostram ainda a existência de quatro filogrupos distintos para a espécie, com áreas de distribuição parcialmente sobrepostas. Análises populacionais e filogeográficas incluiram comparação de distância genética P, estruturação populacional baseada em distribuição de haplótipos e índices de diversidade, testes de neutralidade, índice de fixação FST, análise de variância molecular (AMOVA), análise espacial de variância molecular (SAMOVA), construção de rede haplotípica de parcimônia, e análise de clados hierarquizados (NCPA). Os resultados mostram 48 haplótipos repartidos em doze populações bem estruturadas, com baixo ou nenhum fluxo gênico entre si. Eventos de expansão geográfica podem ser identificados ao longo da história demográfica, sugerindo que a estruturação encontrada atualmente reflete não só as características ecológicas da espécie, como também uma história de mudanças nas condições ambientais, eventualmente favoráveis a migração e dispersão. Contatos entre populações de diferentes bacias podem ser mais frequentes através de capturas de cabeceiras do que ao longo do corpo dos rios principais. A hipótese mais plausível para a presença da espécie na bacia do Ribeira é a de uma captura de cabeceira do alto rio Tietê. Apesar de ser formado por quatro filogrupos distintos, algumas linhagens derivadas de H. ancistroides apresentam sobreposição de suas áreas de distribuição. Esse contato secundário revelado apenas por um marcador de herança matrilineal impossibilita a delimitação de diferentes espécies correspondentes aos filogrupos, sob os paradigmas clássicos de especiação em peixes neotropicais. / The genus Hypostomus (Siluriformes: Loricariidae), comprising ca. 130 nominal species, is one of the most species-rich and widely distributed genera of neotropical freshwater fish. Because of its wide distribution and vast diversity, knowledge on the taxonomy, phylogenetic relationships and biogeography of Hypostomus is still severely incomplete. Consequently, little is known about the processes involved in the diversification and morphological variation for the genus. Hypostomus ancistroides is a species described from the upper Rio Paraná drainage, a freshwater ecoregion known for its ichthyological endemism, also occurring in the coastal basin of Rio Ribeira de Iguape. This species shows considerable morphological, karyotypic and isoenzimatic variation among different populations, suggesting the existence of a species complex. Its wide distribution area, coupled with recent understanding on biogeographic patterns of several fish species from the Upper Parana, reinforces that possibility. However, morphological variation in populations of H. ancistroides is wide and continuous, and does not allow recognition of potential different species by means of traditional taxonomic approaches. Thus, this paper uses tools from molecular systematics, population genetics, and phylogeography in order to answer major questions about the evolution of this potential species complex. Complete sequences of the mitochondrial marker ATP synthase (subunits 6 and 8; 842 bp) were obtained for several species of Hypostomus, including 162 specimens of H. ancistroides from twelve localities covering its entire area of distribution, plus other loricariid genera as outgroups. Phylogenetic analysis using methods of Maximum Likelihood, Maximum Parsimony, Neighbor Joining and Bayesian Inference resulted in mostly similar topologies, supporting the monophyly of the species, and showing as its closest relatives other species from river basins bordering the Upper Parana. Results also reveal four distinct phylogroups for the species, with partially overlapping distribution areas. Population and phylogeographic analysis included comparisons of genetic distance P, population structure based on the haplotype distribution and diversity indices, neutrality tests, fixation index FST, analysis of molecular variance (AMOVA), spatial analysis of molecular variance (SAMOVA), construction of a parsimony haplotype network, and nested clade phylogeographical analysis (NCPA). Results show 48 haplotypes distributed into twelve well-structured populations with little or no gene flow. Geographic range expansion events can be identified along the demographic history of H. ancistroides, suggesting that the structure found today reflects not only the ecology of the species, but also a history of changing environmental conditions that on occasion weree favorable for migration and dispersal. Contact between populations from differente basins may be more intense through headwater stream capture than through the river channel. The most supported hypothesis for the presence of the species in the Rio Ribeira basin is a headwater capture from the upper Rio Tiete. Although H. ancistroides is split into four distinct phylogroups, some derived lineages of the species have overlapping distribution ranges. Such secondary contact is revealed only by a matrilineal inheritance marker and does not allow the recognition of separate species for the different phylogroups under the current paradigm of speciation and species limits in Neotropical fishes.

O cluster Drosophila buzzatii é formado por sete espécies endêmicas da América do Sul e que apresentam relação ecológica obrigatória com cactos. Dentre estas espécies, Drosophila serido possui ampla distribuição geográfica, na Caatinga e ao longo da costa Atlântica, e é considerada uma espécie politípica sendo dividida em dois grupos: populações do nordeste e do litoral. Com o objetivo de compreender os processos que moldaram a distribuição atual das populações de D. serido foram realizadas análises com sequências dos genes nucleares period e kl-5, ligados aos cromossomos sexuais X e Y, respectivamente, genes nucleares autossômicos GstD1 e E5, e gene mitocondrial COI. Dentre os resultados obtidos, a homogeneidade genética entre as populações do Nordeste e a divisão norte-sul entre as populações da costa Atlântica foram observadas em todos os marcadores. Três padrões quanto à estruturação populacional na costa Atlântica foram observados para os diferentes marcadores. A hipótese de que a Chapada Diamantina seja o centro de dispersão para a espécie foi confirmada pelo presente trabalho, no entanto, o TMRCA estimado para populações de Santa Catarina sugerem que estas sejam populações ancestrais de D. serido, sendo que o Nordeste teria sido colonizado a partir delas. Eventos de expansão de área e fragmentação alopátrica foram sugeridos como inferências filogeográficas para explicar o isolamento atual de populações de D. serido em Goiás e Minas Gerais. De acordo com as estimativas do TMRCA, é possível que os eventos causais dos processos históricos inferidos estejam relacionados à influencia das flutuações climáticas do Quaternário na distribuição geográfica da vegetação/cactos, afetando indiretamente as populações de moscas cactofílicas. É possível que eventos de seleção, associado aos fatores ecológicos quanto ao uso de cactos, também possam ter contribuído para o processo de diversificação populacional, uma vez que foi encontrada evidência de seleção positiva para os genes autossômicos. / Drosophila buzzatii cluster comprises seven species endemic of South America and that present a mandatory ecological association with cacti. Among these species, Drosophila serido has a wide geographical range, in Caatinga and along Atlantic coast, and is considered as a polytypic species, divided in two groups: northeast and coast populations. The purpose of this study was understand the process that shaped the current distribution of D. serido populations through genetic analysis using sequences of nuclear genes period and kl-5, X- and Y-linked, respectively, autosomal genes GstD1 e E5, and mitochondrial gene COI. The genetic homogeneity among Northeast populations and the north-south division among coast Atlantic populations were observed for all markers. Three patterns related to population structure in coast Atlantic were seen for the different markers. Hypothesis that Diamantina Plateau was the dispersion center for the species were confirmed at this study, although, TMRCA estimated for Santa Catarina populations suggested that these ones were ancestral, and that Northeast would be colonized from them. Expansion range and allopatric fragmentation were historical events suggested as phylogeographic inferences to explain the current isolation of D. serido populations in Goiás and Minas Gerais. According to TMRCA estimations, it is possible that causal events of historical process inferred were related to the influence of climatic fluctuations during Quaternary in the geographic distribution range of vegetation/cacti, indirectly affecting the populations of cactofilic flies. Furthermore, selection events, associated with ecological factors due to cacti use, as well as contributed to diversification process in populations, once it was found evidence of positive selection at autosomal genes.