Το γένος Trachelipus περιλαμβάνει οργανισμούς σχετικά στενόοικους οι οποίοι ζουν είτε στην παρόχθια βλάστηση ρεμάτων και ποταμών είτε σε υγρά δάση. Στη χώρα μας έχουν καταγραφεί 8 από τα 50 είδη του γένους, 4 από τα οποία είναι ενδημικά της Ελλάδας. Το ένα από αυτά εξαπλώνεται από την Κρήτη μέχρι την Ήπειρο, ένα στα νησιά του κεντρικού Αιγαίου, ένα στην Κρήτη και ένα στο νότιο Ευβοϊκό. Η κατανομή κάθε είδους είναι ασυνεχής, είτε λόγω γεωγραφικών (νησιωτικοί πληθυσμοί κλπ) είτε λόγω ενδιαιτηματικών παραγόντων. Η διάκριση μεταξύ των ειδών έχει γίνει βάσει περιορισμένου αριθμού μορφολογικών χαρακτήρων και δεν είναι βέβαιο ότι αντανακλά τις πραγματικές φυλογενετικές σχέσεις τους. Από τα αποτελέσματα προηγούμενης μελέτης διαπιστώθηκε έντονη απόκλιση μεταξύ των προτύπων της γενετικής ποικιλότητας και εκείνης της τρέχουσας ταξινόμησης σε ορισμένες ομάδες πληθυσμών του γένους αυτού. Επιπλέον, φάνηκε σημαντικός βαθμός γενετικής απομόνωσης μεταξύ των πληθυσμών ενός είδους, ενισχύοντας την άποψη περί ισχυρής μεταπληθυσμιακής συγκρότησής τους. Στην παρούσα μελέτη, συλλέχθηκαν 47 πληθυσμοί στην ηπειρωτική Ελλάδα, οι οποίοι στη μεγάλη τους πλειοψηφία ανήκαν στο είδος Trachelipus kytherensis (σύμφωνα με την ισχύουσα ταξινόμηση). Σε αυτούς προστέθηκαν και τα δεδομένα των Parmakelis et al 2008 (16 πληθυσμοί) έτσι ώστε να είναι πιο ολοκληρωμένη η μελέτη και η εξαγωγή συμπερασμάτων για το γένος Trachelipus. Συνολικά μελετήθηκαν γενετικά 63 πληθυσμοί του γένους, χρησιμοποιώντας ως μοριακούς δείκτες τα μιτοχονδριακά γονίδια 16S rRNA και COI. Έπειτα από απομόνωση του DNA και τον πολλαπλασιασμό των συγκεκριμένων τμημάτων με PCR προσδιορίστηκε η αλληλουχία των βάσεων, και υπολογίστηκε η γενετική διαφοροποίηση εντός και μεταξύ των πληθυσμών. Για την ανάλυση των φυλογενετικών σχέσεων μεταξύ των πληθυσμών ή/και των ειδών χρησιμοποιήθηκαν οι μέθοδοι της Σύνδεσης Γειτόνων (Neighbor Joining-NJ), της Μέγιστης Φειδωλότητας (Maximum Parsimony-MP) και της Μπεϊεσιανής Συμπερασματολογίας (Bayesian Inference-BI). Το τελικό μήκος των αλληλουχιών μετά την επεξεργασία ήταν 386 θέσεις για το γενετικό τόπο 16S rRNA και 512 θέσεις για το γενετικό τόπο COI. Με τα δεδομένα αυτά δεδομένα πραγματοποιήθηκε τόσο ανεξάρτητη όσο και συνδυασμένη ανάλυση. Από τα αποτελέσματα φαίνονται πληθυσμοί οι οποίοι παρα το ότι είναι πολύ κοντινοί γεωγραφικά, και μέχρι σήμερα θεωρείται πως ανήκουν στο ίδιο είδος (Trachelipus kytherensis), εμφανίζουν μεγάλες γενετικές αποστάσεις μεταξύ τους και ομαδοποιούνται σε διαφορετικούς και αρκετά απομακρυσμένους κλάδους των δένδρων σε όλες τις αναλύσεις (NJ, MP, BI). Η τοπολογία των κλάδων, καθώς και η απουσία σαφούς γεωγραφικού προτύπου στην ομαδοποίηση των πληθυσμών του T. kytherensis, καταδεικνύει ότι πιθανότατα δεν έχουμε να κάνουμε με ένα μόνο είδος, αλλά με περισσότερα που είναι δύσκολο να διακριθούν μορφολογικά, τουλάχιστον με τους μέχρι σήμερα χρησιμοποιούμενους ταξινομικούς διαγνωστικούς χαρακτήρες. Αυτό ενισχύεται και από τις γενετικές αποστάσεις που καταγράφηκαν στην παρούσα μελέτη και εμφανίζονται ιδιαίτερα αυξημένες (μέγιστες παρατηρηθείσες γενετικές απόστασεις: 27,3% COI, 17,6% 16S rRNA) ακόμα και σε σχέση με αυτές που έχουν αναφερθεί σε άλλες έρευνες για τη διάκριση ειδών ισοπόδων. Επισημαίνεται η ιδιαίτερα μεγάλη γενετική διαφοροποίηση μεταξύ των αντιπροσώπων του γένους. Επιπλέον καταδεικνύεται πως η Πελοπόννησος φιλοξενεί τα είδη Trachelipus ‘kytherensis’ και T. aegaeus (τουλάχιστον στη χερσόνησο της Αργολίδας) αλλά και πιθανόν μια τρίτη μορφή στα βόρεια (νέο είδος;) η οποία εμφανίζεται ευρύτερα στην ηπειρωτική Ελλάδα. Θα είχε ιδιαίτερο ενδιαφέρον λοιπόν να μελετηθούν αυτές οι πιθανές «ζώνες επαφής» ως προς τη γονιδιακή τους ροή, ώστε να εκτιμηθεί το ποσοστό απομόνωσης των πληθυσμών και, κατ’ επέκταση, του κάθε είδους. / The phylogenetic relationships among terrestrial isopod species are still largely unknown because robust analyses have started to appear only relatively recently. Species-level taxonomy has been based mainly on a few secondary sexual characters of males, although recent analyses based on molecular markers have indicated that species definitions based on morphology may underestimate the true levels of divergence among populations. Furthermore, within several genera or species groups, morphological characters do not provide clear-cut taxonomic resolution, so that many changes in the interpretation of nominal species have appeared in the literature. The genus Trachelipus comprises of relatively stenoecious animals living in habitats generally threatened by human activities, such as humid forest sites and riparian habitats. It includes some 50 species distributed around the Palaearctic, with 8 species recorded from Greece, 4 endemic to the country. The distribution of species is discontinuous due to the increasing fragmentation of its habitats and the expansion of agricultural land and dry woodland. Projected climatic change will restrict further gene flow between Trachelipus populations, as dry habitats are expected to expand in Greece. Species–level taxonomy has been based on a few morphological characters, mainly the secondary sexual characters of males, exhibiting significant variation, and is controversial. Very high intraspecific genetic divergence among several populations has been documented. In this study we attempt a phylogeographic analysis among the Greek endemic species of the genus. We sampled 47 populations from several sites in mainland Greece. In our analyses we incorporated data from previous work (16 populations) in order to better estimate possible geographic structure in the patterns of divergence among populations, and to throw new light in the systematics of the species. Overall, 63 populations were considered. After total DNA extraction, we sequenced the two PCR amplified mtDNA gene fragments, namely 16S rRNA and cytochrome oxidase subunit I (COI), and calculated the genetic divergence within and among the populations studied, as well as their phylogenetic relationships. The methods for phylogenetic reconstruction used were Neighbor Joining (NJ), Maximum Parsimony (MP) and Bayesian Inference (BI) for each mtDNA sequence data and the concatenated dataset. The phylogenetic trees obtained from the molecular data – from all three phylogenetic methods (NJ, MP, BI) - produced trees with quite congruent topologies. Some populations that are considered conspecific exhibit large genetic distances and cluster in different clades. The highly-structured phylogenetic tree and the lack of an overall geographic pattern in the clustering of Trachelipus populations indicates that very probably we are not dealing with a single species, but rather with a number of cryptic species, hardly distinguished by means of currently used morphological characters. This is further corroborated by the genetic distances separating the clades hosting nominal T. kytherensis populations (max_dCOI=27.3% and max_d16S rRNA=17.6%). In general, it can be argued that the genetic distances recorded in the present study are quite large compared with those reported for different species and even genera in other studies of terrestrial isopods. Furthermore, it is evident than there are two species present in the Peloponnese, i.e. Trachelipus ‘kytherensis’ and T. aegaeus (in Argolis peninsula). In northern Peloponnese, a third form is also present (new species?) that occurs throughout the central and northern part of mainland Greece. These ‘contact zones’ should be further investigated in terms of genetic flow and isolation of the populations and/or species. Both the phylogeny presented here and the genetic distances separating populations appear to justify the necessity of further investigation into the phylogeny of the Greek Trachelipus species using a population by population approach. It is likely that morphology inadequately describes real variation inside and among species; hence, diagnoses based on the morphological characters used so far for the delineation of Trachelipus species should be reconsidered under the light of more extensive molecular phylogenetic analyses.

Submitted by Marco Antônio de Ramos Chagas (mchagas@ufv.br) on 2017-06-06T11:18:38Z No. of bitstreams: 1 texto completo.pdf: 909512 bytes, checksum: 95d360795ba1a42ae10b3949c99caca0 (MD5) / Made available in DSpace on 2017-06-06T11:18:38Z (GMT). No. of bitstreams: 1 texto completo.pdf: 909512 bytes, checksum: 95d360795ba1a42ae10b3949c99caca0 (MD5) Previous issue date: 2005-12-14 / Fundação de Amparo a Pesquisa do Estado de Minas Gerais / Os ovinos foram introduzidos no Brasil principalmente pelos portugueses e espanhóis durante o processo de colonização. Por motivos sócio-culturais, a criação desses animais foi considerada no Brasil uma atividade de categoria inferior, de modo que foram criados somente para subsistência. Esse descaso fez com que os produtos derivados de ovinos (lã, carne, pele) perdessem competitividade frente aos produtores de outros países. Para que ocorra uma mudança desse cenário, é necessária uma profunda modificação logística de todas as classes envolvidas na produção de ovinos, visto que os ovinos representam, principalmente nas regiões Sul e Nordeste, uma fonte de recursos importante do ponto de vista social, cultural e histórico. O objetivo desse trabalho foi realizar um conjunto de técnicas moleculares que permitam a caracterização genética das principais raças e/ou estoques de ovinos naturalizados do Brasil de modo a.oferecer subsídios para a elaboração de programas estratégicos de conservação e melhoramento desta espécie. Foram utilizadas quatro classes de marcadores moleculares (RAPD, microssatélites, sequenciamento do DNA mitocondrial e do cromossomo Y) em até 11 raças de ovinos naturalizadas e comerciais existentes no Brasil. Os resultados permitiram identificar padrões de estruturação genética existentes nessa espécie no Brasil, bem como demonstraram a viabilidade de aplicação de marcadores moleculares para: 1) monitoramento genético de rebanhos; 2) testes de exclusão de paternidade para controle de pedigrees; 3) origem geográfica de raças ou populações; 4) inferências filogenéticas intra- específicas. / In Brazil, sheep breeds were introduced during the colonization process by Spanish and Portuguese settlers. Social and cultural factors determined that sheep rearing was considered a low-status activity, and therefore, sheep were raised only to meet subsistence goals. The outcome of this is that products derived from sheep such as wool, meat and hides are non competitive in the international market. A change of this scenario requires a profound logistic alteration involving all sheep production-related groups, particularly in the northern and southern regions in the country, where sheep are of high cultural, social and historical relevance. The objective of this work was to characterize the main naturalized Brazilian sheep breeds using molecular markers. Our results will be a baseline for the development of management and conservation programs. Four kinds of molecular markers were used (RAPD, microsatellites, and sequences of mtDNA and Y chromosome) and were applied on 11 breeds of naturalized and commercial breeds. Results identified the genetic structure of the species in the Country and demonstrated the efficiency of molecular markers for 1) herd genetic monitoring, 2) paternity (exclusion) analyses, 3) for determining the geographic origin of breeds and populations, and 4) for investigating within-species phylogenies.

Golden mice (Ochrotomys nuttalli) are generally an elusive and rare species throughout their geographic range in the southeastern United States. They are considered to be habitat specialists that prefer dense understory consisting of shrubs and vines. Golden mice are less vagile, and likely disperse shorter distances than other sympatric species such as the white-footed mouse (Peromyscus leucopus). Conversely, white-footed mice are considered habitat generalists that inhabit a variety of habitat types, are more vagile, and disperse farther than golden mice. Because of this it is likely that golden mice have a lower genetic diversity and are more genetically subdivided than white-footed mice. In southern Illinois, golden mice are on the periphery of their range, which is one of the reasons they are on the state-threatened list in Illinois. It has been hypothesized that populations on the periphery of a species range will have more population structure and lower genetic diversity than populations in the core of the range. Tissue samples for golden mice and white-footed mice were collected from 24 sites throughout southern Illinois and 24 sites throughout the golden mouse core range. I analyzed 13 and 10 microsatellite markers as well as 594 and 624 base pairs of the mitochondrial control region for golden mice and white-footed mice, respectively, to characterize and compare the genetic diversity and population structure of both species. Overall haplotype diversity (0.76) and nucleotide diversity (0.20%) was lower in golden mice compared to white footed mice (0.99 and 1.97%). Results of an AMOVA using the mitochondrial control region revealed more subdivision among the 3 populations of golden mice (Φst = 0.099, P < 0.001) than among the 3 populations of white-footed mice (Φst = 0.058, P < 0.001). Microsatellite loci showed a similar trend with overall FST values of 0.027 (P < 0.001) for golden mice and 0.004 (P = 0.137) for white-footed mice. I intended to compare golden mouse individuals from southern Illinois and the core of the range, but too few individuals were collected from the core. More samples need to be collected throughout the core of the range to better understand the population genetics of golden mice in the core of the range compared to the periphery.

Este trabalho teve como meta principal contribuir para elucidar algumas das questões em aberto pertinentes à história evolutiva e antropológica de populações nativas americanas. Para isso investigou-se marcadores uniparentais paternos, ligados à NRY, e materno, mtDNA. Para o cromossomo Y foram investigados 108 indivíduos (85 sulameríndios de 16 tribos, pertencentes a 5 grupos lingüísticos, além de 23 asiáticos (siberianos), compreendendo 6 grupos étnicos distintos). Para o mtDNA foram investigados 160 indivíduos (homens e mulheres), compreendendo 10 tribos sulamericanas, pertencentes a 5 grupos lingüísticos distintos. Para o cromossomo Y foram utilizados 26 marcadores (SNPs). Para o mtDNA a região controladora-RC (HVS-I: da posição 16.024 até 16.569, e HVS-II: da posição 001 até 576) e a região imediatamente 5’ à região controladora foram seqüenciadas. Foi possível determinar para o cromossomo Y que Q1a3a* (autóctone nativo-americano, de provável origem beringiana) está fixado em 63% das tribos; o haplogrupo Q1a3*, que por outro lado também é encontrado na Ásia, foi observado entre os Araweté (25%), Jamamadi (100%), Lengua (25%) e esquimós asiáticos (17%). Merece destaque que Q1a3* parece ser o que até agora era identificado como sendo apenas “haplogrupo Q*”, ou seja, cromossomo Y portador do alelo derivado no loco M242, mas com alelo ancestral para o M3. Nenhuma das novas mutações mencionadas na atual árvore filogenética do cromossomo Y (com exceção do M346, que define Q1a3*) foram encontradas. O seqüenciamento de regiões do cromossomo Y não revelou nenhuma nova mutação. No caso do mtDNA, os indígenas do tronco Ge mostram os haplogrupos B e A como sendo os mais freqüentes, enquanto que nos Tupi esses haplogrupos apresentam freqüências mais elevadas apenas em regiões bastante restritas, ficando o haplogrupo D como o mais freqüente. Cabe salientar que o haplogrupo C apresenta freqüência muito baixa tanto para os Ge quanto para os Tupi, sendo que freqüências um pouco mais elevadas estão quase que geograficamente opostas, ficando no sul do Brasil para os Ge e no norte para os Tupi. Avaliando o modelo de fissão-fusão pôde-se sugerir que: 1) As linhagens mitocondriais tribo-específicas dentro das tribos Kayapó aqui investigadas dificilmente representariam linhagens autóctones, já que o tempo de surgimento de cada tribo por processo de fissão é pequeno para comportar uma rede de novas mutações. As especificidades poderiam estar vinculadas ao modelo de fissão envolvendo grupos de pessoas aparentadas via materna. Nesse caso, grupos de parentes carregariam para fora do grupo parental todas as seqüências pertencentes a uma determinada linhagem. Assim a linhagem estaria presente somente no grupo derivado e não mais no parental; 2) Perda de linhagens parentais na dispersão e/ou por deriva na formação do novo grupo, o que resultaria na diferença encontrada entre os grupos derivados; 3) Embora não se possa excluir alguma fusão posterir a fissão, a quantidade de linhages exclusivas nas tribos Kayapó estaria indicando relativo isolamento dos grupos depois da fissão (ausência ou baixa freqüência de fluxo gênico entre os grupos fissionados levando à relativa baixa freqüência de linhagens compartilhadas), o que denota o fato do fenômeno ser recente (atritos ainda presentes na memória coletiva e/ou familiar dos grupos fissionados) como estabelecido pelos dados históricos (início do século XVII). Esse fato poderia sugerir que a fusão demanda mais tempo para ocorrer; 4) O compartilhamento das linhagens mais comuns, normalmente na raiz das networks, entre os Tupi e os Ge, parece denotar mais ancestralidade comum do que importante fluxo gênico depois da formação desses dois grandes estoques lingüísticos. / This work has as its main aim to elucidate some of the still open questions about the evolutive and anthropological history of the Native American populations. Paternal uniparental markers, in the NRY, and maternal, mtDNA, were investigated to do that. For the Y chromosome, 108 individuals were investigated (85 South-Amerindians from 16 tribes, belonging to 5 linguistic groups, and 23 Asians (Siberians), covering 6 distinct ethnical groups). For the mtDNA, 160 individuals (men and women) were evaluated, covering 10 South-American tribes, belonging to 5 distinct linguistic groups. For the Y chromosome 26 SNPs were tested and some regions sequenced. For the mtDNA the control region-CR (HVS-I: from position 16.024 to 16.569, and HVS-II: from position 001 to 576) and the region immediately 5’ of the control region were sequenced. It was possible to determine that Q1a3a* (a Native American autoctonous chromosome, probably of Beringian origin) is fixed in 63% of the tribes; the haplogroup Q1a3*, which, moreover, is also encountered in Asia, was observed in Araweté (25%), Jamamadi (100%), Lengua (25%) and Asian Eskimos (17%). It is worth mentioning that Q1a3* appears to be what until now has been identified as “haplogroup Q*” only, that is, Y chromosome carrier of the derived allele in the M242 locus, but with an ancestral allele for M3. Any of the new mutations mentioned in the current Y chromosome phylogenetic tree (except M346, which defines Q1a3*) were encountered. Sequencing of Y chromosome regions hasn’t revealed any new mutation. In the mtDNA’s case, the Ge indians show the haplogroups B and A as the most frequent ones, while in the Tupi indians these haplogroups show high frequencies only in very restrict regions, being haplogroup D the most frequent. It should be noted that haplogroup C shows very low frequency in both Ge and Tupi, the slightly higher frequencies occuping almost geographically opposite locations, at the South of Brazil for the Ge and on the North for the Tupi. On evaluating the fission-fusion model it could be suggested that: 1) Tribe-specific lineages in the Kayapó tribes investigated here would hardly represent autoctonous lineages, since the time of emergence of each tribe by fission process is small to bear a web of new mutations. The specificities could be related to the fission model involving maternally related groups of people. In this case, groups of relatives would carry out of the parental group all the sequences belonging to a determined lineage. Therefore the lineage would be present only in the derived group and not in the parental anymore; 2) Loss of parental lineages in the dispersion and/or by drift in the new group’s formation, which would result in the differences found between the derived groups; 3) Though some fusion posterior to the fission cannot be excluded, the amount of exclusive lineages in the Kayapó tribes would indicate a relative isolation of the groups after the fission (absence or low frequency of gene flow between the fissioned groups leading to relative low frequency of the shared lineages), which denotes the fact of the phenomenon being recent (struggles still present in the collective and/or familiar memories of the fissioned groups) as estabilished by historical data (beginning of the XVII century). This fact could suggest that the fusion demands more time to occur; 4) The sharing of the more common lineages, normally in the networks’ nodes, between Tupi and Ge, appears to denote more common ancestrality than important gene flow after the formation of these two great linguistic stocks.

Este trabalho teve como meta principal contribuir para elucidar algumas das questões em aberto pertinentes à história evolutiva e antropológica de populações nativas americanas. Para isso investigou-se marcadores uniparentais paternos, ligados à NRY, e materno, mtDNA. Para o cromossomo Y foram investigados 108 indivíduos (85 sulameríndios de 16 tribos, pertencentes a 5 grupos lingüísticos, além de 23 asiáticos (siberianos), compreendendo 6 grupos étnicos distintos). Para o mtDNA foram investigados 160 indivíduos (homens e mulheres), compreendendo 10 tribos sulamericanas, pertencentes a 5 grupos lingüísticos distintos. Para o cromossomo Y foram utilizados 26 marcadores (SNPs). Para o mtDNA a região controladora-RC (HVS-I: da posição 16.024 até 16.569, e HVS-II: da posição 001 até 576) e a região imediatamente 5’ à região controladora foram seqüenciadas. Foi possível determinar para o cromossomo Y que Q1a3a* (autóctone nativo-americano, de provável origem beringiana) está fixado em 63% das tribos; o haplogrupo Q1a3*, que por outro lado também é encontrado na Ásia, foi observado entre os Araweté (25%), Jamamadi (100%), Lengua (25%) e esquimós asiáticos (17%). Merece destaque que Q1a3* parece ser o que até agora era identificado como sendo apenas “haplogrupo Q*”, ou seja, cromossomo Y portador do alelo derivado no loco M242, mas com alelo ancestral para o M3. Nenhuma das novas mutações mencionadas na atual árvore filogenética do cromossomo Y (com exceção do M346, que define Q1a3*) foram encontradas. O seqüenciamento de regiões do cromossomo Y não revelou nenhuma nova mutação. No caso do mtDNA, os indígenas do tronco Ge mostram os haplogrupos B e A como sendo os mais freqüentes, enquanto que nos Tupi esses haplogrupos apresentam freqüências mais elevadas apenas em regiões bastante restritas, ficando o haplogrupo D como o mais freqüente. Cabe salientar que o haplogrupo C apresenta freqüência muito baixa tanto para os Ge quanto para os Tupi, sendo que freqüências um pouco mais elevadas estão quase que geograficamente opostas, ficando no sul do Brasil para os Ge e no norte para os Tupi. Avaliando o modelo de fissão-fusão pôde-se sugerir que: 1) As linhagens mitocondriais tribo-específicas dentro das tribos Kayapó aqui investigadas dificilmente representariam linhagens autóctones, já que o tempo de surgimento de cada tribo por processo de fissão é pequeno para comportar uma rede de novas mutações. As especificidades poderiam estar vinculadas ao modelo de fissão envolvendo grupos de pessoas aparentadas via materna. Nesse caso, grupos de parentes carregariam para fora do grupo parental todas as seqüências pertencentes a uma determinada linhagem. Assim a linhagem estaria presente somente no grupo derivado e não mais no parental; 2) Perda de linhagens parentais na dispersão e/ou por deriva na formação do novo grupo, o que resultaria na diferença encontrada entre os grupos derivados; 3) Embora não se possa excluir alguma fusão posterir a fissão, a quantidade de linhages exclusivas nas tribos Kayapó estaria indicando relativo isolamento dos grupos depois da fissão (ausência ou baixa freqüência de fluxo gênico entre os grupos fissionados levando à relativa baixa freqüência de linhagens compartilhadas), o que denota o fato do fenômeno ser recente (atritos ainda presentes na memória coletiva e/ou familiar dos grupos fissionados) como estabelecido pelos dados históricos (início do século XVII). Esse fato poderia sugerir que a fusão demanda mais tempo para ocorrer; 4) O compartilhamento das linhagens mais comuns, normalmente na raiz das networks, entre os Tupi e os Ge, parece denotar mais ancestralidade comum do que importante fluxo gênico depois da formação desses dois grandes estoques lingüísticos. / This work has as its main aim to elucidate some of the still open questions about the evolutive and anthropological history of the Native American populations. Paternal uniparental markers, in the NRY, and maternal, mtDNA, were investigated to do that. For the Y chromosome, 108 individuals were investigated (85 South-Amerindians from 16 tribes, belonging to 5 linguistic groups, and 23 Asians (Siberians), covering 6 distinct ethnical groups). For the mtDNA, 160 individuals (men and women) were evaluated, covering 10 South-American tribes, belonging to 5 distinct linguistic groups. For the Y chromosome 26 SNPs were tested and some regions sequenced. For the mtDNA the control region-CR (HVS-I: from position 16.024 to 16.569, and HVS-II: from position 001 to 576) and the region immediately 5’ of the control region were sequenced. It was possible to determine that Q1a3a* (a Native American autoctonous chromosome, probably of Beringian origin) is fixed in 63% of the tribes; the haplogroup Q1a3*, which, moreover, is also encountered in Asia, was observed in Araweté (25%), Jamamadi (100%), Lengua (25%) and Asian Eskimos (17%). It is worth mentioning that Q1a3* appears to be what until now has been identified as “haplogroup Q*” only, that is, Y chromosome carrier of the derived allele in the M242 locus, but with an ancestral allele for M3. Any of the new mutations mentioned in the current Y chromosome phylogenetic tree (except M346, which defines Q1a3*) were encountered. Sequencing of Y chromosome regions hasn’t revealed any new mutation. In the mtDNA’s case, the Ge indians show the haplogroups B and A as the most frequent ones, while in the Tupi indians these haplogroups show high frequencies only in very restrict regions, being haplogroup D the most frequent. It should be noted that haplogroup C shows very low frequency in both Ge and Tupi, the slightly higher frequencies occuping almost geographically opposite locations, at the South of Brazil for the Ge and on the North for the Tupi. On evaluating the fission-fusion model it could be suggested that: 1) Tribe-specific lineages in the Kayapó tribes investigated here would hardly represent autoctonous lineages, since the time of emergence of each tribe by fission process is small to bear a web of new mutations. The specificities could be related to the fission model involving maternally related groups of people. In this case, groups of relatives would carry out of the parental group all the sequences belonging to a determined lineage. Therefore the lineage would be present only in the derived group and not in the parental anymore; 2) Loss of parental lineages in the dispersion and/or by drift in the new group’s formation, which would result in the differences found between the derived groups; 3) Though some fusion posterior to the fission cannot be excluded, the amount of exclusive lineages in the Kayapó tribes would indicate a relative isolation of the groups after the fission (absence or low frequency of gene flow between the fissioned groups leading to relative low frequency of the shared lineages), which denotes the fact of the phenomenon being recent (struggles still present in the collective and/or familiar memories of the fissioned groups) as estabilished by historical data (beginning of the XVII century). This fact could suggest that the fusion demands more time to occur; 4) The sharing of the more common lineages, normally in the networks’ nodes, between Tupi and Ge, appears to denote more common ancestrality than important gene flow after the formation of these two great linguistic stocks.

Made available in DSpace on 2016-06-02T19:26:21Z (GMT). No. of bitstreams: 1 RODRIGUES_Eduardo_2011.pdf: 3957020 bytes, checksum: 1b7344009b2439ce9b066bb71c3ffb02 (MD5) Previous issue date: 2011-12-12 / Financiadora de Estudos e Projetos / The taxonomic classification system of all organisms has been traditionally based in the comparative analysis of a wide range of morphological structures. In the last decades, the potential of physiological, cellular and molecular characteristics have been recognized in taxonomy, including phylogenetic and biogeographic aspects. This study focuses on the structural and evolutionary characterization of a region encompassing the 3 end of the mtDNA gene COI from sarcophagids and analyzed the contribution of this information for species identification, increasing the knowledge related to this family in the neotropical region. The Sarcophagidae family has approximately 2,600 species and their phylogenetic relationships are not well established for most genera and sub-genera. In this scenario, the characterization of nucleotide sequences for species identification in Sarcophagidae is a strategic approach that contributes for inferring phylogenetic relationships in this family. In this study, a 470 bp region from the COI gene was sequenced and characterized by structural and evolutionary analyses for five species: Peckia anguilla, Peckia collusor, Peckia ingens, Oxysarcodexia admixta e Oxysarcodexia paulistanensis. For comparative analyses we included ortholog sequences from three other sarcophagid species (P. intermutans, O. ventricosa e S. carnaria) and from the species C. hominivorax (Calliphoridae) e Haematobia irritans (Muscidae) available in GenBank. The intraspecific variation showed values between 0 e 0,01 and the interspecific variation varied from 0,07 - 0,151. Similarly to other Diptera families, the nucleotide composition of this region showed a high content of A and T (on average: A = 30.2%; T = 38.7%; C = 17.3% and G = 13.8%). The aminoacid composition presents higher abundance of Leucine, Phenylalanine and Tyrosine. Only eight divergent aminoacid positions were identified in comparative analysis of sarcophagid species, in addition to 3 positions that diverges from the insect COI protein structural model. Neighbor-joining analysis using Kimura-2P, an usual procedure in DNA barcodes analysis, distributed all species in monophyletic clusters, however the utility of this approach for resolving taxonomical conflicts requires additional sampling of specimens/species including a wide geographical coverage in order to provide a better characterization of intraspecific variation in these species. / O sistema de classificação taxonômica dos seres vivos tem sido tradicionalmente baseado na comparação de uma ampla gama de estruturas morfológicas. Nas últimas décadas, o potencial taxonômico de características fisiológicas, celulares e moleculares tem sido reconhecido, além de aspectos filogenéticos e biogeográficos. Este estudo focou a caracterização estrutural e evolutiva da região 3 do gene COI do DNAmt de espécies de sarcofagídeos e analisou a contribuição desta informação para fins de identificação taxonômica, ampliando o conhecimento sobre esta família na região neotropical. A família Sarcophagidae contém aproximadamente 2.600 espécies e suas relações filogenéticas não estão bem estabelecidas entre gêneros e sub-gêneros. Neste cenário, a caracterização de sequências nucleotídicas para identificação de espécies de Sarcophagidae é uma abordagem estratégica que também poderá contribuir na investigação de relações filogenéticas. Neste trabalho, foi seqüenciada e caracterizada estrutural e evolutivamente uma região de 470 pb do gene COI de cinco espécies de sarcofagídeos: Peckia anguilla, Peckia collusor, Peckia ingens, Oxysarcodexia admixta e Oxysarcodexia paulistanensis. Para as análises comparativas foram incluídas sequências ortólogas de outras 3 espécies de Sarcophagidae (P. intermutans, O. ventricosa e S. carnaria) e das espécies C. hominivorax (Calliphoridae) e Haematobia irritans (Muscidae) disponíveis no GenBank. A variação intraespecífica apresentou valores entre 0 e 0,01 e variação interespecífica variou entre 0,07 - 0,151. Similarmente a outras famílias de Diptera, a composição de nucleotídeos desta região apresentou uma maior abundância de A e T (em média: A = 30.2%; T = 38.7%; C = 17.3% e G = 13.8%). A composição de aminoácidos apresentou maior abundância de Leucina, Fenilalanina e Treonina. Foram identificadas apenas oito posições de aminoácidos divergentes nas análises comparativas entre as espécies de sarcofagídeos analisadas, além de 3 divergências (inserções) com relação ao modelo estrutural da proteína COI de insetos. A análise de Neighbor-joining utilizando Kimura-2P, procedimento utilizado em análises de DNA Barcodes , distribuíram as espécies em clados monofiléticos, entretanto a validação desta abordagem para auxiliar na resolução de conflitos taxonômicos requer a análise de uma amostragem maior de indivíduos de cada espécie - incluindo maior distribuição geográfica para caracterizar a amplitude da variação intraespecífica nestas espécies.

Submitted by Izabel Franco (izabel-franco@ufscar.br) on 2016-09-26T18:53:54Z No. of bitstreams: 1 TeseLS.pdf: 6231137 bytes, checksum: 82ce7c68a05ca7eb79c0ea1da7fe74e9 (MD5) / Approved for entry into archive by Marina Freitas (marinapf@ufscar.br) on 2016-09-27T19:39:44Z (GMT) No. of bitstreams: 1 TeseLS.pdf: 6231137 bytes, checksum: 82ce7c68a05ca7eb79c0ea1da7fe74e9 (MD5) / Approved for entry into archive by Marina Freitas (marinapf@ufscar.br) on 2016-09-27T19:39:56Z (GMT) No. of bitstreams: 1 TeseLS.pdf: 6231137 bytes, checksum: 82ce7c68a05ca7eb79c0ea1da7fe74e9 (MD5) / Made available in DSpace on 2016-09-27T19:40:04Z (GMT). No. of bitstreams: 1 TeseLS.pdf: 6231137 bytes, checksum: 82ce7c68a05ca7eb79c0ea1da7fe74e9 (MD5) Previous issue date: 2015-06-23 / Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) / The penaeid shrimp (Crustacea, Decapoda, Penaeidae) are the most economically fishing resource of the greatest global importance both for fisheries and the aquaculture industry. Shrimp fishing is one of the pillars of national economy in Mozambique, where they provide around USD 80,000,000 per year in export earnings. In recent years there has been observing a reduction in the shrimp fishery industry probably due the over-exploitation or due the presence of other shrimp species that were not been observed on the coast Mozambique before which may competing for the ecological niche. Despite the great fishing economic importance of penaeid shrimps in Mozambique, there is no genetic scientific literature available thus far on their genetic characteristics. Therefore, this is the first work addressing the genetic diversity of penaeids species of greatest economic value from Mozambique coast F. indicus and M. monoceros, for the first time shrimp from this coast were identified using DNA Barcoding tool. In addition, for the first time sequences of penaeid shrimp from Mozambique coast were deposited in GenBank and Bold system. The objective of this study was to evaluate the genetic diversity and population structure of the species F. indicus and M. monoceros, and identify nine species of penaeids from the Mozambican coast. To assess the genetic diversity and structure of F. indicus and M. monoceros, 160 samples were collected along the Mozambique coast. Three mitochondrial genes (COI, Cyt b, and the control region D-loop) were analyzed. A great genetic diversity was observed, however, the D-loop presented higher values (F. indicus: Hd = 1, h = 13; Hi = 0.0133, M. monoceros Hd = 0,99; H-24; and Hi = 0.0092). D-loop showed unique haplotypes; the Tajima D test and Fu Fs values were negative and significant for the COI and Cyt b genes. The mismatch distribution curves suggested that the two espéceis undergone to a recent population expansion (10.397 to 28.418) years ago F. indicus and M. monoceros respectively. The AMOVA analysis showed that over 99% of the variation occurs within populations. The Fst Pairwise values pointed to a non structured population. The nature of ocean currents along the Mozambique channel as well as the complete absence of physical and / or environmental barriers may be the main factors that influence the non structure of these two species. To identify shrimp penaeids from Mozambique based on DNA barcondig, a total of 69 samples were collected in the Maputo Bay. The genetic distance tree grouped six species into two clades as to the place of origin, suggesting the presence of cryptic species. The intraspecific genetic distance ranged from (0 to 8.636) and interspecific distance from (3.897 to 21.558). The distance distribution analysis 10 of the nearest neighbor ranged from (3.897-18.971). The DNA Barcoding identification tool was efficient to identify the Penaeid species from mozambican coast. However the presence of cryptic species pointed the need for further studies which must be conducted using molecular analyzes; morphological taxonomy and the ecological treats to evaluate each of the sibling species to reach a correct decision of the taxonomic status. / Os camarões peneídeos (Crustacea, Decapoda, Penaeidae) constituem um recurso pesqueiro de grande importância econômica mundial tanto para a indústria pesqueira quanto para a aquicultura. Em Moçambique, a indústria pesqueira constitui uma das bases da sua economia, onde a pesca do camarão chega a render cerca de 80 milhões de dólares anuais. Nos últimos anos, tem-se verificado uma redução na pesca do camarão, provavelmente devido à sobrexplotação e à presença de espécies exóticas. Este é o primeiro estudo genético envolvendo as espécies de maior valor econômico de Moçambique. O objetivo deste estudo foi avaliar a diversidade genética e a estrutura populacional das espécies Fenneropeaneus indicus e Metapenaeus monoceros e identificar através do DNA barcoding nove espécies de camarão peneídeo. Para avaliar a diversidade e a estrutura genética de F. indicus e M. monoceros, foram coletadas 160 amostras ao longo da costa de Moçambique e analisados os genes mitocondriais COI (citocromo oxidase subunidade 1), Cyt b (citocromo oxidase subunidade b) e a região controle D-loop. Foi observada uma alta diversidade genética, sendo que o D-loop apresentou os valores mais elevados (F. indicus: Hd=1; h=13; Hi=0,0133; M. monoceros: Hd=0,99; h=24; e Hi=0,0092). O D-loop apresentou haplótipos únicos. Os valores do teste D de Tajima e Fs de Fu foram negativos e significativos para os genes COI e Cyt b. As curvas de distribuição mismatch sugeriram que as duas espécies passaram por uma expansão populacional recente de 10,397 e 28,418 anos para F. indicus e M. monoceros, respectivamente. A AMOVA referente aos genes COI e Cyt b mostrou que mais de 99% da variação ocorre dentro das populações. Os valores de FST par a par indicaram não haver estruturação populacional. A natureza das correntes marinhas ao longo do canal de Moçambique, bem como a ausência completa de barreiras físicas e/ou ambientais podem ser os principais fatores que influenciam a manutenção destas duas espécies como populações únicas. Para a identificação dos peneídeos de Moçambique com base no DNA barcondig, um total de 69 amostras foi coletado na Baía de Maputo. A árvore de distância genética agrupou seis espécies em dois clados com relação ao lugar de origem, sugerindo a presença de duas linhagens. A distância genética intraespecífica variou de 0 a 8,636 e a distância interespecífica variou de 3,897 a 21,558. A análise da distribuição de distância para o vizinho mais próximo variou de 3, 897 a 18,971. A ferramenta de identificação DNA barcoding, foi eficiente na identificação das espécies de peneídeos da costa moçambicana.

The diversity and biogeography of three dominant cichlid genera (Australoheros, Gymnogeophagus and Crenicichla) is reviewed within the Argentinean province of Misiones based on newly collected material specifically for this study. The results have revealed strikingly different structuring and origin of diversity between the three genera with implications for a future PhD study. The biogeographic implications of the reconstructed phylogenies using mitochondrial DNA have been compared with the geological history of the area revealing many new insights.

A seqüência completa do genoma mitocondrial de uma espécie pode ajudar no mapeamento de restrição e desenho de primers para PCR. Estes poderão servir para amplificação e posterior seqüenciamento de regiões específicas de outras espécies e populações relacionadas, para estudos filogenéticos e de dinâmica populacional. Até o momento, temos na literatura a seqüência completa do DNA mitocondrial (DNAmt) de um único himenóptero, Apis mellifera, espécie que é endêmica do Velho Mundo. Nenhum genoma mitocondrial de uma espécie de abelha nativa do Brasil foi até o momento descrito. Com a devastação crescente dos ecossistemas, há a perda de espécies de abelhas ainda pouco estudadas, e talvez até outras ainda não conhecidas. Entre os meliponíneos, há espécies-chave de diversos ecossistemas brasileiros, tendo portanto uma enorme importância ecológica. No decorrer deste projeto, foram amplificados via PCR e seqüenciados 77% do genoma mitocondrial da abelha sem ferrão Melipona bicolor (Apidae, Meliponini), contendo todos os 13 genes mitocondriais codificadores para proteínas, 18 dos 22 genes para RNAt e os dois genes para RNAr (sendo um integral e o outro parcialmente seqüenciado). Além do seqüenciamento, foram realizados neste trabalho: análise da organização do genoma (conteúdo e ordem gênica); análise da tradução dos genes para proteínas e código genético; análise de outras características moleculares (freqüência das bases, códons utilizados, iniciação e terminação de genes, freqüência de aminoácidos etc); e comparação das características acima mencionadas com o genoma mitocondrial de A. mellifera e também com outros insetos. O viés para o uso de bases A+T, bastante evidente em A. mellifera, mostrou-se ainda mais acentuado em M. bicolor. Foram encontradas diferenças no tamanho e composição dos genes. Pelo menos nove rearranjos na ordem gênica mitocondrial foram observados entre as duas espécies de abelhas, um fenômeno raro entre organismos tão próximos. Considerando que essas espécies compartilham um comportamento intrigante, a eussocialidade, esses rearranjos podem servir como um excelente marcador para estudar a origem e a evolução desse comportamento no grupo. / The complete sequence of the mitochondrial genome of a species may help on restriction mapping and to design PCR primers. These can be useful to amplify and sequence specific regions from other species and analyze populations, in phylogenetic and demographic studies. So far, there was reported on literature the mtDNA complete sequence for only one hymenopteran, Apis mellifera, endemic from the Old World. No mitocondrial genome of a Brazilian native bee was ever described. With the increasing devastation of natural environments, several bee species can be led to extinction, including those poorly studied and maybe some unknown species. The meliponines (stingless bees) include key species to several Brazilian ecosystems, so they play an important ecological role. In this project, we have PCR amplified and sequenced 77% of the mitochondrial genome of the stingless bee Melipona bicolor (Apidae, Meliponini). The sequenced region contains all of the 13 mitochondrial protein-coding genes, 18 of 22 tRNA genes, and both rRNA genes (one of them was only partially sequenced). Besides sequencing, this work consisted of: analysis of genome organization (gene content and order); analysis of gene translation and genetic code; analysis of other molecular features (base frequencies, codon usage, gene initiation and termination, amino acid frequencies etc.); and comparison of the characteristics mentioned above with A. mellifera mitocondrial genome and also other insects. The highly biased A+T content is a typical characteristic of A. mellifera mitochondrial genome, and it is even more extreme on M. bicolor mtDNA. There are length and compositional differences on genes between M. bicolor and A. mellifera. At least nine gene order rearrangements were observed by comparing the mtDNA of these species, what is a rare event on closely related organisms. Considering that both species share an intriguing behavior, eusociality, these gene rearrangements may be used as an excellent marker to study the origin and evolution of that behavior on bees.

O gênero Pagurus é um táxon heterogêneo de ermitões, com ampla distribuição mundial, descrito há mais de duzentos anos. A sistemática do grupo é complexa com uma longa história de rearranjos taxonômicos. A classificação conta com a inclusão de numerosas novas espécies e separação de algumas inicialmente contidas no táxon estabelecendo-se novos gêneros. Devido à extensa distribuição das espécies que compõem o táxon, foi necessário restringir o objetivo deste estudo. Assim foi avaliado o status taxonômico das espécies que ocorrem nas costas Pacífica e Atlântica da América do Sul, por meio da combinação de análises morfológicas e moleculares das espécies, utilizando dois marcadores genéticos (16S rDNA e Histona 3). As análises taxonômicas mostraram uma alta variabilidade morfológica nas 22 espécies examinadas. As espécies se encaixam perfeitamente em quatro dos onze grupos preestabelecidos dentro de Pagurus. Além disso, foram fornecidos os caracteres morfológicos que definem um desses grupos. Adicionalmente foi incluída uma chave para ajudar na identificação de todas as espécies. As análises independentes dos dados moleculares mostraram resultados contrastantes. O gene mitocondrial foi mais variável e portanto mais informativo, proporcionando uma hipótese mais clara das relações internas entre os membros de Pagurus. Assim, as topologias moleculares resultantes, concordaram em vários aspectos com o reportado nos dados morfológicos das espécies. De modo que, as semelhanças morfológicas foram refletidas na formação dos nós internos. Assim, as análises do gene 16S e H3 mostraram-se concordante com a morfologia, refletindo-se na formação de alguns dos grupos previamente propostos. Como ponto importante, ressalta-se a separação das espécies que compõe o grupo provenzanoi como um táxon diferenciado dentro de Pagurus. Ao mesmo tempo, as análises com o gene H3 mostraram a espécie Propagurus gaudichaudii inserida dentro de Pagurus, questionando a validade taxonômica de Propagurus. Como só foi incluída uma das cinco espécies do gênero, é claramente necessário a inclusão de outras espécies contidas neste táxon, bem como alguns outros genes uma revisão das espécies contidas neste táxon, junto com análises de outros genes, a fim de resolver definitivamente o status taxonômico de Propagurus. / The genus Pagurus is a heterogeneous taxon of hermit crabs, with worldwide distribution which was described more than two hundred years ago. Systematics of the group is complex and with a long history of taxonomic rearrangements. Thus current classification accounts for inclusion of many new species and splitting-off of some of the original species in order to establish new genera. Because of the extensive distribution of the species that conform this taxon it was necessary to restrict the aim of this study. Thus I evaluated the taxonomic status of the species found in the Pacific and Atlantic coasts of South America using a combination of both morphologic and molecular analyses (16S rDNA and Histona 3). The taxonomic analysis showed high morphological variation among all the 21 examined species. The analyzed species seemed to perfectly fit four out of the eleven morphologically pre-established groups of Pagurus. Furthermore I provide morphological characters that define one of these groups. Additionally, I included a key to aid in the identification of all the target species. Independent analysis of the molecular data showed contrasting results. The mitochondrial gene was the most variable and thus the most informative, providing a clearer hypothesis of the internal relationships among members of Pagurus. Therefore, both 16S and H3 analyses were in general agreement with the morphology. Thus, the resultant molecularly based topologies reflected some of the groups previously proposed. It is important to point out that all the included species belonging to the provenzanoi group were clustered together separated from other clades within Pagurus. At the same time, the analysis with the gen H3 showed Propagurus gaudichaudii clustered within Pagurus, thus questioning the taxonomic validity of Propagurus. As I only included one of the five species of the genus, it is obviously necessary to include other the species contained in this taxon, as well as some other genes in order to definitely solve the taxonomic status of Propagurus.