Disorders of ATP synthase, the key enzyme of mitochondrial energy provision belong to the most severe metabolic diseases presenting mostly as early-onset mitochondrial encephalo-cardio-myopathies. Mutations in four nuclear genes can result in isolated deficiency of ATP synthase, all sharing a similar biochemical phenotype - pronounced decrease in the content of fully assembled and functional ATP synthase complex. The thesis summarises studies on two distinct causes of ATP synthase deficiency. First is TMEM70 protein, a novel ancillary factor of ATP synthase, which represents most frequent determinant of severe inborn deficiency of ATP synthase. TMEM70 is a 21 kDa protein of the inner mitochondrial membrane, facilitating the biogenesis of mitochondrial ATP synthase, possibly through TMEM70 protein region exposed to the mitochondrial matrix, but the proper regulatory mechanism remains to be elucidated. In TMEM70-lacking patient fibroblasts the low content of ATP synthase induces compensatory adaptive upregulation of mitochondrial respiratory chain complexes III and IV, interestingly by a posttranscriptional mechanisms. The second type of ATP synthase deficiency studied was mtDNA m.9205delTA mutation affecting maturation of MT-ATP8/MT-ATP6/MT-CO3 mRNA and thus biosynthesis of Atp6 (subunit a) and Cox3...

The Red Sea region is one of the important places that allow us to uncover traces of the evolution of anatomically modern humans. Besides the questions related to its expansion out of Africa, this region is also important in terms of the mutual influence between populations of Africa and Arabia that after a long period of isolation and genetic differentiation related to climate change in the Pleistocene and subsequent development of seaways and land routes in the Holocene began to contact with each other more frequently. Number of genetic analyzes has been done but some issues concerning on the later development still remain inadequately answered, mainly because of insufficient material. This work is focused on the analysis of 200 mtDNA sequences of four Sudanese populations - two populations of nomadic herdsmen Rashaida and Beja living in the close neighborhood around the city of Kassala and speaking different languages and two populations of the Nile Valley with settled way of life. Analysis of the intrapopulation level revealed much higher diversity of the sedentary populations (in this work the sedentary populations are represented by the Nubians and Arabs). Interpopulation variability and genetic distances within other 46 populations of the Red Sea showed that although Rashaida and Beja people...

Climate change is one of the most important factor determining species ranges. In Europe there is now evidence for northward areal expansion in many Mediterranean insects including the praying mantis (Mantis religiosa). This species is the only representative of the order Mantodea inhabiting central Europe. The northern edge of the species distribution currently reaches latitude 53ř North. Although, the praying mantis is well known insect there is not enough evidence about its phylogeography. In this work three mitochondrial genes (COI, COII, Cyt b) were selected for phylogenetic study. Results indicate three statistically supported distinct lineages in Europe: Eastern European, Central European and Western European. Presumably these lineages are consistent with isolation during the last glacial and re-colonization from glacial refugia. Reduced haplotype diversity on the northern edge suggests currently established populations at the northern distribution border. To validate mtDNA results it was also considered four microsatellite loci. Due to different type of inheritance mtDNA and nuclear DNA it is possible to compare two independent genetic datasets. Microsatellite analysis confirmed results obtained on mitochondrial data. Three major genetic clusters were found: east, west and central. Spatial...

Phylogeny of selected genera of geckos in the Mediterranean and adjacent regions Jan Červenka Ph.D. thesis Abstract This Ph.D. thesis is composed of three published articles and one manuscript, and is focused on the phylogenetic relationships of selected species of geckos from the Mediterranean and surrounding areas. The group of geckos of interest shares the common characteristic of an absence of adhesive lamellas on their toes. Historically, it was assumed that these species were closely related. Molecular-phylogenetic approaches were used in order to reveal the phylogenetic relationships within this group, especially using the sequential data from mitochondrial genes. Morphological characteristics commonly used in lizards were studied in connection with the ecology of the group. This thesis provides the first more detailed view of the phylogeny of the studied species. The results show that the genus Cyrtopodion, previously considered as monophyletic, in fact is not monophyletic as the genera Bunopus and Agamura represent its inner groups. Mediodactylus, the subgenus of Cyrtopodion, forms monophylum but is not closely related to the other members of the genus and so was reclassified as the independent genus. The enigmatic and yet so far very poorly studied genus Carinatogecko was discovered to be the...

<p>U radu je analzirana struktura populacija i stepen genetičke varijabilnosti u<br />populacijama divlje svinje u Evropi.&nbsp; Određena je polimorfnost jedanaest<br />tetranukleotidnih mikrosatelita u uzorku od 664 divljih svinja u Evropi, utvrđivanjem<br />alela prisutnih u populacijama i utvrđivanjem njihove frekvencije. U analiziranom<br />uzorku definisano je prisustvo 13 subpopulacija divljih svinja u Evropi i određeni su<br />osnovni parametri intra-&nbsp; i interpopulacione varijabilnosti. Pokazano je da je&nbsp; protok<br />gena između definisanih subpopulacija relativno mali&nbsp; obzirom da je utvrđen&nbsp; srednji i<br />visok nivo genetičke divergencije između definisanih subpopulacija. Utvrđen je visok<br />nivo genetičkog diverziteta u populacijama divlje svinje Evrope, &scaron;to ukazuje na<br />činjenicu da populacije ove vrste poseduju visok genetički potencijal.&nbsp; Analizom<br />polimorfnosti&nbsp; CR1-mtDNK nađeni su jedinstveni haplotipovi za Balkansko<br />poluostrvo i utvrđena je stuktuiranost populacija divljih svinja na Balkanu.<br />Poređenjem dobijenih sekvenci CR1-mtDNK sa dostupnim sekvencama divljih svinja<br />iz čitavog sveta rasvetljena je demografska i filogeografska istorija vrste&nbsp; <em>Sus scrofa</em>&nbsp; i<br />potvrđeno je važna uloga Balkana u rekolonizaciji Evrope nakon poslednjeg ledenog<br />doba.&nbsp; Pokazano je da su sva tri južna poluostrva Evrope (Balkansko, Iberijsko i<br />Apeninsko) učestvovala&nbsp; u rekolonizaciji Evrope i da se filogeografska&nbsp; istorija&nbsp; vrste<br /><em>Sus scrofa</em> može predstaviti u tri koraka: (1) povlačenje jedinki iz Centralne Evrope u<br />južna poluostrva tokom poslednjeg ledenog doba, (2) nezavisna diverzifikacija u<br />svakom od tri poluostrva, (3) rekolonizacija Evrope od strane haplotipova koji su bili<br />na severu poluostrva (u ekspazivnom frontu).&nbsp; Na osnovu rezultata ovog istraživanja<br />data je preporuka da&nbsp; za svaku definisanu subpopulaciju treba razviti odgovarajuće<br />strategije menadžmenta u skladu sa njenim genetičkim potencijalom, a u cilju<br />očuvanja evolucionog potencijala svake od njih kako bi se obezbedila i očuvala<br />stabilnost vrste.</p> / <p>In this paper an assessment of the wild boar genetic structure and phylogeography was&nbsp;performed&nbsp; based on the analysis of microsatellites and CR-1 region of mitochondrial&nbsp;DNA. Polymorphism of eleven tetranucletide microsatellites was determined in a&nbsp;sample of 664 wild boars in Europe&nbsp; by detection of&nbsp; alleles present in the populations&nbsp;and their frequency. In the analyzed sample of 664 wild boars, 13 genetically different&nbsp;subpopulations were defined and basic parameters of intra-&nbsp; and interpopulation&nbsp;variability were estimated.&nbsp; It was shown that&nbsp; gene flow&nbsp; between&nbsp; defined&nbsp;subpopulations&nbsp; is relatively&nbsp; small&nbsp; since estimated genetic distances between&nbsp;subpopulations indicated a moderate to high genetic differentiation.&nbsp; According to&nbsp;derived data,&nbsp; high genetic diversity is present in wild boar populations in &nbsp;Europe,&nbsp;indicating high genetic potential of the species.&nbsp; In the analysis of mtDNA control&nbsp;region sequences in wild boars from the Balkan peninsula unique haplotypes &nbsp;were&nbsp;found and population structure was observed.&nbsp; A detailed inspection of results reveals&nbsp;that a similar phylogeographic pattern emerges in all&nbsp; southern European peninsulas,&nbsp;arising from post-LGM expansion, and that all three peninsulas had a similar role in&nbsp;the wild boar post-glacial recolonization of Europe.&nbsp; This pattern could be explained&nbsp;by: the southward migration of Central-European haplotypes during the LGM to&nbsp;southern peninsulas; independent diversification in each peninsula; and post-LGM&nbsp;leading edge recolonization of Europe&nbsp; involving all three peninsulas.&nbsp; Based on the&nbsp;results of this research, it was recommended that&nbsp; for each defined subpopulation&nbsp;adequate&nbsp; manegament strategies should be defined and each subpopulation&nbsp; should be&nbsp;managed separately in order to preserve their evolutionary potential and to secure the&nbsp;long-term stability of wild resources.</p>

<p>Taksonomija&nbsp; i&nbsp; sistematika&nbsp; su&nbsp; okosnica&nbsp; nauke&nbsp; o biodiverzitetu,&nbsp; obzirom&nbsp; da&nbsp; su&nbsp; osnova&nbsp; za identifikaciju&nbsp; i&nbsp; razdvajanje&nbsp; jedinstvenih filogenetskih&nbsp; entiteta&nbsp; (vrsta),&nbsp; ali&nbsp; i&nbsp; vi&scaron;ih taksonomskih&nbsp; kategorija.&nbsp; Rod&nbsp;<em> Merodon&nbsp;</em> Meigen,1803&nbsp; pripada&nbsp; familiji&nbsp; Syrphidae,&nbsp; podfamiliji Eristalinae,&nbsp; tribusu&nbsp; Merodontini.&nbsp; Vodeći&nbsp; je&nbsp; rod osolikih muva po bogatstvu vrstama u Evropi (124 vrsta).&nbsp; Sirfide&nbsp; predstavljaju&nbsp; veoma&nbsp; važnu&nbsp; grupu<br />organizama&nbsp; i&nbsp; njihov&nbsp; značaj&nbsp; u&nbsp; prirodi&nbsp; je&nbsp; vi&scaron;estruk (polinacija,&nbsp; regulatori&nbsp; brojnosti&nbsp; &scaron;tetnih&nbsp; insekata bioindikatori&nbsp; stani&scaron;ta,&nbsp; razlagači&nbsp; materija&nbsp; u raspadanju&nbsp; itd).&nbsp; Iako&nbsp; su&nbsp; se&nbsp; istraživanjima&nbsp; roda Merodon&nbsp; bavili&nbsp; brojni&nbsp; autori,&nbsp; dosada&scaron;nje filogenetske&nbsp; analize&nbsp; nisu&nbsp; u&nbsp; potpunosti&nbsp; rasvetlile njegovu sistematsku poziciju, kao i položaj taksona na&nbsp; filogenetskom&nbsp; stablu.&nbsp; U&nbsp; cilju&nbsp; &scaron;to&nbsp; boljeg razumevanja sistematike i filogenije roda&nbsp; <em>Merodon</em>, neophodno&nbsp; je&nbsp; analizirati&nbsp; genske&nbsp; regione&nbsp; koji evoluiraju različitim mutacionim stopama, kao i &scaron;to veći&nbsp; broj&nbsp; filogenetski&nbsp; informativnih&nbsp; morfolo&scaron;kih karaktera. U&nbsp; ovom&nbsp; radu&nbsp; su&nbsp; u&nbsp; cilju&nbsp; istraživanja sistematike&nbsp; roda&nbsp; <em>Merodon&nbsp; </em>analizirani&nbsp; molekularni (mtDNK, 18S rRNK, 28S rRNK) i 250 morfolo&scaron;kih<br />karaktera&nbsp; (pomoću&nbsp; binokularne&nbsp; lupe&nbsp; i&nbsp; Skening elektronskog&nbsp; mikroskopa),&nbsp; pojedinačno&nbsp; i kombinovano&nbsp; a&nbsp; upotrebom&nbsp; metoda&nbsp; za&nbsp; filogenetsku analizu-&nbsp; <em>maximum&nbsp; parsimony</em>&nbsp; (MP)&nbsp; i&nbsp;<em> maximumlikelihood (</em>ML). Analizirano je ukupno 329 jedinki. Pokazalo&nbsp; se&nbsp; da&nbsp; je&nbsp; u&nbsp; ovakvom&nbsp; tipu&nbsp; istraživanja neophodan&nbsp; integrativni&nbsp; pristup,&nbsp; odnosno kombinacija&nbsp; &scaron;to&nbsp; vi&scaron;e&nbsp; karaktera&nbsp; poreklom&nbsp; iz različitih&nbsp; izvora.&nbsp; Na&nbsp; osnovu&nbsp; ML&nbsp; stabla&nbsp; svih&nbsp; gena tribus&nbsp; Merodontini&nbsp; je&nbsp; monofiletski&nbsp; gde&nbsp; se&nbsp; vrsta<br /><em>Nausigaster&nbsp; meridionalis</em>&nbsp; pojavljuje&nbsp; kao&nbsp; sestrinska ostalim rodovima tribusa (<em>Azpeytia, Platynochaetus, Megatrigon,&nbsp; Eumerus&nbsp;&nbsp; tricolor&nbsp;</em> kladi&nbsp; i&nbsp; ostalim vrstama&nbsp; roda&nbsp;<em> Eumerus</em>).&nbsp; Rod&nbsp; <em>Eumerus&nbsp;</em> je parafiletski&nbsp; i&nbsp; sastoji&nbsp; se&nbsp; iz&nbsp; dve&nbsp; monofiletske&nbsp; linije: <em>Eumerus&nbsp; tricolor&nbsp;</em> klade&nbsp; (potencijalnog&nbsp; roda)&nbsp; i ostalih&nbsp; vrsta&nbsp; roda&nbsp; Eumerus.&nbsp; Rod&nbsp; Merodon&nbsp; je monofiletski&nbsp; prema&nbsp; analizama&nbsp; kombinovane matrice&nbsp;&nbsp; molekularnih&nbsp; i&nbsp; morfolo&scaron;kih&nbsp; podataka,&nbsp; 5&#39; kraja&nbsp; mtDNK&nbsp; COI&nbsp; i&nbsp; analize&nbsp; matrice&nbsp; morfolo&scaron;kih karaktera.&nbsp; U&nbsp; okviru&nbsp; roda&nbsp; <em>Merodon</em>&nbsp; detektovano&nbsp; je ukupno&nbsp; pet&nbsp; klada&nbsp; (<em>aureus,&nbsp; albifrons,&nbsp; desuturinus, natans&nbsp; i&nbsp; avidus</em>),&nbsp; odnosno&nbsp; četiri&nbsp; glavne&nbsp; evolutivne linije,&nbsp; potencijalna&nbsp; podroda:&nbsp; aureus,&nbsp; albifrons&nbsp; + desuturinus,&nbsp; natans&nbsp; i&nbsp; avidus.&nbsp; Mitohondrijalni&nbsp; geni pokazali su se veoma informativnim u sagledavanju<br />filogenetskih odnosa i izdvajanja većine klada, kao i grupa&nbsp; vrsta,&nbsp; &scaron;to&nbsp; ukazuje&nbsp; na&nbsp; veću&nbsp; varijabilnost sekvenci&nbsp; COI&nbsp; gena&nbsp; u&nbsp; odnosu&nbsp; na&nbsp; nuklearne&nbsp; gene. Nuklearni&nbsp; geni&nbsp; samostalno&nbsp; nisu&nbsp; doprineli rasvetljavanju&nbsp; filogenetskih&nbsp; odnosa&nbsp; između&nbsp; klada<br />(28S&nbsp; rRNK&nbsp; izdvaja&nbsp; samo&nbsp; natans&nbsp; kladu)&nbsp; u&nbsp; okviru roda&nbsp;<em> Merodon</em>,&nbsp; ali&nbsp; su&nbsp; izdvojili&nbsp; tribus<em>&nbsp; Merodontini,</em>kao&nbsp; i&nbsp;<em> Eumerus&nbsp; tricolor&nbsp; </em>liniju.&nbsp; Nuklearni&nbsp; geni&nbsp; su izdvojili&nbsp; i&nbsp; pojedine&nbsp; grupe&nbsp; vrsta&nbsp; u&nbsp; okviru&nbsp; roda <em>Merodon</em>,&nbsp; &scaron;to&nbsp; govori&nbsp; u&nbsp; prilog&nbsp; tome&nbsp; da&nbsp; nuklearni geni mogu biti informativni kako na vi&scaron;im, tako i na nižim&nbsp; taksonomskim&nbsp; nivoima.&nbsp; Mala&nbsp; varijabilnost nuklearnog&nbsp; gena&nbsp; u&nbsp; okviru&nbsp; roda&nbsp; Merodon,&nbsp; naročito<br />slučaju&nbsp; 18S&nbsp; rRNK,&nbsp; govori&nbsp; o&nbsp; njegovoj konzervativnosti.&nbsp; Utvrđeno&nbsp; je&nbsp; da&nbsp; morfolo&scaron;ki<br />karakteri genitalija mužjaka nose važan filogenetski signal&nbsp; za&nbsp; izdvajanje&nbsp; klada&nbsp; i&nbsp; grupa&nbsp; vrsta&nbsp; te&nbsp; upravo kombinacija&nbsp; različitih&nbsp; morfolo&scaron;kih&nbsp; struktura&nbsp; i njihova uloga sa različitim stepenom selekcije koja deluje&nbsp; na&nbsp; njih,&nbsp; uslovljava&nbsp; i&nbsp; njihovu&nbsp; evolucionu diverzifikaciju.&nbsp; Ipak,&nbsp; analize&nbsp; molekularnog&nbsp; i morfolo&scaron;kog&nbsp; seta&nbsp; karaktera&nbsp; pojedinačno&nbsp; nisu&nbsp; u potpunosti&nbsp; rasvetlili&nbsp; filogenetske&nbsp; odnose&nbsp; u&nbsp; okviru<br />roda&nbsp;<em> Merodon</em>,&nbsp; &scaron;to&nbsp; opravdava&nbsp; potrebu&nbsp; za kombinovanom analizom.&nbsp;</p> / <p>Taxonomy&nbsp; and&nbsp; systematics&nbsp; provide&nbsp; the&nbsp; framework&nbsp; for&nbsp; biodiversity&nbsp; research, since&nbsp; they represent a foundation for identification&nbsp; and&nbsp; delimitation&nbsp; of&nbsp; phylogenetic&nbsp; units&nbsp; (species), as well as higher taxonomic ranks. Genus<em>&nbsp; Merodon&nbsp; </em>Meigen,&nbsp; 1803&nbsp; belongs&nbsp; to family&nbsp; Syrphidae,&nbsp; subfamily&nbsp; Eristalinae, tribus&nbsp; Merodontini.&nbsp; Hoverflies&nbsp; play&nbsp; crucial&nbsp; ecological&nbsp; roles&nbsp; (pollination,&nbsp; decomposition&nbsp; and&nbsp; recycling&nbsp; of&nbsp; a&nbsp; vast&nbsp; range&nbsp; of&nbsp; materials, bioindicators&nbsp; etc).&nbsp; Despite&nbsp; the&nbsp; fact&nbsp; that genus<em>&nbsp; Merodon</em>&nbsp; is&nbsp; the&nbsp; species&nbsp; richest hoverfly&nbsp; genus&nbsp; in&nbsp; Europe&nbsp; (124&nbsp; described&nbsp; species so far), only few authors have dealt with&nbsp; its&nbsp; systematics&nbsp; and&nbsp; phylogenetic&nbsp; relationships&nbsp; of&nbsp; this&nbsp; large&nbsp; phytophagous genus. In order to understand the systematics and&nbsp; phylogeny&nbsp; of&nbsp; genus&nbsp; Merodon,&nbsp; it&nbsp; is&nbsp; necessary to analyze comprehensive number of&nbsp; gene&nbsp; regions&nbsp; known&nbsp; to&nbsp; evolve&nbsp; with various&nbsp; mutational&nbsp; rates,&nbsp; and&nbsp; as&nbsp; many&nbsp; feasible,&nbsp; phylogenetically&nbsp; important&nbsp; morphological&nbsp; characters.&nbsp; In&nbsp; this&nbsp; thesis, molecular (mtDNA, 18S rRNA, 28S rRNA)and&nbsp; 250&nbsp; morphological&nbsp; characters&nbsp; (with&nbsp; the aid&nbsp; of&nbsp; binocular&nbsp; and&nbsp; scanning&nbsp; electron microscope)&nbsp; were&nbsp; analyzed,&nbsp; separately&nbsp; and combined,&nbsp; with&nbsp; phylogenetic&nbsp; methods <em>maximum&nbsp; parsimony&nbsp; </em>(MP)&nbsp; and&nbsp; <em>maximum likelihood</em>&nbsp; (ML).&nbsp; In&nbsp; total&nbsp; 329&nbsp; specimens were&nbsp; analyzed.&nbsp; It&nbsp; has&nbsp; been&nbsp; proven&nbsp; that&nbsp; in these types of research integrative approach is crucial, as it considers a large&nbsp; amount of data from various sources. In ML analysis of all&nbsp; genes&nbsp; tribus&nbsp; Merodontini&nbsp; is monophyletic,&nbsp; with&nbsp; Nausigaster meridionalis&nbsp; grouping&nbsp; as&nbsp; a&nbsp; sister&nbsp; to&nbsp; the remaining&nbsp; Merodontini&nbsp; (<em>Azpeytia, Platynochaetus,&nbsp; Megatrigon,&nbsp; Eumerus&nbsp; </em>and <em>Eumerus&nbsp; tricolor&nbsp;</em> lineage). Genus&nbsp;<em> Eumerus </em>is&nbsp; paraphyletic,&nbsp; and&nbsp; within&nbsp; this&nbsp; genus&nbsp; two main&nbsp; monophyletic&nbsp; lineages&nbsp; can&nbsp; be identified:&nbsp;<em> Eumerus&nbsp; tricolor&nbsp; </em>clade&nbsp; (putative genera)&nbsp; and&nbsp; the&nbsp; remaining&nbsp; taxa&nbsp; of&nbsp; genus Eumerus.&nbsp; Genus&nbsp; <em>Merodon</em>&nbsp; monophyly&nbsp; is confirmed,&nbsp; based&nbsp; on&nbsp; all&nbsp; data&nbsp; analysis&nbsp; 5&#39; mtDNA&nbsp; COI&nbsp; and&nbsp; morphological&nbsp; dataset. Within&nbsp; genus&nbsp; <em>Merodon</em>&nbsp; five&nbsp; monophyletic clades&nbsp; can&nbsp; be&nbsp; identified&nbsp; (<em>aureus,&nbsp; albifrons, desuturinus,&nbsp; natans&nbsp; and&nbsp; avidus</em>),&nbsp; or&nbsp; four evolutionary&nbsp; lineages,&nbsp; putative&nbsp; subgenera: aureus,&nbsp; albifrons&nbsp; +&nbsp; desuturinus,&nbsp; natans&nbsp; and avidus.&nbsp; Mitochondrial DNA is proved to be very&nbsp; informative&nbsp; in&nbsp; resolving&nbsp; systematic position&nbsp; of&nbsp; clades,&nbsp; species&nbsp; groups&nbsp; and&nbsp; taxa, which confirms the higher variability of COI mtDNA&nbsp; sequences&nbsp; compared&nbsp; to&nbsp; nuclear genes. Nuclear genes alone didn&#39;t resolve the systematic&nbsp; position&nbsp; and&nbsp; phylogenetic relationships&nbsp; between&nbsp; most&nbsp; clades&nbsp; (28S rRNA&nbsp; identified&nbsp; only&nbsp; natans&nbsp; clade)&nbsp; within genus&nbsp; <em>Merodon,</em>&nbsp; but&nbsp; these&nbsp; genes&nbsp; confirmed the&nbsp; monophyly&nbsp; of&nbsp; tribus&nbsp; Merodontini&nbsp; and putative&nbsp; genera&nbsp; <em>Eumerus&nbsp; tricolo</em>r.&nbsp; Nuclear genes&nbsp; were&nbsp; also&nbsp; informative&nbsp; for&nbsp; some species&nbsp; groups,&nbsp; which&nbsp; implies&nbsp; that&nbsp; nuclear genes&nbsp; could&nbsp; be&nbsp; beneficial&nbsp; in&nbsp;&nbsp; resolving systematic position of both lower and higher taxonomic ranks. Low&nbsp; variability of nuclear genes within genus <em>Merodon</em>, especially 18SrRNA,&nbsp; proves&nbsp; the&nbsp; fact&nbsp; that&nbsp; they&nbsp; are&nbsp; conservative&nbsp; genes.&nbsp; Morphological&nbsp; characters&nbsp; of&nbsp; male&nbsp; genitalia&nbsp; carry&nbsp; the strongest&nbsp; phylogenetic&nbsp; signal,&nbsp; since&nbsp; they show a great evolutionary divergence in the shape&nbsp; and&nbsp; structural&nbsp; complexity,&nbsp; as&nbsp; a&nbsp; result of&nbsp; sexual&nbsp; selection.&nbsp; As&nbsp; molecular&nbsp; nor morphological&nbsp; characters&nbsp; alone&nbsp; couldn&#39;t fully&nbsp; resolve&nbsp; the&nbsp; phylogenetic&nbsp; relationships&nbsp; within genus&nbsp; <em>Merodon</em>,&nbsp; all data&nbsp; approach is proven&nbsp; to&nbsp; be&nbsp; necessary&nbsp; in&nbsp; this&nbsp; type&nbsp; of&nbsp; research.<br />&nbsp;</p>

Submitted by JOSIANE SANTOS DE OLIVEIRA (josianeso) on 2017-12-06T13:59:20Z No. of bitstreams: 1 Tainã Coelho Quevedo_.pdf: 1779262 bytes, checksum: 1c805c11de74d708f12d1e1a98e63886 (MD5) / Made available in DSpace on 2017-12-06T13:59:20Z (GMT). No. of bitstreams: 1 Tainã Coelho Quevedo_.pdf: 1779262 bytes, checksum: 1c805c11de74d708f12d1e1a98e63886 (MD5) Previous issue date: 2017-08-21 / CAPES - Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / PROSUP - Programa de Suporte à Pós-Gradução de Instituições de Ensino Particulares / Os cachalotes, Physeter macrocephalus Linnaeus, 1758, são amplamente distribuídos por todos os oceanos do mundo. Todavia, os machos e fêmeas têm diferenças marcadas em seu padrão de distribuição. Globalmente, estudos genéticos, ecológicos e de comportamento vocal comparando populações sugerem a existência de uma forte estrutura social matrilinear com alta filopatria das fêmeas nas regiões tropicais, sendo o fluxo gênico mediado pelos machos. As populações do oceano Atlântico Sul Ocidental (ASO) ainda são tidas como as menos pesquisadas e conhecidas. A fim de identificar possíveis unidades de manejo da espécie na região, o presente estudo apresentou a primeira análise da diversidade genética e a avaliação da potencial estruturação das populações de cachalotes ao longo do ASO, utilizando sequências da região controladora do DNA mitocondrial (DNAmt) de 565 pb obtidas de amostras coletadas na região. Além disso, objetivou-se também estabelecer as relações filogeográficas entre estas populações do ASO e as do resto do mundo. Para a realização deste estudo foram analisadas 58 amostras de cachalotes de três áreas geográficas na costa brasileira (nordeste =15, sudeste =3, sul = 36) e uma da costa argentina (n = 4), e comparadas com 1.577 sequências de outros oceanos, disponíveis publicamente no GenBank (Atlântico = 362, Índico = 159 e Pacífico = 1.056). Além disso, o sexo de 39 espécimes foi determinado molecularmente, a fim de se testar a existência de mais de uma população de cachalotes no ASO, a partir da detecção de fêmeas em áreas além do nordeste brasileiro. A análise das sequências do DNAmt revelou a existência de quatro grupos genéticos e sete haplótipos no ASO. As diversidades haplotípica (Hd) e nucleotídica (π) observadas para a espécie como um todo no ASO foram Hd = 0,6824 e π = 0,002296, respectivamente. Os testes de neutralidade seletiva não sugeriram mudanças significativas no tamanho efetivo e nem expansão populacional recente da espécie no ASO. Os resultados das análises de variância molecular (AMOVA) revelaram que entre 9,14% (ΦST) e 12,31% (FST) da variação genética observada deve-se a diferenças entre as populações. Contudo, essa diferenciação geográfica só foi significativa entre as populações do nordeste e sudeste-sul do Brasil, as quais possuíam altos índices de fixação entre si (nordeste e sudeste-sul do Brasil: FST = 0,1089; ΦST = 0,1378; nordeste do Brasil e Argentina: FST = -0,1076; ΦST = -0,0512; sudeste-sul do Brasil e Argentina: FST = 0,0742; ΦST = 0,1206; P<0,00001). A população do nordeste do Brasil apresentou a diversidade genética mais baixa do estudo (Hd = 0,5128 e π = 0,001796), quando comparada com as populações do sudeste-sul (Hd = 0,6659 e π = 0,002482), e Argentina (Hd = 0,8333 e π = 0,002043). A costa sudeste-sul do Brasil apresentou três haplótipos exclusivos num total de sete, enquanto a costa da Argentina apresentou um haplótipo particular. Apenas a região sudeste-sul apresentou um grupo genético exclusivo, sugerindo que a distribuição da variação genética é melhor compreendida com a existência de três grupos ao longo do ASO (nordeste, sudeste-sul e Argentina), os quais seriam considerados diferentes unidades de manejo. Em relação a comparação mundial entres as populações de cachalotes, foram recuperados 39 haplótipos e quatro grupos genéticos, sendo que apenas o oceano Pacífico apresentou um grupo genético exclusivo. A AMOVA revelou que entre 8,89% (FST) e 16,39% (ΦST) da variação genética observada deve-se a diferenças entre as populações do mundo. A AMOVA indicou que há diferenciação geográfica entre o ASO e os demais oceanos, os quais possuíam altos índices de fixação entre si (ASO e Atlântico Norte: FST = 0,1837; ΦST = 0,3142; Atlântico Sul Ocidental e Índico: FST = 0,0898; ΦST = 0,1661; Atlântico Sul Ocidental e Pacífico: FST = 0,1140; ΦST = 0,0757; P<0,00001). A amostra unificada do oceano ASO não apresentou haplótipos exclusivos. Entretanto, os indivíduos da região sudeste-sul do Brasil compartilharam seis dos seus sete haplótipos com a população do oceano Pacífico. Dos 39 cachalotes com sexo determinado molecularmente nove eram machos e 30 fêmeas, tendo sido encontradas 18 fêmeas na região sul, fora da região tropical, sugerindo que há pelo menos mais de uma população reprodutiva no ASO. Estes resultados, aliados as diferenças de variabilidade genética e ao pouco compartilhamento de haplótipos entre as populações estudadas, sugere que os cachalotes do sudeste-sul do Brasil seriam uma unidade de manejo, potencialmente isolada em termos reprodutivos das demais. Contudo, o DNAmt é um marcador matrilinear e apresenta exclusivamente a história evolutiva das fêmeas. Desta forma, a continuidade destes estudos, incluindo novas amostras e marcadores nucleares, será fundamental para a identificação de reais unidades de manejo da espécie no ASO e principalmente em águas brasileiras. / Sperm whales, Physeter macrocephalus Linnaeus, 1758, are widely distributed throughout the world's oceans. However, males and females have marked differences in their distribution pattern. Worldwide studies on genetics, ecology and vocal behavior comparing populations suggested the existence of a strong matrilineal social structure with female high philopatry in tropical regions, and gene flow mediated by males. The populations of the southwestern Atlantic Ocean (SWA) are still considered the least known and studied. In order to identify possible management units of the species in the SWA, the present study presented the first analysis of the genetic diversity and the evaluation of the potential structuring of the sperm whale populations along the SWA, using sequences from the mitochondrial DNA control region (mtDNA) of 565 bp obtained from samples collected in the region. In addition, it was also aimed to establish the phylogeographic relationships among these SWA populations and those of the rest of the world. Fifty-eight sperm whales from three geographic areas on the Brazilian coast (northeast = 15, southeast = 3, south = 36) and one from the coast of Argentina (n = 4) were analyzed and compared with 1577 sequences from other oceans and available in GenBank (Atlantic = 362, Indian = 159 and Pacific = 1056). In addition, the sex of 39 specimens was molecularly determined in order find females outside of the northeastern coast of Brazil, which would confirm the existence of more than one sperm whale population in the SWA. The analysis of mtDNA sequences revealed the existence of four genetic groups and seven haplotypes in SWA. The haplotype (Hd) and nucleotide (π) diversities observed for the species as a whole in SWA were Hd = 0.6824 e π = 0.002296, respectively. The selective neutrality tests did not suggest significant changes in the effective population size or recent population expansion for the species in SWA. The results of the molecular analysis of variance (AMOVA) revealed that between 9.14% (ΦST) and 12.31% (FST) of the genetic diversity variation observed are due to differences between populations. However, this geographical differentiation was only significant between the populations of northeast and southeast-south Brazil, which had the highest fixation index between them (northeast and southeast-south Brazil: FST = 0.1089, ΦST = 0.1378; northeast Brazil and Argentina: FST = - 0.1076; ΦST = - 0.0512; southeast-south of Brazil and Argentina: FST=0.0742; ΦST=0.1206; P<0.00001). The population of northeastern Brazil had the lowest genetic diversity of the study (Hd = 0.5128 and π = 0.001796), when compared to the southeast-south populations (Hd = 0.6659 and π = 0.002482), and Argentina (Hd = 0.8333 and π = 0.002043). The southeast-south coast of Brazil presented three exclusive haplotypes in a total of seven, while the coast of Argentina presented a particular haplotype. Only the samples from the southeast-south region of Brazil presented an exclusive genetic group, suggesting that the distribution of the genetic variation is better understand with the existence of three groups of sperm whales along the SWA (northeast of Brazil, southeast-south of Brazil and Argentina), which could be considered as different management units. Regarding the worldwide genetic structure of sperm whales, 39 haplotypes and four genetic groups were recovered, and only the Pacific Ocean presented an exclusive genetic group. AMOVA revealed that between 8.89% (FST) and 16.39% (ΦST) of the observed genetic variation was due to differences among the populations of the world. AMOVA indicated that there is a geographical differentiation between the SWA and the other oceans, which had high indexes of fixation between them (SWA and North Atlantic: FST = 0.1837, ΦST = 0.3142, SWA and Indian Ocean: FST = 0.0898; ΦST = 0.1661; SWA and Pacific: FST = 0.11140; ΦST = 0.0757; P<0.00001). The unified sample of the SWA did not present exclusive haplotypes. However, individuals from the southeast-south of Brazil only shared six of seven haplotypes with the population of the Pacific Ocean. From 39 sperm whales with sex molecularly determined, nine were males and 30 females, 18 females were found in the southern region, outside the tropical region, suggesting that there are at least more than one reproductive population in WSA. These results, together with the differences in genetic variability and the lack of sharing of haplotypes among the studied populations, suggest that sperm whales from southeast-south of Brazil would be a management unit, potentially isolated, in reproductive terms, from the others. However, mtDNA is a matrilineal marker and exclusively presents the evolutionary history of females. In this context, the continuity of these studies, including new samples and nuclear markers, will be fundamental for the identification of real units of management of the species in the SWA and particularly in Brazilian waters.

Saccharomyces yeasts are ideal candidates for genomic and evolutionary studies in eukaryotes due to their small genome, short generation time and availability of genomic data. Species freely hybridize producing viable but largely sterile cells. A hybridization event can be a swift mechanism for evolutionary innovation that if successful, may produce individuals fitter than either parents. It is largely unclear which mechanisms contribute to such hybrid vigour. This thesis investigated three mechanisms by which a natural hybrid may utilise one or both subgenomes to its advantage: recombination, the formation of chimeric protein complexes and the inheritance of mitochondrial DNA. Three strains of Saccharomyces pastorianus, a natural hybrid of Saccharomyces cerevisiae and Saccharomyces eubayanus, used in the lager fermentation process were sequenced using a NGS SOLiD platform. An analysis of recombination between each subgenome revealed the presence of 30 breakpoints, 28 of which are found within coding regions. Two breakpoints, present within the genes XRN1 and HSP82 have been reused in all three strains of S. pastorianus. This thesis investigated the formation of chimeric protein complexes in S. pastorianus by determining the configuration of protein complex-forming gene pairs to see whether they were mainly uni-specific, with all members belonging to the same parent, or chimeric, comprising one member from each parental species. A total of 21 pairwise protein complexes were found to be obligatorily chimeric in three strains of S. pastorianus. We used PCR-mediated gene deletion to recreate chimeric protein complexes in laboratory hybrids of S. cerevisiae and S. uvarum. The allelic configuration of one protein-complex forming gene pair, MLP2 and SPC110, impacted the growth of hybrid strains in a temperature-dependent manner. Finally, we looked at the mitochondrial inheritance in hybrids. Yeast hybrids can initially inherit mitochondrial DNA (mtDNA) from both parents, but rapidly become homoplasmic. To investigate the mechanisms influencing mtDNA inheritance, strains of Saccharomyces cerevisiae and Saccharomyces uvarum were crossed under different environmental conditions. The majority of hybrids inherited S. cerevisiae mtDNA when crossed in glycerol, a carbon source that can only be respired by yeast, in a range of temperatures. Those crossed in glucose, a fermentable source, did not show a preference for the inheritance of mtDNA at 30°, but at 10°C preferentially inherited S. uvarum mtDNA. In subsequent growth assays, hybrids with S. cerevisiae mtDNA grew better than those with S. uvarum mtDNA at 30°C and 20°C. However, at 10°C, the reverse was true: hybrids with S. uvarum mtDNA grew better that those with S. cerevisiae mtDNA, although only in glycerol. Overall this works sheds light on the molecular mechanisms contributing to fitness and evolutionary vigour in yeast hybrids.

A superfamília Majoidea é dividida em seis famílias: Epialtidae, Hymenosamatidae, Inachidae, lnachoididae, Majidae e Oregoniidae. A família Epialtidae engloba 76 gêneros, dentre eles Acanthonyx e Epialtus com 17 e 11 espécies, respectivamente. No litoral brasileiro, ocorrem três espécies do gênero Acanthonyx, A. dissimulatus, A. scutiformis e A. petiverii; e duas de Epialtus, E. bituberculatus e E. brasiliensis. As dúvidas quanto à sistemática destes gêneros, a diversidade de formas de seus indivíduos e a escassez de revisões abordando-os, destaca a necessidade de uma revisão taxonômica das espécies brasileiras combinando diferentes ferramentas metodológicas como morfologia e análise molecular. Uma lista de caracteres foi analisada e apresentada nas descrições de A. dissimulatus, A. petiverii, A. scutiformis, E. bituberculatus e E. brasiliensis. Adicionalmente, exemplares das cinco espécies reportadas para o Brasil, oriundas de diferentes localidades, tiveram DNA amplificado usando marcadores para os genes mitocondriais 16S e COI. As sequências resultantes foram comparadas no sistema BLAST para confirmação de suas identidades, editadas e alinhadas em CIustal W no programa BioEdit. As distâncias genéticas foram calculadas no programa MEGA5 e representadas por meio de matrizes. Os filogramas foram construídos pelo método de Máxima Verossimilhança na plataforma online CIPRES. As redes de haplótipos foram obtidas pelo Median-Joining no programa Network. As três espécies de Acanthonyx são muito semelhantes e difíceis de identificar. Os filogramas e as redes de haplótipos mostraram que E. brasiliensis inseriu-se no grupo de E. bituberculatus, e que A. dissimulatus e A. scutiformis se inserem em A. petiverii, permitindo questionar a validade taxonômica destas espécies. Os dados moleculares corroboraram a morfologia de Acanthonyx; a divisão dos espécimes de A. petiverii em dois grupos distintos e bem suportados indicou que há diferenças genéticas entre estas populações, mas que ainda ocorre fluxo gênico. Entre as espécies de Epialtus, não houve alta divergência genética e o compartilhamento de haplótipos indicou fluxo gênico entre E. brasiliensis e E. bituberculatus, indicando a presença de uma única espécie no Brasil. Dessa forma, pode ser que a presença ou ausência do espinho proximal ventral nos últimos pares de pernas locomotoras seja um caráter plástico em relação ao meio em que vivem. Nos filogramas e nas redes de haplótipos, os espécimes de Epialtus separaram-se em Caribe e Brasil, mas não foram distinguidos morfologicamente. Por fim, sugere-se a sinonimização de A. dissimulatus e A. scutiformis com A. petiverii, e a ocorrência de E. bituberculatus no Caribe e E. brasiliensis no Brasil. / The Superfamily Majoidea consists of six families: Epialtidae, Hymenosamatidae, Inachidae, Inachoididae, Majidae and Oregoniidae. The family Epialtidae includes 76 genera, among them Acanthonyx and Epialtus with 17 and 11 valid species, respectively. In the Brazilian coast there are three Acanthonyx species, A. dissimulatus, A. scutiformis and A. petiverii; and two Epialtus, E. bituberculatus and E. brasiliensis. Doubts about the systematic of these genus, the high diversity of forms and the lack of revisions addressing them, highlight the necessity for a taxonomic revision of the Brazilian species using different methodological tools such as morphology and molecular analysis together. A list of characters was analyzed and descriptions were made for A. dissimulatus, A. petiverii, A. scutiformis, E. bituberculatus and E. brasiliensis. For molecular data, DNA of specimens from different localities was amplified using markers for the mitochondrial genes 16S and COI. AII sequences were confirmed in BLAST system; they were edited and aligned using Clustal W with interface to BioEdit. Genetic distances were calculated in the program Mega5 and represented through matrices. The construction of the trees was performed using Maximum Likelihood in the online platform CIPRES. Haplotype networks were based on Median-Joining analysis and performed in the program Network. The three species of Acanthonyx were similar morphologically and could not be separated. Trees and the haplotype network showed that E. brasiliensis was into the group of E. bituberculatus; and A. dissimulatus and A. scutiformis were within A. petiverii branch, which means that taxonomic status of these species may be questioned. There is a correspondence between morphologic and molecular data among the three species of Acanthonyx; the division in two distinct groups observed in specimens of A. petiverii was weII supported and indicated that there are genetic differences between these populations, but gene flow still occurs. Between both species of Epialtus, the results from molecular markers were in conflict with the morphological classification, and sharing of haplotypes indicated gene flow between E. brasiliensis and E. bituberculatus, which means that there is only one species in Brazil. Hence, the presence or absence of the spine on the propodus\'s ventral surface in the Iast ambulatory pereopods can be related to ecological plasticity developed in response to the environment where these crabs Iive. Phylograms and the haplotype network showed that specimens of Epialtus were separated in two groups, Caribbean and Brazil, but they were not distinguished morphologically. In this way, we propose that A. dissimulatus and A. scutiformis as junior synonyms of A. petiverii; and the occurrence of E. bituberculatus in the Caribbean and E. brasiliensis in Brazil.

Made available in DSpace on 2015-04-11T13:38:42Z (GMT). No. of bitstreams: 1 Tese Conceicao.pdf: 3479286 bytes, checksum: e423419bc970a5fbce6d4829446d589e (MD5) Previous issue date: 2010-09-24 / Fundação de Amparo à Pesquisa do Estado do Amazonas / The floodplain ecosystem shelters and supports most of the fish stocks of commercial importance, such as the tambaqui, Colossoma macropomum, which is considered a key species of this ecosystem. This fish is the largest characin of the Amazon and it is highly appreciated as food by the local population. Currently the tambaqui represents 70% of the regional pisciculture, but despite increasing aquiculture output, wild populations have been experiencing severe over-exploitation. To manage natural stocks of tambaqui it is necessary to access a range of information from diverse areas of knowledge, including genetics. It is thus of fundamental importance to access levels of genetic variability and how this variability is distributed throughout the Amazon region where the species occurs. This information is necessary to guide management strategies and conservation of this species. To obtain such information, mitochondrial (control region and ATPase gene) and nuclear (microsatellites) molecular markers were used. In this study 14 highly polymorphic microsatellite loci for the tambaqui were developed. These molecular markers were successfully transferred to other species of serrasalmids. For the genetic characterization of the tambaqui, 21 localities in the Amazon basin were sampled. We sequenced 1561pb (control region + ATPase gene) from 539 individuals finding 444 haplotypes, of which 440 were unique. The haplotype diversity was high and relatively homogeneous among all localities, however diversity was smallest in Porto Velho. Data from 12 microsatellite loci were collected from 604 individuals, showing an average of 21,4 alleles per locus. Total HE was 0,78 and heterozygosity levels were homogeneous among sampled localities. Porto Velho and Guaporé showed lower values of HE. These results suggest high levels of genetic variability in the tambaqui. AMOVA and other tests to detect population structure based on both markers indicated that within the Brazilian Amazon basin, the tambaqui comprises a single large population, supported by high gene flow between localities. These results indicate that species management in this area can be unified. Considering the entire sampling scheme, the data suggest a metapopulation scenario between the Brazilian and Bolivian basins, with low genetic differentiation between the basins and restricted gene flow due to isolation by distance. The rapids of the Tapajós and Madeira Rivers are not barriers to gene flow among population samples of tambaqui. A demographically stable population was detected in the Bolivian basin and a historical demographic expansion in the Amazon basin, supported by the large number of haplotypes and the presence of unique alleles in Brazilian localities. The migration rates were higher from white water tributaries to the main channel, while the opposite was true for the clear waters of Tapajós River. The effective population size (Ne) was greater in the channel, and in Jacareacanga and Boca do Acre. Genetic effects of over-exploitation were not detected in the tambaqui due to the high genetic diversity found. However, these findings are showing the historical status compatible with a large effective population size of the species in the past since the time of over-exploitation is still be short to be registered genetically. / O ecossistema de várzea amazônica abriga e sustenta a maior parte dos estoques de peixes de importância comercial, como o tambaqui Colossoma macropomum. Este peixe é o maior caracídeo da Amazônia e é muito apreciado como alimento pela população local. Atualmente corresponde com 70% da piscicultura regional, mas apesar da crescente produtividade cultivada, esta espécie na natureza vem experimentando uma intensa sobre-exploração. Para gerenciar os estoques naturais de tambaqui é necessário acessar um conjunto de informações de diversas áreas do conhecimento e, concernente à genética, é de fundamental importância acessar a variabilidade genética e a forma como esta variabilidade está distribuída ao longo da região Amazônica. Estas informações são importantes para direcionar estratégias de manejo e conservação para espécie. Para obter tais informações, foram utilizados marcadores moleculares mitocondriais (região controle e gene da ATPase) e nucleares (microssatélites). No presente estudo foram isolados 14 locos de microssatélites altamente polimórficos para tambaqui. Estes marcadores moleculares foram transferidos com sucesso para outras espécies de serrasalmídeos. Para a caracterização genética do tambaqui, 21 localidades foram amostradas na bacia Amazônica, e 1561 pb (região controle + gene da ATPase) foram seqüenciados em 539 indivíduos. Foram encontrados 444 haplótipos, sendo que 440 foram únicos. A diversidade haplotípica foi alta e relativamente homogênea para todas as localidades, mas foi menor em Porto Velho. Para dados de microssatélites foram utilizados 12 locos em 604 indivíduos, sendo encontrada uma média de 21,4 alelos por loco. A HE total foi de 0,78, sendo em geral, homogênea para as localidades amostrada. Para Porto Velho e Guaporé a HE apresentou os menores valores. Estes resultados sugerem altos níveis de variabilidade genética em tambaqui. AMOVA e as demais análises para detectar estrutura populacional, com base em ambos marcadores, indicaram que dentro da bacia Amazônica brasileira o tambaqui forma uma única e grande população, suportado por um intenso fluxo gênico entre as localidades. Estes resultados indicam que o manejo da espécie nesta área pode ser unificado. Considerando toda a amostragem do estudo, evidenciou-se um cenário de metapopulação entre as bacias hidrográficas brasileiras e bolivianas. As corredeiras presentes nos rios Tapajós e Madeira não representam uma barreira ao fluxo gênico entre as amostras populacionais de tambaqui. Uma estabilidade populacional foi detectada para a bacia Boliviana e uma expansão para a bacia Amazônica, suportado pelo grande número de haplótipos únicos e a presença de alelos exclusivos nas localidades brasileiras. As taxas de migração foram maiores das localidades dos tributários de água branca para a calha principal, e desta para o rio Tapajós. Os dados genéticos podem estar configurando a migração reprodutiva ou uma dinâmica nos movimentos da espécie. O tamanho efetivo populacional (Ne) foi maior na calha principal, no rio Tapajós e no rio Purus. Não foram detectados sinais de sobreexploração devido à alta diversidade genética encontrada. No entanto estes achados podem estar mostrando um status histórico da espécie compatível a um enorme tamanho efetivo populacional no passado ou que o tempo de sobreexploração pode ainda ser curto para um registro genético.