<p>Identifikacija genomskih regiona na koje je delovala selekcija tokom stvaranja elitnih<br />sorti soje (<em>Glycine max</em> (L.) Merr.) može ukazati na pozicije gena koji determini&scaron;u<br />važna agronomska svojstva ili su odgovorni za adaptabilnost. U radu su sagledani<br />efekti oplemenjivanja u agroklimatskim uslovima centralne i istočne Evrope koristeći<br />pristup&nbsp; &ldquo;<em>hitchhiking</em>&rdquo;&nbsp; mapiranja i analizu&nbsp; pedigrea. U ovu svrhu&nbsp; su&nbsp; primenjeni<br />molekularni markeri, mikrosateliti i&nbsp; principi populacione genetike, koristeći vi&scaron;e<br />različitih pristupa za identifikaciju selektivno značajnih lokusa. Analiza je obuhvatila<br />populacije soje koje su se sastojale od predačkih genotipova i elitnih genotipova koji<br />su nastali u Institutu za ratarstvo i povrtarstvo u Novom Sadu. Analizom pedigrea je<br />potvrđena uska genetička osnova sorti soje elitne populacije.&nbsp; Kao posledica<br />dugogodi&scaron;njeg oplemenjivanja, svi analizirani parametri su&nbsp; ukazali na statistički<br />značajno smanjenje genetičkog diverziteta elitne populacije u odnosu na predačku.<br />Usled specifične strukture populacija soje, koja je u velikoj meri bila pod uticajem<br />pedigrea&nbsp; elitnih genotipova,&nbsp; uočen je nizak nivo genetičke diferencijacije među<br />ispitivanim populacijama. Primenom najmanje dva različita pristupa identifikovano je<br />devet mikrosatelitskih lokusa koji su ukazivali na regione genoma na koje je delovala<br />selekcija,&nbsp; a koji su bili uključeni u proces adaptacija u agroklimatskim uslovima<br />centralne i istočne Evrope.&nbsp; U elitnoj populaciji je potvrđeno povećanje stope<br />gametskog disekvilibrijuma, najverovatnije kao posledica delovanja selekcije.<br />&bdquo;<em>Bottleneck</em>&rdquo; test je ukazao na značajno smanjenje diverziteta samo kod lokusa na koje je&nbsp; delovala&nbsp; selekcija&nbsp; u&nbsp; elitnoj&nbsp; populaciji, &scaron;to&nbsp; najverovatnije&nbsp; nije uzrokovano<br />demografskim faktorima, nego takođe predstavlja posledicu delovanja selekcije.<br />Analizom kolokacije poznatih QTL regiona i identifikovanih, selektivno značajnih<br />genomskih regiona, uočeno je ukupno 264 QTL-ova, od kojih su najzastupljeniji bili<br />lokusi koji su determinisali svojstva u vezi sa reproduktivnim razvojem biljke.<em> In silico</em><br />analizom je utvrđeno&nbsp; da su lokusi&nbsp; na koje je delovala selekcija,&nbsp; determinisali<br />agronomski značajna svojstva&nbsp; koja su na direktan ili indirektan način&nbsp; uticala na<br />povećanje prinosa elitnih sorti soje u specifičnim agroklimatskim uslovima gajenja.<br />Rezultati istraživanja su takođe ukazali da E1 gen, koji ima važnu ulogu u regulisanju<br />vremena cvetanja i sazrevanja kod soje, ili region u okolini ovog gena, verovatno ima<br />glavni&nbsp; uticaj&nbsp; na&nbsp; adaptaciju&nbsp; na&nbsp; agroklimatske&nbsp; uslove&nbsp; područja&nbsp; centralne&nbsp; i&nbsp; istočne<br />Evrope. Takođe se pretpostavlja da je najveći broj selektivno značajnih gena imao<br />regulatornu ulogu, delujući kao&nbsp; transkripcioni faktori, kao i ulogu u&nbsp; procesima<br />transporta.&nbsp; Identifikovani&nbsp; selektivno&nbsp; značajni&nbsp; genomski&nbsp; regioni&nbsp; u&nbsp; okviru<br />oplemenjivačkog programa mogu imati praktičnu primenu u povećanju efikasnosti<br />oplemenjivanja u narednom periodu.</p> / <p>The identification of genomic regions affected by selection during breeding of soybean<br />(<em>Glycine max</em> (L.) Merr.) may indicate the positions of important agronomic traits<br />genes or genes underlying adaptation to a specific target environment. This study<br />investigated the effects of breeding in Central-East European environments by a<br /><em>hitchhiking </em>mapping approach and pedigree analysis. Population genetic principles<br />were applied to microsatellite markers using multiple outlier detection tests. The<br />analysed populations comprised ancestral genotypes and elite varieties, developed at<br />the Institute of Field and Vegetable Crops, Novi Sad. The pedigree analysis confirmed<br />narrow genetic base of elite genotypes. As a result of long-term breeding, all analysed<br />parameters showed significant reduction in genetic diversity in the elite population,<br />compared to the ancestral. Specific population structure of analysed varieties, which<br />has been largely influenced by the pedigree, probably caused a low level of genetic<br />differentiation between the populations. Using at least two approaches, nine markers<br />were considered as strong positive selection candidates, indicating regions involved in<br />the adaptation to Central-East Europe environments. Also, an excess of linkage<br />disequilibrium was confirmed in the elite population, probably caused by selection.<br /><em>Bottleneck</em> tests provided evidence of population bottlenecks only for the candidate<br />positive selection loci in the elite population, suggesting that selection might shaped<br />the pattern of genetic diversity in these regions. The co-localisation analysis of the<br />candidate positive selection loci and previously mapped quantitative trait loci (QTLs),<br />identified in total 264 QTLs in selectively important genomic regions. The highest<br />number of identified QTLs had impact on the reproductive period.<em> In silico </em>analysis<br />revealed a high level of agreement between the identified QTLs and the traits expected<br />to be under selection during soybean breeding, indicating that selection was mostly<br />directed towards increasing the yield of elite varieties in a specific environmental<br />conditions. Furthermore, E1 gene that controls flowering time and maturity in soybean,<br />or its surrounding region, seems to be a major contributor for adaptation to<br />environmental conditions of Central-East Europe. It is assumed that most of the<br />selectively important genes had regulatory role, acting as transcription factors, as well<br />as a role in the processes of transport. The identified selectively important genomic<br />regions in a specific breeding program could have practical importance for future<br />breeding and yield improvement.</p>

O MHC é uma região genômica que contém genes de papel central na resposta imune adaptativa. Genes do MHC e, particularmente, genes HLA em humanos, estão envolvidos susceptibilidade e resistência a doenças infecciosas, na predisposição a doenças autoimunes e na rejeição de órgãos transplantados. Essas descobertas incentivaram uma série de estudos sobre padrões da variabilidade genética em genes HLA, que demonstraram possuir uma variação bastante distinta da expectativa neutra. Essa contundente evidência de seleção natural, ímpar no genoma humano, levanta uma série de perguntas a respeito das forças evolutivas específicas que agem nesses genes e as implicações genômicas para a evolução da região como um todo. O presente estudo investiga como a seleção natural afeta e é afetada pela diversidade de genes que estão ligados fisicamente a outros que constituem alvos de seleção. Nossa expectativa é que seleção balanceadora forte sobre genes HLA interfere na eficácia com que a seleção purificadora remove variantes deletérias em loci próximos. Especificamente, a partir da anotação funcional de variantes genéticas, testamos se grupos de genes ligados fisicamente aos genes HLA apresentam uma diversidade mais alta do que seria esperado na ausência de seleção balanceadora e de carona genética causada por ela, e se essa diversidade é enriquecida com variantes possivelmente deletérias. Por meio da análise de razão entre polimorfismos não-sinônimos e sinônimos (e diversas outras estatísticas relacionadas), fomos capazes de observar que loci próximos a genes HLA acumulam um excesso de variação não-sinônima (e portanto potencialmente deletéria). O grau de deleteriedade foi confirmado pelo emprego do software Polyphen 2, que utiliza como critério de classificação a conservação das sequências nucleotídicas e informação das estruturas protéicas, e pela análise de estatísticas como Pdel/Pn e Pdel/Ps. De acordo com testes de McDonald-Kreitman e o Índice de Neutralidade, entretanto, parte dessa variação deletéria se fixa em longo prazo, o que sugere que a seleção em genes HLA pode interferir tanto nos padrões de polimorfismos como de divergência / The MHC is a genomic region that contains genes with a central role in the adaptive immune response. Genes in the MHC region, in particular the HLA genes of humans, are involved in the differential susceptibility and resistance to infectious diseases, predisposition to autoimmune diseases and the rejection of transplanted organs. These findings have fueled a series of studies on patterns of genetic variation at HLA genes, which have conclusively demonstrated that their variation deviates from neutral expectations. Such strong evidence of natural selection, with few counterparts in the remainder of the human genome, raise a series of questions concerning the specific evolutionary forces acting on this region and their genomic implications for the evolution of the region as a whole. This work investigates how natural selection affects and is affected by the diversity of genes that are physically linked to those that are units of selection. Our expectation is that strong selection on HLA genes may interfere with the efficacy of selection in removing deleterious variants at closely linked loci. Specifically, by using functional annotations of genetic variants, we test whether sets of genes physically linked to the strongly selected HLA loci show a higher diversity than would be expected in the absence of balancing selection and genetic hitchhiking caused by it, and if this diversity is enriched for putatively deleterious variants. By analyzing the ratio of nonsynonymous to synonymous polymorphisms (and several related statistics) we were able to show that loci close to HLA genes are harboring an excess of nonsynonymous (and hence potentially deleterious) variation. The deleteriousness was confirmed by employing Polyphen 2 - a software that uses nucleotide sequence conservation and protein structure information to classify variants as deleterious or not - and computing statistics such as Pdel/Pn and Pdel/Ps. According to McDonald-Kreitman tests and the Neutrality Index, however, part of this putatively deleterious variation reaches fixation over long timespans, suggesting that selection at the HLA genes may be interfering with both the transient patterns of polymorphism and substitution processes

O MHC é uma região genômica que contém genes de papel central na resposta imune adaptativa. Genes do MHC e, particularmente, genes HLA em humanos, estão envolvidos susceptibilidade e resistência a doenças infecciosas, na predisposição a doenças autoimunes e na rejeição de órgãos transplantados. Essas descobertas incentivaram uma série de estudos sobre padrões da variabilidade genética em genes HLA, que demonstraram possuir uma variação bastante distinta da expectativa neutra. Essa contundente evidência de seleção natural, ímpar no genoma humano, levanta uma série de perguntas a respeito das forças evolutivas específicas que agem nesses genes e as implicações genômicas para a evolução da região como um todo. O presente estudo investiga como a seleção natural afeta e é afetada pela diversidade de genes que estão ligados fisicamente a outros que constituem alvos de seleção. Nossa expectativa é que seleção balanceadora forte sobre genes HLA interfere na eficácia com que a seleção purificadora remove variantes deletérias em loci próximos. Especificamente, a partir da anotação funcional de variantes genéticas, testamos se grupos de genes ligados fisicamente aos genes HLA apresentam uma diversidade mais alta do que seria esperado na ausência de seleção balanceadora e de carona genética causada por ela, e se essa diversidade é enriquecida com variantes possivelmente deletérias. Por meio da análise de razão entre polimorfismos não-sinônimos e sinônimos (e diversas outras estatísticas relacionadas), fomos capazes de observar que loci próximos a genes HLA acumulam um excesso de variação não-sinônima (e portanto potencialmente deletéria). O grau de deleteriedade foi confirmado pelo emprego do software Polyphen 2, que utiliza como critério de classificação a conservação das sequências nucleotídicas e informação das estruturas protéicas, e pela análise de estatísticas como Pdel/Pn e Pdel/Ps. De acordo com testes de McDonald-Kreitman e o Índice de Neutralidade, entretanto, parte dessa variação deletéria se fixa em longo prazo, o que sugere que a seleção em genes HLA pode interferir tanto nos padrões de polimorfismos como de divergência / The MHC is a genomic region that contains genes with a central role in the adaptive immune response. Genes in the MHC region, in particular the HLA genes of humans, are involved in the differential susceptibility and resistance to infectious diseases, predisposition to autoimmune diseases and the rejection of transplanted organs. These findings have fueled a series of studies on patterns of genetic variation at HLA genes, which have conclusively demonstrated that their variation deviates from neutral expectations. Such strong evidence of natural selection, with few counterparts in the remainder of the human genome, raise a series of questions concerning the specific evolutionary forces acting on this region and their genomic implications for the evolution of the region as a whole. This work investigates how natural selection affects and is affected by the diversity of genes that are physically linked to those that are units of selection. Our expectation is that strong selection on HLA genes may interfere with the efficacy of selection in removing deleterious variants at closely linked loci. Specifically, by using functional annotations of genetic variants, we test whether sets of genes physically linked to the strongly selected HLA loci show a higher diversity than would be expected in the absence of balancing selection and genetic hitchhiking caused by it, and if this diversity is enriched for putatively deleterious variants. By analyzing the ratio of nonsynonymous to synonymous polymorphisms (and several related statistics) we were able to show that loci close to HLA genes are harboring an excess of nonsynonymous (and hence potentially deleterious) variation. The deleteriousness was confirmed by employing Polyphen 2 - a software that uses nucleotide sequence conservation and protein structure information to classify variants as deleterious or not - and computing statistics such as Pdel/Pn and Pdel/Ps. According to McDonald-Kreitman tests and the Neutrality Index, however, part of this putatively deleterious variation reaches fixation over long timespans, suggesting that selection at the HLA genes may be interfering with both the transient patterns of polymorphism and substitution processes

This thesis muddies the idea of singular being, tracing the footprints of nature writer and poet Edward Thomas, from the beginning of his epically creative final four years, to the site where he died in 1917, during the Battle of Arras. It is presented as a series of engagements with landscape, writing, and poetry; affective mapping, chasing memory-prompts, bookmarks and the shock of the poetic. The journeys seek to return to an ‘open’ idea of the geographical imagination, negating a negative, reductionist form of geography; shifting the focus away from sociologically determined notions of mobility. A resident of England for all his life, but with Welsh heritage, Edward Thomas believed he belonged nowhere. His texts: little time capsules, admixtures of social commentary, environmental action, and personal musings, are archaeological exercises, presenting a complicated picture of loss, demonstrating the value of artistic imagination. Loss - and subsequent estrangement from the world - would become his poetic source. This thesis is about trying to understand the relationship between poetry - indeed all ‘land writing’ - and place. How it affects in-place, what it does in-place? To understand this relationship properly it was necessary to consider why, as humans, we write? To find out what the subjective condition of the poet, or writer, emerges out of - in order to relay the experience of meeting poetry in-place. Edward Thomas began as a nature writer and became a poet after much agonizing. This made him a useful subject (object) (neither). Furthermore he suffered a long period of introspection and had a knowledge of Freud and psychoanalysis - which he underwent in 1912. This was played out in what Edna Longley (2008) terms; ‘poetic psychodrama.’ His poems often feature a split self or switch between patient and analyst (Longley, 2008). The Other Man, is his doppelganger, who he plays himself off against: the poems are, as such, multi-voiced, counterpointed, intersubjective. Deleuze and Guattari wrote in A Thousand Plateaus (1988: 3): ‘since each of us was already several, there was already quite a crowd.’ Edward Thomas knew this all too well. From the beginning of this ambulatory homage my psyche became inextricably linked with his.

É o processo de mutação que, em última instância, introduz diversidade nas populações. Quando a mutação é pontual e segrega na população, recebe o nome de polimorfismo de nucleotídeo único (ou SNP, de Single Nucleotide Polymorphism). Caso esse SNP seja vantajoso, ele aumenta de frequência na população e estabelece um forte desequilíbrio de ligação com seus SNPs vizinhos, consequência do processo chamado de efeito de carona genética. Esse efeito pode ter duas consequências na proximidade dos sítios selecionados: (1) pode levar ao aumento de frequência de mutações neutras ligadas a mutação vantajosa ou (2) pode reduzir o tamanho efetivo da população Ne nessas regiões, e, consequentemente aumentar a importância da deriva genética na variação genética dessas regiões. Como consequência, é comum que a região próxima a sítios vantajosos apresente acúmulo de mutações neutras com frequências acima do esperado sob neutralidade. No entanto, a maior parte de novas mutações são deletérias e seria esperado que fossem removidas da população por seleção purificadora. Entretanto, como os padrões de variabilidade observados no genoma resultam de processos seletivos atuando em conjunto com a deriva genética, não é incomum SNPs fracamente deletérios atingirem frequências elevadas nos diferentes contextos de história demográfica e seletiva das populações. O acúmulo desses SNPs fracamente deletérios no genoma reduz progressivamente a aptidão média da população, o que representa um aumento de sua carga genética. Neste estudo investigamos se na vizinhança de sítios vantajosos selecionados há um acúmulo de SNPs deletérios, contribuindo para a carga genética da população. Para responder essa questão, dividimos nosso estudo em três passos. Primeiro, desenvolvemos uma nova metodologia para estimar a diferença na carga genética entre região vizinha a sítios selecionados e o resto do genoma. Nossa metodologia é mais robusta do que a tradicionalmente utilizada pois garante que a região influenciada pela seleção natural e o controle apresentem o mesmo número de SNPs, e possibilita controlar para variáveis confundidoras, como a frequência dos polimorfismos, permitindo explorar regiões alvo com diferentes características e reduzir resultados espúrios. Em seguida, utilizamos nossa metodologia para testar se a carga genética na região vizinha a sítios sob seleção positiva é maior do que no restante do genoma. Identificamos um acúmulo de SNPs deletérios em europeus e leste asiáticos para amostras do projeto 1000 genomas.Mostramos também que as mesmas regiões exploradas em populações sob efeito de seleção positiva não apresentaram carga genética aumentada em populações nas quais essas regiões não experimentaram seleção positiva. Por último, utilizamos essa mesma metodologia para avaliar a carga genética em genes sob seleção balanceadora, os genes clássicos do HLA de classe I. Esses genes compõe uma das famílias gênicas mais estudadas em humanos e para os quais existem evidências indicando os sítios específicos que estão sob seleção balanceadora. Nosso teste mostrou que as regiões vizinhas aos sítios sob seleção balanceadora dentro dos genes do HLA apresentam acúmulo de SNPs deletérios para pelo menos dois agrupamentos populacionais. Assim, com os três passos aqui descritos, conseguimos apontar o aumento da carga genética em regiões próximas a sítios sob dois regimes de seleção distintos, utilizando uma metodologia capaz de considerar características específicas das regiões estudadas / It is the mutation process that ultimately introduces diversity into populations. When a mutation is punctual and segregates in the population, it is called a single nucleotide polymorphism (SNP). If this mutation is advantageous, it increases in frequency in the population and creates strong linkage disequilibrium with its neighboring loci, as a consequence of the hitchhiking effect. This effect can have two consequences in the vicinity of the selected sites: (1) it can increase the frequency of neutral mutations linked to this advantageous mutation or (2) can reduce the effective population size Ne in the region around the selected site, and consequently increase the importance of genetic drift in the genetic variation of these regions. As a consequence, it is common that the region around sites under advantageous selection to accumulate more neutral mutations at high frequencies than expected under neutrality. However, most new mutation are deleterious and it is expected that these mutation will be removed from the population by purifying selection. However, since the patterns of variability observed in the genome result from selective processes interacting with genetic drift, it is common for weakly deleterious SNPs to reach high frequencies in different population demographic histories. The accumulation of these weakly deleterious SNPs in the genome progressively reduces the population\'s fitness, increasing their genetic load. In this study we investigated whether in the neighborhood of selected sites there is an accumulation of deleterious SNPs due to hitchhiking, contributing to the genetic load of the population. To answer this question, we divided our study into three steps. First, we developed a new methodology to estimate the genetic load difference between the region around selected sites and the rest of the genome. Our methodology is more robust than those traditionally used one because it ensures that both the region influenced by natural selection and control have the same number of SNPs, reducing the probability of spurious results, and is flexible to different genome peculiarities, making it possible to explore target regions with different characteristics. We then used our methodology to test whether genetic load in the region around sites under positive selection is greater than in the rest of the genome. We found consistent evidence of an accumulation of deleterious SNPs in European and East Asian continental groups. We also showed that these same region do not present the same deleterious SNP accumulation in populations in which these region did not experience positive selection. Finally, we used this same methodology to evaluate the genetic load in genes under the balancing selection, the classic HLA class I genes. These genes are one of the most studied in humans and there is evidence that indicates the specific sites within these genes that are under balancing selection. We found that the regions around these sites under balancing selection within the HLA genes had deleterious SNPs accumulating for at least two continental groups. Thus, with the three steps described here, we were able to point out the increase of genetic load in regions around selected sites for two distinct selective regimes using a methodology that takes into account specific characteristics of the studied regions

Η περιέλιξη του σώματος είναι ένα φαινόμενο που συναντάται αποκλειστικά στα Γαστερόποδα και παρουσιάζει ιδιαίτερο ενδιαφέρον για τη γενετική, την εξελικτική και την αναπτυξιακή βιολογία. Η κατεύθυνση της περιέλιξης (δεξιόστροφη ή αριστερόστροφη) καθορίζεται από ένα άγνωστο γονίδιο, το οποίο παρουσιάζει μητρικό επηρεασμό. Στα περισσότερα είδη, τα άτομα αντίστροφης περιέλιξης δεν μπορούν να ζευγαρώσουν, συνεπώς η αλλαγή στην κατεύθυνση της περιέλιξης προκαλεί αναπαραγωγική απομόνωση. Η συντριπτική πλειονότητα των ειδών στο γένος Albinaria έχει αριστερόστροφη περιέλιξη. Οι μόνες δεξιόστροφες μορφές εμφανίζονται αποκλειστικά στη νότια Πελοπόννησο. Όλες οι δεξιόστροφες μορφές θεωρείται, με βάση τα μορφολογικά δεδομένα, ότι ανήκουν σε ένα είδος, το Albinaria voithii. Ωστόσο, επειδή η μορφολογική και η γενετική διαφοροποίηση στα χερσαία μαλάκια και ειδικότερα στο γένος Albinaria συχνά δείχνει αντικρουόμενα αποτελέσματα και καθώς δεν υπάρχουν στοιχεία σχετικά με τη φυλογένεση του συγκεκριμένου ζώου, δεν έχει αποσαφηνιστεί εάν όλοι οι δεξιόστροφοι πληθυσμοί συγκροτούν μία μονοφυλετική ομάδα και αν η αντιστροφή της περιέλιξης συνέβη μία ή περισσότερες φορές. Επιπλέον, πολλές φορές τα δεξιόστροφα άτομα ζουν συμπάτρια με αριστερόστροφα, αλλά σπανίως διασταυρώνονται με αυτά. Προκύπτει έτσι το ερώτημα εάν η αντιστροφή της περιέλιξης εμφανίστηκε ως ένα μέσο μείωσης της γονιδιακής ροής για να αποφευχθεί η δημιουργία υβριδίων με χαμηλή αρμοστικότητα. Σε αυτήν την εργασία ελέγξαμε εάν οι δεξιόστροφοι πληθυσμοί της Albinaria συγκροτούν μια μονοφυλετική ομάδα και εάν αντιστοίχως το φαινόμενο της αντιστροφής της περιέλιξης έχει συμβεί μία ή περισσότερες ανεξάρτητες φορές. Για το σκοπό αυτό χρησιμοποιήσαμε αριστερόστροφα και δεξιόστροφα άτομα που συλλέχθηκαν από 25 τοποθεσίες της Πελοποννήσου. Στις 10 περιοχές υπήρχαν μόνο αριστερόστροφοι αντιπρόσωποι, στις 8 μόνο δεξιόστροφοι, ενώ στις υπόλοιπες 7 περιοχές υπήρχε συμπάτρια παρουσία αριστερόστροφων και δεξιόστροφων πληθυσμών. Η εκτίμηση της γενετικής ποικιλότητας και ο προσδιορισμός των φυλογενετικών σχέσεων αυτών των πληθυσμών έγινε χρησιμοποιώντας έναν πυρηνικό (ITS1) και δύο μιτοχονδριακούς μοριακούς δείκτες (COΙ και 16S). Οι φυλογενετικές αναλύσεις του πυρηνικού και των μιτοχονδριακών δεικτών οδήγησαν στην παραγωγή δέντρων ανόμοιας τοπολογίας. Τα δέντρα των μιτοχονδριακών δεικτών έχουν τρεις δεξιόστροφους και τρεις αριστερόστροφους κλάδους, ενώ στα δέντρα του πυρηνικού υπάρχουν δύο αριστερόστροφοι κλάδοι, ένας δεξιόστροφος και ένας με αριστερόστροφα και δεξιόστροφα άτομα. Από τις φυλογενετικές αναλύσεις του πυρηνικού δείκτη συμπεραίνουμε ότι τα δεξιόστροφα άτομα δεν συγκροτούν μία μονοφυλετική ομάδα και ότι η δεξιοστροφία στο γένος Albinaria έχει εμφανιστεί ανεξάρτητα τουλάχιστον δύο φορές, καθώς τα δεξιόστροφα άτομα τοποθετούνται σε δύο διαφορετικούς κλάδους, αλλά το δεξιόστροφο αλληλόμορφο εμφανίστηκε μόνο μία φορά. Επίσης, η εμφάνιση της δεξιοστροφίας πρέπει να είναι ένα παλιό εξελικτικό γεγονός που συνέβη πριν από αρκετά εκατομμύρια χρόνια, καθώς τα συμπάτρια αριστερόστροφα και δεξιόστροφα άτομα δεν έχουν πρόσφατο κοινό πρόγονο. Ακόμα, μπορούμε να συμπεράνουμε ότι δεν υπάρχει γονιδιακή ροή ανάμεσα στα συμπάτρια δεξιόστροφα και αριστερόστροφα άτομα, επειδή αυτά τοποθετούνται σε διαφορετικούς κλάδους. Μία πιθανή ερμηνεία της τοπολογίας του δέντρου των μιτοχονδριακών δεικτών είναι ότι ο μητρικός κυτταροπλασματικός παράγοντας που καθορίζει την κατεύθυνση της περιέλιξης στο έμβρυο, πιθανώς συμπαρασύρει τη μεταβίβαση ενός τύπου μιτοχονδρίου. / Body coiling is a phenomenon occurring exclusively in gastropods and it has important implications for their genetics, evolution and development. The direction of coiling (dextral or sinistral) is determined by an unknown gene that has maternal effect. In most species, individuals with reverse coiling cannot mate, thus the inversion of coiling might cause reproductive isolation. The vast majority of species and populations in the pulmonate genus Albinaria coil sinistrally. The only dextral morphs can be found restricted in southern Peloponissos and according to their morphology they belong to a single species, Albinaria voithii. However, morphological and genetic differentiation in mollusks, (especially in genus Albinaria), often show conflicting results and since phylogenetic studies are lacking, it is not clear whether all dextral populations form a monophyletic group and if the inversion of coiling has occurred more than once. Moreover, dextral populations are often found in sympatry with sinistral ones, but rarely mate with them. Therefore, it is interesting to examine if the inversion of coiling emerged as a means to reduce gene flow and the production of unfitted hybrids. In this study we tested whether dextral populations form a monophyletic group and if the inversion of coiling occurred independently more than once. For this purpose we used dextral and sinistral individuals collected from 25 localities in Peloponissos. In 10 localities there were only sinistral populations, in 8 only dextral ones, while in the remaining 7 localities sympatric sinistral and dextral populations were found. The assessment of genetic diversity and the determination of phylogenetic relationships of these populations were performed using a nuclear (ITS1) and two mitochondrial markers (COI and 16S). Phylogenetic analyses of nuclear and mitochondrial markers produced trees with different topologies. Trees of mitochondrial markers have three dextral and three sinistral clades, whereas the trees of nuclear marker have two sinistral clades, one dextral and one clade with both sinistral and dextral individuals. From the phylogenetic analyses of the nuclear marker we can conclude that dextral individuals do not form a monophyletic group and that dextrality has evolved independently at least twice within the genus Albinaria, as dextral individuals are placed in two different clades. However, it seems that the dextral allele appeared only once. Also, the evolution of dextrality must be an old evolutionary event that occurred before several million years, because sympatric sinistral and dextral individuals do not share a recent common ancestor. Moreover, we can conclude that there is no gene flow between sympatric dextral and sinistral individuals because they are placed in different clades. A possible scenario that explains the topology of the tree of mitochondrial markers is that the maternal cytoplasmic factor that determines the direction of coiling in the embryo probably causes the inheritance of mitochondria of a certain type.

abstract: Building mathematical models and examining the compatibility of their theoretical predictions with empirical data are important for our understanding of evolution. The rapidly increasing amounts of genomic data on polymorphisms greatly motivate evolutionary biologists to find targets of positive selection. Although intensive mathematical and statistical studies for characterizing signatures of positive selection have been conducted to identify targets of positive selection, relatively little is known about the effects of other evolutionary forces on signatures of positive selection. In this dissertation, I investigate the effects of various evolutionary factors, including purifying selection and population demography, on signatures of positive selection. Specifically, the effects on two highly used methods for detecting positive selection, one by Wright's Fst and its analogues and the other by footprints of genetic hitchhiking, are investigated. In Chapters 2 and 3, the effect of purifying selection on Fst is studied. The results show that purifying selection intensity greatly affects Fst by modulating allele frequencies across populations. The footprints of genetic hitchhiking in a geographically structured population are studied in Chapter 4. The results demonstrate that footprints of genetic hitchhiking are significantly influenced by geographic structure, which may help scientists to infer the origin and spread of the beneficial allele. In Chapter 5, the stochastic dynamics of a hitchhiking allele are studied using the diffusion process of genetic hitchhiking conditioned on the fixation of the beneficial allele. Explicit formulae for the conditioned two-locus diffusion process of genetic hitchhiking are derived and stochastic aspects of genetic hitchhiking are investigated. The results in this dissertation show that it is essential to model the interaction of neutral and selective forces for correct identification of the targets of positive selection. / Dissertation/Thesis / Ph.D. Biology 2011

Recent studies have demonstrated that phages can be co-transported with motile non-host bacteria, thereby enabling their invasion of biofilms and control of biofilm composition. Here, we developed a novel approach to isolate non-host bacteria able to co-transport phages from soil. It is based on the capability of phage-carrying non-host bacteria to move along mycelia out of soil and form colonies in plaques of their co-transported phages. The approach was tested using two model phages of differing surface hydrophobicity, i.e., hydrophobic Escherichia virus T4 (T4) and hydrophilic Pseudoalteromonas phage HS2 (HS2). The phages were mixed into soil and allowed to be transported by soil bacteria along the mycelia of Pythium ultimum. Five phage-carrying bacterial species were isolated (Viridibacillus sp., Enterobacter sp., Serratia sp., Bacillus sp., Janthinobacterium sp.). These bacteria exhibited phage adsorption efficiencies of ≈90–95% for hydrophobic T4 and 30–95% for hydrophilic HS2. The phage adsorption efficiency of Viridibacillus sp. was ≈95% for both phages and twofold higher than T4-or HS2-adsorption to their respective hosts, qualifying Viridibacillus sp. as a potential super carrier for phages. Our approach offers an effective and target-specific way to identify and isolate phage-carrying bacteria in natural and man-made environments.

Les bases génétiques et l'histoire de la différenciation adaptative ont été étudiées chez les moules du complexe d'espèces Mytilus edulis qui représente un modèle d'étude intéressant pour mieux comprendre comment se propage et se distribue la différenciation adaptative en population structurée. Grâce à la technique AFLP, une approche de génomique des populations (« scan génomique ») a été utilisée pour mesurer la différenciation entre des populations isolées sur des échelles de temps et d'espaces contrastées. Notre objectif était de vérifier si la différenciation génétique n'avait pas une origine plus complexe qu'habituellement proposé. Trois parties s'articulent autour de cette question centrale. La première s'intéresse à la différenciation entre l'Atlantique et la Méditerranée chez l'espèce M. galloprovincialis et a montré que la structure génétique était la conséquence d'un différentiel d'introgression avec l'espèce sœur M. edulis. Dans la deuxième partie de ce travail nous avons mis en évidence qu'une sélection directe, soit balancée soit intermittente, sur un polymorphisme pré-existant expliquait le niveau de différenciation anormalement élevé d'un gène de l'immunité entre populations de la côte européenne chez M. edulis. Enfin, la troisième partie s'est intéressée à revisiter un exemple classique de la littérature de la génétique des populations: le cas des M. edulis du détroit de Long Island et a permis de suggérer que la structure observée à très petite échelle spatiale correspondait probablement à un contact secondaire entre des moules européennes introduites et les moules américaines. D'une manière générale nos résultats démontrent que, quelque soit l'échelle à laquelle nous nous plaçons, la différentiation génétique tire son origine d'une histoire souvent plus complexe qu'attendu. / The genetic basis and history of adaptive differentiation were studied in the species complex M. edulis which is an interesting model system to understand how adaptive differentiation spreads and structure itself in subdivided populations. Using the AFLP technique, a genome scan approach was undertaken to measure differentiation between populations on contrasted spacial and temporal scales. Our objective was to verify wether the origin of genetic differentiation could be more complex than anticipated. This question was addressed in three chapters. The first one focuses on the differentiation between populations of the Atlantic Ocean and Mediterranean Sea in M. galloprovincialis. Our results show that the genetic structure was the result of differential introgression with the sister hybridizing species M. edulis. In the second chapter of this work we demonstrated that direct selection on a pre-existing polymorphism explained the unusually high level of differentiation at a defensin locus between populations of the European coast in M. edulis. Finally, in the third chapter we revisited a classic example of the population genetics literature: the aminopeptidase cline in M. edulis populations of the Long Island Sound. We obtained evidence that the genetic differentiation observed at a very fine spatial scale in the sound was the consequence of a secondary contact between introduced mussels from Europe and indigenous American mussels. Whatever the spatio-temporal scale at which we analyzed genetic differentiation, its origin proved to originate from an unsuspectedly long and complex history.

Les génomes sont affectés par des régimes de sélection conflictuels. Ceci est particulièrement bien illustré par le concept de barrière semi-perméable au flux génique, issu de la littérature des zones hybrides. Certains gènes contribuent à empêcher le mélange entre lignées génétiques différenciées, soit parce qu'ils participent à l'adaptation aux conditions environnementales locales, soit parce qu'ils sont incompatibles avec les gènes d'autres lignées. D'autres parties du génome sont soit neutres, soit soumises à une sélection qui tend à homogénéiser les différentes lignées entre elles. Dans la première partie de cette thèse, des modèles d'évolution de l'isolement reproductif sont présentés pour expliquer les patrons d'isolements observés dans les expériences d'hybridation au laboratoire. Par modélisation classique d'incompatibilités génétiques de type Dobzhansky-Muller, il est montré que l'asymétrie et la complexité des incompatibilités sont imparfaitement expliquées par un filtre évolutif, c.a.d. une vitesse d'accumulation différente entre types d'incompatibilité. Une approche complémentaire de modélisation quantitative à l'aide d'une extension du modèle géométrique de Fisher a permis de préciser quelles conditions de divergence entre lignées isolées conduisaient à un effet fortement délétère des mutations dans les génotypes hybrides. L'importance relative du niveau d'épistasie moyen, de la distribution des effets des mutations et des modalités de l'adaptation de chaque lignée est discutée. La seconde partie de cette thèse profite des avancées techniques de la génomique pour étudier l'histoire de la spéciation et de l'adaptation dans un complexe d'espèces non-modèles, les moules du genre Mytilus. Une méthode statistique d'inférence de scénarios de spéciation est présentée. Les résultats montrent que les moules Européennes ont connu une histoire complexe de divergence stricte suivie d'une période de connectivité périodique. En accord avec le concept de barrière semi-perméable au flux génique, il est montré que les taux d'introgression sont hétérogènes le long du génome. Ensuite, des scans génomiques de la différenciation ont été menés entre paires de populations du complexe d'espèces. L'analyse de la variation génétique et des généalogies d'allèles sur une échelle chromosomique localisée a permis de reconstituer l'histoire évolutive de plus de 1000 régions du génome des moules. Cette analyse a révélé qu'une cause majeure, mais insoupçonnée, de la différenciation génétique intraspécifique est l'introgression différentielle d'allèles étrangers. Globalement, cette thèse montre non seulement le rôle majeur de la biogéographie de la spéciation, c.a.d. des patrons temporels et spatiaux du flux de gènes, dans notre compréhension de la biodiversité actuelle, mais aussi sa surprenante complexité et l'étendue de ses conséquences sur l'évolution des génomes. / Genomes are affected by conflicting selective regimes. This is particularly well illustrated by the concept of semi-permeable barriers to gene flow, as found in the hybrid zones literature. Some genes contribute to the prevention of mixing between differentiated genetic lineages, either because they are involved in adaptation to local environmental conditions, or because they are incompatible with alleles from other genetic lineages. Other parts of the genome are either neutral, or subjected to selection which tends to homogenize the genetic lineages. In the first part of this thesis, models of the evolution of reproductive isolation are presented to explain the isolation patterns observed in experimental hybridizing crosses between incipient species. Using standard models of Dobzhansky-Muller genetic incompatibilities, it is shown that the asymmetry and complexity of incompatibilities are not well explained by there being an “evolutionary sieve”, i.e. a different rate of accumulation between incompatibilities. A complementary approach to quantitative modeling (an extension of Fisher's Geometric Model) then clarifies which conditions of divergence between allopatric lines led to highly deleterious effects in hybrid genotypes. The relative importance of mean levels of fitness epistasis, the distribution of mutation sizes, and the way lineages adapt to new environmental conditions is discussed. The second part of this thesis takes advantage of technical advances in genomics to study the history of speciation and adaptation in a non-model species complex, Mytilus mussels. A statistical method of inferring speciation scenarios is presented. Results show that European mussels experienced a complex history of strict divergence followed by a period of periodic connectivity. In agreement with the concept of semi-permeable barriers to gene flow, it is shown that introgression rates are heterogeneous along the genome. Next, genome scans of differentiation were conducted between pairs of populations of the species complex. The analysis of genetic variation and allele genealogies on a small chromosomal scale allowed to reconstruct the evolutionary history of more than 1000 genomic regions. This analysis reveals that a major cause of intraspecific differentiation is the differential introgression of foreign alleles. Overall, this thesis shows not only that biogeography of speciation, i.e. the temporal and spatial patterns of gene flow, play a major role in our understanding of existing biodiversity, but also its amazing complexity and extent of its impact on genome evolution.