Indiana University-Purdue University Indianapolis (IUPUI) / 2022-08-31

Analyzing regions in the genome with low levels of recombination helps understand the prevalence of sexual reproduction. Here, I show that variability in regions of reduced recombination in Drosophila can be explained by interference among strongly deleterious mutations; selection becomes progressively less effective in influencing the behaviour of neighbouring sites as the number of closely linked sites on a chromosome increases. I also show that the accumulation of loss-of-function mutations on the neo-Y chromosome of Drosophila miranda is compatible with a model of selection against such mutations alone, without the need to invoke the action of selective sweeps. I describe the discovery of two new sex-linked genes in the plant Silene latifolia, SlCyt and SlX9/SlY9. SlCyt has been recently translocated from an autosome to the X and shows signs of a selective sweep. Its possible role in having caused recombination arrest between the evolving X and Y chromosome is discussed. SlX9 still has an intact Y-linked copy that is presumably functional. Nucleotide diversity at SlY9 is very low, whereas SlX9 has an unusually high diversity and shows signs of introgression from S. dioica into S. latifolia, but the effect of this seems very localized.

<p>The aim of this study was to investigate the forensic usefulness of various Y-chromosome short tandem repeat loci among South African sub-populations. Three different sets of Y-chromosome short tandem repeat loci were chosen for investigation.</p>

Y chromosome is due to its special characteristics the ideal tool of archaeogenetic studies. Its diversity is influenced by several factors and I analysed two of them (geographical location and subsistence). I generated SNPs and STRs data from several loci of samples from Slovakia (156 samples, 5 regions) and sub-Saharan Africa, where I analysed samples of sedentary farmers (481 samples, 18 regions) and nomadic pastorals (405 samples, 16 regions). Slovakia is situated at the meeting point of two migration ways. First of them was spread from the east to the west and is associated with enlargement of haplogroup R1a in Europe. The second came from the Iberian Peninsula eastward and is associated with enlargement of haplogroup R1b. Results of MDS graphs replicate the geographical map of Europe. Slovakia is situated in the middle of Russian, Balkanian and Iberian samples. Correlation between genetics and geographic distances is indicated by hierarchical AMOVA analysis and Mantel tests. Populations in sub-Saharan Africa differ from each other by the subsistence pattern. Different life style influence the diversity of the Y chromosome. Nomadic pastoralists and sedentary farmers share different haplogroups, for example, while haplogroup R1b was detected only in nomadic pastoral groups, sedentary farmers...

A análise do conteúdo gênico do cromossomo Y em 12 espécies de Drosophila com genoma sequenciado em 2008 mostrou que o Y é pouco conservado entre espécies e está em processo de aquisição de genes, o que contradiz o modelo atual de evolução de cromossomos sexuais que o descreve como um homólogo degenerado do X, com constante perda de genes. Este resultado inicial incitou o estudo espécies adicionais de Drosophila e de gêneros próximos. Uma dificuldade relevante para obtenção de espécimes é que muitos grupos taxonômicos de drosofilídeos não estão disponíveis nos &ldquo;stock-centers&rdquo;, e seus hábitos de vida são pouco conhecidos. Muitas espécies são encontradas na natureza associadas a fungos, flores, ou exsudados vegetais, e raramente são atraídas por isca com banana fermentada, que é o método usual de coleta de drosofilídeos. Os objetivos do presente trabalho foram: I) analisar o conteúdo gênico do cromossomo Y de drosofilídeos provenientes de substratos &ldquo;não usuais&rdquo;, II) determinar substratos de desenvolvimento larval e identificar espécies novas, e III) analisar a composição de bases de genes no Y. Os resultados revelam a natureza dinâmica de aquisição e perdas de genes do cromossomo Y na família Drosophilidae que, em poucos casos, inclui um movimento de todo o cromossomo (p.e., fusão do Y a um autossomo). Descrevemos uma nova espécie, Drosophila calatheae, cuja larva se desenvolve em flores do gênero Calathea (Marantaceae). Uma segunda espécie, provisoriamente codificada como Drosophila I4, e cujas larvas também se desenvolvem nessas flores, está em fase de descrição. A partir de análise morfológica, nenhuma dessas duas espécies pôde ser incluídas em algum dos grupos de espécies conhecidos. Uma filogenia molecular preliminar com dois genes do cromossomo Y (kl-3 and kl-5) sugere que ambas pertencem à radiação virilis-repleta e que D. calatheae tem relações (morfológicas e moleculares) com as espécies do grupo bromeliae. A análise do conteúdo GC de genes no Y mostrou que genes neste cromossomo são enriquecidos em AT em relação a genes autossômicos, e esta diferença na composição de bases é proporcional ao tempo que um gene está presente no Y. Portanto, o conteúdo GC pode servir como ferramenta no estudo da evolução do cromossomo Y ao determinar o estado ancestral de um gene (autossômico vs. ligado ao Y) e datar o movimento de genes entre esses dois compartimentos genômicos / The analyses of the Y chromosome gene content in 12 Drosophila species whose genome were sequenced in 2008 showed that the Y is not well conserved among species and is currently in the process of acquiring genes, contradicting the current model of sex chromosome evolution that describes the Y as a degenerate homolog of the X, in constant gene loss. This initial result prompted the study of additional Drosophila species and related genera. One of the difficulties in obtaining specimens is the fact that drosophilids from many taxonomic groups are not available in stock- centers and little is known about their ecology. Many species are found in nature associated with fungi, flowers, or plant exudates, and are rarely attracted to baits with fermented banana, the usual method of collecting drosophilids. The objectives of this study were: I) analysis of the Y chromosome gene content of species from \"unusual\" substrates, II) determination of drosophilids breeding / larval development sites, and III) analysis of the base composition of genes in the Y chromosome. The results emphasize the Y-chromosome dynamic nature of genes acquisition and loss in the family Drosophilidae, including a few cases of whole chromosome movements (p.e., Y-autosome fusion). We describe a new species, Drosophila calatheae, whose larvae develop in flowers of the genus Calathea (Marantaceae). Drosophila I4 (to be described) also breeds in these flowers. None of these two species could be included in a known taxonomic group of species. A phylogeny with two Y-chromosome genes (kl-3 and kl-5) suggests that they belong to the virilis-repleta radiation and D. calatheae is related to the bromeliae group. Analysis of base composition of Y-chromosome genes shows that they are AT-rich when compared to autosomal genes, and this difference is proportional to the time that a gene has been in the Y. Thus, GC content can be a tool to study the evolution of this chromosome

The domestic dog was probably the first domesticated animal, and the only one to spread to all continents in ancient times. The dog is one of the most phenotypically diverse animals, a result of human selection throughout dog history. Studies of the genetic origins and early spread of domestic dogs is important to gather information about biological and cultural mechanisms behind domestication but also to investigate early human history. The step from a hunter and gatherer lifestyle to farming is one of the most important steps in human history. In this thesis I will present work aimed at understanding both domestic dog origins and dispersal. In order to be able to investigate dog origins based on a second haploid chromosome we identified 14,437 bp of Y-chromosomal DNA sequence. Based on this we show that dogs in Asia south of Yangtze River (ASY) has the highest genetic diversity and was founded from a large number of wolf founders confirming earlier mtDNA results. Early dog dispersal is tightly coupled to human history with the dog brought along as a cultural item. We have for the first time investigated the dog dispersal into Polynesia and Australia and our data can be used as evidence for a more complex settlement of Polynesia than earlier indicated from archaeological and linguistic studies. Analysis of Y-chromosome SNPs in Australian dingoes confirms earlier mtDNA genetic studies that the dingo is part of the domestic dog phylogeny and was founded from a small population of domestic dogs. We have also for the first time investigated the dog population on Madagascar and our data strongly indicates a mainland African origin for the Madagascan dogs. Finally, we have investigated the American dog population sampled from throughout the continent and also for the first time included putative indigenous breed dogs such as Chihuahua and Pero Sín Pelo del Peru, and the free-ranging Carolina dogs from southern USA. Our data clearly indicates a primarily Old World origin for the indigenous breed dogs and also for the free-ranging Carolina dogs in USA. We can also for the first time present evidence for continuity between the ancient and extant dog population with e.g. exclusive sharing of a haplotype between a modern sample of Chihuahua and an ancient Mexican sample. / QC 20120510

published_or_final_version / Medical Sciences / Master / Master of Medical Sciences

SRY (Sex determining Region of Y chromosome) is the master gene initiating testis determination in mammals. To shed light on the molecular mechanism of SRY action during testicular differentiation, we examined the effects of TAT-HMG fusion protein on gonadal sex differentiation in culture. HMG is the DNA binding motif of SRY and "TAT" is a protein transduction domain. Each pair of CD1 mouse gonadal primordia at 11.5 days post coitum (dpc) was cultured with or without TAT-HMG dissolved in dimethyl sulfoxide (DMSO) up to 3 days. Immunocytochemical labeling and Real-time RT-PCR of Sry, Sox9 and Mis indicated that DMSO blocked testicular differentiation, Sertoli cell differentiation and testis cords formation, downstream of SRY. TUNEL showed a massive mesenchymal cell death, which might be responsible for disruption of testis cord formation. Treatment with TAT-HMG rescued Sertoli cell differentiation, probably by up regulation of Sry, but not testis cord formation or cell death.

Mapping studies of the centromeric region of the human Y chromosome Construction of a map of a human centromeric region is very important in order to understand the organisation of this essential part of the chromosome. A YAC contig map has been assembled of the pericentric 10 Mb of the human Y chromosome, giving coverage of Yp from the large X-Y homologous region through to the alphoid satellite of the centromere, and from the alphoid DNA to the proximal unique sequences on Yq. The Yp map has one remaining gap between TSPY1 and the AMELY region, while two gaps separate the satellite region on Yq from the other two contigs. After constructing the map, the known genes were localised to the region. One Yq gene, DFFRY, was discounted as a potential anti-Turner syndrome gene by analysis of rearranged Y chromosomes. Detection of a block of duplicated sequence on Yp led to the confirmation of the existence of an inversion polymorphism, which was then found to be correlated with a major subclass of sex-reversed individuals, who have X-Y chromosomal breakpoints within the inverted region. These results not only give a far more extensive and detailed map of this region than before, but also show that understanding the organisation of the region has important consequences for a number of genetic disorders.

The objective of this dissertation is the isolation of DNA sequences that are differentially represented in males and females of the Oriental fruit fly Bactrocera dorsalis, specifically by initiating a molecular characterization of Y chromosome sequences in this species. Cytological observations have established the presence of a diminutive Y chromosome in B. dorsalis males. To isolate DNA sequences from the Y chromosome, a special method of genomic DNA isolation known as Representational Difference Analysis (RDA) was utilized to obtain DNA sequences unique to the B. dorsalis male genome. Genomic DNA from B. dorsalis males served as the "tester" DNA and female genomic DNA as the "driver" DNA. Six distinct RDA products were obtained following two complete rounds of DNA hybridization and difference enrichment via the Polymerase Chain Reaction (PCR). One ofthese products (RDA product 1) was used to isolate a genomic DNA clone (3.1a) from a B. dorsalis male genomic DNA minilibrary. This sequence shows similarity to the reverse transcriptase of R1 retrotransposable elements. The presence of R1 elements in the Tephritid insects has heretofore been undescribed, although these elements have been previously described in the genomes of other Dipteran species. Oligonucleotide primers for PCR were designed for the 3.1a clone. These primers consistently produce different amplification patterns in PCRs ofgenomic DNA from B. dorsalis males vs. females. Amplification using male genomic DNA produces 325 bp and 2.6 kb products while only a 2.6 kb product is obtained from female DNA. The amplification products obtained with these primers are also produced in PCRs of genomic DNA from B. dorsalis embryos and third instar larvae, suggesting the ability of this method to infer sex at pre-adult stages ofthe B. dorsalis life cycle. Similar amplification products have also been obtained in other Bactrocera species. Both the 325 bp male PCR product and the 2.6 kb products have regions of sequence similarity to R1 elements. The 2.6 kb product contains a putative 1.7 kb open reading frame (ORF) encoding 583 amino acids. Three amino acid motifs found in Drosophila R1 element reverse transcriptases are present in comparable locations within the hypothetical ORF product. Both of these sequences are also repetitively represented in the B. dorsalis male and female genomes. However, the 325 bp male product produces some bands that are male specific when used as a probe for Southern blots of B. dorsalis male and female genomic DNA. The amplification pattern produced by the 3.1a primers is consistent with what would be expected if the 2.6 kb and 325 bp PCR products originated from the B. dorsalis X and Y chromosomes, respectively. Thus, the cloned male-specific sequence recovered here is potentially useful both as a gateway into the relatively uncharacterized B. dorsalis Y chromosome and as a tool for the characterization of other aspects of the B. dorsalis genome.