By increasing genomic size, whole-genome duplication (WGD) is considered a major source of evolutionary innovation and speciation. We examined sequence evolution and expression divergence following WGD in a tetraploid African clawed frog (\textit{Silurana}). We hypothesized that the redundancy generated by WGD might allow for sex-specific and/or tissue-specific divergence, contributing to sexual dimorphism in this frog, and that such changes could be detected at both the expression and sequence levels. We investigated this hypothesis with a transcriptome-based approach, comparing both sexes across brain, heart and liver. We compared molecular evolution and expression divergence of duplicate gene homeologs to singleton genes and to an extant diploid relative, and identified genes with evidence for sex-biased expression. In doing so, we provide evidence for an allopolyploid mechanism of WGD and speciation in \textit{Silurana}. Additionally, we find that female-biased gene expression is more prevalent among duplicate genes than male-biased expression, particularly in brain where expression levels are highest. We similarly identified antagonistically sex-biased homeologs with indication of positive selection. Our results indicate that divergent evolution at both the sequence and expression levels following WGD favors the co-option of female-biased gene expression and may help resolve sexually antagonistic selection in this frog, thereby facilitating the evolution of sexual dimorphism. / Thesis / Master of Science (MSc) / Whole-genome duplication (WGD) is considered a major source of evolutionary innovation and a driver of speciation. By increasing genetic content and introducing redundancy, selective pressures are reduced and paralogous pairs diverge. We investigate how sex and tissue type contribute to duplicate gene divergence following WGD in a tetraploid African clawed frog. We find evidence for sex-dependent variation in sex-biased expression patterns of duplicate genes in brain, heart and liver, and evaluate how molecular evolution of duplicate genes accounts for expression divergence between sexes. This thesis provides a general framework for investigating sex-biased duplicate gene evolution in an amphibious tetrapod.

Sex biased expression characterizes ~1,000 genes in mammalian liver, and impart sex differences in metabolism and disease susceptibility. The sex-dependent temporal patterns of pituitary growth hormone (GH) secretion, pulsatile in males and more continuous in females, are known to sex-differentially activate transcriptional regulators (TFs), leading to widespread sex-differences in the mouse liver transcriptome. This thesis elucidates sex-biased gene expression patterns in the following studies. Gene structures, expression patterns and species conservation are characterized for ~15,000 liver-expressed intergenic long noncoding RNAs (lncRNAs), many of which are novel. Analysis of intergenic lncRNA promoters revealed unexpected high conservation and significant enrichment of TF binding compared to protein-coding promoters. A subset of intergenic lncRNAs showed strong sex-specific and GH-dependent gene expression, and whose transcription was tightly correlated with the surrounding chromatin environment and TF binding patterns. The pervasive role of genetic factors to regulate sex-biased genes was revealed by analyzing livers with matched genotype and gene expression data from Diversity Outbred (DO) mice, an outbred population with high natural allelic variance derived from eight inbred strains. Significant associations between genetic variants and gene expression (eQTLs) were identified, including many eQTLs with a strong sex-biased association. Remarkably, a large fraction of these sex-biased eQTLs were linked to either gain or loss of sex-specific gene expression in the DO founder strain predicted to be regulated by the eQTL. Thus, genetic factors are a major contributor to the variability of sex-biased genes, which has important consequences related to the individual variability of liver phenotypes with known sex-differences. Natural genetic perturbations in DO mice were leveraged to identify candidate lncRNAs that may regulate hypophysectomy (hypox) responsiveness. Co-regulated protein-coding gene clusters were discovered based on gene expression correlations across DO mouse livers, many of which are enriched for distinct hypox response classes. LncRNAs whose expression showed unexpected significant negative correlation with protein-coding gene clusters enriched for genes of the opposite-sex bias and inverse hypox class were hypothesized to play negative regulatory role. In sum, these studies expand the characterization of the sex-biased hepatic transcriptome and reveal contributions of genetic factors to the regulation of sex bias in mammalian liver. / 2020-11-27T00:00:00Z

Today, groups considered Hispanic in the United States consist of populations whose complex genetic structures reflect intermixed diverse groups of people who came in contact during Spanish colonization in Latin America. After coming in contact and wiping out most of the Native Americans who occupied North and Latin America, the Spanish also introduced West African individuals for labor to begin developing crops to be shipped back to Europe, resulting in the Trans-Atlantic African slave trade. These migration events and differential gene flow among males and females that occurred throughout Latin America have led to populations that have been genetically transformed from what they were prior to Spanish arrival (Madrigal, 2006). Genetic research commonly refers to individuals considered Hispanic as "tri-hybrids" of Native American, European, and African ancestry (Bertoni et al., 2003; Gonz[aacute]lez-Andrade et al., 2007). This research focuses on populations from present-day Mexico, Puerto Rico, and Cuba, all of whom experienced various population histories as these three ancestral groups came in contact. Published genetic research demonstrates that individuals from Mexico tend to have the highest mean proportion of Native American ancestry, while Puerto Rican individuals have the highest mean proportion of European ancestry, and Cuban individuals have the highest mean proportion of African ancestry (Bonilla et al., 2005; Lisker et al., 1990; Mendizabal et al., 2008; Tang et al., 2007; Via et al., 2011). The present research utilizes craniometric data from these three groups to determine whether the cranial morphology reflects similar population relationships and mean ancestry proportions as found in genetic research through Mahalanobis distance (D2), canonical discriminant function, and normal mixture cluster analyses. Sex-biased ancestry asymmetry was also tested by separating each group by sex and running the same analyses. The results show that all three groups considered Hispanic (Mexico, Puerto Rico, and Cuba) are significantly different from each other; however, when proxy ancestral groups are included (Guatemalan Mayan, Indigenous Caribbean, Spanish, and West African), the Mexican and Guatemalan Mayan samples are the most similar, followed by the Mexican and Indigenous Caribbean samples and the Puerto Rican and Cuban samples. The results of the normal mixture analyses indicate that Mexico has the highest mean ancestry proportion of Native American (Guatemalan Mayan) (72.9%), while the Puerto Rican and Cuban samples both have a higher mean European ancestry proportion, with 81.34% and 73.6% respectively. While the Cuban sample is not reflective of the genetic research in regards to ancestry proportion results, with the highest proportion of African ancestry over European and Native American ancestry, it does have the highest proportion of African ancestry among the three groups (18.4%). When separated by sex, the results indicate that the Mexican and Puerto Rican samples may show some evidence in sex-biased ancestry proportions, with the male individuals having a larger proportion of European ancestry and the female individuals having a larger proportion of Native American or African ancestry. Cuba, on the other hand, does not follow this trend and instead displays a higher proportion of European ancestry in females and a higher proportion of Native American and African ancestry in the males. Techniques in the field of forensic anthropology in the United States are constantly being reanalyzed and restructured based on the changing demographics of the population, especially with the arrival of individuals from Latin America (Ennis et al., 2011). Recent samples of American Black and White individuals were included in the Mahalanobis distance (D2) and canonical discriminant function analyses in place of the ancestral proxy groups to determine the craniometric relationship of the groups within the United States. The results show that the Mexico and Guatemala samples are the most similar (D2=2.624), followed by the Cuba and American Black samples (D2=3.296) and the Puerto Rico and American White samples (D2=4.317), which each cluster together in pairs. These results reflect the population histories that took place during colonialism, with the largest amount of slave trade occurring in Cuba over the other two countries. From an applied perspective, clarification is needed in the biological definition of Hispanic and the degree of heterogeneity in each social group, as well as the relationship among groups, in order to accurately develop techniques in forensic anthropology for human identification.

Studies of the maternally inherited mitochondrial DNA in loggerhead sea turtles (Caretta caretta) demonstrate that females are philopatric, returning to nest in the region where they hatched. Eleven genetic stocks of maternal lineages have been identified in the Atlantic Ocean. An analysis of the conventionally-used 380 bp of the mitochondrial control region of a sample of individuals from the genetic stock of loggerheads in Mexico (N = 175) revealed 13 haplotypes. When a longer sequence read of 815 bp was analyzed, 17 haplotypes were uncovered. In the genetic stock of loggerheads in northwestern Florida (N = 25), three haplotypes were identified with both control region sequence lengths. Based on the currently known distributions of the three long CC-A1 and CC-A2 haplotypes, two of each are unique to Mexico. This makes the longer sequence reads useful for stock identification. Within Mexico, there was evidence of significant population structuring between Cozumel and the northern region of the sampling area on mainland Mexico (pairwise ϕST = 0.1003, p = 0.0197), but not after Bonferroni correction. A direct comparison of female and male nuclear microsatellite genotypes indicated male-biased dispersal between Mexico and northwestern Florida. Within Mexico, microsatellite analysis indicated significant structuring of females between sampling years and between the northern and the southern region of the sampling area on the mainland. Consequently, this genetic stock, while perhaps not in equilibrium, shows signs of female natal homing. An analysis of clutches indicated that significantly more clutches in Mexico had multiple paternity compared to the northwestern Florida (66% and 23%, respectively). The frequency of multiple paternity was not correlated with female abundance, nest density or sex ratio of reproductively successful individuals. There was no evidence of females benefiting through increased reproductive success from multiple paternity. This is consistent with other studies of sea turtles.

Die Beziehung zwischen Genen und Verhalten ist in der Evolutionsbiologie von besonderem Interesse. Bestimmte Verhaltensweisen können die genetische Struktur natürlicher Populationen gestalten, dadurch deren genetische Diversität verändern und so ihr evolutives Schicksal beeinflussen. Abwanderung aus der Geburtsgruppe ist eine dieser Verhaltensweisen. Sie beeinflusst Genfluss, dessen Ausmaß die genetische Struktur von Populationen bestimmt. Paviane (Gattung Papio) sind ein besonders interessantes Forschungssystem um die Beziehung zwischen Verhalten und populationsgenetischer Struktur zu untersuchen. Die Evolution der Paviane wurde sowohl von historischem als auch gegenwärtigem Genfluss geprägt. Innerhalb dieser Gattung treten sowohl die überwiegende Abwanderung von Männchen als auch die überwiegende Abwanderung von Weibchen auf. Zudem wurde ihre gegenwärtige Verbreitung maßgeblich von Populationsausbreitung und –rückzug beeinflusst und es tritt häufig Genfluss zwischen verschiedenen Arten auf. In meiner Doktorarbeit untersuchte ich, wie verschiedene Abwanderungsmuster den Genfluss bei Pavianen beeinflussen. Damit hoffe ich zu einem besseren Ver-ständnis der Wechselbeziehung zwischen Verhaltensökologie und Genetik in natürlichen Populationen beizutragen. Ich fokussierte mich darauf, wie Unterschiede in den Sozialsystemen unterschiedlicher Pavianarten deren genetische Struktur beeinflussen. Die beobachteten Muster nutzte ich, um auf das geschlechtsspezifische Abwanderungsmuster bei Guineapavianen zu schließen, eine der am wenigsten untersuchten Pavianarten. Zudem untersuchte ich, wie sowohl historischer als auch gegenwärtiger Genfluss die genetische Struktur der Guineapaviane formten und ob es möglich ist von der Populationsausbreitung der Paviane Rückschlüsse auf die menschliche Evolutionsgeschichte zu ziehen. Um diese Fragen zu beantworten nutzte ich einen populationsgenetischen Ansatz, basierend auf im gesamten Verbreitungsgebiet gesammelten Kotproben, deren exakter geographischer Ursprung bekannt war. Ich analysierte sowohl autosomale Mikrosatelliten als auch Sequenzen der mitochondrialen Hypervariablen Region I. Meine Ergebnisse zeigen, dass die genetische Struktur der Guineapaviane am besten durch die überwiegende Abwanderung von Weibchen erklärt werden kann, sowohl in einem lokalen als auch im globalen Kontext. Weiblicher Genfluss führt zu einer hohen Diversität innerhalb von Populationen sowie einem Fehlen von genetisch-geographischer Struktur in mitochondrialer DNA. Nukleäre DNA hingegen zeigt eine starke globale geographische Struktur und Männchen sind im Vergleich zu Weibchen durch eine stärkere lokale Struktur gekennzeichnet. Dies entspricht den Vorhersagen für ein System, in welchem hauptsächlich Weibchen abwandern und Männchen in ihrer Geburtsgruppe verbleiben. Insgesamt scheint lokal begrenzte Abwanderung den wirksamen Genfluss auf eine Distanz unter 200 km zu beschränken, was zu einem starken Isolation-durch-Distanz Effekt und genetisch differenzierten Populationen führt. Anzeichen für Populationsausbreitung, die graduelle Struktur genetischer Variation, und mögliche Hinweise auf das “Allele-surfing” Phänomen, deuten auf eine historische westwärts gerichtete Ausbreitung von Guineapavianen hin. Introgressive Hybridisierung mit benachbarten Anubispavianen könnte genetische Muster im Bereich der Kontaktzone erklären, muss aber im Detail noch untersucht werden. Zusätzlich konnte ich zeigen, dass Mantelpaviane vermutlich im gleichen Zeitraum des Späten Pleistozäns von Afrika nach Arabien wanderten, wie Hypothesen für den modernen Menschen vorschlagen. Meine Studie ist die erste umfassende Analyse der genetischen Populationsstruktur der Guineapaviane und liefert Belege für die überwiegende Abwanderung von Weibchen in dieser Art. Dies untersützt die Ansicht, dass das Sozialsystem der Guineapaviane einige vergleichbare Merkmale zum System der Mantelpaviane aufweist und deutet somit darauf hin, dass während der Evolution dieser beiden Arten besondere evolutionäre Drücke gewirkt haben, die sie von allen anderen Pavianarten abgrenzen. In Kombination mit dem starken Einfluss von Populationsausbreitungen auf ihre Verbreitung und genetische Diversität, bekräftigt meine Arbeit Paviane als interssanten analogen Modellorganismus, der helfen kann, die Prozesse die während der Evolution des Menschen maßgeblich waren, aufzuklären.

The goal of this study was to examine several aspects of the population genetics and population biology of the Nigeria-Cameroon chimpanzee at seven sampling locations in the south of Taraba State, Nigeria. Three of the sampling locations are within GGNP and two are situated just outside the southern boundary of GGNP. The final two sampling locations are found within Ngel Nyaki forest reserve, at each of the two forest fragments inside the reserve. Ngel Nyaki forest reserve was the focus of the study and the principal goal was to 16 determine if the community of chimpanzees at Ngel Nyaki forest reserve has become isolated from the chimpanzees at GGNP using microsatellite loci extracted from non-invasive sources of DNA. In Chapter two, the methods used to extract and amplify the DNA and the protocols used to confirm the genotypes are outlined. Chapter three examines the population structure of the chimpanzees among the regions sampled in this study, particularly addressing the question as to whether the chimpanzees at Ngel Nyaki forest reserve are isolated from the chimpanzees at GGNP. Chapter four investigates patterns of sex biased dispersal in the Nigeria-Cameroon chimpanzee. In Chapter five, population viability analysis is used to determine the fate of the chimpanzees at Ngel Nyaki forest reserve under a range of management scenarios. Chapter six summarizes the conclusions of the study and presents a conservation strategy to ensure the viability of the population of chimpanzees at Ngel Nyaki forest reserve.

Newts of the genus Taricha have long been studied due to the powerful neurotoxin found in their skin. Tetrodotoxin (TTX) acts by blocking receptors in sodium channels, ultimately resulting in death via asphyxiation. The only documented predators of species in this genus have been snakes of the genus Thamnophis. Recently, predation on Taricha in Ledson Marsh in Annadel State Park, Santa Rosa, CA was discovered. Predation was in the form of laceration or evisceration, and tracking of predation from 1998-2008 showed that it was male-biased. Two species of Taricha were found living sympatrically at this location, the California newt (T. torosa) and the rough-skinned newt (T. granulosa). Fluorometric High Phase Liquid Chromatography (HPLC) analysis was used in order to quantify TTX levels in the skin of ten male and ten female newts of each species. Quantification of TTX was done to determine the influence, if any, that TTX levels may have on sex-biased predation in this population. I predicted that levels of TTX would be greater in females than males, and greater in T. granulosa than T. torosa since very few T. granulosa were preyed upon during the study period. My results indicated that there were significant differences between the sexes, and T. torosa were significantly more toxic than T. granulosa. An in-depth ecological study of relative abundances of both species and identification of the predator are needed at this site to obtain a clear picture of the predator-prey dynamics at Ledson Marsh

Sexual dimorphism, i.e., differences in morphology, physiology, and behavior between conspecific males and females, is ubiquitous, extensive, and often species-specific, indicative of its rapidly evolving nature. Ever since Darwin first described a general theory of sexual selection to explain the extraordinary differences between males and females of the same species, biologists have proposed a variety of mechanisms ranging from runaway selection to good genes to sexual conflict. While a popular approach is studying the effects of sexual selection on different components of fitness, the results of these studies are generally difficult to interpret and are typically not generalizable across populations, let alone taxa. Recent advances in the “omics” field are transforming the way that we study patterns and processes involved in sexual selection. At the molecular level, sexual dimorphism is present in gene expression differences between the sexes, providing a powerful framework to study sexual selection. By studying genes that are sex-biased in expression, we will better understand the underlying genetic basis of traits that are sexually dimorphic. Alreadly, studies of sex-biased genes in model organisms, particularly Drosophila, have revealed that male-biased genes are among the most rapidly evolving functional classes of genes. However, while a number of intrinsic factors appear to correlate with evolutionary rate (e.g., gene expression level, codon bias), it is unclear whether any of these factors drive the rapid divergence of male-biased genes. Another important discovery is the prevalence of sex-biased gene expression. However, even with widespread sexual dimorphism at the phenotypic level, it remains unknown the extent to which sex-biased gene expression exists in humans and their primate relatives. In fact, studies of sexual dimorphism on a molecular level in primates have been very few, even though understanding this phenomenon in humans could further our knowledge of the nature of sex-biased phenotypes and diseases. In this thesis, I advance our knowledge of the genetic bases and mechanisms that shape sexual dimorphism. First, I review a classic framework that biologists have traditionally applied to define and partition fitness measures between males and females in the model system, Drosophila. Second, I apply a molecular framework to compare the relative roles of intrinsic factors on the evolutionary rate of rapidly evolving male-biased genes in Drosophila. Third, I review the current state of our knowledge of sexual dimorphism and sex-biased gene expression in humans. Fourth, I present a bioinformatics framework to identify the extent of sex-biased expression in primate tissue and to examine the selective forces involved in their evolution. Overall, I demonstrate the effectiveness of using a functional comparative genomics approach in studying the nature of sexual dimorphism at the molecular level across multiple taxa. / Biology

<p>The common shrew, <i>Sorex araneus</i>, has one of the most variable karyotypes among mammals, displaying numerous chromosomes races throughout its distribution, which can be categorized into different karyotypic groups. The objective of this thesis was to examine the postglacial population history of Fennoscandian common shrews using autosomal microsatellites, mitochondrial DNA (mtDNA) and a Y chromosome specific microsatellite (L8Y).</p><p>Autosomal microsatellites and mtDNA revealed weak genetic structure over a hybrid zone between the karyotypically divergent Northern and Western karyotypic groups. However, the genetic structure displayed by the Y chromosome microsatellite was orders of magnitude higher. Hence, considerable chromosomal differences between the groups do not prevent female gene flow, while male gene flow is reduced (cf. Haldane's rule). Further, the results suggest that the Haldane effect may be caused by the chromosomal differences between the karyotypic groups.</p><p>No mtDNA differentiation was observed either between chromosome races or between the Northern and Western karyotypic groups in Fennoscandia. The combined pattern of karyotypic and mtDNA variation of Fennoscandian common shrews, suggest bi-directional postglacial recolonisation from a single refugium in Europe. The variation of the Y-linked microsatellite supported this conclusion. In contrast, significant mtDNA structure, discordant with the karyotypic variation, revealed that common shrews in southern Finland belong to a different lineage than remaining Fennoscandian regions, implying postglacial recolonisation from a different source.</p><p>MtDNA variation of the chromosome races in Sweden supports the hypothesis that three races of the Western karyotypic group have been formed through whole arm reciprocal translocations (WARTs), as suggested by their mutual karyotypic variation. The variation of the molecular markers supports the theory of rapid karyotypic evolution in the common shrew.</p>

The common shrew, Sorex araneus, has one of the most variable karyotypes among mammals, displaying numerous chromosomes races throughout its distribution, which can be categorized into different karyotypic groups. The objective of this thesis was to examine the postglacial population history of Fennoscandian common shrews using autosomal microsatellites, mitochondrial DNA (mtDNA) and a Y chromosome specific microsatellite (L8Y). Autosomal microsatellites and mtDNA revealed weak genetic structure over a hybrid zone between the karyotypically divergent Northern and Western karyotypic groups. However, the genetic structure displayed by the Y chromosome microsatellite was orders of magnitude higher. Hence, considerable chromosomal differences between the groups do not prevent female gene flow, while male gene flow is reduced (cf. Haldane's rule). Further, the results suggest that the Haldane effect may be caused by the chromosomal differences between the karyotypic groups. No mtDNA differentiation was observed either between chromosome races or between the Northern and Western karyotypic groups in Fennoscandia. The combined pattern of karyotypic and mtDNA variation of Fennoscandian common shrews, suggest bi-directional postglacial recolonisation from a single refugium in Europe. The variation of the Y-linked microsatellite supported this conclusion. In contrast, significant mtDNA structure, discordant with the karyotypic variation, revealed that common shrews in southern Finland belong to a different lineage than remaining Fennoscandian regions, implying postglacial recolonisation from a different source. MtDNA variation of the chromosome races in Sweden supports the hypothesis that three races of the Western karyotypic group have been formed through whole arm reciprocal translocations (WARTs), as suggested by their mutual karyotypic variation. The variation of the molecular markers supports the theory of rapid karyotypic evolution in the common shrew.