+publisher:"University of Illinois – Urbana-Champaign" +contributor:("Malhi, Ripan S")

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University of Illinois – Urbana-Champaign

1. Lindo, John. Paleogenomics in the Americas: demography, adaptations, and resilience.

Degree: PhD, Anthropology, 2015, University of Illinois – Urbana-Champaign

URL: http://hdl.handle.net/2142/88175

► This work covers the evolutionary history of an indigenous population from the Americas through the lens of ancient DNA. In recent years, major advances in… (more)

▼ This work covers the evolutionary history of an indigenous population from the Americas through the lens of ancient DNA. In recent years, major advances in DNA sequencing have allowed for the utilization of ancient DNA on a grand scale. We now have the ability to examine the whole genomes of ancient individuals and examine the forces of evolution though space and time. Through these advances, this project addresses questions that would have otherwise been difficult to address with modern DNA alone. These questions span a period of 10,000 years and broach both local and continental demographic histories. In doing so, a comprehensive genetic picture of an indigenous population, with a history characteristic of other native groups, emerges so as to explain nuanced migration patterns, the historical experiences of Native Americans with European-borne pathogens, and the long-lasting genomic effects of European contact. This work was made possible through the collaborative efforts of Northwest Coast First Nations. The first topic presented here focuses on the highly debated processes behind the initial peopling of the Americas and, more specifically, the Northwest Coast. Over the past decades, this region has received a great deal of a attention due to the Northwest Coast’s proximity to Beringia and its prime location with respect to the coastal migration model, which holds that the first migration wave into the Americas occurred along the Pacific coast. Recent research, utilizing genome-wide data of both ancient and modern native individuals, has pointed to a primary migration that extends an ancestral lineage to most indigenous groups living today. Previous research, however, utilizing paternal and maternal genetic lineages, have found distributions of genetic markers that are difficult to reconcile into a single migration event. To address this discrepancy, the genomes of three ancient individuals from the Northwest Coast, ranging in age from 10,000 to 1,500 years Before Present (BP), were sequenced and compared to previously described ancient individuals from the Americas. The results suggest that the Northwest Coast was populated by two sources, which may represent two separate migrations into the region. I present analyses suggesting that the first source was part of a primary migration that led to the peopling of both continents. The second source may have been a result of a migration that occurred during the Holocene, which further diversified the gene pool and directly links to the current indigenous populations of the Northwest Coast. This analysis reconciles modern distributions of genetic markers, which are missing from North America but are prevalent on the southern continent. These markers, which are evident in the most ancient individuals of the region, are gradually replaced through time, which may be indicative of additional gene flow that entered the area after the primary migration wave made its way southward. The next period of inquiry moves forward to the era of European colonization and addresses… Advisors/Committee Members: Champaign%22%20%2Bcontributor%3A%28%22Malhi%2C%20Ripan%20S.%22%29&pagesize-30">Malhi, Ripan S. (advisor), Champaign%22%20%2Bcontributor%3A%28%22Malhi%2C%20Ripan%20S.%22%29&pagesize-30">Malhi, Ripan S. (Committee Chair), Champaign%22%20%2Bcontributor%3A%28%22Roseman%2C%20Charles%20C.%22%29&pagesize-30">Roseman, Charles C. (committee member), Champaign%22%20%2Bcontributor%3A%28%22Lugo%2C%20Alejandro%22%29&pagesize-30">Lugo, Alejandro (committee member), Champaign%22%20%2Bcontributor%3A%28%22DeGiorgio%2C%20Michael%22%29&pagesize-30">DeGiorgio, Michael (committee member).

Subjects/Keywords: Ancient DNA; Native Americans; Colonization

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Lindo, J. (2015). Paleogenomics in the Americas: demography, adaptations, and resilience. (Doctoral Dissertation). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/88175

Chicago Manual of Style (16^th Edition):

Lindo, John. “Paleogenomics in the Americas: demography, adaptations, and resilience.” 2015. Doctoral Dissertation, University of Illinois – Urbana-Champaign. Accessed March 03, 2021. http://hdl.handle.net/2142/88175.

MLA Handbook (7^th Edition):

Lindo, John. “Paleogenomics in the Americas: demography, adaptations, and resilience.” 2015. Web. 03 Mar 2021.

Vancouver:

Lindo J. Paleogenomics in the Americas: demography, adaptations, and resilience. [Internet] [Doctoral dissertation]. University of Illinois – Urbana-Champaign; 2015. [cited 2021 Mar 03]. Available from: http://hdl.handle.net/2142/88175.

Council of Science Editors:

Lindo J. Paleogenomics in the Americas: demography, adaptations, and resilience. [Doctoral Dissertation]. University of Illinois – Urbana-Champaign; 2015. Available from: http://hdl.handle.net/2142/88175

University of Illinois – Urbana-Champaign

2. Witt Dillon, Kelsey E. A demographic and dietary history of ancient dogs in the Americas using ancient DNA.

Degree: PhD, Ecol, Evol, Conservation Biol, 2017, University of Illinois – Urbana-Champaign

URL: http://hdl.handle.net/2142/98204

► Dogs were domesticated more than 15,000 years ago, and since then they have become an integral part of human lives. They have served as hunters,… (more)

▼ Dogs were domesticated more than 15,000 years ago, and since then they have become an integral part of human lives. They have served as hunters, guards, and pets, and have migrated with humans to multiple continents, including the Americas and Australia. The close relationship between humans and dogs makes dogs a valuable proxy when studying human history. In this study, we use ancient dog remains from the Americas to gain an understanding of their demographic and dietary history, as well as that of humans. Mitochondrial DNA sequences of the hypervariable region of ancient dogs were compared to modern and ancient American dogs to model dog demography and compare populations to identify shared haplotypes. This study identified multiple founding haplotypes, and suggested that dogs arrived to the Americas after the initial human migration. The majority of published ancient American dog DNA sequences is of the hypervariable region, so this comparison gives us the opportunity to look at the largest number of dogs across the Americas. We also sequenced complete mitochondrial genomes (mitogenomes), to determine if mitogenome data could be used to confirm the hypotheses made about ancient American dog demography using the hypervariable region. Mitogenome sequences show a higher-resolution perspective on dog diversity, and the longer sequences revealed different aspects of dog demography. We were able to support the hypotheses that suggest that dogs migrated to the Americas with humans, and that dog populations vary in genetic diversity, but were not able to support the hypotheses that ancient and modern dogs show continuity, and that dogs arrived to the Americas later in time. We also found that ancient dog demography mirrors ancient Native American demography in specific regions of North America, such as the Pacific Coast and Southeast. Finally, we assessed the diet in dogs from the American Bottom using both stable isotopes and shotgun sequencing of dog coprolites, and used the findings about dog diet to infer human diet during the Late Woodland and Mississippian periods. We found that dogs (and humans) ate no maize during the Late Woodland Period, but were consuming large amounts of maize as early as 1010 AD, and maize was likely present in the American Bottom by 900 AD. Additionally, Mississippian dogs and humans supplemented their diet of maize with other foods including squash and fish. The analysis of the history of dogs has yielded a wealth of information about how dogs and humans interacted in the Americas. Advisors/Committee Members: Champaign%22%20%2Bcontributor%3A%28%22Malhi%2C%20Ripan%20S%22%29&pagesize-30">Malhi, Ripan S (advisor), Champaign%22%20%2Bcontributor%3A%28%22Malhi%2C%20Ripan%20S%22%29&pagesize-30">Malhi, Ripan S (Committee Chair), Champaign%22%20%2Bcontributor%3A%28%22Kukekova%2C%20Anna%20V%22%29&pagesize-30">Kukekova, Anna V (committee member), Champaign%22%20%2Bcontributor%3A%28%22Roca%2C%20Alfred%20%20L%22%29&pagesize-30">Roca, Alfred L (committee member), Champaign%22%20%2Bcontributor%3A%28%22Ambrose%2C%20Stanley%20H%22%29&pagesize-30">Ambrose, Stanley H (committee member), Champaign%22%20%2Bcontributor%3A%28%22Kemp%2C%20Brian%20M%22%29&pagesize-30">Kemp, Brian M (committee member).

Subjects/Keywords: Ancient deoxyribonucleic acid (DNA); Domestic dog; Population genetics; Demography; Mitochondrial deoxyribonucleic acid (DNA); Americas; Stable isotopes; Diet

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Witt Dillon, K. E. (2017). A demographic and dietary history of ancient dogs in the Americas using ancient DNA. (Doctoral Dissertation). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/98204

Chicago Manual of Style (16^th Edition):

Witt Dillon, Kelsey E. “A demographic and dietary history of ancient dogs in the Americas using ancient DNA.” 2017. Doctoral Dissertation, University of Illinois – Urbana-Champaign. Accessed March 03, 2021. http://hdl.handle.net/2142/98204.

MLA Handbook (7^th Edition):

Witt Dillon, Kelsey E. “A demographic and dietary history of ancient dogs in the Americas using ancient DNA.” 2017. Web. 03 Mar 2021.

Vancouver:

Witt Dillon KE. A demographic and dietary history of ancient dogs in the Americas using ancient DNA. [Internet] [Doctoral dissertation]. University of Illinois – Urbana-Champaign; 2017. [cited 2021 Mar 03]. Available from: http://hdl.handle.net/2142/98204.

Council of Science Editors:

Witt Dillon KE. A demographic and dietary history of ancient dogs in the Americas using ancient DNA. [Doctoral Dissertation]. University of Illinois – Urbana-Champaign; 2017. Available from: http://hdl.handle.net/2142/98204

University of Illinois – Urbana-Champaign

3. Shattuck, Milena. The Molecular Evolution of the Serotonin System in Macaques (MACACA): a Detailed Survey of Four Serotonin-Related Genes.

Degree: PhD, 0340, 2011, University of Illinois – Urbana-Champaign

URL: http://hdl.handle.net/2142/26115

► Serotonin, a hormone produced in the brain, has long been implicated in the regulation of critical behaviors, such as those related to aggression or impulse… (more)

▼ Serotonin, a hormone produced in the brain, has long been implicated in the regulation of critical behaviors, such as those related to aggression or impulse control. However, most research on serotonin has focused on the proximate connection to behavior, and little is known about its evolution. This is unfortunate, since the serotonin system has great potential to inform our understanding of behavioral evolution. I seek to address this gap in knowledge by investigating the molecular evolution of the serotonin system in macaques (genus Macaca). The macaque genus represents a useful model for understanding behavioral evolution. Comprised of approximately 19 species, macaques display a wide range of behaviors. It is likely that behavioral differences are caused by differences in neuroendocrinology. Therefore, the serotonin system provides one potential mechanism through which evolution may act to shape macaque behavior. In this dissertation, I sequence four genes that are known to influence serotonin functioning and behavior: HTR1A, HTR1B, TPH2, and SLC6A4. I examine the pattern of genetic variation within and between several species of macaque, and, using an approach based on molecular evolutionary theory, discern which evolutionary force ??? positive selection, balancing selection, purifying selection, or random genetic drift ??? is most likely to have acted on these genes. Three out of the four genes (HTR1B, TPH2, and SLC6A4), show a low level of overall genetic variation within the coding regions, suggesting that purifying selection is the predominate force acting on these genes. Within non-coding regions, the patterns of genetic variation found are consistent with genetic drift. Thus, positive selection does not seem to be affecting these genes. The genetic variation for these genes may contribute to the behavioral variation found in macaques; however, any effect that these genes have on behavior is likely due to non-adaptive evolutionary forces. In contrast to the other genes, HTR1A shows a pattern that is clearly distinct. HTR1A displays an unusually high level of interspecific variation, which is consistent with positive selection. Moreover, a subset of macaque species share a codon loss, an extremely rare event in gene evolution, and analyses of the coding region indicate a significant elevation of protein evolution among certain sites of the gene. These results suggest that positive selection has played a significant role in the evolution of the serotonin system and it is likely that the effects of positive selection on HTR1A contributed to macaque behavioral evolution. This research provides an important first step towards gaining a more thorough understanding of the mechanisms underlying the evolution of behavior. Advisors/Committee Members: Champaign%22%20%2Bcontributor%3A%28%22Malhi%2C%20Ripan%20S.%22%29&pagesize-30">Malhi, Ripan S. (advisor), Champaign%22%20%2Bcontributor%3A%28%22Malhi%2C%20Ripan%20S.%22%29&pagesize-30">Malhi, Ripan S. (Committee Chair), Champaign%22%20%2Bcontributor%3A%28%22Leigh%2C%20Steven%20R.%22%29&pagesize-30">Leigh, Steven R. (committee member), Champaign%22%20%2Bcontributor%3A%28%22Roseman%2C%20Charles%20C.%22%29&pagesize-30">Roseman, Charles C. (committee member), Champaign%22%20%2Bcontributor%3A%28%22Konigsberg%2C%20Lyle%20W.%22%29&pagesize-30">Konigsberg, Lyle W. (committee member).

Subjects/Keywords: serotonin; macaques; evolution; behavior; genetics

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Shattuck, M. (2011). The Molecular Evolution of the Serotonin System in Macaques (MACACA): a Detailed Survey of Four Serotonin-Related Genes. (Doctoral Dissertation). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/26115

Chicago Manual of Style (16^th Edition):

Shattuck, Milena. “The Molecular Evolution of the Serotonin System in Macaques (MACACA): a Detailed Survey of Four Serotonin-Related Genes.” 2011. Doctoral Dissertation, University of Illinois – Urbana-Champaign. Accessed March 03, 2021. http://hdl.handle.net/2142/26115.

MLA Handbook (7^th Edition):

Shattuck, Milena. “The Molecular Evolution of the Serotonin System in Macaques (MACACA): a Detailed Survey of Four Serotonin-Related Genes.” 2011. Web. 03 Mar 2021.

Vancouver:

Shattuck M. The Molecular Evolution of the Serotonin System in Macaques (MACACA): a Detailed Survey of Four Serotonin-Related Genes. [Internet] [Doctoral dissertation]. University of Illinois – Urbana-Champaign; 2011. [cited 2021 Mar 03]. Available from: http://hdl.handle.net/2142/26115.

Council of Science Editors:

Shattuck M. The Molecular Evolution of the Serotonin System in Macaques (MACACA): a Detailed Survey of Four Serotonin-Related Genes. [Doctoral Dissertation]. University of Illinois – Urbana-Champaign; 2011. Available from: http://hdl.handle.net/2142/26115

University of Illinois – Urbana-Champaign

4. Rogers, Mary Patricia. Variation in age at menarche and adult reproductive function: the role of energetic and psychosocial stressors.

Degree: PhD, Anthropology, 2018, University of Illinois – Urbana-Champaign

URL: http://hdl.handle.net/2142/101759

► Reproductive ecology has long examined the flexibility of women’s reproductive function in the face of variable environments. The timing of a woman’s first menses, or… (more)

▼ Reproductive ecology has long examined the flexibility of women’s reproductive function in the face of variable environments. The timing of a woman’s first menses, or age at menarche, is both used as a proxy of childhood stressors and correlated with adolescent and adult reproductive function. This research seeks to understand the connections between childhood environments, pubertal timing, and adult reproductive function, and I specifically 1) identify a need for including social support measures in studies of pubertal timing through empirical evidence that positive parental-child interactions affect age at menarche, 2) demonstrate that psychosocial and energetic stressors experienced during childhood correlate with pubertal timing and adult reproductive function, 3) compare timing of menarche and variation in reproductive hormones between two populations with similar geographic origins but different subsistence environments, and 4) investigate gene methylation as a potential mechanism mediating the relationship between key stressors and reproductive function. I first investigated relationships between parent-adolescent communication and age at menarche in a diverse sample of 128 post-menarcheal, American girls aged 12-17. I found that measures of close family relationships, specifically open communication with parents, were correlated with age at menarche in this sample. I further found that mother-adolescent and father-adolescent open communication scores had opposing directional effects on menarcheal timing. These findings suggest that maternal and paternal communication may signal different things about the developmental and reproductive environment. This research underscores the importance of including measures of family support in future studies of adolescent reproductive trait timing, as well as the consideration that positive psychosocial factors, rather than only negative psychosocial factors, may be associated with accelerated menarcheal development. I further investigated the secular trend of declining ages at menarche in in the rural Beskid Wyspowy region of southern Poland and investigated relationships between childhood stressors, age at menarche, and adult reproductive function. I found that age at menarche has declined over time in rural Poland. Helping on farms and with farm animals as a child were associated with later ages at menarche. Women with a higher number of adverse childhood experiences tended to have earlier age at menarche, although this difference was not statistically significant. Despite different effects on age at menarche, all types of childhood stressors were associated with lower adult E1G concentrations. The results of this study support a model under which developmental conditions affect adult reproductive function, but challenge the use of age at menarche alone as a proxy for childhood stressors. I compared differences in reproductive traits between women in rural Poland and Polish American women in urban areas of the United States. We found that ages at menarche are… Advisors/Committee Members: Champaign%22%20%2Bcontributor%3A%28%22Clancy%2C%20Kathryn%20B.H.%22%29&pagesize-30">Clancy, Kathryn B.H. (advisor), Champaign%22%20%2Bcontributor%3A%28%22Malhi%2C%20Ripan%20S.%22%29&pagesize-30">Malhi, Ripan S. (advisor), Champaign%22%20%2Bcontributor%3A%28%22Clancy%2C%20Kathryn%20B.H.%22%29&pagesize-30">Clancy, Kathryn B.H. (Committee Chair), Champaign%22%20%2Bcontributor%3A%28%22Malhi%2C%20Ripan%20S.%22%29&pagesize-30">Malhi, Ripan S. (Committee Chair), Champaign%22%20%2Bcontributor%3A%28%22Roseman%2C%20Charles%22%29&pagesize-30">Roseman, Charles (committee member), Champaign%22%20%2Bcontributor%3A%28%22Uddin%2C%20Monica%22%29&pagesize-30">Uddin, Monica (committee member).

Subjects/Keywords: age at menarche; reproductive ecology; gene methylation; epigenetics; reproductive function; energetic stressors; psychosocial stressors; estradiol; progesterone

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Rogers, M. P. (2018). Variation in age at menarche and adult reproductive function: the role of energetic and psychosocial stressors. (Doctoral Dissertation). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/101759

Chicago Manual of Style (16^th Edition):

Rogers, Mary Patricia. “Variation in age at menarche and adult reproductive function: the role of energetic and psychosocial stressors.” 2018. Doctoral Dissertation, University of Illinois – Urbana-Champaign. Accessed March 03, 2021. http://hdl.handle.net/2142/101759.

MLA Handbook (7^th Edition):

Rogers, Mary Patricia. “Variation in age at menarche and adult reproductive function: the role of energetic and psychosocial stressors.” 2018. Web. 03 Mar 2021.

Vancouver:

Rogers MP. Variation in age at menarche and adult reproductive function: the role of energetic and psychosocial stressors. [Internet] [Doctoral dissertation]. University of Illinois – Urbana-Champaign; 2018. [cited 2021 Mar 03]. Available from: http://hdl.handle.net/2142/101759.

Council of Science Editors:

Rogers MP. Variation in age at menarche and adult reproductive function: the role of energetic and psychosocial stressors. [Doctoral Dissertation]. University of Illinois – Urbana-Champaign; 2018. Available from: http://hdl.handle.net/2142/101759

University of Illinois – Urbana-Champaign

5. Brandt, Jessica R. Conservation and population genetics of African and Asian rhinoceros.

Degree: PhD, Animal Sciences, 2016, University of Illinois – Urbana-Champaign

URL: http://hdl.handle.net/2142/92892

► There are five living species of rhinoceros inhabiting Africa and Asia: black rhinoceros (Diceros bicornis), white rhinoceros (Ceratotherium simum), Indian rhinoceros (Rhinoceros unicornis), Javan rhinoceros… (more)

▼ There are five living species of rhinoceros inhabiting Africa and Asia: black rhinoceros (Diceros bicornis), white rhinoceros (Ceratotherium simum), Indian rhinoceros (Rhinoceros unicornis), Javan rhinoceros (Rhinoceros sondaicus) and Sumatran rhinoceros (Dicerorhinus sumatrensis). Anthropogenic activities, such as poaching and habitat disruption, have led to steep declines in the population size of all rhinoceros species, placing them in danger of extinction. The development of genetic markers for assessment of diversity at neutral and adaptive loci can be used to address a number of questions that will aid in the conservation of rhinoceros populations both ex situ and in the wild. In order to evaluate genetic diversity in rhinoceros populations, I investigated three research questions that will contribute substantially to the conservation and management of rhinoceros species. (1) Accurate estimates of population size are often difficult to obtain for rhinoceros species that are elusive or prefer dense habitat. Knowing the precise number of individuals in an area is essential for managers to develop and implement conservation plans that address the issues facing a particular population. To enable the use of molecular methods for censusing of rhinoceros populations 29 novel Sumatran rhinoceros microsatellites and 17 novel black rhinoceros microsatellites were characterized from next generation sequencing data for use with low quality DNA extracted from non-invasively collected fecal samples. A subset of these markers is sufficient for identification of individuals based on PID and PID(sib) values. Through a series of optimization steps I was able to show that these markers can be successfully used to obtain genotypes from fecal samples. These markers are of particularly importance for Sumatran rhinoceros populations since the reported number of individual has been difficult to accurately estimate and drastically overstated. Studies aimed at implementing these markers for estimating census size in wild rhinoceros populations are ongoing. (2) The Sumatran rhinoceros, once widespread across Southeast Asia, now consists of ca. 100 individuals primarily found in three isolated populations on the island of Sumatra. No studies have examined the population genetic structure of Sumatran rhinoceros using techniques beyond mitochondrial restriction mapping analysis. Given the requirement for substantial management of the remaining Sumatran rhino populations in the wild and in ex situ breeding facilities, more information regarding their genetic status needs to be available. I used mitochondrial DNA sequences from modern and archival museum samples to assess genetic diversity and structure. Among all samples, haplotype diversity was high; samples identified as being members of the subspecies D. s. sumatrensis formed a cluster containing ten haplotypes. The number of haplotypes and the haplotype diversity among the museum samples of D. s. sumatrensis were higher than in the modern samples even after rarefaction, suggesting… Advisors/Committee Members: Champaign%22%20%2Bcontributor%3A%28%22Roca%2C%20Alfred%20L%22%29&pagesize-30">Roca, Alfred L (advisor), Champaign%22%20%2Bcontributor%3A%28%22Roca%2C%20Alfred%20L%22%29&pagesize-30">Roca, Alfred L (Committee Chair), Champaign%22%20%2Bcontributor%3A%28%22Fischer%2C%20Amy%20E%22%29&pagesize-30">Fischer, Amy E (committee member), Champaign%22%20%2Bcontributor%3A%28%22Malhi%2C%20Ripan%20S%22%29&pagesize-30">Malhi, Ripan S (committee member), Champaign%22%20%2Bcontributor%3A%28%22Kukekova%2C%20Anna%22%29&pagesize-30">Kukekova, Anna (committee member).

Subjects/Keywords: Conservation ecology; Rhinoceros; Population genetics; Immunogenetics

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Brandt, J. R. (2016). Conservation and population genetics of African and Asian rhinoceros. (Doctoral Dissertation). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/92892

Chicago Manual of Style (16^th Edition):

Brandt, Jessica R. “Conservation and population genetics of African and Asian rhinoceros.” 2016. Doctoral Dissertation, University of Illinois – Urbana-Champaign. Accessed March 03, 2021. http://hdl.handle.net/2142/92892.

MLA Handbook (7^th Edition):

Brandt, Jessica R. “Conservation and population genetics of African and Asian rhinoceros.” 2016. Web. 03 Mar 2021.

Vancouver:

Brandt JR. Conservation and population genetics of African and Asian rhinoceros. [Internet] [Doctoral dissertation]. University of Illinois – Urbana-Champaign; 2016. [cited 2021 Mar 03]. Available from: http://hdl.handle.net/2142/92892.

Council of Science Editors:

Brandt JR. Conservation and population genetics of African and Asian rhinoceros. [Doctoral Dissertation]. University of Illinois – Urbana-Champaign; 2016. Available from: http://hdl.handle.net/2142/92892

University of Illinois – Urbana-Champaign

6. de Flamingh, Alida. Conservation genetics of African elephants.

Degree: PhD, Ecol, Evol, Conservation Biol, 2020, University of Illinois – Urbana-Champaign

URL: http://hdl.handle.net/2142/107911

► Elephant population numbers are plummeting across the African continent. Habitat loss as a consequence of anthropogenic landscape transformation, and the poaching of elephants for the… (more)

▼ Elephant population numbers are plummeting across the African continent. Habitat loss as a consequence of anthropogenic landscape transformation, and the poaching of elephants for the illegal ivory trade, has reduced and fragmented elephant populations to a fraction of their former population size and range. It has therefore become necessary to develop and implement proactive and targeted conservation initiatives that aim at maintaining or restoring spatial and genetic connectivity between populations. In this thesis, I use a conservation genetic approach to study African elephant populations with the aim of developing methodologies and providing applications that could inform conservation planning for African elephants. In Chapter 1, I introduce and discuss the need for proactive African elephant conservation initiatives. In Chapter 2, I develop and evaluate an approach to delineate functional landscape linkages (FLL) for African elephant conservation planning, and I use this approach to create a fine-scale map that demarcates FLL for elephant populations in southern Africa. The results of Chapter 3 provide support for conservation initiatives that aim at increasing connectivity through FLL. In Chapter 3, I show that Kruger National Park’s elephant population forms part of a functional entity in which migration helped to maintain a relatively diverse gene pool. Chapter 4 benefits elephant conservation by increasing our understanding of historical elephant population ecology and genetics. Here I show that contemporary West African forest elephant populations have limited genetic diversity compared to the genetic diversity found in historical populations. Chapter 4 highlights the need for proactive and preventative conservation strategies that aim to conserve the genetic diversity within remaining forest elephant populations. In Chapter 5 I adapt a method previously developed for sex identification of human remains for use with non-human taxa, and I successfully identify the sex of modern and ancient elephants from low coverage genome data. Sex identification of ancient animal biological remains can benefit conservation by increasing our understanding of historical population structure, demography and social behavior. In this thesis I develop and apply genetic and spatial analyses to extinct and extant elephant populations to inform local and regional African elephant conservation strategies. This thesis provides an interdisciplinary toolset and framework for future conservation genetic studies that focus on African elephant conservation planning. Advisors/Committee Members: Champaign%22%20%2Bcontributor%3A%28%22Roca%2C%20Alfred%20L%22%29&pagesize-30">Roca, Alfred L (advisor), Champaign%22%20%2Bcontributor%3A%28%22Roca%2C%20Alfred%20L%22%29&pagesize-30">Roca, Alfred L (Committee Chair), Champaign%22%20%2Bcontributor%3A%28%22Malhi%2C%20Ripan%20S%22%29&pagesize-30">Malhi, Ripan S (committee member), Champaign%22%20%2Bcontributor%3A%28%22Schooley%2C%20Robert%20L%22%29&pagesize-30">Schooley, Robert L (committee member), Champaign%22%20%2Bcontributor%3A%28%22van%20Aarde%2C%20Rudi%20J%22%29&pagesize-30">van Aarde, Rudi J (committee member).

Subjects/Keywords: conservation genetics; molecular ecology; conservation genomics; megafauna

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

de Flamingh, A. (2020). Conservation genetics of African elephants. (Doctoral Dissertation). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/107911

Chicago Manual of Style (16^th Edition):

de Flamingh, Alida. “Conservation genetics of African elephants.” 2020. Doctoral Dissertation, University of Illinois – Urbana-Champaign. Accessed March 03, 2021. http://hdl.handle.net/2142/107911.

MLA Handbook (7^th Edition):

de Flamingh, Alida. “Conservation genetics of African elephants.” 2020. Web. 03 Mar 2021.

Vancouver:

de Flamingh A. Conservation genetics of African elephants. [Internet] [Doctoral dissertation]. University of Illinois – Urbana-Champaign; 2020. [cited 2021 Mar 03]. Available from: http://hdl.handle.net/2142/107911.

Council of Science Editors:

de Flamingh A. Conservation genetics of African elephants. [Doctoral Dissertation]. University of Illinois – Urbana-Champaign; 2020. Available from: http://hdl.handle.net/2142/107911

University of Illinois – Urbana-Champaign

7. Dong, Yu. Eating identity: food, gender, and social organization in late Neolithic northern China.

Degree: PhD, 0340, 2013, University of Illinois – Urbana-Champaign

URL: http://hdl.handle.net/2142/45643

► The Dawenkou Neolithic Culture (ca. 4300-2600 cal. BC) in Shandong, northern Jiangsu and Anhui Provinces, China, has been intensively investigated because it provides insights into… (more)

▼ The Dawenkou Neolithic Culture (ca. 4300-2600 cal. BC) in Shandong, northern Jiangsu and Anhui Provinces, China, has been intensively investigated because it provides insights into the origin of complex stratified societies. Dawenkou is well known for its extremely elaborate burials indicating incipient social stratification. The initial spread of rice from southern China to the millet agriculture-based societies of the Yellow River Valley, including Dawenkou region, also occurred during this period. Dawenkou is also the assumed critical transitional period during which societies were changing from matrilineal/matriarchal clans to patrilineal/patriarchal families. In this thesis, I shall argue that rice consumption had been used as an important identity marker (including ethnicity, gender, and social status) of individuals at some Dawenkou site, and the introduction of rice possibly facilitated the development of incipient social stratification. I shall also argue that the assumed transition to patrilineal/patriarchal families did not occur simultaneously across all Dawenkou sites. Some late Dawenkou site was still matrilineal, while females seem to have special status than males at some other late Dawenkou site. My thesis focuses on the questions of the relationships among social organization, gender relations, and staple food preferences in identity formation and the development of social complexity in four Dawenkou sites (Dongjiaying, Fujia, Huating, and Liangwangcheng). Key to understanding these questions are the integration of mortuary evidence, radiocarbon dating, stable isotope analysis, and ancient DNA analysis of human remains. My radiocarbon dating results suggest that Liangwangcheng, Fujia, and Huating all date to 2800-2500 cal. BC, while Dongjiaying is a few centuries later (2600-2300 cal. BC). The contemporary nature of these sites permits synchronic and diachronic comparisons of diet composition and burial customs among communities over a few centuries. Despite the contemporaneity there is significant variation in the development of social stratification. Huating seems to be the most stratified with evidence of human sacrifices in some burials. Liangwangcheng also shows signs of social stratification by the lavishness of some burials, and the inclusion of exotic goods that suggest long distance trade. In addition, some females seem to have privilege over others in the community. There is no evidence supporting the hypothesis that a transition to patriarchal families occurred at this late Neolithic site with increasing social complexity. Based on the limited information available, Fujia community seems to be more egalitarian. My stable isotopic analysis of human and faunal remains from these sites suggests that food consumption varied across landscape and among different individuals within sites. Fujia and Dongjiaying human diets were dominated by millets and millet-fed pigs, while Huating and Liangwangcheng people had more diverse diets, including significant amount of C3 plants such as rice and… Advisors/Committee Members: Champaign%22%20%2Bcontributor%3A%28%22Ambrose%2C%20Stanley%20H.%22%29&pagesize-30">Ambrose, Stanley H. (advisor), Champaign%22%20%2Bcontributor%3A%28%22Ambrose%2C%20Stanley%20H.%22%29&pagesize-30">Ambrose, Stanley H. (Committee Chair), Champaign%22%20%2Bcontributor%3A%28%22Underhill%2C%20Anne%20P.%22%29&pagesize-30">Underhill, Anne P. (committee member), Champaign%22%20%2Bcontributor%3A%28%22Malhi%2C%20Ripan%20S.%22%29&pagesize-30">Malhi, Ripan S. (committee member), Champaign%22%20%2Bcontributor%3A%28%22Lucero%2C%20Lisa%20J.%22%29&pagesize-30">Lucero, Lisa J. (committee member).

Subjects/Keywords: Neolithic China; stable isotope analysis; ancient DNA analysis; complex societies; rice agriculture; food and identity; Kinship

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Dong, Y. (2013). Eating identity: food, gender, and social organization in late Neolithic northern China. (Doctoral Dissertation). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/45643

Chicago Manual of Style (16^th Edition):

Dong, Yu. “Eating identity: food, gender, and social organization in late Neolithic northern China.” 2013. Doctoral Dissertation, University of Illinois – Urbana-Champaign. Accessed March 03, 2021. http://hdl.handle.net/2142/45643.

MLA Handbook (7^th Edition):

Dong, Yu. “Eating identity: food, gender, and social organization in late Neolithic northern China.” 2013. Web. 03 Mar 2021.

Vancouver:

Dong Y. Eating identity: food, gender, and social organization in late Neolithic northern China. [Internet] [Doctoral dissertation]. University of Illinois – Urbana-Champaign; 2013. [cited 2021 Mar 03]. Available from: http://hdl.handle.net/2142/45643.

Council of Science Editors:

Dong Y. Eating identity: food, gender, and social organization in late Neolithic northern China. [Doctoral Dissertation]. University of Illinois – Urbana-Champaign; 2013. Available from: http://hdl.handle.net/2142/45643

University of Illinois – Urbana-Champaign

8. Brandt, Adam. African elephant conservation and population genetics.

Degree: PhD, 0002, 2015, University of Illinois – Urbana-Champaign

URL: http://hdl.handle.net/2142/72995

► Despite advances in technology and management practices, countless species of wildlife continue to decline and become threatened with extinction, largely due to human activities such… (more)

▼ Despite advances in technology and management practices, countless species of wildlife continue to decline and become threatened with extinction, largely due to human activities such as poaching and habitat destruction. The field of conservation genetics aims to reduce the rate and severity of species decline by better understanding their genetics and making relevant information available to conservation and management entities. African elephants are in decline and the research here aims to answer important questions relevant to conservation efforts. (1) Phylogeographic patterns between nuclear and mitochondrial DNA in African elephants are often incongruent, which has been attributed to sex-biased dispersal and variance in reproductive success. To examine this, we sequenced the mitochondrial genome of two African forest elephants and examined the coalescent dates within the elephantid lineage. Comparing mitochondrial and nuclear coalescence dates, we found the ratio to be much greater than 0.25, which is consistent with the expectation that sex differences in dispersal and in variance of reproductive success would have increased the effective population size of mtDNA relative to nuclear markers in elephantids, thus contributing to the persistence of incongruent mtDNA phylogeographic patterns. (2) Past research on African elephant genetics has focused heavily on the phylogenetic relationship of forest and savanna elephants. Few studies have examined savanna elephant population genetics exclusively; those that have were limited in geographic scope or relied on mitochondrial DNA which has been shown to be a poor indicator of nuclear population structure. In this study we determined the extent of range wide, intra-species genetic variation for the African savanna elephant using multilocus genotype data. Our findings indicated that African savanna elephants have not undergone a population bottleneck within the last 2 to 4 NE generations. Additionally, there was strong support for isolation by distance at the continental scale and there was evidence that localities in north-central Africa are distinct. (3) Many elephant populations in Africa are isolated within fragmented habitat and persist in low numbers. The elephants of Gash-Barka, Eritrea have become completely isolated, lacking any gene flow from other elephant populations. Using DNA isolated from dung, we examined nuclear and mitochondrial markers to better understand genetic variation and affinities to elephants elsewhere on the continent for conservation purposes. Elephants in Eritrea have low genetic diversity and a close affinity to savanna elephants in Eastern Africa. Conservation efforts should aim to protect Eritrean elephants and their habitat in the short run, with restoration of habitat connectivity and genetic diversity as long-term goals. (4) While conservation genetics aims to reduce species decline, research is often limited by the availability of high quality DNA samples like blood or tissue. Obtaining these samples requires direct contact and… Advisors/Committee Members: Champaign%22%20%2Bcontributor%3A%28%22Roca%2C%20Alfred%20L.%22%29&pagesize-30">Roca, Alfred L. (advisor), Champaign%22%20%2Bcontributor%3A%28%22Roca%2C%20Alfred%20L.%22%29&pagesize-30">Roca, Alfred L. (Committee Chair), Champaign%22%20%2Bcontributor%3A%28%22Fischer%2C%20Amy%20E.%22%29&pagesize-30">Fischer, Amy E. (committee member), Champaign%22%20%2Bcontributor%3A%28%22Malhi%2C%20Ripan%20S.%22%29&pagesize-30">Malhi, Ripan S. (committee member), Champaign%22%20%2Bcontributor%3A%28%22Swanson%2C%20Kelly%20S.%22%29&pagesize-30">Swanson, Kelly S. (committee member).

Subjects/Keywords: Proboscidea; savanna elephant; forest elephant; fecal DNA; Loxodonta; microsatellites; mitochondrial DNA; single nucleotide polymorphism

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Brandt, A. (2015). African elephant conservation and population genetics. (Doctoral Dissertation). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/72995

Chicago Manual of Style (16^th Edition):

Brandt, Adam. “African elephant conservation and population genetics.” 2015. Doctoral Dissertation, University of Illinois – Urbana-Champaign. Accessed March 03, 2021. http://hdl.handle.net/2142/72995.

MLA Handbook (7^th Edition):

Brandt, Adam. “African elephant conservation and population genetics.” 2015. Web. 03 Mar 2021.

Vancouver:

Brandt A. African elephant conservation and population genetics. [Internet] [Doctoral dissertation]. University of Illinois – Urbana-Champaign; 2015. [cited 2021 Mar 03]. Available from: http://hdl.handle.net/2142/72995.

Council of Science Editors:

Brandt A. African elephant conservation and population genetics. [Doctoral Dissertation]. University of Illinois – Urbana-Champaign; 2015. Available from: http://hdl.handle.net/2142/72995

University of Illinois – Urbana-Champaign

9. Mallott, Elizabeth K. Social, ecological, and developmental influences on fruit and invertebrate foraging strategies and gut microbial communities in white-faced capuchins (Cebus capucinus).

Degree: PhD, Anthropology, 2016, University of Illinois – Urbana-Champaign

URL: http://hdl.handle.net/2142/93005

► Primates are challenged by spatiotemporal variation in resource availability, and a central question in biological anthropology is how primates compensate for seasonal variation in food… (more)

▼ Primates are challenged by spatiotemporal variation in resource availability, and a central question in biological anthropology is how primates compensate for seasonal variation in food resources by adjusting their foraging strategies. How primates respond to variation in invertebrate availability has rarely been the focus of studies of primate foraging ecology. This dissertation examines the role of insectivory in shaping foraging strategies, elucidates developmental differences in invertebrate foraging strategies, and investigates the role of the gut microbiome in mediating dietary changes in white-faced capuchins. White-faced capuchins (Cebus capucinus) are an instructive model for examining the influences of changes in both fruit and arthropod availability on foraging strategies, as they devote a mean of 44.4% of feeding and foraging time to fruit, 38.0% to invertebrates, and 1.2% to vertebrates. A group of 20-22 white-faced capuchins was studied from January 2013 through January 2014 at La Suerte Biological Field Station in northeastern Costa Rica. Data was collected from individually recognizable adult and juvenile capuchins on diet (fruit, invertebrates, leaves, seeds, vertebrates, other), activity budget (feeding, foraging, traveling, resting, social, other), affiliative and agonistic interactions, nearest neighbor identity and distance, foraging subgroup size and spread, and geographic location at 2-minute intervals during 1-hour focal follows. Crown volume, diameter at breast height, number of food items in the crown, and average mass of five food items was collected for each tree in which the group fed for more than four minutes in order to assess patch productivity. Every two weeks, fruit resource availability was tracked using 25 100x4 meter phenology transects, and invertebrate resource availability was assessed using 10 composite insect traps and sweep net sites. Fecal samples were collected throughout the study period (n=225). DNA was extracted from fecal samples, and the COI mtDNA and the v3-v5 region of the 16S rRNA genes were amplified and sequenced to identify invertebrates consumed and the gut microbial community structure. The second chapter uses social network analysis to quantify group-level responses of white-faced capuchins to changes in food availability. The results indicate that increases in fruit abundance and decreases in patch density increase group cohesion (network density = 0.48±0.01 during periods of high abundance and patch density, network density = 0.40±0.07 during periods of low abundance and patch density), indicating that individuals may be decreasing group cohesion as fruit resources become less available in order to avoid feeding competition. Additionally, the abundance and distribution of invertebrate resources does not have a consistent effect on group cohesion, and the results suggest that capuchins do not see invertebrates as a uniform resource. In the third chapter of my dissertation, innovative molecular methods are used to identify the taxa of invertebrates present… Advisors/Committee Members: Champaign%22%20%2Bcontributor%3A%28%22Garber%2C%20Paul%20A%22%29&pagesize-30">Garber, Paul A (advisor), Champaign%22%20%2Bcontributor%3A%28%22Garber%2C%20Paul%20A%22%29&pagesize-30">Garber, Paul A (Committee Chair), Champaign%22%20%2Bcontributor%3A%28%22Malhi%2C%20Ripan%20S%22%29&pagesize-30">Malhi, Ripan S (committee member), Champaign%22%20%2Bcontributor%3A%28%22Stumpf%2C%20Rebecca%20M%22%29&pagesize-30">Stumpf, Rebecca M (committee member), Champaign%22%20%2Bcontributor%3A%28%22MacKinnon%2C%20Katherine%20C%22%29&pagesize-30">MacKinnon, Katherine C (committee member).

Subjects/Keywords: white-faced capuchins; foraging ecology; DNA metabarcoding; gut microbiome

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Mallott, E. K. (2016). Social, ecological, and developmental influences on fruit and invertebrate foraging strategies and gut microbial communities in white-faced capuchins (Cebus capucinus). (Doctoral Dissertation). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/93005

Chicago Manual of Style (16^th Edition):

Mallott, Elizabeth K. “Social, ecological, and developmental influences on fruit and invertebrate foraging strategies and gut microbial communities in white-faced capuchins (Cebus capucinus).” 2016. Doctoral Dissertation, University of Illinois – Urbana-Champaign. Accessed March 03, 2021. http://hdl.handle.net/2142/93005.

MLA Handbook (7^th Edition):

Vancouver:

Mallott EK. Social, ecological, and developmental influences on fruit and invertebrate foraging strategies and gut microbial communities in white-faced capuchins (Cebus capucinus). [Internet] [Doctoral dissertation]. University of Illinois – Urbana-Champaign; 2016. [cited 2021 Mar 03]. Available from: http://hdl.handle.net/2142/93005.

Council of Science Editors:

Mallott EK. Social, ecological, and developmental influences on fruit and invertebrate foraging strategies and gut microbial communities in white-faced capuchins (Cebus capucinus). [Doctoral Dissertation]. University of Illinois – Urbana-Champaign; 2016. Available from: http://hdl.handle.net/2142/93005

10. Amato, Katherine. Black howler monkey (Alouatta pigra) nutrition: Integrating the study of behavior, feeding ecology, and the gut microbial community.

Degree: PhD, 5107, 2013, University of Illinois – Urbana-Champaign

URL: http://hdl.handle.net/2142/45368

► All animals, including primates, face the challenge of obtaining sufficient energy and nutrients despite 1) variation in food availability across habitats and seasons and 2)… (more)

▼ All animals, including primates, face the challenge of obtaining sufficient energy and nutrients despite 1) variation in food availability across habitats and seasons and 2) temporal fluctuations in nutritional requirements due to life history processes. Because variation in food availability or nutritional requirements requires animals to vary energy and nutrient intake, vary energy and nutrient expenditure, or vary digestion and assimilation of energy and nutrients to meet demands, many studies of primates examine shifts in primate activity budgets and foraging patterns across seasons and life history stages. However, few studies establish a direct relationship between activity and diet composition and energy and nutrient intake. Additionally, the mechanisms that primates use to digest and assimilate their food are largely overlooked. Mutualistic gut microbial communities impact host digestive efficiency and assimilation by breaking down otherwise indigestible material and providing hosts with energy and nutrients. Laboratory studies have demonstrated that gut microbial communities shift in response to changes in host diet and physiology, and while these shifts may allow hosts to digest food items more efficiently to meet energy and nutrient demands, no data are currently available to explore this relationship in wild primates. This dissertation describes an integrated 10-month field study investigating the behavioral and physiological mechanisms used by non-human primates to satisfy nutritional demands in response to changes in diet and physiology. Specifically, it examines the relationship between behavior, physiology and nutrition in two groups (N = 16 individuals) of wild, black howler monkeys (Alouatta pigra) in Palenque National Park, Chiapas. The first chapter explores patterns in black howler monkey nutritional intake across time to determine whether howlers employ a foraging strategy that regulates energy and/or nutrient intake and whether this strategy changes in response to the amount of ripe fruits or leaves in the howler diet. The second investigates the response of the howler monkey gut microbial community to changes in diet composition across time and the potential effects of changes in the gut microbial community on howler digestive efficiency and nutrition. Finally, the third chapter examines differences in activity, diet, and the gut microbiota among adult male, adult female, and juvenile howler monkeys to determine whether behavioral or physiological mechanisms allows adult females and juveniles to compensate for the increased nutritional demands of reproduction and growth. The data presented in this dissertation suggest that although they are able to consume large quantities of leaves periodically, on an annual basis, black howler monkeys consume more ripe fruits than leaves. They also exhibit a protein-regulating foraging strategy similar to that of ripe-fruit-specialist spider monkeys and consume more protein energy and more total energy than spider monkeys. These results indicate… Advisors/Committee Members: Champaign%22%20%2Bcontributor%3A%28%22Garber%2C%20Paul%20A.%22%29&pagesize-30">Garber, Paul A. (advisor), Champaign%22%20%2Bcontributor%3A%28%22Garber%2C%20Paul%20A.%22%29&pagesize-30">Garber, Paul A. (Committee Chair), Champaign%22%20%2Bcontributor%3A%28%22Kent%2C%20Angela%20D.%22%29&pagesize-30">Kent, Angela D. (committee member), Champaign%22%20%2Bcontributor%3A%28%22Leigh%2C%20Steven%20R.%22%29&pagesize-30">Leigh, Steven R. (committee member), Champaign%22%20%2Bcontributor%3A%28%22Malhi%2C%20Ripan%20S.%22%29&pagesize-30">Malhi, Ripan S. (committee member).

Subjects/Keywords: gut microbiota; nutrition; primate; Alouatta; feeding ecology

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Amato, K. (2013). Black howler monkey (Alouatta pigra) nutrition: Integrating the study of behavior, feeding ecology, and the gut microbial community. (Doctoral Dissertation). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/45368

Chicago Manual of Style (16^th Edition):

Amato, Katherine. “Black howler monkey (Alouatta pigra) nutrition: Integrating the study of behavior, feeding ecology, and the gut microbial community.” 2013. Doctoral Dissertation, University of Illinois – Urbana-Champaign. Accessed March 03, 2021. http://hdl.handle.net/2142/45368.

MLA Handbook (7^th Edition):

Amato, Katherine. “Black howler monkey (Alouatta pigra) nutrition: Integrating the study of behavior, feeding ecology, and the gut microbial community.” 2013. Web. 03 Mar 2021.

Vancouver:

Amato K. Black howler monkey (Alouatta pigra) nutrition: Integrating the study of behavior, feeding ecology, and the gut microbial community. [Internet] [Doctoral dissertation]. University of Illinois – Urbana-Champaign; 2013. [cited 2021 Mar 03]. Available from: http://hdl.handle.net/2142/45368.

Council of Science Editors:

Amato K. Black howler monkey (Alouatta pigra) nutrition: Integrating the study of behavior, feeding ecology, and the gut microbial community. [Doctoral Dissertation]. University of Illinois – Urbana-Champaign; 2013. Available from: http://hdl.handle.net/2142/45368

11. Olds, Brett. Analysis of genetic variation in Pediculus humanus and Populus trichocarpa.

Degree: PhD, 0314, 2013, University of Illinois – Urbana-Champaign

URL: http://hdl.handle.net/2142/44336

► With the advent of sequencing technologies that are both affordable and readily available, biologists are now able to address questions that were previously intractable. New… (more)

▼ With the advent of sequencing technologies that are both affordable and readily available, biologists are now able to address questions that were previously intractable. New species are having their genomes mapped at an increasing rate, including non-model organisms. Two such organisms are the human body louse, Pediculus humanus corporis and the black cottonwood, Populus trichocarpa. While unrelated, these two organisms each represent a study system with questions that challenge our current understanding of each organism. Body and head lice, while closely related, are thought to be separate species with their most important difference being that only body lice vector disease to humans. The first question is: Are body lice (Pediculus humanus coporis) and head lice (Pediculus humanus capitis) the same species? A total of 10,771 body louse and 10,770 head louse transcripts were predicted from a combined assembly of Roche 454 and Illumina sequenced cDNAs from whole body tissues collected at all life stages and during pesticide exposure and bacterial infection treatments. Illumina reads mapped to the 10,775 draft body louse gene models from the whole genome assembly predicted nine presence/absence differences, but PCR confirmation resulted in a single gene difference. One novel microRNA was predicted in both lice species and 99% of the 544 transcripts from Candidatus riesia indicate that they share the same endosymbiont. Overall, few differences exist, which supports the hypothesis that these two organisms are ecotypes of the same species. A second question is: Are there gene expression differences between these two organisms that cause the body louse to vector disease to humans while head lice do not? We utilized an RNAseq analysis on 7-day old head and body lice fed blood infected with Bartonella quintana, the bacterium that causes trench fever, and control individuals to elicit gene expression differences. Eight immunoresponse genes came out significant, many associated with the Toll pathway; Fibrinogen-related protein (PHUM500950), Spaetzle (PHUM595260), Defensin 1 (PHUM365700) and 2 (PHUM595870), Serpin (PHUM311330), Cactus (PHUM345810), Scavenger receptor A (ScavA; PHUM066640) and Apolipoprotein D (PHUM427700). Increased expression of Fibrinogen-related protein and Spaetzle, both related to the Toll pathway, in treated body lice supports the hypothesis that body lice are fighting infection from B. quintana. But conflicting results in Defensin 1 and 2 based upon validation method suggest another mechanism in head lice alternative to the Toll pathway might be involved. Additionally, Scavenger receptor A was higher in both control and treated head lice, suggesting higher phagocytotic activity in head lice to curb infection. In 1981, Whitham and Slobodchikoff hypothesized that long-lived plant species, like black cottonwood, that propagate both asexually and sexually, might develop, through accumulation of somatic mutations, as genetic mosaics, providing the potential to respond to or even outrun their insect… Advisors/Committee Members: Champaign%22%20%2Bcontributor%3A%28%22Paige%2C%20Ken%20N.%22%29&pagesize-30">Paige, Ken N. (advisor), Champaign%22%20%2Bcontributor%3A%28%22Pittendrigh%2C%20Barry%20R.%22%29&pagesize-30">Pittendrigh, Barry R. (advisor), Champaign%22%20%2Bcontributor%3A%28%22Paige%2C%20Ken%20N.%22%29&pagesize-30">Paige, Ken N. (Committee Chair), Champaign%22%20%2Bcontributor%3A%28%22Pittendrigh%2C%20Barry%20R.%22%29&pagesize-30">Pittendrigh, Barry R. (Committee Chair), Champaign%22%20%2Bcontributor%3A%28%22Hudson%2C%20Matthew%20E.%22%29&pagesize-30">Hudson, Matthew E. (committee member), Champaign%22%20%2Bcontributor%3A%28%22Malhi%2C%20Ripan%20S.%22%29&pagesize-30">Malhi, Ripan S. (committee member).

Subjects/Keywords: body louse; Pediculus humanus; Bartonella quintana; disease vector competency; black cottonwood; Populus trichocarpa; somatic mutation

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Olds, B. (2013). Analysis of genetic variation in Pediculus humanus and Populus trichocarpa. (Doctoral Dissertation). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/44336

Chicago Manual of Style (16^th Edition):

Olds, Brett. “Analysis of genetic variation in Pediculus humanus and Populus trichocarpa.” 2013. Doctoral Dissertation, University of Illinois – Urbana-Champaign. Accessed March 03, 2021. http://hdl.handle.net/2142/44336.

MLA Handbook (7^th Edition):

Olds, Brett. “Analysis of genetic variation in Pediculus humanus and Populus trichocarpa.” 2013. Web. 03 Mar 2021.

Vancouver:

Olds B. Analysis of genetic variation in Pediculus humanus and Populus trichocarpa. [Internet] [Doctoral dissertation]. University of Illinois – Urbana-Champaign; 2013. [cited 2021 Mar 03]. Available from: http://hdl.handle.net/2142/44336.

Council of Science Editors:

Olds B. Analysis of genetic variation in Pediculus humanus and Populus trichocarpa. [Doctoral Dissertation]. University of Illinois – Urbana-Champaign; 2013. Available from: http://hdl.handle.net/2142/44336

12. Yan, Caie. Social interaction and dispersal patterns of golden snub-nosed monkeys (Rhinopithecus roxellana) living in multi-level societies.

Degree: PhD, 0340, 2012, University of Illinois – Urbana-Champaign

URL: http://hdl.handle.net/2142/31175

► This study aimed to explore the benefits that individuals gain from group living and the role of kin and nonkin affiliation and cooperation in the… (more)

▼ This study aimed to explore the benefits that individuals gain from group living and the role of kin and nonkin affiliation and cooperation in the formation of social networks in primates by investigating the multi-level social structures exhibited by Sichuan snub-nosed monkeys (Rhinopithecus roxellana). The multi-level social network of snub-nosed monkeys composed of over 100 individuals, in which individuals form one-male breeding units (OMUs, which include one adult male, several adult females, and their offspring), all male units (AMUs), and bands (several OMUs that travel, feed and rest together). Given the fact that the majority of Asian colobines exhibit a harem social organization, multi-level societies of R. roxellana are proposed to have evolved through the aggregation of individual one-male groups. The specific objectives of this study are to explore 1) the social factors that help to maintain the stability of multilevel societies, 2) the benefits to individuals of forming a higher level social structure, 3) the presence and complexity of kinship networks and dispersal patterns in R. roxellana based on genetic data, and 4) the behavioral mechanisms regulating social interactions within multi-level social networks, and whether these are most consistent with kin selection theory, reciprocity theories, or biological market theory. Behavioral observations for this study were conducted at Zhouzhi National Natural Reserve, Shaanxi, China. A habituated band of snub-nosed monkeys was followed from September 2007 to August 2008. Along with behavioral observations, fecal samples were collected from the focal band and two neighboring bands. DNA was extracted from the fecal samples. The d-loop region of the mitochondrial DNA was amplified and sequenced for each sample. The behavioral data indicate that OMUs were socially and sexual independent since the majority of social and sexual interactions were restricted to members of the same OMU. Both direct affiliative and agonistic interactions between members of different OMUs were infrequent. Compared to the harems formed by other Asian colobines, the OMUs of R. roxellana were more cohesive. Leader males played a critical role in maintaining the cohesion of his OMU by actively threatening or chasing both adult and juvenile members of other OMUs that were within 5 meters of his harem. It is likely that the formation of multi-level societies in R. roxellana is the result of social and spatial tolerance among harem males in response to the foraging requirements associated with the exploitation of highly seasonal and low productive habitat. Three distinct haplotypes were found among 99 samples collected from the three neighboring bands. Based on the assumption that individuals with less frequent haplotypes represent immigrants from other bands, it was estimated that approximately 17-21% of females and 8-15% of males immigrated from neighboring bands. The genetic data also indicated that females transfer between OMUs within the same band since females with the same… Advisors/Committee Members: Champaign%22%20%2Bcontributor%3A%28%22Garber%2C%20Paul%20A.%22%29&pagesize-30">Garber, Paul A. (advisor), Champaign%22%20%2Bcontributor%3A%28%22Garber%2C%20Paul%20A.%22%29&pagesize-30">Garber, Paul A. (Committee Chair), Champaign%22%20%2Bcontributor%3A%28%22Malhi%2C%20Ripan%20S.%22%29&pagesize-30">Malhi, Ripan S. (committee member), Champaign%22%20%2Bcontributor%3A%28%22Stumpf%2C%20Rebecca%20M.%22%29&pagesize-30">Stumpf, Rebecca M. (committee member), Champaign%22%20%2Bcontributor%3A%28%22Swedell%2C%20Larissa%22%29&pagesize-30">Swedell, Larissa (committee member).

Subjects/Keywords: Rhinopithecus roxellana; snub-nosed monkey; multi-level society; social interaction; dispersal pattern; kin selection; reciprocity; biological market theory

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APA (6^th Edition):

Yan, C. (2012). Social interaction and dispersal patterns of golden snub-nosed monkeys (Rhinopithecus roxellana) living in multi-level societies. (Doctoral Dissertation). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/31175

Chicago Manual of Style (16^th Edition):

Yan, Caie. “Social interaction and dispersal patterns of golden snub-nosed monkeys (Rhinopithecus roxellana) living in multi-level societies.” 2012. Doctoral Dissertation, University of Illinois – Urbana-Champaign. Accessed March 03, 2021. http://hdl.handle.net/2142/31175.

MLA Handbook (7^th Edition):

Yan, Caie. “Social interaction and dispersal patterns of golden snub-nosed monkeys (Rhinopithecus roxellana) living in multi-level societies.” 2012. Web. 03 Mar 2021.

Vancouver:

Yan C. Social interaction and dispersal patterns of golden snub-nosed monkeys (Rhinopithecus roxellana) living in multi-level societies. [Internet] [Doctoral dissertation]. University of Illinois – Urbana-Champaign; 2012. [cited 2021 Mar 03]. Available from: http://hdl.handle.net/2142/31175.

Council of Science Editors:

Yan C. Social interaction and dispersal patterns of golden snub-nosed monkeys (Rhinopithecus roxellana) living in multi-level societies. [Doctoral Dissertation]. University of Illinois – Urbana-Champaign; 2012. Available from: http://hdl.handle.net/2142/31175

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Open Access Theses and Dissertations