College of Agriculture & Natural Resources
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The collections in this community comprise faculty research works, as well as graduate theses and dissertations.
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Item Population Declines and Genetic Variation: Effects of Serial Bottlenecks(2015) Callicrate, Taylor Eilers; Song, Jiuzhou; Fleischer, Robert C; Animal Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Islands foster unique biodiversity, yet also present biogeographic limitations that impose increased risk for population extinction through demographic and genetic constraints and decreased probability of surviving a catastrophe. Of particular interest, especially with regard to endangered species, is the genetic response of insular species to severe population declines or translocations. Both types of events, considered population bottlenecks, are expected to reduce genetic variation, and correspondingly, adaptive potential. For these reasons, it is important to understand how bottlenecks interact with insular population dynamics to affect genetic diversity. I used a combination of a laboratory model experiment and population genetics study of an in situ bottleneck in an endangered species to investigate how quantitative and molecular genetic variation are affected during bottlenecks. I used a laboratory animal model (red flour beetle, Tribolium castaneum) to compare how quantitative genetic variation is affected if a serial bottleneck occurs in a novel versus familiar environment. The experiment was designed to model a founder event or translocation to a new island with a novel environment. I found that phenotypic and additive variance for a quantitative trait were larger following a bottleneck occurring in the novel environment, suggesting that the novel environment could improve adaptive potential in bottlenecked populations. Next, I used molecular genetic markers to assess variation and signatures of selection in the Laysan finch (Telespiza cantans), a Hawaiian honeycreeper endemic to a small Northwestern Hawaiian island. Laysan finches experienced a major bottleneck on Laysan in the early 20th century, followed by a translocation and series of founder events as populations were established on the islets of Pearl and Hermes Reef (PHR) in the 1960s – 70s. I found that, contrary to expectation, bottlenecked Laysan finch populations did not show declines in genetic variation and were not differentiated as a result of genetic drift. These results are potentially caused by insular demographic dynamics. I identified loci with extreme differentiation between modern populations, potentially indicating genomic signals of selection. These regions could be important for adaptation to the novel environment on PHR and are candidates for future study.Item GENETIC DIVERSITY AND LINKAGE DISEQUILIBRIUM IN WILD SOYBEAN, LANDRACES, ANCESTRAL, AND ELITE SOYBEAN POPULATIONS(2005-04-20) Hyten, Jr., David Lee; Costa, Jose M.; Plant Science and Landscape Architecture (PSLA); Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Domestication, founder effects, and artificial selection can impact populations by reducing genome diversity and increasing the extent of linkage disequilibrium (LD). To understand the impact of these genetic bottlenecks and selection on sequence diversity and LD within soybean [Glycine max (L.) Merr.], 111 genes and three chromosomal regions located on linkage groups A2, G, and J were characterized in soybean. Four soybean populations were evaluated: 1) the wild ancestor of soybean (G. soja), 2) the population resulting from domestication (landraces), 3) Asian introductions from which North American cultivars were developed (ancestors), and 4) elite cultivars from the 1980's (elite). A total of 438 single nucleotide polymorphisms (SNPs) and 58 insertions-deletions were discovered within the 102 genes. Sequence diversity was lower than expected in G. soja with an overall theta equal to 0.00235, and was less than half that value (theta = 0.00115) in the landraces. Domestication eliminated most unique haplotypes with G. soja containing 240 unique haplotypes while the landraces only contained 42 unique haplotypes. The founder effect of the introduction of soybean to North America followed by intensive artificial selection, resulted in only a 30% decrease in nucleotide diversity. A total of 738 SNPs were discovered and genotyped in the four populations throughout three chromosomal regions. In G. soja LD did not extend past 100 kb while in the three cultivated soybean populations LD extended from 90 kb up to 600+ kb, most likely as a result of increased inbreeding and domestication. The three chromosomal regions varied in the extent of LD within the populations. G. soja is the greatest resource for unique alleles and may be best suited for fine mapping utilizing association analysis. The landraces do not contain much more variability than the elite cultivars but may have enough diversity to facilitate genetic improvement of elite cultivars. Finally, due to the extended levels of LD in the landraces and the elite cultivars, whole genome association analysis may be possible for the discovery of QTL.