Methods for statistical and population genetics analyses.

Genetics studies have advanced rapidly, from candidate region studies to genome wide association studies (GWAS) and next generation sequencing projects. The emergence of new technologies has brought with it an array of statistical challenges. In this thesis, we propose methods for statistical and population genetics in our effort to better understand the underlying architecture of our genomes. GWAS rely on indirect association, testing a reduced set of representative markers (tagSNPs) instead of all variants present in the genome. In the first chapter, we propose a graph-based method to select the optimal set of tagSNPs. We apply our method to chromosome-wide data and show that it outperforms the widely used greedy approach, selecting fewer tagSNPs while maintaining high correlation with non-tagSNPs variants. Alignment to a reference sequence is an integral step in many sequencing studies. Multiply mapped reads, reads that align to multiple locations in the reference, are discarded from downstream analyses, resulting in a loss of information. We develop a Gibbs sampling approach to identify the true location of multiply mapped reads obtained from the alignment step. We validate our method using simulation studies. We use the improvement in variant discovery to quantify the effect of including multiply mapped reads in downstream analyses. In the third chapter, we explore the feasibility of admixture mapping, a population genetics tool, in identifying regions harboring rare susceptibility variants. We compare the power of admixture mapping to single marker association studies in detecting causal regions. We find that admixture mapping performs better over a wide range of risk allele frequencies. The site frequency spectrum (SFS) is an important summary statistic in population genetics, encompassing information on selection and demographic history. We show that estimates of the SFS obtained from genotype calling methods underestimate the number of rare variants, especially singletons and doubletons. We derive a maximum likelihood estimate for the SFS. We demonstrate that our method performs better than SFS obtained from genotype calling algorithms using both simulated and real data examples.Ph.D.BiostatisticsUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/89609/1/gopalakr_1.pd

Economic impact of fluctuations in oilsardine landings in India

The Indian oilsardine Sardinella longiceps  (Valenciennes, 1847) is a significant contributor to the marine fisheries economy of India. The species showed wide fluctuations in landings in the past and during recent years, the decline in landings is an issue of concern for sustainable harvest of the resourcee specially in the context of climate change regime.The paper analysed the economic impacts of fluctuations in oilsardine landings in terms of gross earnings realised at landing centre and retail levels; inflation in the domestic markets and external trade during the 2000-2018 period. The analysis indicated that the decline in landings was more in the state of Kerala as compared to all India landings. The inflation at point of first sales (landing centre level) was more during 2000-09 period whereas at retail market level inflation was highest during 2010-18. The inflationary pressure on domestic consumers in Kerala was more during 2010-18 period. The growth in external trade of sardines was in tune with the Indian oilsardine landings in the country

Structure and regeneration status of mangrove patches along the estuarine and coastal stretches of Kerala, India

This study presents the structural characteristics and regeneration potential of mangrove patches in the estuarine and coastal areas of Kerala, a tropical maritime state in India. Field surveys were carried out at 46 selected sites during August 2015 to May 2016. In each site, the vegetative structure and regeneration status were assessed using the quadrat method. Altogether 219 quadrates were laid out and a total of 13 true mangrove species, belonging to 5 families and 8 genera, were recorded. The total tree density and stand basal area of the study region was 1678.08/ha and 20.33 m2/ha respectively. The low basal areas indicate the reduced structural development in mangroves. Of the 13 tree species, Avicennia constitutes 56% of the total Important Value Index (IVI) and Avicennia officinalis represents 41% of the IVI in Kerala, followed by Avicennia marina (15%), Rhizophora mucronata (15%), Sonneratia alba (8%) Rhizophora apiculata (7%) and Excoecaria agallocha (7%). The diameter at breast height (DBH) in the study area revealed that 47% of the tree species came under the 1–10 cm DBH class. Total sapling and seedling density in Kerala was 2238.35 and 3232.42 individuals/ha respectively. Density of young plants (seedlings ? saplings) was only 31% greater of tree density and varied from 3–63%, which indicates poor regeneration potential. The Maturity index value (MIV) and complexity index (Ic) value of mangroves were 18.30 and 109.81 respectively. However, the low Ic value (\10) observed in seven out of ten coastal districts indicated poor structural development of mangroves in Kerala. Therefore, locationspecific conservation and management measures, guided by the knowledge on spatial distribution and habitat requirements of mangrove varieties should be taken to preserve the mangrove diversity of Kerala

Conservation genomics of the endangered Seychelles Magpie‐Robin (Copsychus sechellarum):a unique insight into the history of a precious endemic bird

The Seychelles Magpie-Robin Copsychus sechellarum is an IUCN Red-List Endangered species endemic to the Seychelles, whose population was reduced to eight individuals on a single island in the 1960s. Translocations from the remaining population to four additional islands have been an integral factor in their recovery, but the potential genetic consequences of their translocation history have not previously been explored. We resequenced the genomes of 141 individuals sampled across the five current island populations and analysed the data to characterize their population structure, as well as to explore suspected inbreeding. Overall, very low levels of heterozygosity were observed, all coupled with long homozygous segments that suggest recent inbreeding, probably the consequence of a population bottleneck in the 1960s. Three of the four translocated populations displayed less genetic diversity than the founder population from which they were taken, a familiar pattern observed as a result of the evolutionary force of genetic drift following founder events. Furthermore, and perhaps surprising given the recent time since the new populations were established, population structure was observed within these same three populations. New awareness of inbreeding in the Seychelles Magpie-Robin populations, and continued genetic monitoring, will allow for genetically informed management decisions. This is particularly prudent in maximizing the success of the future conservation translocation planned for this species

The extinct Sicilian wolf shows a complex history of isolation and admixture with ancient dogs

The Sicilian wolf remained isolated in Sicily from the end of the Pleistocene until its extermination in the 1930s–1960s. Given its long-term isolation on the island and distinctive morphology, the genetic origin of the Sicilian wolf remains debated. We sequenced four nuclear genomes and five mitogenomes from the seven existing museum specimens to investigate the Sicilian wolf ancestry, relationships with extant and extinct wolves and dogs, and diversity. Our results show that the Sicilian wolf is most closely related to the Italian wolf but carries ancestry from a lineage related to European Eneolithic and Bronze Age dogs. The average nucleotide diversity of the Sicilian wolf was half of the Italian wolf, with 37–50% of its genome contained in runs of homozygosity. Overall, we show that, by the time it went extinct, the Sicilian wolf had high inbreeding and low-genetic diversity, consistent with a population in an insular environmen

Article The extinct Sicilian wolf shows a complex history of isolation and admixture with ancient dogs

The Sicilian wolf remained isolated in Sicily from the end of the Pleistocene until its extermination in the 1930s-1960s. Given its long-term isolation on the island and distinctive morphology, the genetic origin of the Sicilian wolf remains debated. We sequenced four nuclear genomes and five mitogenomes from the seven existing museum specimens to investigate the Sicilian wolf ancestry, rela-tionships with extant and extinct wolves and dogs, and diversity. Our results show that the Sicilian wolf is most closely related to the Italian wolf but carries ancestry from a lineage related to European Eneolithic and Bronze Age dogs. The average nucleotide diversity of the Sicilian wolf was half of the Italian wolf, with 37-50% of its genome contained in runs of homozygosity. Overall, we show that, by the time it went extinct, the Sicilian wolf had high inbreeding and low-genetic diversity, consistent with a population in an insular environment

Travel Tales of a Worldwide Weed: Genomic Signatures of Plantago major L. Reveal Distinct Genotypic Groups With Links to Colonial Trade Routes

Retracing pathways of historical species introductions is fundamental to understanding the factors involved in the successful colonization and spread, centuries after a species’ establishment in an introduced range. Numerous plants have been introduced to regions outside their native ranges both intentionally and accidentally by European voyagers and early colonists making transoceanic journeys; however, records are scarce to document this. We use genotyping-by-sequencing and genotype-likelihood methods on the selfing, global weed, Plantago major, collected from 50 populations worldwide to investigate how patterns of genomic diversity are distributed among populations of this global weed. Although genomic differentiation among populations is found to be low, we identify six unique genotype groups showing very little sign of admixture and low degree of outcrossing among them. We show that genotype groups are latitudinally restricted, and that more than one successful genotype colonized and spread into the introduced ranges. With the exception of New Zealand, only one genotype group is present in the Southern Hemisphere. Three of the most prevalent genotypes present in the native Eurasian range gave rise to introduced populations in the Americas, Africa, Australia, and New Zealand, which could lend support to the hypothesis that P. major was unknowlingly dispersed by early European colonists. Dispersal of multiple successful genotypes is a likely reason for success. Genomic signatures and phylogeographic methods can provide new perspectives on the drivers behind the historic introductions and the successful colonization of introduced species, contributing to our understanding of the role of genomic variation for successful establishment of introduced taxa.info:eu-repo/semantics/publishedVersio

Travel Tales of a Worldwide Weed: Genomic Signatures of Plantago major L. Reveal Distinct Genotypic Groups With Links to Colonial Trade Routes

Retracing pathways of historical species introductions is fundamental to understanding the factors involved in the successful colonization and spread, centuries after a species’ establishment in an introduced range. Numerous plants have been introduced to regions outside their native ranges both intentionally and accidentally by European voyagers and early colonists making transoceanic journeys; however, records are scarce to document this. We use genotyping-by-sequencing and genotype-likelihood methods on the selfing, global weed, Plantago major, collected from 50 populations worldwide to investigate how patterns of genomic diversity are distributed among populations of this global weed. Although genomic differentiation among populations is found to be low, we identify six unique genotype groups showing very little sign of admixture and low degree of outcrossing among them. We show that genotype groups are latitudinally restricted, and that more than one successful genotype colonized and spread into the introduced ranges. With the exception of New Zealand, only one genotype group is present in the Southern Hemisphere. Three of the most prevalent genotypes present in the native Eurasian range gave rise to introduced populations in the Americas, Africa, Australia, and New Zealand, which could lend support to the hypothesis that P. major was unknowlingly dispersed by early European colonists. Dispersal of multiple successful genotypes is a likely reason for success. Genomic signatures and phylogeographic methods can provide new perspectives on the drivers behind the historic introductions and the successful colonization of introduced species, contributing to our understanding of the role of genomic variation for successful establishment of introduced taxa.publishedVersio