Reconstructing the Population Genetic History of the Caribbean

The Caribbean basin is home to some of the most complex interactions in recent history among previously diverged human populations. Here, we investigate the population genetic history of this region by characterizing patterns of genome-wide variation among 330 individuals from three of the Greater Antilles (Cuba, Puerto Rico, Hispaniola), two mainland (Honduras, Colombia), and three Native South American (Yukpa, Bari, and Warao) populations. We combine these data with a unique database of genomic variation in over 3,000 individuals from diverse European, African, and Native American populations. We use local ancestry inference and tract length distributions to test different demographic scenarios for the pre- and post-colonial history of the region. We develop a novel ancestry-specific PCA (ASPCA) method to reconstruct the sub-continental origin of Native American, European, and African haplotypes from admixed genomes. We find that the most likely source of the indigenous ancestry in Caribbean islanders is a Native South American component shared among inland Amazonian tribes, Central America, and the Yucatan peninsula, suggesting extensive gene flow across the Caribbean in pre-Columbian times. We find evidence of two pulses of African migration. The first pulse—which today is reflected by shorter, older ancestry tracts—consists of a genetic component more similar to coastal West African regions involved in early stages of the trans-Atlantic slave trade. The second pulse—reflected by longer, younger tracts—is more similar to present-day West-Central African populations, supporting historical records of later transatlantic deportation. Surprisingly, we also identify a Latino-specific European component that has significantly diverged from its parental Iberian source populations, presumably as a result of small European founder population size. We demonstrate that the ancestral components in admixed genomes can be traced back to distinct sub-continental source populations with far greater resolution than previously thought, even when limited pre-Columbian Caribbean haplotypes have survived.     

Habitat restoration and native grass conservation: a case study of switchgrass (Panicum virgatum)

Switchgrass (Panicum virgatum) has been planted extensively for habitat restoration across the United States, such as with the Conservation Reserve Program (CRP). However, genetic profiles of these populations have never been studied nor compared with those of remnant prairies or cultivars. In this study, we sampled 16 CRP and 17 prairie populations across eastern Kansas. We assessed ploidy levels of all populations and compared genetic diversity and structure of 10 prairies, 10 CRP areas, and 5 standard cultivars, using nine simple sequence repeat (SSR) DNA markers. All CRP and prairie populations were octaploid (8x), except two prairies with both hexaploid (6x) and octaploid (8x) individuals. Based on the results of SSR analyses, there were no significant differences between CRP and prairie populations in genetic diversity, and 94% of total variation was partitioned within populations. Similarities among prairie and CRP populations were also observed in Bayesian clustering algorithms and principal coordinate analysis, suggesting that they had similar genetic compositions. In addition, positive spatial autocorrelations were detected up to 42 and 46 km among prairie and among CRP populations, respectively. To conclude, the CRP and prairie populations shared similar genetic profiles. However, remnant prairies still harbored unique genotypes and a high level of genetic diversity, highlighting the importance of seed sources for restoration efforts, that is using local wild seeds or cultivars from the same geographical region. A popular tetraploid (4x) cultivar known as “Kanlow” was genetically distinct from the prairie populations and therefore is not recommended for habitat restoration in this region.     

Reinvestigation of the O-antigens of Yersinia pseudotuberculosis: revision of the O2c and confirmation of the O3 antigen structures

Structures of the O-antigens of Yersinia pseudotuberculosis O2c and O3 were reinvestigated by NMR spectroscopy, including 2D (1)H,(1)H COSY, TOCSY, ROESY, (1)H,(13)C HSQC, and HMBC experiments. The following revised structure of the O2c tetrasaccharide repeating unit was established, which differs from the structure proposed earlier in the glycosylation pattern of the mannose residue at the branching point: where Abe stands for 3,6-dideoxy-d-xylo-hexose. The structure of the Y. pseudotuberculosis O3 antigen reported earlier was confirmed.     

Decoding Diffusivity in Multiple Sclerosis: Analysis of Optic Radiation Lesional and Non-Lesional White Matter

Objectives

Diffusion tensor imaging (DTI) has been suggested as a new promising tool in MS that may provide greater pathological specificity than conventional MRI, helping, therefore, to elucidate disease pathogenesis and monitor therapeutic efficacy. However, the pathological substrates that underpin alterations in brain tissue diffusivity are not yet fully delineated. Tract-specific DTI analysis has previously been proposed in an attempt to alleviate this problem. Here, we extended this approach by segmenting a single tract into areas bound by seemingly similar pathological processes, which may better delineate the potential association between DTI metrics and underlying tissue damage.

Method

Several compartments were segmented in optic radiation (OR) of 50 relapsing-remitting MS patients including T2 lesions, proximal and distal parts of fibers transected by lesion and fibers with no discernable pathology throughout the entire length of the OR.

Results

Asymmetry analysis between lesional and non-lesional fibers demonstrated a marked increase in Radial Diffusivity (RD), which was topographically limited to focal T2 lesions and potentially relates to the lesional myelin loss. A relative elevation of Axial Diffusivity (AD) in the distal part of the lesional fibers was observed in a distribution consistent with Wallerian degeneration, while diffusivity in the proximal portion of transected axons remained normal. A moderate, but significant elevation of RD in OR non-lesional fibers was strongly associated with the global (but not local) T2 lesion burden and is probably related to microscopic demyelination undetected by conventional MRI.

Conclusion

This study highlights the utility of the compartmentalization approach in elucidating the pathological substrates of diffusivity and demonstrates the presence of tissue-specific patterns of altered diffusivity in MS, providing further evidence that DTI is a sensitive marker of tissue damage in both lesions and NAWM. Our results suggest that, at least within the OR, parallel and perpendicular diffusivities are affected by tissue restructuring related to distinct pathological processes.     

The response of stream periphyton to Pacific salmon: using a model to understand the role of environmental context

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The Characterization of Twenty Sequenced Human Genomes

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