Dimensions of distance: international flight connections, historical determinism, and economic relations in Africa

Purpose: The paper examines how distance manifests in terms of air passenger transport links between countries and focuses on the 48 countries of sub-Saharan Africa (SSA). It asks to what extent do existing flight connections reflect economic relations between countries and if so, do they represent past, current or future relations? It asks whether the impact of distance is similar for all countries and at different stages of development. Design/methodology/approach: Passenger flight connection data was extracted to generate map images and flight frequencies in order to observe inter-relationships between different locations and to observe emerging patterns. The paper uses ESRIs ArcGIS software to visualise all these data into maps. Findings: SSA is poorly connected both intra- and inter-continentally. Cultural and historical ties dominate and elements of historical determinism appear within flight connections in SSA reflecting the biases associated with colonialism. Larger economies in SSA are less dependent on these past ties and their flight connections reveal a greater level of diversity and interests. SSA has generally been slow to develop flight routings to the new emerging markets. Originality/value: Its contribution lies not only in examining these flight patterns for an under-researched region but aides in future work on SSA and its integration into the global economy and international business networks. It argues that whilst distance matters; how it matters varies

Chromosomal distribution of new genes.

<p>Most of the new genes are located on the unassembled contigs (U).</p

Additional file 2: of Detecting false positive sequence homology: a machine learning approach

Density estimation of RNA-seq base coverage used in [ 32 ]. (PDF 75 kb

Annotation pipeline.

<p>Four samples of <i>D. pseudoobscura</i> are independently annotated with Cufflinks and then merged with cuffcompare. Isoforms confirmed in at least two samples and having at least 2-fold coverage by unambiguous reads are retained. The filtered annotation is compared against the FlyBase annotation using cuffcompare retaining extended FlyBase isoforms ( = ), new isoforms (j), new genes located in introns (i) or intergenic regions (u). Gene fusions are filtered out from the extended and new isoforms with intersectBed. New genes overlapping FlyBase genes directly or indirectly through transcripts detected in only one sample are removed using intersectBed.</p

Comparison of reference-based approaches.

<p>¹Base level accuracy and percentage of confirmed junctions with different combinations of mapper and assembler on the sample ps94 males compared to the orthology annotation and the EST annotation (²based on 48 M reads).</p

Women's fear in sports and competition climbing

Summary of DROSO RNA-seq libraries. (XLSX 40 kb

Evaluation of Different Reference Based Annotation Strategies Using RNA-Seq – A Case Study in <i>Drososphila pseudoobscura</i>

<div><p>RNA-Seq is a powerful tool for the annotation of genomes, in particular for the identification of isoforms and UTRs. Nevertheless, several software tools exist and no standard strategy to obtain a reliable annotation is yet established. We tested different combinations of the most commonly used reference-based alignment tools (TopHat, GSNAP) in combination with two frequently used reference-based assemblers (Cufflinks, Scripture) and evaluated the potential of RNA-Seq to improve the annotation of <i>Drosophila pseudoobscura</i>. While GSNAP maps a higher proportion of reads, TopHat resulted in a more accurate annotation when used in combination with Cufflinks. Scripture had the lowest sensitivity. Interestingly, after subsampling to the same coverage for GSNAP and TopHat, we find that both mappers have similar performance, implying that the advantage of TopHat is mainly an artifact of the lower coverage. Overall, we observed a low concordance among the different approaches tested both at junction and isoform levels. Using data from both sexes of two adult strains of <i>D. pseudoobscura</i> we detected alternative splicing for about 30% of the FlyBase multiple-exon genes. Moreover, we extended the boundaries for 6523 genes (about 40%). We annotated 669 new genes, 45% of them with splicing evidence. Most of the new genes are located on unassembled contigs, reflecting their incomplete annotation. Finally, we identified 99 additional new genes that are not represented in the current genome contigs of <i>D. pseudoobscura</i>, probably due to location in genomic regions that are difficult to assemble (e.g. heterochromatic regions).</p></div

Comparison of our annotation <i>vs.</i> the FlyBase annotation r2.23.

<p>¹only considering multiple exon genes,</p><p>²only for the longest isoforms of each gene.</p

Alternative splicing in <i>D. pseudoobscura</i>.

<p>a) Distribution of number of isoforms per gene, b) Distribution of alternative splicing modes.</p

Effects of alternative splicing events on the coding sequence (CDS) in <i>D. pseudoobscura</i>.

<p>Stop codons are rare in all alternative splicing (AS) modes. Frameshifts show a more heterogeneous distribution, with intron retention events harboring most frameshifts.</p