Whole Genome Phylogenetic Tree Reconstruction Using Colored de Bruijn Graphs

We present kleuren, a novel assembly-free method to reconstruct phylogenetic trees using the Colored de Bruijn Graph. kleuren works by constructing the Colored de Bruijn Graph and then traversing it, finding bubble structures in the graph that provide phylogenetic signal. The bubbles are then aligned and concatenated to form a supermatrix, from which a phylogenetic tree is inferred. We introduce the algorithms that kleuren uses to accomplish this task, and show its performance on reconstructing the phylogenetic tree of 12 Drosophila species. kleuren reconstructed the established phylogenetic tree accurately, and is a viable tool for phylogenetic tree reconstruction using whole genome sequences. Software package available at: https://github.com/Colelyman/kleurenComment: 6 pages, 3 figures, accepted at BIBE 2017. Minor modifications to the text due to reviewer feedback and fixed typo

Light environment drives evolution of color vision genes in butterflies and moths

Opsins, combined with a chromophore, are the primary light-sensing molecules in animals and are crucial for color vision. Throughout animal evolution, duplications and losses of opsin proteins are common, but it is unclear what is driving these gains and losses. Light availability is implicated, and dim environments are often associated with low opsin diversity and loss. Correlations between high opsin diversity and bright environments, however, are tenuous. To test if increased light availability is associated with opsin diversification, we examined diel niche and identified opsins using transcriptomes and genomes of 175 butterflies and moths (Lepidoptera). We found 14 independent opsin duplications associated with bright environments. Estimating their rates of evolution revealed that opsins from diurnal taxa evolve faster—at least 13 amino acids were identified with higher dN/dS rates, with a subset close enough to the chromophore to tune the opsin. These results demonstrate that high light availability increases opsin diversity and evolution rate in Lepidoptera

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

Targeted Amplicon Sequencing (TAS): A Scalable Next-Gen Approach to Multilocus, Multitaxa Phylogenetics

Next-gen sequencing technologies have revolutionized data collection in genetic studies and advanced genome biology to novel frontiers. However, to date, next-gen technologies have been used principally for whole genome sequencing and transcriptome sequencing. Yet many questions in population genetics and systematics rely on sequencing specific genes of known function or diversity levels. Here, we describe a targeted amplicon sequencing (TAS) approach capitalizing on next-gen capacity to sequence large numbers of targeted gene regions from a large number of samples. Our TAS approach is easily scalable, simple in execution, neither time-nor labor-intensive, relatively inexpensive, and can be applied to a broad diversity of organisms and/or genes. Our TAS approach includes a bioinformatic application, BarcodeCrucher, to take raw next-gen sequence reads and perform quality control checks and convert the data into FASTA format organized by gene and sample, ready for phylogenetic analyses. We demonstrate our approach by sequencing targeted genes of known phylogenetic utility to estimate a phylogeny for the Pancrustacea. We generated data from 44 taxa using 68 different 10-bp multiplexing identifiers. The overall quality of data produced was robust and was informative for phylogeny estimation. The potential for this method to produce copious amounts of data from a single 454 plate (e.g., 325 taxa for 24 loci) significantly reduces sequencing expenses incurred from traditional Sanger sequencing. We further discuss the advantages and disadvantages of this method, while offering suggestions to enhance the approach

Reflectance spectra of Heliconiine butterfly yellow wing pigments

Reflectance spectra of yellow wing colors of Heliconius butterflies and their relatives used in the color space model of birds and butterflies shown in Figure 4 of Bybee et al. Averaged reflectances and location of individual measurements on the wings are shown in Appendix

Appendix: Wing photomicrographs and averaged yellow reflectance spectra

Photomicrographs of butterfly wings and averaged yellow reflectance spectra. Color-coded circles indicate the location from which the associated reflectance spectra were sampled. N=number of individual specimens measured. Left column: Dorsal wings and dorsal reflectance spectra, Right column: Ventral wings and ventral reflectance spectra. FD, forewing dorsal; FV, forewing ventral; HD, hindwing dorsal; HV, hindwing ventral

UV opsin nucleotide sequences

Fasta file for UV opsin gene tree

BEAST XML file

BEAST XML file used for the best analysis based on MLE comparison and including 2 uncorrelated lognormal clocks and a birth death Tree mode

File S2 - MrBayes input file

MrBayes input file for the phylogenetic inferenc