02729nas a2200313 4500008004100000022001400041245014100055210006900196260001600265300001200281490000700293520176300300653001002063653001502073653001602088653001802104653001802122100001902140700002102159700002302180700002202203700001802225700002502243700002102268700002002289700002202309700002302331856006102354 2017 eng d a1063-515700aPhylogenomics using Target-restricted Assembly Resolves Intra-generic Relationships of Parasitic Lice (Phthiraptera: Columbicola)0 aPhylogenomics using Targetrestricted Assembly Resolves Intragene cJul-01-2018 a896-9110 v663 a

Parasitic “wing lice” (Phthiraptera: Columbicola) and their dove and pigeon hosts are a well-recognized model system for coevolutionary studies at the intersection of micro- and macroevolution. Selection on lice in microevolutionary time occurs as pigeons and doves defend themselves against lice by preening. In turn, behavioral and morphological adaptations of the lice improve their ability to evade host defense. Over macroevolutionary time wing lice tend to cospeciate with their hosts; yet, some species of Columbicola have switched to new host species. Understanding the ecological and evolutionary factors that influence coadaptation and codiversification in this system will substantially improve our understanding of coevolution in general. However, further work is hampered by the lack of a robust phylogenetic framework for Columbicola spp. and their hosts. Previous attempts to resolve the phylogeny of Columbicola based on sequences from a few genes provided limited support. Here, we apply a new approach, target restricted assembly, to assemble 977 orthologous gene sequences from whole-genome sequence data generated from very small, ethanol-preserved specimens, representing up to 61 species of wing lice. Both concatenation and coalescent methods were used to estimate the species tree. These two approaches yielded consistent and well-supported trees with 90% of all relationships receiving 100% support, which is a substantial improvement over previous studies. We used this new phylogeny to show that biogeographic ranges are generally conserved within clades of Columbicola wing lice. Limited inconsistencies are probably attributable to intercontinental dispersal of hosts, and host switching by some of the lice.

10aaTRAM10acoalescent10acoevolution10aconcatenation10aspecies tree.1 aBoyd, Bret, M.1 aAllen, Julie, M.1 aNguyen, Nam-phuong1 aSweet, Andrew, D.1 aWarnow, Tandy1 aShapiro, Michael, D.1 aVilla, Scott, M.1 aBush, Sarah, E.1 aClayton, Dale, H.1 aJohnson, Kevin, P. uhttps://academic.oup.com/sysbio/article/66/6/896/292940203205nas a2200313 4500008004100000022001400041245005800055210005800113260001600171300001200187490000700199520223300206653006002439100002102499700001902520700002302539700002402562700001802586700002102604700002502625700002002650700002202670700002202692700002702714700003002741700002002771700002302791856007702814 2017 eng d a1063-515700aPhylogenomics from Whole Genome Sequences Using aTRAM0 aPhylogenomics from Whole Genome Sequences Using aTRAM cJan-01-2019 a786-7980 v663 a

Abstract.—Novel sequencing technologies are rapidly expanding the size of data sets that can be applied to phylogenetic studies. Currently the most commonly used phylogenomic approaches involve some form of genome reduction. While these approaches make assembling phylogenomic data sets more economical for organisms with large genomes, they reduce the genomic coverage and thereby the long-term utility of the data. Currently, for organisms with moderate to small genomes (<1000 Mbp) it is feasible to sequence the entire genome at modest coverage (10−30×). Computational challenges for handling these large data sets can be alleviated by assembling targeted reads, rather than assembling the entire genome, to produce a phylogenomic data matrix. Here we demonstrate the use of automated Target Restricted Assembly Method (aTRAM) to assemble 1107 single-copy ortholog genes from whole genome sequencing of sucking lice (Anoplura) and out-groups. We developed a pipeline to extract exon sequences from the aTRAM assemblies by annotating them with respect to the original target protein. We aligned these protein sequences with the inferred amino acids and then performed phylogenetic analyses on both the concatenated matrix of genes and on each gene separately in a coalescent analysis. Finally, we tested the limits of successful assembly in aTRAM by assembling 100 genes from close- to distantly related taxa at high to low levels of coverage.
Both the concatenated analysis and the coalescent-based analysis produced the same tree topology, which was consistent with previously published results and resolved weakly supported nodes. These results demonstrate that this approach is successful at developing phylogenomic data sets from raw genome sequencing reads. Further, we found that with coverages above 5−10×, aTRAM was successful at assembling 80–90% of the contigs for both close and distantly related taxa. As sequencing costs continue to decline, we expect full genome sequencing will become more feasible for a wider array of organisms, and aTRAM will enable mining of these genomic data sets for an extensive variety of applications, including phylogenomics.

10aaTRAM; gene assembly; genome sequencing; phylogenomics.1 aAllen, Julie, M.1 aBoyd, Bret, M.1 aNguyen, Nam-phuong1 aVachaspati, Pranjal1 aWarnow, Tandy1 aHuang, Daisie, I1 aGrady, Patrick, G.S.1 aBell, Kayce, C.1 aCronk, Quentin, C1 aMugisha, Lawrence1 aPittendrigh, Barry, R.1 aLeonardi, MarĂ­a, Soledad1 aReed, David, L.1 aJohnson, Kevin, P. uhttps://academic.oup.com/sysbio/article-lookup/doi/10.1093/sysbio/syw105