Michael James Barker

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Chapters

• Barker, M. S. (2013). Karyotype and genome evolution in Pteridophytes. In Plant Genome Diversity, Volume 2(pp 245-253). Vienna: Springer.
• Barker, M. S., Baute, G. J., & Liu, S. (2012). Duplications and turnover in plant genomes. In Plant Genome Diversity, Volume 1(pp 155-169). Vienna: Springer.

Journals/Publications

• Barker, M. S., Arrigo, N., Baniaga, A. E., Li, Z., & Levin, D. A. (2015). On the relative abundance of autopolyploids and allopolyploids. New Phytologist.
• Edger, P. P., Heidel-Fischer, H. M., Bekaert, M., Rota, J., Gl{\"o}ckner, G., Platts, A. E., Heckel, D. G., Der, J. P., Wafula, E. K., Tang, M., & others, . (2015). The butterfly plant arms-race escalated by gene and genome duplications. Proceedings of the National Academy of Sciences, 112, 8362--8366.
• Li, Z., Baniaga, A. E., Sessa, E. B., Scascitelli, M., Graham, S. W., Rieseberg, L. H., & Barker, M. S. (2015). Early genome duplications in conifers and other seed plants. Science advances, 1, e1501084.
• Marques, I., Montgomery, S. A., Barker, M. S., Macfarlane, T. D., Conran, J. G., Catal{\'a}n, P., Rieseberg, L. H., Rudall, P. J., & Graham, S. W. (2015). Transcriptome-derived evidence supports recent polyploidization and a major phylogeographic division in Trithuria submersa (Hydatellaceae, Nymphaeales). New Phytologist.
• Mayrose, I., Zhan, S. H., Rothfels, C. J., Arrigo, N., Barker, M. S., Rieseberg, L. H., & Otto, S. P. (2015). Methods for studying polyploid diversification and the dead end hypothesis: a reply to Soltis et al. (2014). The New phytologist, 206(1), 27-35.
• Hodgins, K. A., Lai, Z., Oliveira, L. O., Still, D. W., Scascitelli, M., Barker, M. S., Kane, N. C., Dempewolf, H., Kozik, A., Kesseli, R. V., Burke, J. M., Michelmore, R. W., & Rieseberg, L. H. (2014). Genomics of compositae crops: Reference transcriptome assemblies and evidence of hybridization with wild relatives. Molecular Ecology Resources, 14(1), 166-177.
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  Abstract: Although the Compositae harbours only two major food crops, sunflower and lettuce, many other species in this family are utilized by humans and have experienced various levels of domestication. Here, we have used next-generation sequencing technology to develop 15 reference transcriptome assemblies for Compositae crops or their wild relatives. These data allow us to gain insight into the evolutionary and genomic consequences of plant domestication. Specifically, we performed Illumina sequencing of Cichorium endivia, Cichorium intybus, Echinacea angustifolia, Iva annua, Helianthus tuberosus, Dahlia hybrida, Leontodon taraxacoides and Glebionis segetum, as well 454 sequencing of Guizotia scabra, Stevia rebaudiana, Parthenium argentatum and Smallanthus sonchifolius. Illumina reads were assembled using Trinity, and 454 reads were assembled using MIRA and CAP3. We evaluated the coverage of the transcriptomes using BLASTX analysis of a set of ultra-conserved orthologs (UCOs) and recovered most of these genes (88-98%). We found a correlation between contig length and read length for the 454 assemblies, and greater contig lengths for the 454 compared with the Illumina assemblies. This suggests that longer reads can aid in the assembly of more complete transcripts. Finally, we compared the divergence of orthologs at synonymous sites (Ks) between Compositae crops and their wild relatives and found greater divergence when the progenitors were self-incompatible. We also found greater divergence between pairs of taxa that had some evidence of postzygotic isolation. For several more distantly related congeners, such as chicory and endive, we identified a signature of introgression in the distribution of Ks values. © 2013 John Wiley & Sons Ltd.
• Matasci, N., Hung, L., Yan, Z., Carpenter, E. J., Wickett, N. J., Mirarab, S., Nguyen, N., Warnow, T., Ayyampalayam, S., Barker, M., Burleigh, J. G., Gitzendanner, M. A., Wafula, E., Der, J. P., dePamphilis, C. W., Roure, B., Philippe, H., Ruhfel, B. R., Miles, N. W., , Graham, S. W., et al. (2014). Data access for the 1,000 Plants (1KP) project. GigaScience, 3, 17.
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  The 1,000 plants (1KP) project is an international multi-disciplinary consortium that has generated transcriptome data from over 1,000 plant species, with exemplars for all of the major lineages across the Viridiplantae (green plants) clade. Here, we describe how to access the data used in a phylogenomics analysis of the first 85 species, and how to visualize our gene and species trees. Users can develop computational pipelines to analyse these data, in conjunction with data of their own that they can upload. Computationally estimated protein-protein interactions and biochemical pathways can be visualized at another site. Finally, we comment on our future plans and how they fit within this scalable system for the dissemination, visualization, and analysis of large multi-species data sets.
• Sessa, E. B., Banks, J. A., Barker, M. S., Der, J. P., Duffy, A. M., Graham, S. W., Hasebe, M., Langdale, J., Li, F., Marchant, D. B., Pryer, K. M., Rothfels, C. J., Roux, S. J., Salmi, M. L., Sigel, E. M., Soltis, D. E., Soltis, P. S., Stevenson, D. W., & Wolf, P. G. (2014). Between two fern genomes. GigaScience, 3, 15.
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  Ferns are the only major lineage of vascular plants not represented by a sequenced nuclear genome. This lack of genome sequence information significantly impedes our ability to understand and reconstruct genome evolution not only in ferns, but across all land plants. Azolla and Ceratopteris are ideal and complementary candidates to be the first ferns to have their nuclear genomes sequenced. They differ dramatically in genome size, life history, and habit, and thus represent the immense diversity of extant ferns. Together, this pair of genomes will facilitate myriad large-scale comparative analyses across ferns and all land plants. Here we review the unique biological characteristics of ferns and describe a number of outstanding questions in plant biology that will benefit from the addition of ferns to the set of taxa with sequenced nuclear genomes. We explain why the fern clade is pivotal for understanding genome evolution across land plants, and we provide a rationale for how knowledge of fern genomes will enable progress in research beyond the ferns themselves.
• Wickett, N. J., Mirarab, S., Nguyen, N., Warnow, T., Carpenter, E., Matasci, N., Ayyampalayam, S., Barker, M. S., Burleigh, J. G., Gitzendanner, M. A., Ruhfel, B. R., Wafula, E., Der, J. P., Graham, S. W., Mathews, S., Melkonian, M., Soltis, D. E., Soltis, P. S., Miles, N. W., , Rothfels, C. J., et al. (2014). Phylotranscriptomic analysis of the origin and early diversification of land plants. Proceedings of the National Academy of Sciences of the United States of America, 111(45), E4859-68.
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  Reconstructing the origin and evolution of land plants and their algal relatives is a fundamental problem in plant phylogenetics, and is essential for understanding how critical adaptations arose, including the embryo, vascular tissue, seeds, and flowers. Despite advances in molecular systematics, some hypotheses of relationships remain weakly resolved. Inferring deep phylogenies with bouts of rapid diversification can be problematic; however, genome-scale data should significantly increase the number of informative characters for analyses. Recent phylogenomic reconstructions focused on the major divergences of plants have resulted in promising but inconsistent results. One limitation is sparse taxon sampling, likely resulting from the difficulty and cost of data generation. To address this limitation, transcriptome data for 92 streptophyte taxa were generated and analyzed along with 11 published plant genome sequences. Phylogenetic reconstructions were conducted using up to 852 nuclear genes and 1,701,170 aligned sites. Sixty-nine analyses were performed to test the robustness of phylogenetic inferences to permutations of the data matrix or to phylogenetic method, including supermatrix, supertree, and coalescent-based approaches, maximum-likelihood and Bayesian methods, partitioned and unpartitioned analyses, and amino acid versus DNA alignments. Among other results, we find robust support for a sister-group relationship between land plants and one group of streptophyte green algae, the Zygnematophyceae. Strong and robust support for a clade comprising liverworts and mosses is inconsistent with a widely accepted view of early land plant evolution, and suggests that phylogenetic hypotheses used to understand the evolution of fundamental plant traits should be reevaluated.
• Barker, M., Arrigo, N., Therrien, J., Anderson, C. L., Windham, M. D., Haufler, C. H., & Barker, M. S. (2013). A total evidence approach to understanding phylogenetic relationships and ecological diversity in Selaginella subg. Tetragonostachys. American journal of botany, 100(8).
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  Several members of Selaginella are renowned for their ability to survive extreme drought and "resurrect" when conditions improve. Many of these belong to subgenus Tetragonostachys, a group of ∼45 species primarily found in North and Central America, with substantial diversity in the Sonoran and Chihuahuan Deserts. We evaluated the monophyly and the age of subgenus Tetragonostachys and assess how drought tolerance contributed to the evolution of this clade.
• Arrigo, N., & Barker, M. S. (2012). Rarely successful polyploids and their legacy in plant genomes. Current Opinion in Plant Biology, 15(2), 140-146.
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  PMID: 22480430;Abstract: Polyploidy, or whole genome duplication, is recognized as an important feature of eukaryotic genome evolution. Among eukaryotes, polyploidy has probably had the largest evolutionary impact on vascular plants where many contemporary species are of recent polyploid origin. Genomic analyses have uncovered evidence of at least one round of polyploidy in the ancestry of most plants, fueling speculation that genome duplications lead to increases in net diversity. In spite of the frequency of ancient polyploidy, recent analyses have found that recently formed polyploid species have higher extinction rates than their diploid relatives. These results suggest that despite leaving a substantial legacy in plant genomes, only rare polyploids survive over the long term and most are evolutionary dead-ends. © 2012 Elsevier Ltd.
• Barker, M., Arrigo, N., Albert, L. P., Mickelson, P. G., & Barker, M. S. (2012). Quantitative visualization of biological data in Google Earth using R2G2, an R CRAN package. Molecular ecology resources, 12(6).
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  We briefly introduce R2G2, an R CRAN package to visualize spatially explicit biological data within the Google Earth interface. Our package combines a collection of basic graph-editing features, including automated placement of dots, segments, polygons, images (including graphs produced with R), along with several complex three-dimensional (3D) representations such as phylogenies, histograms and pie charts. We briefly present some example data sets and show the immediate benefits in communication gained from using the Google Earth interface to visually explore biological results. The package is distributed with detailed help pages providing examples and annotated source scripts with the hope that users will have an easy time using and further developing this package. R2G2 is distributed on http://cran.r-project.org/web/packages.
• Bowers, J. E., Nambeesan, S., Corbi, J., Barker, M. S., Rieseberg, L. H., Knapp, S. J., & Burke, J. M. (2012). Development of an Ultra-Dense Genetic Map of the Sunflower Genome Based on Single-Feature Polymorphisms. PLoS ONE, 7(12).
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  PMID: 23284684;PMCID: PMC3526535;Abstract: The development of ultra-dense genetic maps has the potential to facilitate detailed comparative genomic analyses and whole genome sequence assemblies. Here we describe the use of a custom Affymetrix GeneChip containing nearly 2.4 million features (25 bp sequences) targeting 86,023 unigenes from sunflower (Helianthus annuus L.) and related species to test for single-feature polymorphisms (SFPs) in a recombinant inbred line (RIL) mapping population derived from a cross between confectionery and oilseed sunflower lines (RHA280×RHA801). We then employed an existing genetic map derived from this same population to rigorously filter out low quality data and place 67,486 features corresponding to 22,481 unigenes on the sunflower genetic map. The resulting map contains a substantial fraction of all sunflower genes and will thus facilitate a number of downstream applications, including genome assembly and the identification of candidate genes underlying QTL or traits of interest. © 2012 Bowers et al.
• Lai, Z., Kane, N. C., Kozik, A., Hodgins, K. A., Dlugosch, K. M., Barker, M. S., Matvienko, M., Qian, Y. u., Turner, K. G., Pearl, S. A., D., G., Zou, Y., Grassa, C., Guggisberg, A., Adams, K. L., Anderson, J. V., Horvath, D. P., Kesseli, R. V., Burke, J. M., , Michelmore, R. W., et al. (2012). Genomics of compositae weeds: EST libraries, microarrays, and evidence of introgression. American Journal of Botany, 99(2), 209-218.
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  PMID: 22058181;Abstract: Premise of study: Weeds cause considerable environmental and economic damage. However, genomic characterization of weeds has lagged behind that of model plants and crop species. Here we describe the development of genomic tools and resources for 11 weeds from the Compositae family that will serve as a basis for subsequent population and comparative genomic analyses. Because hybridization has been suggested as a stimulus for the evolution of invasiveness, we also analyze these genomic data for evidence of hybridization. Methods: We generated 22 expressed sequence tag (EST) libraries for the 11 targeted weeds using Sanger, 454, and Illumina sequencing, compared the coverage and quality of sequence assemblies, and developed NimbleGen microarrays for expression analyses in five taxa. When possible, we also compared the distributions of Ks values between orthologs of congeneric taxa to detect and quantify hybridization and introgression. Results: Gene discovery was enhanced by sequencing from multiple tissues, normalization of cDNA libraries, and especially greater sequencing depth. However, assemblies from short sequence reads sometimes failed to resolve close paralogs. Substantial introgression was detected in Centaurea and Helianthus, but not in Ambrosia and Lactuca. Conclusions: Transcriptome sequencing using next-generation platforms has greatly reduced the cost of genomic studies of nonmodel organisms, and the ESTs and microarrays reported here will accelerate evolutionary and molecular investigations of Compositae weeds. Our study also shows how ortholog comparisons can be used to approximately estimate the genome-wide extent of introgression and to identify genes that have been exchanged between hybridizing taxa. © 2012 Botanical Society of America.
• Banks, J. A., Nishiyama, T., Hasebe, M., Bowman, J. L., Gribskov, M., DePamphilis, C., Albert, V. A., Aono, N., Aoyama, T., Ambrose, B. A., Ashton, N. W., Axtell, M. J., Barker, E., Barker, M. S., Bennetzen, J. L., Bonawitz, N. D., Chapple, C., Cheng, C., Gustavo, L., , Dacre, M., et al. (2011). The Selaginella genome identifies genetic changes associated with the evolution of vascular plants. Science, 332(6032), 960-963.
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  PMID: 21551031;PMCID: PMC3166216;Abstract: Vascular plants appeared ∼410 million years ago, then diverged into several lineages of which only two survive: the euphyllophytes (ferns and seed plants) and the lycophytes. We report here the genome sequence of the lycophyte Selaginella moellendorffii (Selaginella), the first nonseed vascular plant genome reported. By comparing gene content in evolutionarily diverse taxa, we found that the transition from a gametophyte- to a sporophyte-dominated life cycle required far fewer new genes than the transition from a nonseed vascular to a flowering plant, whereas secondary metabolic genes expanded extensively and in parallel in the lycophyte and angiosperm lineages. Selaginella differs in posttranscriptional gene regulation, including small RNA regulation of repetitive elements, an absence of the trans-acting small interfering RNA pathway, and extensive RNA editing of organellar genes.
• Der, J. P., Barker, M. S., Wickett, N. J., dePamphilis, C. W., & Wolf, P. G. (2011). De novo characterization of the gametophyte transcriptome in bracken fern, Pteridium aquilinum. BMC Genomics, 12.
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  PMID: 21303537;PMCID: PMC3042945;Abstract: Background: Because of their phylogenetic position and unique characteristics of their biology and life cycle, ferns represent an important lineage for studying the evolution of land plants. Large and complex genomes in ferns combined with the absence of economically important species have been a barrier to the development of genomic resources. However, high throughput sequencing technologies are now being widely applied to non-model species. We leveraged the Roche 454 GS-FLX Titanium pyrosequencing platform in sequencing the gametophyte transcriptome of bracken fern (Pteridium aquilinum) to develop genomic resources for evolutionary studies.Results: 681,722 quality and adapter trimmed reads totaling 254 Mbp were assembled de novo into 56,256 unique sequences (i.e. unigenes) with a mean length of 547.2 bp and a total assembly size of 30.8 Mbp with an average read-depth coverage of 7.0×. We estimate that 87% of the complete transcriptome has been sequenced and that all transcripts have been tagged. 61.8% of the unigenes had blastx hits in the NCBI nr protein database, representing 22,596 unique best hits. The longest open reading frame in 52.2% of the unigenes had positive domain matches in InterProScan searches. We assigned 46.2% of the unigenes with a GO functional annotation and 16.0% with an enzyme code annotation. Enzyme codes were used to retrieve and color KEGG pathway maps. A comparative genomics approach revealed a substantial proportion of genes expressed in bracken gametophytes to be shared across the genomes of Arabidopsis, Selaginella and Physcomitrella, and identified a substantial number of potentially novel fern genes. By comparing the list of Arabidopsis genes identified by blast with a list of gametophyte-specific Arabidopsis genes taken from the literature, we identified a set of potentially conserved gametophyte specific genes. We screened unigenes for repetitive sequences to identify 548 potentially-amplifiable simple sequence repeat loci and 689 expressed transposable elements.Conclusions: This study is the first comprehensive transcriptome analysis for a fern and represents an important scientific resource for comparative evolutionary and functional genomics studies in land plants. We demonstrate the utility of high-throughput sequencing of a normalized cDNA library for de novo transcriptome characterization and gene discovery in a non-model plant. © 2011 Der et al; licensee BioMed Central Ltd.
• Kane, N. C., Barker, M. S., Zhan, S. H., & Rieseberg, L. H. (2011). Molecular evolution across the asteraceae: Micro-and macroevolutionary processes. Molecular Biology and Evolution, 28(12), 3225-3235.
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  PMID: 21693439;Abstract: The Asteraceae (Compositae) is a large family of over 20,000 wild, weedy, and domesticated species that comprise approximately 10% of all angiosperms, including annual and perennial herbs, shrubs and trees, and species on every continent except Antarctica. As a result, the Asteraceae provide a unique opportunity to understand the evolutionary genomics of lineage radiation and diversification at numerous phylogenetic scales. Using publicly available expressed sequence tags from 22 species representing four of the major Asteraceae lineages, we assessed neutral and nonneutral evolutionary processes across this diverse plant family. We used bioinformatic tools to identify candidate genes under selection in each species. Evolution at silent and coding sites were assessed for different Gene Ontology functional categories to compare rates of evolution over both short and long evolutionary timescales. Our results indicate that patterns of molecular change across the family are surprisingly consistent on a macroevolutionary timescale and much more so more than would be predicted from the analysis of one (or many) examples of microevolution. These analyses also point to particular classes of genes that may be crucial in shaping the radiation of this diverse plant family. Similar analyses of nuclear and chloroplast genes in six other plant families confirm that many of these patterns are common features of the plant kingdom. © 2011 The Author.
• Mayrose, I., Zhan, S. H., Rothfels, C. J., Magnuson-Ford, K., Barker, M. S., Rieseberg, L. H., & Otto, S. P. (2011). Recently formed polyploid plants diversify at lower rates. Science, 333(6047), 1257-.
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  PMID: 21852456;
• Barker, M. S., & Wolf, P. G. (2010). Unfurling fern biology in the genomics age. BioScience, 60(3), 177-185.
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  Abstract: Twenty-first century technology is addressing many of the questions posed by 20th-century biology. Although the new approaches, especially those involving genomic data and bioinformatic tools, were first applied to model organisms, they are now stretching across the tree of life. Here, we review some recent revelations in the ferns. We first examine how DNA sequence data have contributed to our understanding of fern phylogeny. We then address evolution of the fern plastid genome, including reports of high levels of RNA editing. Recent studies are also shedding light on the evolution of fern nuclear genomes. Initial analyses of genomic data suggest that despite their very high chromosome numbers homosporous ferns may have experienced relatively few rounds of genome duplication. Genomic data are enabling researchers to examine speciation rates and the mechanisms underlying the formation of new fern species. We also describe genetic tools that have been used to study gene function and development in ferns. Recent findings in fern biology are providing insights that are not only pertinent to this major component of the land flora but can also help to provide an improved evolutionary context for research on flowering plants. © 2010 by American Institute of Biological Sciences. All rights reserved.
• Barker, M. S., Dlugosch, K. M., Dinh, L., Challa, R. S., Kane, N. C., King, M. G., & Rieseberg, L. H. (2010). Evopipes.net: Bioinformatic tools for ecological and evolutionary genomics. Evolutionary Bioinformatics, 2010(6), 143-149.
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  PMID: 21079755;PMCID: PMC2978936;Abstract: Recent increases in the production of genomic data are yielding new opportunities and challenges for biologists. Among the chief problems posed by next-generation sequencing are assembly and analyses of these large data sets. Here we present an online server, http://EvoPipes.net, that provides access to a wide range of tools for bioinformatic analyses of genomic data oriented for ecological and evolutionary biologists. The EvoPipes.net server includes a basic tool kit for analyses of genomic data including a next-generation sequence cleaning pipeline (SnoWhite), scaffolded assembly software (SCARF), a reciprocal best-blast hit ortholog pipeline (RBH Orthologs), a pipeline for reference protein-based translation and identification of reading frame in transcriptome and genomic DNA (TransPipe), a pipeline to identify gene families and summarize the history of gene duplications (DupPipe), and a tool for developing SSRs or microsatellites from a transcriptome or genomic coding sequence collection (findSSR). EvoPipes.net also provides links to other software developed for evolutionary and ecological genomics, including chromEvol and NU-IN, as well as a forum for discussions of issues relating to genomic analyses and interpretation of results. Overall, these applications provide a basic bioinformatic tool kit that will enable ecologists and evolutionary biologists with relatively little experience and computational resources to take advantage of the opportunities provided by next-generation sequencing in their systems. © the author(s), publisher and licensee Libertas Academica Ltd.
• Dempewolf, H., Kane, N. C., Ostevik, K. L., Geleta, M., Barker, M. S., Lai, Z., Stewart, M. L., Bekele, E., M., J., C., Q., & Rieseberg, L. H. (2010). Establishing genomic tools and resources for Guizotia abyssinica (L.f.) Cass.-the development of a library of expressed sequence tags, microsatellite loci, and the sequencing of its chloroplast genome. Molecular Ecology Resources, 10(6), 1048-1058.
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  PMID: 21565115;Abstract: We present an EST library, chloroplast genome sequence, and nuclear microsatellite markers that were developed for the semi-domesticated oilseed crop noug (Guizotia abyssinica) from Ethiopia. The EST library consists of 25-711 Sanger reads, assembled into 17-538 contigs and singletons, of which 4781 were functionally annotated using the Arabidopsis Information Resource (TAIR). The age distribution of duplicated genes in the EST library shows evidence of two paleopolyploidizations-a pattern that noug shares with several other species in the Heliantheae tribe (Compositae family). From the EST library, we selected 43 microsatellites and then designed and tested primers for their amplification. The number of microsatellite alleles varied between 2 and 10 (average 4.67), and the average observed and expected heterozygosities were 0.49 and 0.54, respectively. The chloroplast genome was sequenced de novo using Illumina's sequencing technology and completed with traditional Sanger sequencing. No large re-arrangements were found between the noug and sunflower chloroplast genomes, but 1.4% of sites have indels and 1.8% show sequence divergence between the two species. We identified 34 tRNAs, 4 rRNA sequences, and 80 coding sequences, including one region (trnH-psbA) with 15% sequence divergence between noug and sunflower that may be particularly useful for phylogeographic studies in noug and its wild relatives. © 2010 Blackwell Publishing Ltd.
• Dlugosch, K. M., Barker, M. S., & Rieseberg, L. H. (2010). NU-IN: Nucleotide evolution and input module for the EvolSimulator genome simulation platform. BMC Research Notes, 3.
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  PMID: 20678216;PMCID: PMC3161368;Abstract: Background. There is increasing demand to test hypotheses that contrast the evolution of genes and gene families among genomes, using simulations that work across these levels of organization. The EvolSimulator program was developed recently to provide a highly flexible platform for forward simulations of amino acid evolution in multiple related lineages of haploid genomes, permitting copy number variation and lateral gene transfer. Synonymous nucleotide evolution is not currently supported, however, and would be highly advantageous for comparisons to full genome, transcriptome, and single nucleotide polymorphism (SNP) datasets. In addition, EvolSimulator creates new genomes for each simulation, and does not allow the input of user-specified sequences and gene family information, limiting the incorporation of further biological realism and/or user manipulations of the data. Findings. We present modified C++ source code for the EvolSimulator platform, which we provide as the extension module NU-IN. With NU-IN, synonymous and non-synonymous nucleotide evolution is fully implemented, and the user has the ability to use real or previously-simulated sequence data to initiate a simulation of one or more lineages. Gene family membership can be optionally specified, as well as gene retention probabilities that model biased gene retention. We provide PERL scripts to assist the user in deriving this information from previous simulations. We demonstrate the features of NU-IN by simulating genome duplication (polyploidy) in the presence of ongoing copy number variation in an evolving lineage. This example is initiated with real genomic data, and produces output that we analyse directly with existing bioinformatic pipelines. Conclusions. The NU-IN extension module is a publicly available open source software (GNU GPLv3 license) extension to EvolSimulator. With the NU-IN module, users are now able to simulate both drift and selection at the nucleotide, amino acid, copy number, and gene family levels across sets of related genomes, for user-specified starting sequences and associated parameters. These features can be used to generate simulated genomic datasets under an extremely broad array of conditions, and with a high degree of biological realism. © 2010 Dlugosch et al; licensee BioMed Central Ltd.
• Mayrose, I., Barker, M. S., & Otto, S. P. (2010). Probabilistic models of chromosome number evolution and the inference of polyploidy. Systematic Biology, 59(2), 132-144.
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  PMID: 20525626;Abstract: Polyploidy, the genome wide duplication of chromosome number, is a key feature in eukaryote evolution. Polyploidy exists in diverse groups including animals, fungi, and invertebrates but is especially prevalent in plants with most, if not all, plant species having descended from a polyploidization event. Polyploids often differ markedly from their diploid progenitors in morphological, physiological, and life history characteristics as well as rates of adaptation. The altered characteristics displayed by polyploids may contribute to their success in novel ecological habitats. Clearly, a better understanding of the processes underlying changes in the number of chromosomes within genomes is a key goal in our understanding of speciation and adaptation for a wide range of families and genera. Despite the fundamental role of chromosome number change in eukaryotic evolution, probabilistic models describing the evolution of chromosome number along a phylogeny have not yet been formulated. We present a series of likelihood models, each representing a different hypothesis regarding the evolution of chromosome number along a given phylogeny. These models allow us to reconstruct ancestral chromosome numbers and to estimate the expected number of polyploidization events and single chromosome changes (dysploidy) that occurred along a phylogeny. We test, using simulations, the accuracy of this approach and its dependence on the number of taxa and tree length. We then demonstrate the application of the method for the study of chromosome number evolution in 4 plant genera: Aristolochia, Carex, Passiflora, and Helianthus. Considering the depth of the available cytological and phylogenetic data, formal models of chromosome number evolution are expected to advance significantly our understanding of the importance of polyploidy and dysploidy across different taxonomic groups.
• Shi, T., Huang, H., & Barker, M. S. (2010). Ancient genome duplications during the evolution of kiwifruit (Actinidia) and related Ericales. Annals of Botany, 106(3), 497-504.
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  PMID: 20576738;PMCID: PMC2924827;Abstract: Background and AimsTo assess the number and phylogenetic distribution of large-scale genome duplications in the ancestry of Actinidia, publicly available expressed sequenced tags (ESTs) for members of the Actinidiaceae and related Ericales, including tea (Camellia sinensis), were analysed.MethodsSynonymous divergences (Ks) were calculated for all duplications within gene families and examined for evidence of large-scale duplication events. Phylogenetic comparisons for a selection of orthologues among several related species in Ericales and two outgroups permitted placement of duplication events in relation to lineage divergences. Gene ontology (GO) categories were analysed for each whole-genome duplication (WGD) and the whole transcriptome.Key ResultsEvidence for three ancient WGDs in Actinidia was found. Analyses of paleologue GO categories indicated a different pattern of retained genes for each genome duplication, but a pattern consistent with the dosage-balance hypothesis among all retained paleologues.ConclusionsThis study provides evidence for one independent WGD in the ancestry of Actinidia (Ad-), a WGD shared by Actinidia and Camellia (Ad-), and the well-established At- WGD that occurred prior to the divergence of all taxa examined. More ESTs in other taxa are needed to elucidate which groups in Ericales share the Ad- or Ad- duplications and their impact on diversification. © The Author 2010.
• Barker, M. S., Dlugosch, K. M., Reddy, C. C., Amyotte, S. N., & Rieseberg, L. H. (2009). SCARF: Maximizing next-generation EST assemblies for evolutionary and population genomic analyses. Bioinformatics, 25(4), 535-536.
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  PMID: 19129211;Abstract: Scaffolded and Corrected Assembly of Roche 454 (SCARF) is a next-generation sequence assembly tool for evolutionary genomics that is designed especially for assembling 454 EST sequences against high-quality reference sequences from related species. The program was created to knit together 454 contigs that do not assemble during traditional de novo assembly, using a reference sequence library to orient the 454 sequences. © The Author 2009. Published by Oxford University Press. All rights reserved.
• Kane, N. C., King, M. G., Barker, M. S., Raduski, A., Karrenberg, S., Yatabe, Y., Knapp, S. J., & Rieseberg, L. H. (2009). Comparative genomic and population genetic analyses indicate highly porous genomes and high levels of gene flow between divergent helianthus species. Evolution, 63(8), 2061-2075.
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  PMID: 19473382;PMCID: PMC2731706;Abstract: While speciation can be found in the presence of gene flow, it is not clear what impact this gene flow has on genome- and range-wide patterns of differentiation. Here we examine gene flow across the entire range of the common sunflower, H. annuus, its historically allopatric sister species H. argophyllus and a more distantly related, sympatric relative H. petiolaris. Analysis of genotypes at 26 microsatellite loci in 1015 individuals from across the range of the three species showed substantial introgression between geographically proximal populations of H. annuus and H. petiolaris, limited introgression between H. annuus and H. argophyllus, and essentially no gene flow between the allopatric pair, H. argophyllus and H. petiolaris. Analysis of sequence divergence levels among the three species in 1420 orthologs identified from EST databases identified a subset of loci showing extremely low divergence between H. annuus and H. petiolaris and extremely high divergence between the sister species H. annuus and H. argophyllus, consistent with introgression between H. annuus and H. petiolaris at these loci. Thus, at many loci, the allopatric sister species are more genetically divergent than the more distantly related sympatric species, which have exchanged genes across much of the genome while remaining morphologically and ecologically distinct. © 2009 The Society for the Study of Evolution.
• Wood, T. E., Takebayashi, N., Barker, M. S., Mayrose, I., Greenspoon, P. B., & Rieseberg, L. H. (2009). The frequency of polyploid speciation in vascular plants. Proceedings of the National Academy of Sciences of the United States of America, 106(33), 13875-13879.
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  PMID: 19667210;PMCID: PMC2728988;Abstract: Since its discovery in 1907, polyploidy has been recognized as an important phenomenon in vascular plants, and several lines of evidence indicate that most, if not all, plant species ultimately have a polyploid ancestry. However, previous estimates of the frequency of polyploid speciation suggest that the formation and establishment of neopolyploid species is rare. By combining information from the botanical community's vast cytogenetic and phylogenetic databases, we establish that 15% of angiosperm and 31% of fern speciation events are accompanied by ploidy increase. These frequency estimates are higher by a factor of four than earlier estimates and lead to a standing incidence of polyploid species within genera of 35% (n = 1,506). Despite this high incidence, we find no direct evidence that polyploid lines, once established, enjoy greater net species diversification. Thus, the widespread occurrence of polyploid taxa appears to result from the substantial contribution of polyploidy to cladogenesis, but not from subsequent increases in diversification rates of polyploid lines.
• Barker, M. S., Kane, N. C., Matvienko, M., Kozik, A., Michelmore, R. W., Knapp, S. J., & Rieseberg, L. H. (2008). Multiple paleopolyploidizations during the evolution of the compositae reveal parallel patterns of duplicate gene retention after millions of years. Molecular Biology and Evolution, 25(11), 2445-2455.
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  PMID: 18728074;PMCID: PMC2727391;Abstract: Of the approximately 250,000 species of flowering plants, nearly one in ten are members of the Compositae (Asteraceae), a diverse family found in almost every habitat on all continents except Antarctica. With an origin in the mid Eocene, the Compositae is also a relatively young family with remarkable diversifications during the last 40 My. Previous cytologic and systematic investigations suggested that paleopolyploidy may have occurred in at least one Compositae lineage, but a recent analysis of genomic data was equivocal. We tested for evidence of paleopolyploidy in the evolutionary history of the family using recently available expressed sequence tag (EST) data from the Compositae Genome Project. Combined with data available on GenBank, we analyzed nearly 1 million ESTs from 18 species representing seven genera and four tribes. Our analyses revealed at least three ancient whole-genome duplications in the Compositae - a paleopolyploidization shared by all analyzed taxa and placed near the origin of the family just prior to the rapid radiation of its tribes and independent genome duplications near the base of the tribes Mutisieae and Heliantheae. These results are consistent with previous research implicating paleopolyploidy in the evolution and diversification of the Heliantheae. Further, we observed parallel retention of duplicate genes from the basal Compositae genome duplication across all tribes, despite divergence times of 33-38 My among these lineages. This pattern of retention was also repeated for the paleologs from the Heliantheae duplication. Intriguingly, the categories of genes retained in duplicate were substantially different from those in Arabidopsis. In particular, we found that genes annotated to structural components or cellular organization Gene Ontology categories were significantly enriched among paleologs, whereas genes associated with transcription and other regulatory functions were significantly underrepresented. Our results suggest that paleopolyploidy can yield strikingly consistent signatures of gene retention in plant genomes despite extensive lineage radiations and recurrent genome duplications but that these patterns vary substantially among higher taxonomic categories. © The Author 2008. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved.
• Shaw, S. W., Sprunt, S. V., & Barker, M. S. (2008). Contribution to the Pteridophyte flora of Puerto Rico. American Fern Journal, 98(2), 107-111.
• Brandvain, Y., Barker, M. S., & Wade, M. J. (2007). Gene co-inheritance and gene transfer. Science, 315(5819), 1685-.
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  PMID: 17379800;Abstract: Unexpectedly, in plant taxa that reproduce by self-pollination or cloning, more mitochondrial genes have shifted to the nucleus than in taxa that reproduce sexually.
• Barker, M. S., & Hickey, R. J. (2006). A taxonomic revision of Caribbean Adiantopsis (Pteridaceae). Annals of the Missouri Botanical Garden, 93(3), 371-401.
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  Abstract: Adiantopsis Fée (Pteridaceae) is a relatively unstudied tropical cheilanthoid fern genus. In the present work, we evaluated the taxonomy and relationships among Caribbean Adiantopsis by examining 136 characters from approximately 500 herbarium specimens. This study identified nine Caribbean Adiantopsis species, three of which are newly described (A. parvisegmenta, A. pentagona, and A. vincentii). Additionally, an intriguing pattern of morphological and reticulate evolution was revealed by the analyses. Adiantopsis consists of three different laminar morphologies; palmate, pedate, and pinnate. The two pedate taxa are hypothesized to be fertile allotetraploid derivatives of the palmate A. radiata (L.) Fée and two different pinnate taxa. In this regard they parallel the origin of the South American A. Xaustralopedata Hickey, M. S. Barker & Ponce. Based on our analyses, it appears that pedate laminar morphologies in Adiantopsis independently originated multiple times via hybridization. This study provides testable hypotheses of morphological and reticulate evolution in the genus and presents a novel view of Caribbean Adiantopsis.
• Barker, M. S., Demuth, J. P., & Wade, M. J. (2005). Maternal expression relaxes constraint on innovation of the anterior determinant, bicoid.. PLoS genetics, 1(5), e57.
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  PMID: 16299585;PMCID: PMC1283158;Abstract: The origin of evolutionary novelty is believed to involve both positive selection and relaxed developmental constraint. In flies, the redesign of anterior patterning during embryogenesis is a major developmental innovation and the rapidly evolving Hox gene, bicoid (bcd), plays a critical role. We report evidence for relaxation of selective constraint acting on bicoid as a result of its maternal pattern of gene expression. Evolutionary theory predicts 2-fold greater sequence diversity for maternal effect genes than for zygotically expressed genes, because natural selection is only half as effective acting on autosomal genes expressed in one sex as it is on genes expressed in both sexes. We sample an individual from ten populations of Drosophila melanogaster and nine populations of D. simulans for polymorphism in the tandem gene duplicates bcd, which is maternally expressed, and zerknüllt (zen), which is zygotically expressed. In both species, we find the ratio of bcd to zen nucleotide diversity to be two or more in the coding regions but one in the noncoding regions, providing the first quantitative support for the theoretical prediction of relaxed selective constraint on maternal-effect genes resulting from sex-limited expression. Our results suggest that the accelerated rate of evolution observed for bcd is owing, at least partly, to variation generated by relaxed selective constraint.
• Barker, M. S., Shaw, S. W., Hickey, R. J., Rawlins, J. E., & Fetzner Jr., J. W. (2005). Lepidopteran soral crypsis on Caribbean ferns. Biotropica, 37(2), 314-316.
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  Abstract: Insect-fern interactions are not as well characterized as insect-angiosperm interactions. For example, the imitation of unique fern structures by insects has not been observed. On a recent trip to Puerto Rico, we collected ferns that bore small Lepidoptera imitating fern sori. Herbarium specimen searches indicate that these Lepidoptera are restricted to the Caribbean on ferns with highly visible sporangia. A possible selective pressure for the evolution of lepidopteran soral crypsis is wasp parasitism, as evidence of parasitoid wasps was found. However, it is more likely that soral crypsis evolved to avoid visually oriented predators such as birds or lizards.
• Shaw, S. W., Barker, M. S., & Hickey, R. J. (2004). New records for Puerto Rican pteridophytes. Fern Gazette, 17(2), 97-99.
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  Abstract: During a 2001-2002 collecting trip to Puerto Rico, eleven pteridophytes were collected that are Puerto Rican município records. Of the 11 collections, one is a Puerto Rican endemic Selaginella. For each specimen, we provide full collection data and previously known Puerto Rican distributions for the species.
• Barker, M. S., & Hauk, W. D. (2003). An evaluation of Sceptridium dissectum (Ophioglossaceae) with ISSR markers: Implications for Sceptridium systematics. American Fern Journal, 93(1), 1-19.
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  Abstract: Sceptridium dissectum, the most variable North American grapefern species, demonstrates variation in degree of blade dissection, blade color, pinnule shape, and pinnule margins. Historically, various morphologies have been included within S. dissectum. For example, Clausen's monograph recognized five infraspecific taxa in S. dissectum, of which only the morphologies of variety dissectum and obliquum are currently retained. However, the taxonomic status of the two varieties has been debated. We used ISSR (Inter-Simple Sequence Repeat) markers to assess the genetic distinctness of S. dissectum var. dissectum and var. obliquum in 17 Ohio populations. Five ISSR primers generated 69 reproducible loci. In UPGMA analyses and AMOVA, S. dissectum var. dissectum individuals did not cluster separately from var. obliquum individuals, nor did individuals from the same population cluster together. ISSR markers revealed levels of population genetic structure in S. dissectum similar to levels detected by previous isozyme investigations. Our results concur with recent treatments of S. dissectum that do not formally recognize infraspecific taxa, and may bring into question current species circumscriptions in Sceptridium. We illustrate the use of ISSR markers for examining taxonomic boundaries in Sceptridium.
• Hauk, W. D., & Barker, M. S. (2003). Botrychium lanceolatum subsp. angustisegmentum in Ohio. American Fern Journal, 93(2), 93-94.
• Hickey, R. J., Barker, M. S., & Ponce, M. (2003). An Adiantopsis hybrid from Northeastern Argentina and vicinity. American Fern Journal, 93(1), 42-44.