Data from: Phylogenomic mining of the mints reveals multiple mechanisms contributing to the evolution of chemical diversity in Lamiaceae
Contributors: Mint Evolutionary Genomics Consortium
... The evolution of chemical complexity has been a major driver of plant diversification, with novel compounds serving as key innovations. The species-rich mint family (Lamiaceae) produces an enormous variety of compounds that act as attractants and defense molecules in nature and are used widely by humans as flavor additives, fragrances, and anti-herbivory agents. To elucidate the mechanisms by which such diversity evolved, we combined leaf transcriptome data from 48 Lamiaceae species and four outgroups with a robust phylogeny and chemical analyses of three terpenoid classes (monoterpenes, sesquiterpenes, iridoids) that share and compete for precursors. Our integrated chemical-genomic-phylogenetic approach revealed that: 1) gene family expansion rather than increased enzyme promiscuity of terpene synthases is correlated with mono- and sesqui-terpene diversity; 2) differential expression of core genes within the iridoid biosynthetic pathway is associated with iridoid presence/absence; 3) generally, production of iridoids and canonical monoterpenes appeared to be inversely correlated; and 4) iridoid biosynthesis was significantly associated with expression of geraniol synthase, which diverts metabolic flux away from canonical monoterpenes, suggesting that competition for common precursors can be a central control point in specialized metabolism. These results suggest that multiple mechanisms contributed to the evolution of chemodiversity in this economically important family. ----------MINT EVOLUTIONARY GENOMICS CONSORTIUM MEMBERS: Benoît Boachon¹, C. Robin Buell², Emily Crisovan², Natalia Dudareva¹, Nicolas Garcia³*, Grant Godden² ³, Laura Henry¹, Mohamed O. Kamileen⁴, Heather Rose Kates³, Matthew B. Kilgore¹, Benjamin R. Lichman⁴, Evgeny V. Mavrodiev³, Linsey Newton², Carlos Rodriguez-Lopez⁴, Sarah E. O’Connor⁴, Douglas Soltis³ ⁵, Pamela Soltis³, Brieanne Vaillancourt², Krystle Wiegert-Rininger², Dongyan Zhao² ---------- ¹Department of Biochemistry, Purdue University, West Lafayette, IN 47907-2063, USA ²Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA ³Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA ⁴The John Innes Centre, Department of Biological Chemistry, Norwich, NR4 7UH, UK ⁵Department of Biology, University of Florida, Gainesville, FL 32611, USA ---------- Current address: *Herbario EIF/Laboratorio de Sistemática y Evolución de Plantas, Facultad de Ciencias Forestales y de la Conservación de la Naturaleza, Universidad de Chile, Av. Santa Rosa 11315, La Pintana, Santiago, Chile ---------- For Correspondence: C. Robin Buell; email@example.com; Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA; 517-353-5597
Data from: Finite element analysis of microwave scattering from a three dimensional human head model for brain stroke detection
Contributors: Qureshi, Awais M., Mustansar, Zartasha, Mustafa, Samah
... In this paper, a detailed analysis of microwave scattering from a three dimensional (3-D) anthropomorphic human head model is presented. It is the first time that Finite Element Method (FEM) has been deployed to study the microwave scattering phenomenon of a 3-D realistic head model for brain stroke detection. A major contribution of this paper is to add anatomically more realistic details into the human head model compared to the literature available to-date. Using MRI database, a 3-D numerical head model was developed and segmented into 21 different types through a novel tissue mapping scheme and a mixed-model approach. The heterogeneous and frequency-dispersive dielectric properties to brain tissues were assigned using the same mapping technique. To mimic the simulation setup, an 8-elements antenna array around the head model was designed using dipole antennas. Two types of brain stroke (Hemorrhagic and Ischemic) at various locations inside the head model were then analyzed for possible detection and classification. The transmitted and backscattered signals were calculated by finding out the solution of Helmholtz wave equation in frequency-domain using FEM. FE mesh convergence analysis for electric field values and comparison between different types of iterative solver were also performed to obtain error-free results in a minimum computational time. At the end, a Specific Absorption Rate analysis was conducted to examine the ionization effects of microwave signals to a 3-D human head model. Through computer simulations, it is foreseen that microwave imaging may efficiently be exploited to locate and differentiate two types of brain stroke by detecting abnormal tissue’s dielectric properties. A significant contrast between electric field values of the normal and stroke affected brain tissues was observed at the stroke location. This is a step towards generating microwave scattering information for the development of an efficient image reconstruction algorithm.
Data from: Insular biogeographic origins and high phylogenetic distinctiveness for a recently depleted lizard fauna from Christmas Island, Australia
Contributors: Oliver, Paul M., Blom, Mozes P.K., Cogger, Harold G., Fisher, Robert N., Richmond, Jonathan Q., Woinarski, John C.Z.
... Striking faunal turnover across Asia and Australasia, most famously along the eastern edge of the Sunda Shelf or ‘Wallace’s Line’, has been a focus of biogeographic research for over 150 years. Here we investigate the origins of a highly threatened endemic lizard fauna (4 species) on Christmas Island. Despite occurring less 350 km south of the Sunda Shelf, this fauna mostly comprises species from clades centred on the more distant regions of Wallacea, the Pacific and Australia (> 1000 km east). The three most divergent lineages show Miocene (~23–5mya) divergences from sampled relatives; and have recently become extinct or extinct in the wild, likely due to the recent introduction of a south-east Asian snake (Lycodon capucinus). Insular distributions, deep phylogenetic divergence and recent decline, suggest that rather than dispersal ability or recent origins, environmental and biotic barriers have impeded these lineages from diversifying on the continental Sunda Shelf, and thereby, reinforced faunal differentiation across Wallace’s Line. Our new phylogenetically informed perspective further highlights the rapid loss of ancient lineages that has occurred on Christmas Island, and underlines how the evolutionary divergence and vulnerability of many island-associated lineages may continue to be underestimated.
Data from: Distinguishing between convergent evolution and violation of the molecular clock for three taxa
Contributors: Mitchell, Jonathan D., Sumner, Jeremy G., Holland, Barbara R.
... We give a non-technical introduction to convergence-divergence models, a new modeling approach for phylogenetic data that allows for the usual divergence of lineages after lineage-splitting but also allows for taxa to converge, i.e. become more similar over time. By examining the 3-taxon case in some detail we illustrate that phylogeneticists have been ``spoiled'' in the sense of not having to think about the structural parameters in their models by virtue of the strong assumption that evolution is tree-like. We show that there are not always good statistical reasons to prefer the usual class of tree-like models over more general convergence-divergence models. Specifically we show many 3-taxon data sets can be equally well explained by supposing violation of the molecular clock due to change in the rate of evolution along different edges, or by keeping the assumption of a constant rate of evolution but instead assuming that evolution is not a purely divergent process. Given the abundance of evidence that evolution is not strictly tree-like, our discussion is an illustration that as phylogeneticists we need to think clearly about the structural form of the models we use. For cases with four taxa we show that there will be far greater ability to distinguish models with convergence from non-clock-like tree models.
Data from: Determining the genetic basis of anthracycline-cardiotoxicity by response QTL mapping in induced cardiomyocytes
Contributors: Knowles, David A., Burrows, Courtney K., Blischak, John D., Patterson, Kristen M., Serie, Daniel J., Norton, Nadine, Ober, Carole, Pritchard, Jonathan K., Gilad, Yoav
... Anthracycline-induced cardiotoxicity (ACT) is a key limiting factor in setting optimal chemotherapy regimes, with almost half of patients expected to develop congestive heart failure given high doses. However, the genetic basis of sensitivity to anthracyclines remains unclear. We created a panel of iPSC-derived cardiomyocytes from 45 individuals and performed RNA-seq after 24h exposure to varying doxorubicin dosages. The transcriptomic response is substantial: the majority of genes are differentially expressed and over 6000 genes show evidence of differential splicing, the later driven by reduced splicing fidelity in the presence of doxorubicin. We show that inter-individual variation in transcriptional response is predictive of in vitro cell damage, which in turn is associated with in vivo ACT risk. We detect 447 response-expression QTLs and 42 response-splicing QTLs, which are enriched in lower ACT GWAS p-values, supporting the in vivo relevance of our map of gene tic regulation of cellular response to anthracyclines.
Data from: Reinstatement of the Southern Andean genus Stenodraba (Brassicaceae) based on molecular data and insights from its environmental and geographic distribution
Contributors: Salariato, Diego L., Al-Shehbaz, Ihsan A., Zuloaga, Fernando O.
... Stenodraba (Brassicaceae) included a group of eight species distributed along the Andes of South-Central Argentina and Chile. All of its species were subsequently transferred to other genera and are currently treated in Pennellia (Tribe Halimolobeae) and Weberbauera (Tribe Thelypodieae). However, the phylogeny of Stenodraba and its tribal placement were never analyzed using molecular data. The lack of such studies, as well as paucity of herbarium collections suggesting that some species are vulnerable and/or endangered, prompted us to address the molecular phylogeny of Stenodraba. For this purpose, we generated comprehensive molecular phylogenies using nuclear (ITS) and plastid (trnL-F and trnH-psbA) data, and conducted different niche comparisons in the environmental and geographic space using climate data processed both by ordination and species distribution modelling (SDM) techniques. The results demonstrated that Stenodraba belongs to the South American tribe Eudemeae and is related to the genera Aschersoniodoxa, Brayopsis, Dactylocardamum, and Eudema. Stenodraba species formed two, strongly supported clades, and although molecular data did not recover monophyly of the genus, this hypothesis was not significantly rejected. The main clades were differentiated in their climatic niches (both in the environmental and geographical spaces), and niche overlap was greater within than between clades. Systematic implications, including a key distinguishing Stenodraba from the remaining genera of Eudemeae and a synopsis of its species, are also provided.
Data from: Dispersal is associated with morphological innovation, but not increased diversification, in Cyphostemma (Vitaceae)
Contributors: Hearn, David J, Evans, Margaret, Wolf, Ben, McGinty, Michael, Wen, Jun
... Multiple processes - including dispersal, morphological innovation, and habitat change - are frequently cited as catalysts for increased diversification. We investigate these processes and the causal linkages among them in the genus Cyphostemma (Vitaceae), a clade comprising ~200 species that is unique in the Vitaceae for its diversity of growth habits. We reconstruct time-calibrated evolutionary relationships among 64 species in the genus using five nuclear and chloroplast markers, and infer the group’s morphological and biogeographic history. We test for changes in speciation rate, and evaluate the temporal association and sequencing of events with respect to dispersal, habitat change, and morphological evolution using a Monte Carlo simulation approach. In Cyphostemma, neither dispersal nor morphological evolution is associated with shifts in speciation rate, but dispersal is associated with evolutionary shifts in growth form. Evolution of stem succulence, in particular, is associated with adaptation to local, pre-existing conditions following long-distance dispersal, not habitat change in situ. We suggest that the pattern of association between dispersal, morphological innovation, and diversification may depend on the particular characters under study. Lineages with evolutionarily labile characters, such as stem succulence, do not necessarily conform to the notion of niche conservatism and instead demonstrate remarkable morphological adaptation to local climate and edaphic conditions following dispersal.
Data from: Demography or selection on linked cultural traits or genes? Investigating the driver of low mtDNA diversity in the sperm whale using complementary mitochondrial and nuclear genome analyses
Contributors: Morin, Phillip A., Foote, Andrew D., Baker, C. Scott, Hancock-Hanser, Brittany L., Kaschner, Kristin, Mate, Bruce R., Mesnick, Sarah L., Pease, Victoria L., Rosel, Patricia E., Alexander, Alana
... Mitochondrial DNA has been heavily utilized in phylogeography studies for several decades. However, underlying patterns of demography and phylogeography may be misrepresented due to coalescence stochasticity, selection, variation in mutation rates, and cultural hitchhiking (linkage of genetic variation to culturally transmitted traits affecting fitness). Cultural hitchhiking has been suggested as an explanation for low genetic diversity in species with strong social structures, counteracting even high mobility, abundance and limited barriers to dispersal. One such species is the sperm whale, which shows very limited phylogeographic structure and low mtDNA diversity despite a worldwide distribution and large population. Here, we use analyses of 175 globally distributed mitogenomes and three nuclear genomes to evaluate hypotheses of a population bottleneck/expansion versus a selective sweep due to cultural-hitchhiking or selection on mtDNA as the mechanism contributing to low worldwide mitochondrial diversity in sperm whales. In contrast to mtDNA control region (CR) data, mitogenome haplotypes are largely ocean-specific, with only one of 80 shared between the Atlantic and Pacific. Demographic analyses of nuclear genomes suggest low mtDNA diversity is consistent with a global reduction in population size that ended approximately 125,000 years ago, correlated with the Eemian interglacial. Phylogeographic analysis suggests that extant sperm whales descend from maternal lineages endemic to the Pacific during the period of reduced abundance, and have subsequently colonized the Atlantic several times. Results highlight the apparent impact of past climate change, and suggest selection and hitchhiking are not the sole processes responsible for low mtDNA diversity in this highly social species.
Contributors: Dupuis, Julian, Bremer, Forest, Kauwe, Angela, San Jose, Michael, Leblanc, Luc, Rubinoff, Daniel, Geib, Scott
... High-throughput sequencing has fundamentally changed how molecular phylogenetic datasets are assembled, and phylogenomic datasets commonly contain 50-100-fold more loci than those generated using traditional Sanger-based approaches. Here, we demonstrate a new approach for building phylogenomic datasets using single tube, highly multiplexed amplicon sequencing, which we name HiMAP (Highly Multiplexed Amplicon-based Phylogenomics), and present bioinformatic pipelines for locus selection based on genomic and transcriptomic data resources and post-sequencing consensus calling and alignment. This method is inexpensive and amenable to sequencing a large number (hundreds) of taxa simultaneously, requires minimal hands-on time at the bench (150,000 bp concatenated alignment, ~20% missing character sites across all individuals and amplicons) contained >40,000 phylogenetically informative characters, and although some discordance was observed between analyses, it provided unparalleled resolution of many phylogenetic relationships in this group. Most notably, we found high support for the generic status of Zeugodacus and the sister relationship between Dacus and Zeugodacus. We discuss HiMAP, with regard to its molecular and bioinformatic strengths, and the insight the resulting dataset provides into relationships of this diverse insect group.
Data from: A biting commentary: integrating tooth characters with molecular data doubles known species diversity in a lineage of sea slugs that consume “killer algae”
Contributors: Berriman, John S., Ellingson, Ryan A., Awbrey, Jaymes D., Rico, Diane M., Valdes, Angel A., Wilson, Nerida G., Aguilar, Andres, Herbert, David G., Hirano, Yayoi M., Trowbridge, Cynthia D.
... Predicting biotic resistance to highly invasive strains of “killer algae” (Caulerpa spp.) requires understanding the diversity and feeding preferences of native consumers, including sea slugs in family Oxynoidae. Past studies reported low algal host specificity for Oxynoe (6 spp.) and Lobiger (4 spp.), but these taxonomically challenging slugs may represent species complexes of unrecognized specialists that prefer different Caulerpa spp. Here, we assess global diversity of these genera by integrating gene sequences with morphological data from microscopic teeth and internal shells, the only hard parts in these soft-bodied invertebrates. Four delimitation methods applied to datasets comprising mtDNA and/or nuclear alleles yielded up to 16 species hypotheses for samples comprising five nominal taxa, including five highly divergent species in Lobiger and five in Oxynoe. Depending on the analysis, a further four to six species were recovered in the O. antillarum-viridis complex, a clade in which mitochondrial divergence was low and nuclear alleles were shared among lineages. Bayesian species delimitation using only morphological data supported most candidate species, however, and integrative analyses combining morphological and genetic data fully supported all complex members. Collectively, our findings double the recognized biodiversity in Oxynoidae, and illustrate the value of including data from traits that mediate fast-evolving ecological interactions during species delimitation. Preference for Caulerpa spp. and radular tooth characteristics covaried among newly delimited species, highlighting an unappreciated degree of host specialization and coevolution in these taxa that may help predict their role in containing outbreaks of invasive algae.