22 Works

Exploration of plastid phylogenomic conflict yields new insights into the deep relationships of Leguminosae

Rong Zhang, Yin-Huan Wang, Jian-Jun Jin, Gregory Stull, Anne Bruneau, Domingos Cardoso, Luciano De Queiroz, Michael Moore, Shu-Dong Zhang, Si-Yun Chen, Jian Wang, De-Zhu Li & Ting-Shuang Yi
Phylogenomic analyses have helped resolve many recalcitrant relationships in the angiosperm tree of life, yet phylogenetic resolution of the backbone of the Leguminosae, one of the largest and most economically and ecologically important families, remains poor due to generally limited molecular data and incomplete taxon sampling of previous studies. Here, we resolve many of the Leguminosae's thorniest nodes through comprehensive analysis of plastome-scale data using multiple modified coding and noncoding datasets of 187 species representing...

Minding the gap: Learning and visual scanning behaviour in nocturnal bull ants

Muzahid Islam, Sudhakar Deeti, J. Frances Kamhi & Ken Cheng
Insects possess small brains but exhibit sophisticated behaviour, specifically their ability to learn to navigate within complex environments. To understand how they learn to navigate in a cluttered environment, we focused on learning and visual scanning behaviour in the Australian nocturnal bull ant, Myrmecia midas, which are exceptional visual navigators. We tested how individual ants learn to detour via a gap and how they cope with substantial spatial changes over trips. Homing M. midas ants...

Data from: Electricity and water conservation on college and university campuses in response to national competitions among dormitories: quantifying relationships between behavior, conservation strategies and psychological metrics

John E. Petersen, Cynthia M. Frantz, , Tess M. Yanisch, Evan Tincknell & Noel Myers
“Campus Conservation Nationals” (CCN) is a recurring, nation-wide electricity and water-use reduction competition among dormitories on college campuses. We conducted a two year empirical study of the competition’s effects on resource consumption and the relationship between conservation, use of web technology and various psychological measures. Significant reductions in electricity and water use occurred during the two CCN competitions examined (n = 105,000 and 197,000 participating dorm residents respectively). In 2010, overall reductions during the competition...

Disentangling sources of gene tree discordance in phylogenomic datasets: testing ancient hybridizations in Amaranthaceae s.l.

Diego F. Morales-Briones, Gudrun Kadereit, Delphine Tefarikis, Michael Moore, Stephen Smith, Samuel Brockington, Alfonso Timoneda, Won Yim, John Cushman & Ya Yang
Gene tree discordance in large genomic datasets can be caused by evolutionary processes such as incomplete lineage sorting and hybridization, as well as model violation, and errors in data processing, orthology inference, and gene tree estimation. Species tree methods that identify and accommodate all sources of conflict are not available, but a combination of multiple approaches can help tease apart alternative sources of conflict. Here, using a phylotranscriptomic analysis in combination with reference genomes, we...

Data from: Relationships between spatial metrics and plant diversity in constructed freshwater wetlands

Erika C. Brandt, John E. Petersen, Jake J. Grossman, George A. Allen & David H. Benzing
The diversity of plant species and their distribution in space are both thought to have important effects on the function of wetland ecosystems. However, knowledge of the relationships between plant species and spatial diversity remains incomplete. In this study, we investigated relationships between spatial pattern and plant species diversity over a five year period following the initial restoration of experimental wetland ecosystems. In 2003, six identical and hydrologically-isolated 0.18 ha wetland “cells” were constructed in...

Data from: Widespread paleopolyploidy, gene tree conflict, and recalcitrant relationships among the carnivorous Caryophyllales

Joseph F. Walker, Ya Yang, Moore J. Michael, Jessica Mikenas, Alfonso Timoneda, Samuel Frasier Brockington, Stephen Andrew Smith & Michael J. Moore
PREMISE OF STUDY: The carnivorous members of the large, hyperdiverse Caryophyllales (e.g., Venus flytrap, sundews, and Nepenthes pitcher plants) represent perhaps the oldest and most diverse lineage of carnivorous plants. However, despite numerous studies seeking to elucidate their evolutionary relationships, the early-diverging relationships remain unresolved. METHODS: To explore the utility of phylogenomic data sets for resolving relationships among the carnivorous Caryophyllales, we sequenced 10 transcriptomes, including all the carnivorous genera except those in the rare...

Data from: A population genetics perspective on the evolutionary histories of three clonal, endemic, and dominant grass species of the Qinghai-Tibet Plateau: Orinus (Poaceae)

Yuping Liu, A.J. Harris, Qingbo Gao, Xu Su & Zhumei Ren
We performed analyses of amplified fragment length polymorphism (AFLP) in order to characterize the evolutionary history of Orinus according to its population genetic structure, to investigate putative hybrid origins of O. intermedius, and to provide additional insights on relationships among species. The genus Orinus comprises three clonal grasses that are dominant species within xeric alpine grasslands of the Qinghai-Tibet Plateau (QTP). Here, we used eight selectively-obtained primer pairs of EcoRI/MseI to perform amplifications in 231...

Data from: Dissecting molecular evolution in the highly diverse plant clade Caryophyllales using transcriptome sequencing

Ya Yang, Michael J. Moore, Samuel F. Brockington, Douglas E. Soltis, Gane Ka-Shu Wong, Eric J. Carpenter, Yong Zhang, Li Chen, Zhixiang Yan, Yinlong Xie, Rowan F. Sage, Sarah Covshoff, Julian M. Hibberd, Matthew N. Nelson & Stephen A. Smith
Many phylogenomic studies based on transcriptomes have been limited to “single-copy” genes due to methodological challenges in homology and orthology inferences. Only a relatively small number of studies have explored analyses beyond reconstructing species relationships. We sampled 69 transcriptomes in the hyperdiverse plant clade Caryophyllales and 27 outgroups from annotated genomes across eudicots. Using a combined similarity- and phylogenetic tree-based approach, we recovered 10,960 homolog groups, where each was represented by at least eight ingroup...

Data from: Analysis of phylogenomic datasets reveals conflict, concordance, and gene duplications with examples from animals and plants

Stephen A. Smith, Ya Yang, Joseph W. Brown & Michael J. Moore
Background: The use of transcriptomic and genomic datasets for phylogenetic reconstruction has become increasingly common as researchers attempt to resolve recalcitrant nodes with increasing amounts of data. The large size and complexity of these datasets introduce significant phylogenetic noise and conflict into subsequent analyses. The sources of conflict may include hybridization, incomplete lineage sorting, or horizontal gene transfer, and may vary across the phylogeny. For phylogenetic analysis, this noise and conflict has been accommodated in...

Data from: Phylogenetic signal detection from an ancient rapid radiation: effects of noise reduction, long-branch attraction, and model selection in crown clade Apocynaceae

Shannon C. K. Straub, Michael J. Moore, Pamela S. Soltis, Douglas E. Soltis, Aaron Liston, Tatyana Livshultz & Shannon C.K. Straub
Crown clade Apocynaceae comprise seven primary lineages of lianas, shrubs, and herbs with a diversity of pollen aggregation morphologies including monads, tetrads, and pollinia, making them an ideal group for investigating the evolution and function of pollen packaging. Traditional molecular systematic approaches utilizing small amounts of sequence data have failed to resolve relationships along the spine of the crown clade, a likely ancient rapid radiation. The previous best estimate of the phylogeny was a five-way...

Data from: Phylogenetic utility of ycf1 in orchids: a plastid gene more variable than matK

Kurt M. Neubig, W. Mark Whitten, Barbara S. Carlsward, Mario A. Blanco, Lorena Endara, Norris H. Williams & Michael Moore
Plastid DNA sequences have been widely used by systematists for reconstructing plant phylogenies. The utility of any DNA region for phylogenetic analysis is determined by ease of amplification and sequencing, confidence of assessment in phylogenetic character alignment, and by variability across broad taxon sampling. Often, a compromise must be made between using relatively highly conserved coding regions or highly variable introns and intergenic spacers. Analyses of a combination of these types of DNA regions yield...

Novel approach to delivering pro-environmental messages significantly shifts norms and motivation, but children are not more effective spokespeople than adults

Cynthia Frantz, John Petersen & Kathryn Lucaites
Three studies provided initial laboratory tests of the effectiveness of a novel form of community-based environmental messaging intended to be deployed on public digital signs. In all studies, adult participants watched a slideshow of “Community Voices,” a display that combines community images and quotes to celebrate and empower pro-environmental and pro-community thought and action. In addition to assessing the general efficacy of the approach, a central goal was to assess the impact of alternative messengers...

Influence of anthropogenic landscape modifications and infrastructure on the geological characteristics of liquefaction

Josh Borella, Mark Quigley, Moses Riley, Sarah Trutner, Harry Jol, Maxwell Borella, Sam Hampton & Darren Gravley
Many large cities worldwide are built on natural and engineered geological materials that are highly susceptible to liquefaction and associated ground failure in earthquakes. Constitutive equations describing relationships between sediment geotechnical characteristics, seismological parameters, and liquefaction susceptibility of natural and engineered sediments are well established. What is less understood is the role of anthropogenic landscape modifications (e.g., river channel modifications, sediment engineering and re-distribution) and infrastructure (e.g., buildings, buried infrastructure such as drainage systems) on...

A phylogenomic perspective on gene tree conflict and character evolution in Caprifoliaceae using target enrichment data, with Zabelioideae recognized as a new subfamily

Hong-Xin Wang, Diego F. Morales-Briones, Michael Moore, Jun Wen & Hua-Feng Wang
The use of diverse datasets in phylogenetic studies aiming for understanding evolutionary histories of species can yield conflicting inference. Phylogenetic conflicts observed in animal and plant systems have often been explained by hybridization, incomplete lineage sorting (ILS), or horizontal gene transfer. Here, we employed target enrichment data and species tree and species network approaches to infer the backbone phylogeny of the family Caprifoliaceae, while distinguishing among sources of incongruence. We used 713 nuclear loci and...

Data from: Molecular and morphological evidence reveals a new species of Antiphytum (Echiochiloideae, Boraginaceae) from Guerrero, Mexico

Nidia Mendoza-Díaz, Helga Ochoterena, Michael J. Moore & Hilda Flores-Olvera
Molecular and morphological evidence supports a new species in the genus Antiphytum from the Sierra Madre del Sur, in the state of Guerrero, Mexico, here described as A. brevicalyx. This species is unique in the genus by possessing a calyx shorter than the corolla tube at anthesis; it is similar to A. floribundum in inflorescence arrangement, but differs from that species in lacking a basal leaf rosette and having appendages on the corolla throat. According...

Data from: A long PCR based approach for DNA enrichment prior to next-generation sequencing for systematic studies

Simon Uribe-Convers, Justin R. Duke, Michael J. Moore & David C. Tank
Premise of the study: We present an alternative approach for molecular systematic studies that combines long PCR and next-generation sequencing (NGS). Our approach can be used to generate templates from any DNA source for NGS. Here we test our approach by amplifying complete chloroplast genomes and we present a set of 58 potentially universal primers for angiosperms to do so. Additionally, this approach is likely to be particularly useful for nuclear regions. Methods and Results:...

Data from: Fitness of Arabidopsis thaliana mutation accumulation lines whose spontaneous mutations are known

Charles B. Fenster, Matthew Thomas Rutter, Angela J. Roles, Jeffrey K. Conner, Ruth G. Shaw, Frank Holcomb Shaw, Korbinian Schneeberger, Stephan Ossowski & Detlef Weigel
Despite the fundamental importance of mutation to the evolutionary process, we have little knowledge of the direct consequences of specific spontaneous mutations to the fitness of the organism. Combining results of whole-genome sequencing with repeated field assays of survival and reproduction, we quantify the combined effects on fitness of spontaneous mutations identified in Arabidopsis thaliana. We demonstrate that the effects are beneficial, deleterious or neutral depending on the environmental context. Some lines, bearing mutations disrupting...

Data from: Effectiveness of camera traps for quantifying daytime and nighttime visitation by vertebrate pollinators

Siegfried L. Krauss, David G. Roberts, Ryan D. Phillips & Caroline Edwards
1. Identification of pollen vectors is a fundamental objective of pollination biology. The foraging and social behavior of these pollinators has profound effects on plant mating, making quantification of their behaviour critical for understanding the ecological and evolutionary consequences of different pollinators for the plants they visit. However, accurate quantification of visitation may be problematic, especially for shy animals and/or when the temporal and spatial scale of observation desired is large. Sophisticated heat- and movement-triggered...

Data from: From cacti to carnivores: improved phylotranscriptomic sampling and hierarchical homology inference provide further insight into the evolution of Caryophyllales

Joseph Frederic Walker, Ya Yang, Tao Feng, Alfonso Timoneda, Jessica Mikenas, Vera Hutchison, Caroline Edwards, Ning Wang, Sonia Ahluwalia, Julia Olivieri, Nathanael Walker-Hale, Lucas C. Majure, Raúl Puente, Gudrun Kadereit, Maximillian Lauterbach, Urs Eggli, Hilda Flores-Olvera, Helga Ochoterena, Samuel F. Brockington, Michael J. Moore & Stephen A. Smith
Premise of the Study— The Caryophyllales contains ~12,500 species and is known for its cosmopolitan distribution, convergence of trait evolution, and extreme adaptations. Some relationships within the Caryophyllales, like those of many large plant clades, remain unclear and phylogenetic studies often recover alternative hypotheses. We explore the utility of broad and dense transcriptome sampling across the order for resolving evolutionary relationships in Caryophyllales. Methods— We generated 84 transcriptomes and combined these with 224 publicly available...

Data from: Improved transcriptome sampling pinpoints 26 ancient and more recent polyploidy events in Caryophyllales, including two allopolyploidy events

Ya Yang, Michael J. Moore, Samuel F. Brockington, Jessica Mikenas, Julia Olivieri, Joseph F. Walker & Stephen A. Smith
• Studies of the macroevolutionary legacy of polyploidy are limited by an incomplete sampling of these events across the tree of life. To better locate and understand these events, we need comprehensive taxonomic sampling as well as homology inference methods that accurately reconstruct the frequency and location of gene duplications. • We assembled a dataset of transcriptomes and genomes from 169 species in Caryophyllales, of which 43 were newly generated for this study, representing one...

Data from: Disparity, diversity, and duplications in the Caryophyllales

Stephen A. Smith, Joseph W. Brown, Ya Yang, Riva Bruenn, Chloe P. Drummond, Samuel F. Brockington, Joseph F. Walker, Noah Last, Norman A. Douglas & Michael J. Moore
The role played by whole genome duplication (WGD) in plant evolution is actively debated. WGDs have been associated with advantages such as superior colonization, various adaptations, and increased effective population size. However, the lack of a comprehensive mapping of WGDs within a major plant clade has led to uncertainty regarding the potential association of WGDs and higher diversification rates. Using seven chloroplast and nuclear ribosomal genes, we constructed a phylogeny of 5036 species of Caryophyllales,...

Data from: Salamander climbing behavior varies among species and is correlated with community composition

Tori D. Mezebish, August Blackman & Alexander J. Novarro
Species coexistence is often facilitated by behavioral strategies that minimize competition for limited resources. Terrestrial, lungless salamanders (genus Plethodon) coexist in predictable assemblages of body size guilds, but little is known about the behavioral mechanisms that promote such coexistence. Here, we considered the hypothesis that Plethodon salamanders use climbing behavior to reduce competitive interactions, thereby promoting coexistence through spatial partitioning. To explore this hypothesis, we quantified the frequency of climbing behavior at field sites where...

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