15 Works

Data from: Phylogenomic delineation of Physcomitrium (Bryophyta: Funariaceae) based on targeted sequencing of nuclear exons and their flanking regions rejects the retention of Physcomitrella, Physcomitridium and Aphanorrhegma

Rafael Medina, Matthew G. Johnson, Yang Liu, Norman J. Wickett, A. Jonathan Shaw & Bernard Goffinet
Selection on spore dispersal mechanisms in mosses is thought to shape the transformation of the sporophyte. The majority of extant mosses develop a sporangium that dehisces through the loss of an operculum, and regulates spore release through the movement of articulate teeth, the peristome, lining the capsule mouth. Such complexity was acquired by the Mesozoic Era, but was lost in some groups during subsequent diversification events, challenging the resolution of the affinities for taxa with...

The amount of RNA editing sites in liverwort organellar genes is correlated with GC content and nuclear PPR protein diversity

Shanshan Dong, Chaoxian Zhao, Shouzhou Zhang, Hong Wu, Weixue Mu, Tong Wei, Na Li, Tao Wan, Huan Liu, Jie Cui, Ruiliang Zhu, Bernard Goffinet & Yang Liu
RNA editing occurs in the organellar mRNAs of all land plants but the marchantioid liverworts, making liverworts a perfect group for studying the evolution of RNA editing. Here we profiled the RNA editing of 42 exemplars spanning the ordinal phylogenetic diversity of liverworts, and screened for the nuclear-encoded PPR proteins in the transcriptome assemblies of these taxa. We identified 7,428 RNA editing sites in 128 organellar genes from 31 non-marchantioid liverwort species, and characterized 25,059...

Resource diversity promotes among-individual diet variation, but not genomic diversity, in lake stickleback

Daniel Bolnick & Kimberly Ballare
Many generalist species consist of specialized individuals that use different resources. This within-population niche variation can stabilize population and community dynamics. Consequently, ecologists wish to identify environmental settings that promote such variation. Theory predicts that environments with greater resource diversity favor ecological diversity (via disruptive selection or plasticity). Alternatively, niche variation might be a side-effect of neutral genomic diversity in larger populations. We tested these alternatives in a metapopulation of threespine stickleback. Stickleback consume benthic...

Data from: Assessing combinability of phylogenomic data using Bayes Factors

Suman Neupane, Karolina Fučíková, Louise A Lewis, Lynn Kuo, Ming-Hui Chen & Paul Lewis
With the rapid reduction in sequencing costs of high-throughput genomic data, it has become commonplace to use hundreds of genes to infer phylogeny of any study system. While sampling a large number of genes has given us a tremendous opportunity to uncover previously unknown relationships and improve phylogenetic resolution, it also presents us with new challenges when the phylogenetic signal is confused by differences in the evolutionary histories of sampled genes. Given the incorporation of...

Pseudo-Precipitation: A Continuous Precipitation Variable

Huiling Yuan, Paul Schultz, Edward I. Tollerud, Dingchen Hou, Yuejian Zhu, Malequias Pena, Mike Charles & Zoltan Toth
NOAA Technical Memorandum OAR GSD ; 62

Data from: Biased movement drives local cryptic colouration on distinct urban pavements

Pim Edelaar, Adrian Baños-Villalba, David P. Quevedo, Graciela Escudero, Daniel Bolnick & Aída Jordán-Andrade
Explanations of how organisms might adapt to urban environments have mostly focused on divergent natural selection and adaptive plasticity. However, differential habitat choice has been suggested as an alternative. Here we test for habitat choice in enhancing crypsis in ground-perching grasshoppers colonising an urbanised environment, composed of a mosaic of four distinctly coloured substrates (asphalt roads and adjacent pavements). Additionally, we determine its relative importance compared to present-day natural selection and phenotypic plasticity. We found...

Data from: Complex interactions between local adaptation, phenotypic plasticity, and sex affect vulnerability to warming in a widespread marine copepod

Matthew C. Sasaki, Sydney Hedberg, Kailin Richardson & Hans G. Dam
Predicting the response of populations to climate change requires knowledge of thermal performance. Genetic differentiation and phenotypic plasticity affect thermal performance, but the effects of sex and developmental temperatures often go uncharacterized. We used common garden experiments to test for effects of local adaptation (Florida versus Connecticut temperatures), developmental phenotypic plasticity (18oC vs. 22oC), and individual sex on thermal performance of the ubiquitous copepod, Acartia tonsa. Females had higher thermal tolerance than males in both...

Data from: Were bivalves ecologically dominant over brachiopods in the late Paleozoic? A test using exceptionally preserved fossil assemblages

Shannon Hsieh, Andrew M. Bush & J. Bret Bennington
Interpreting changes in ecosystem structure from the fossil record can be challenging. In a prominent example, the traditional view that brachiopods were ecologically dominant over bivalves in the Paleozoic has been disputed on both taphonomic and metabolic grounds. Aragonitic bivalves may be underrepresented in many fossil assemblages due to preferential dissolution. Abundance counts may further understate the ecological importance of bivalves because they tend to have more biomass and higher metabolic rates than brachiopods. We...

Data from: Repeatability of adaptive radiation depends on spatial scale: regional versus global replicates of stickleback in lake versus stream habitats

Antoine Paccard, Dieta Hanson, Yoel E Stuart, Frank A Von Hippel, Martin Kalbe, Tom Klepaker, Skúli Skúlason, Bjarni K Kristjánsson, Daniel I Bolnick, Andrew P Hendry & Rowan D H Barrett
The repeatability of adaptive radiation is expected to be scale dependent, with determinism decreasing as greater spatial separation among “replicates” leads to their increased genetic and ecological independence. Threespine stickleback (Gasterosteus aculeatus) provide an opportunity to test whether this expectation holds for the early stages of adaptive radiation -their diversification in freshwater ecosystems has been replicated many times. To better understand the repeatability of that adaptive radiation, we examined the influence of geographic scale on...

Data from: Mortality and morphology in egg masses of unisexual and Jefferson Salamanders

Noah Charney, Jacob Kubel, Craig Woodard, Blanca Carbajal-González, Samantha Avis, Julia Blyth, Charles Eiseman, John Castorino & John Malone
Unisexual Ambystoma salamander egg masses have often been observed to exhibit very high rates of embryo mortality. The ecological consequences and underlying mechanisms are of great concern to researchers and managers studying these and other members of the species complex, all of which are listed as rare species throughout much of their range. Substantial embryo mortality is commonly used by field ecologists as an indicator that unisexual salamanders are present in a pond; egg masses...

The hornwort genome and early land plant evolution

Jian Zhang, Xin-Xing Fu, Rui-Qi Li, Xiang Zhao, Yang Liu, Ming-He Li, Arthur Zwaenepoel, Hong Ma, Bernard Goffinet, Yan-Long Guan, Jia-Yu Xue, Yi-Ying Liao, Qing-Feng Wang, Qing-Hua Wang, Jie-Yu Wang, Guo-Qiang Zhang, Zhi-Wen Wang, Yu Jia, Mei-Zhi Wang, Shan-Shan Dong, Jian-Fen Yang, Yuan-Nian Jiao, Ya-Long Guo, Hong-Zhi Kong, An-Ming Lu … & Zhi-Duan Chen
Hornworts, liverworts, and mosses are three early diverging clades of land plants, together composing the bryophytes. Here we report the draft genome sequence of the hornwort Anthoceros angustus. Phylogenomic inferences confirm the monophyly of bryophytes, with hornworts sister to liverworts and mosses. The simple morphology of hornworts correlates with low genetic redundancy in plant body plan while the basic transcriptional regulation toolkit for plant development has already been established in this early land plant lineage....

Data from: Islands of retroelements are major components of Drosophila centromeres

Ching-Ho Chang, Ankita Chanvan, Jason Palladino, Xiaolu Wei, Nuno M. C. Martins, Bryce Santinello, Chin-Chi Chen, Jelena Erceg, Brian J. Beliveau, Chao-Ting Wu, Amanda M. Larracuente & Barbara G Mellone
Centromeres are essential chromosomal regions that mediate kinetochore assembly and spindle attachments during cell division. Despite their functional conservation, centromeres are amongst the most rapidly evolving genomic regions and can shape karyotype evolution and speciation across taxa. Although significant progress has been made in identifying centromere-associated proteins, the highly repetitive centromeres of metazoans have been refractory to DNA sequencing and assembly, leaving large gaps in our understanding of their functional organization and evolution. Here, we...

Data from: Adaptive phenotypic plasticity for life-history and less fitness-related traits

Cristina Acasuso-Rivero, Courtney J. Murren, Carl D. Schlichting & Ulrich Karl Steiner
Organisms are faced with variable environments and one of the most common solutions to cope with such variability is phenotypic plasticity, a modification of the phenotype to the environment. These modifications are commonly modelled in evolutionary theories as adaptive, influencing ecological and evolutionary processes. If plasticity is adaptive, we would predict that the closer to fitness a trait is, the less plastic it would be. To test this hypothesis, we conducted a meta-analysis of 213...

Data from: Resolution of the ordinal phylogeny of mosses using targeted exons from organellar and nuclear genomes

Yang Liu, Matthew G. Johnson, Cymon J. Cox, Rafael Medina, Nicolas Devos, Alain Vanderpoorten, Lars Hedenäs, Neil E. Bell, James R. Shevock, Blanka Aguero, Dietmar Quandt, Norman J. Wickett, A. Jonathan Shaw & Bernard Goffinet
Mosses are a highly diverse lineage of land plants, whose diversification, spanning at least 400 million years, remains phylogenetically ambiguous due to the lack of fossils, massive early extinctions, late radiations, limited morphological variation, and conflicting signal among previously used markers. Here, we present phylogenetic reconstructions based on complete organellar exomes and a comparable set of nuclear genes for this major lineage of land plants. Our analysis of 142 species representing 29 of the 30...

Data from: Invasive species removal increases species and phylogenetic diversity of wetland plant communities

Shane C. Lishawa, Beth A. Lawrence, Dennis A. Albert, Daniel J. Larkin & Nancy C. Tuchman
Plant invasions result in biodiversity losses and altered ecological functions, though quantifying loss of multiple ecosystem functions presents a research challenge. Plant phylogenetic diversity correlates with a range of ecosystem functions, and can be used as a proxy for ecosystem multifunctionality. Laurentian Great Lakes coastal wetlands are ideal systems for testing invasive species management effects because they support diverse biological communities, provide numerous ecosystem services, and are increasingly dominated by invasive macrophytes. Invasive cattails are...

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Affiliations

  • University of Connecticut
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  • Fairy Lake Botanical Garden
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  • Duke University
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  • Gustavus Adolphus College
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  • University of Liège
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  • Cooperative Institute for Research in Environmental Sciences
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  • Ghent University
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  • The University of Texas at Austin
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