Search Results - "Walker, Joseph F"

So many genes, so little time: A practical approach to divergence-time estimation in the genomic era by Smith, Stephen A, Brown, Joseph W, Walker, Joseph F

“…Phylogenomic datasets have been successfully used to address questions involving evolutionary relationships, patterns of genome structure, signatures of…”
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Quartet Sampling distinguishes lack of support from conflicting support in the green plant tree of life by Pease, James B., Brown, Joseph W., Walker, Joseph F., Hinchliff, Cody E., Smith, Stephen A.

“…Premise of the Study Phylogenetic support has been difficult to evaluate within the green plant tree of life partly due to a lack of specificity between…”
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Improved transcriptome sampling pinpoints 26 ancient and more recent polyploidy events in Caryophyllales, including two allopolyploidy events by Yang, Ya, Moore, Michael J., Brockington, Samuel F., Mikenas, Jessica, Olivieri, Julia, Walker, Joseph F., Smith, Stephen A.

“…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…”
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PyPHLAWD: A python tool for phylogenetic dataset construction by Smith, Stephen A., Walker, Joseph F., Cooper, Natalie

“…Comprehensive phylogenetic trees are essential for many ecological and evolutionary studies. Researchers may use existing trees or construct their own. In…”
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Characterizing gene tree conflict in plastome-inferred phylogenies by Walker, Joseph F, Walker-Hale, Nathanael, Vargas, Oscar M, Larson, Drew A, Stull, Gregory W

“…Evolutionary relationships among plants have been inferred primarily using chloroplast data. To date, no study has comprehensively examined the plastome for…”
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Disparity, diversity, and duplications in the Caryophyllales by Smith, Stephen A., Brown, Joseph W., Yang, Ya, Bruenn, Riva, Drummond, Chloe P., Brockington, Samuel F., Walker, Joseph F., Last, Noah, Douglas, Norman A., Moore, Michael J.

“…The role played by whole genome duplication (WGD) in plant evolution is actively debated. WGDs have been associated with advantages such as superior…”
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Characterizing conflict and congruence of molecular evolution across organellar genome sequences for phylogenetics in land plants by Tyszka, Alexa S, Bretz, Eric C, Robertson, Holly M, Woodcock-Girard, Miles D, Ramanauskas, Karolis, Larson, Drew A, Stull, Gregory W, Walker, Joseph F

“…Chloroplasts and mitochondria each contain their own genomes, which have historically been and continue to be important sources of information for inferring…”
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Phyx: phylogenetic tools for unix by Brown, Joseph W, Walker, Joseph F, Smith, Stephen A

“…The ease with which phylogenomic data can be generated has drastically escalated the computational burden for even routine phylogenetic investigations. To…”
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Analyzing Contentious Relationships and Outlier Genes in Phylogenomics by Walker, Joseph F., Brown, Joseph W., Smith, Stephen A.

“…Recent studies have demonstrated that conflict is common among gene trees in phylogenomic studies, and that less than one percent of genes may ultimately drive…”
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Spalt expression and the development of melanic color patterns in pierid butterflies by Stoehr, Andrew M, Walker, Joseph F, Monteiro, Antónia

“…Little is currently known about wing pattern development in the butterfly family Pieridae, which consists mostly of black melanized elements on white or…”
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Phylogenetic Conflicts, Combinability, and Deep Phylogenomics in Plants by Smith, Stephen A., Walker-Hale, Nathanael, Walker, Joseph F., Brown, Joseph W.

“…Studies have demonstrated that pervasive gene tree conflict underlies several important phylogenetic relationships where different species tree methods produce…”
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The N-terminal domains of NLR immune receptors exhibit structural and functional similarities across divergent plant lineages by Chia, Khong-Sam, Kourelis, Jiorgos, Teulet, Albin, Vickers, Martin, Sakai, Toshiyuki, Walker, Joseph F, Schornack, Sebastian, Kamoun, Sophien, Carella, Philip

“…Nucleotide-binding domain and leucine-rich repeat (NLR) proteins are a prominent class of intracellular immune receptors in plants. However, our understanding…”
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Intragenic Conflict in Phylogenomic Data Sets by Smith, Stephen A, Walker-Hale, Nathanael, Walker, Joseph F

“…Most phylogenetic analyses assume that a single evolutionary history underlies one gene. However, both biological processes and errors can cause intragenic…”
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A consensus phylogenomic approach highlights paleopolyploid and rapid radiation in the history of Ericales by Larson, Drew A., Walker, Joseph F., Vargas, Oscar M., Smith, Stephen A.

“…Premise Large genomic data sets offer the promise of resolving historically recalcitrant species relationships. However, different methodologies can yield…”
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Comparative analysis of complete chloroplast genome sequence and inversion variation in Lasthenia burkei (Madieae, Asteraceae) by Walker, Joseph F, Zanis, Michael J, Emery, Nancy C

“…• Premise of the study: Complete chloroplast genome studies can help resolve relationships among large, complex plant lineages such as Asteraceae. We present…”
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Concordance-Based Approaches for the Inference of Relationships and Molecular Rates with Phylogenomic Data Sets by Walker, Joseph F, Smith, Stephen A, Hodel, Richard G J, Moyroud, Edwige

“…Abstract Gene tree conflict is common and finding methods to analyze and alleviate the negative effects that conflict has on species tree analysis is a crucial…”
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Monocotyledonous plants graft at the embryonic root–shoot interface by Reeves, Gregory, Tripathi, Anoop, Singh, Pallavi, Jones, Maximillian R. W., Nanda, Amrit K., Musseau, Constance, Craze, Melanie, Bowden, Sarah, Walker, Joseph F., Bentley, Alison R., Melnyk, Charles W., Hibberd, Julian M.

“…Grafting is possible in both animals and plants. Although in animals the process requires surgery and is often associated with rejection of non-self, in plants…”
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The link between ancient whole‐genome duplications and cold adaptations in the Caryophyllaceae by Feng, Keyi, Walker, Joseph F., Marx, Hannah E., Yang, Ya, Brockington, Samuel F., Moore, Michael J., Rabeler, Richard K., Smith, Stephen A.

“…Premise The Caryophyllaceae (the carnation family) have undergone multiple transitions into colder climates and convergence on cushion plant adaptation,…”
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Sources of inversion variation in the small single copy (SSC) region of chloroplast genomes by Walker, Joseph F., Jansen, Robert K., Zanis, Michael J., Emery, Nancy C.

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Evolution of Portulacineae Marked by Gene Tree Conflict and Gene Family Expansion Associated with Adaptation to Harsh Environments by Wang, Ning, Yang, Ya, Moore, Michael J, Brockington, Samuel F, Walker, Joseph F, Brown, Joseph W, Liang, Bin, Feng, Tao, Edwards, Caroline, Mikenas, Jessica, Olivieri, Julia, Hutchison, Vera, Timoneda, Alfonso, Stoughton, Tommy, Puente, Raúl, Majure, Lucas C, Eggli, Urs, Smith, Stephen A

“…Abstract Several plant lineages have evolved adaptations that allow survival in extreme and harsh environments including many families within the plant clade…”
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