Search Results - "Molecular phylogenetics and evolution"

RASP (Reconstruct Ancestral State in Phylogenies): A tool for historical biogeography by Yu, Yan, Harris, A.J., Blair, Christopher, He, Xingjin

“…[Display omitted] •We introduce software package RASP, which is a tool for historical biogeography.•We improve the widely used S-DIVA method, the DEC model,…”
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Combining phylogenomic and supermatrix approaches, and a time-calibrated phylogeny for squamate reptiles (lizards and snakes) based on 52 genes and 4162 species by Zheng, Yuchi, Wiens, John J.

“…[Display omitted] •Many studies analyze higher-level relationships with many genes but few taxa (e.g. phylogenomic).•Alternately, other studies analyze many…”
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Implementing and testing the multispecies coalescent model: A valuable paradigm for phylogenomics by Edwards, Scott V., Xi, Zhenxiang, Janke, Axel, Faircloth, Brant C., McCormack, John E., Glenn, Travis C., Zhong, Bojian, Wu, Shaoyuan, Lemmon, Emily Moriarty, Lemmon, Alan R., Leaché, Adam D., Liu, Liang, Davis, Charles C.

“…In recent articles published in Molecular Phylogenetics and Evolution, Mark Springer and John Gatesy (S&G) present numerous criticisms of recent…”
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Chloroplast genomic data provide new and robust insights into the phylogeny and evolution of the Ranunculaceae by Zhai, Wei, Duan, Xiaoshan, Zhang, Rui, Guo, Chunce, Li, Lin, Xu, Guixia, Shan, Hongyan, Kong, Hongzhi, Ren, Yi

“…[Display omitted] •Chloroplast (cp) genomes of 35 species representing 31 genera of the 14 tribes of the Ranunculaceae were sequenced, based on which…”
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A 4000-species dataset provides new insight into the evolution of ferns by Testo, Weston, Sundue, Michael

“…[Display omitted] •Ferns and the seed plant clade diverged by the late Silurian.•Most fern lineages are older than previously reported.•Leptosporangiate fern…”
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A large-scale phylogeny of Amphibia including over 2800 species, and a revised classification of extant frogs, salamanders, and caecilians by Alexander Pyron, R., Wiens, John J.

“…[Display omitted] ► Large-scale molecular phylogenetic estimate for Amphibia. ► Based on 2871 species: 41 caecilians, 436 salamanders, and 2394 frogs. ►…”
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Incongruence between gene trees and species trees and phylogenetic signal variation in plastid genes by Gonçalves, Deise J.P., Simpson, Beryl B., Ortiz, Edgardo M., Shimizu, Gustavo H., Jansen, Robert K.

“…[Display omitted] •Current classification of flowering plants is mostly based on plastid phylogenies.•Plastid phylogenies are inferred with full/partial genome…”
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Combining transcriptomes and ultraconserved elements to illuminate the phylogeny of Apidae by Bossert, Silas, Murray, Elizabeth A., Almeida, Eduardo A.B., Brady, Seán G., Blaimer, Bonnie B., Danforth, Bryan N.

“…[Display omitted] •Sequences of ultraconserved elements and transcriptomes often overlap and can be combined.•A large phylogeny of Apidae resolves…”
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Plastid phylogenomic insights into the evolution of Caryophyllales by Yao, Gang, Jin, Jian-Jun, Li, Hong-Tao, Yang, Jun-Bo, Mandala, Venkata Shiva, Croley, Matthew, Mostow, Rebecca, Douglas, Norman A., Chase, Mark W., Christenhusz, Maarten J.M., Soltis, Douglas E., Soltis, Pamela S., Smith, Stephen A., Brockington, Samuel F., Moore, Michael J., Yi, Ting-Shuang, Li, De-Zhu

“…[Display omitted] •Plastomes of 95 species (80 genera) within Caryophyllales were newly sequenced.•The deep-level relationships of Caryophyllales were…”
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Diversification in vipers: Phylogenetic relationships, time of divergence and shifts in speciation rates by Alencar, Laura R.V., Quental, Tiago B., Grazziotin, Felipe G., Alfaro, Michael L., Martins, Marcio, Venzon, Mericien, Zaher, Hussam

“…[Display omitted] •We generated a molecular phylogeny for 79% species of vipers.•We provide divergence time estimates between lineages.•Vipers are…”
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Applications of next-generation sequencing to phylogeography and phylogenetics by McCormack, John E., Hird, Sarah M., Zellmer, Amanda J., Carstens, Bryan C., Brumfield, Robb T.

“…[Display omitted] ► Applications of next-generation sequencing to phylogeography are few. ► We discuss methods for sample preparation and data analysis. ►…”
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Molecular phylogeny of extant Holothuroidea (Echinodermata) by Miller, Allison K., Kerr, Alexander M., Paulay, Gustav, Reich, Mike, Wilson, Nerida G., Carvajal, Jose I., Rouse, Greg W.

“…[Display omitted] •First multigene phylogeny that spans extant Holothuroidea.•A revised taxonomy of Holothuroidea is proposed.•Three families are redefined and…”
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Freshwater mussels (Bivalvia: Unionidae) from the rising sun (Far East Asia): phylogeny, systematics, and distribution by Lopes-Lima, Manuel, Hattori, Akimasa, Kondo, Takaki, Hee Lee, Jin, Ki Kim, Sang, Shirai, Akihisa, Hayashi, Hironori, Usui, Taira, Sakuma, Kanta, Toriya, Taishi, Sunamura, Youhei, Ishikawa, Haruki, Hoshino, Naoki, Kusano, Yushi, Kumaki, Hinata, Utsugi, Yuya, Yabe, Shinnosuke, Yoshinari, Yuma, Hiruma, Hazuki, Tanaka, Akiko, Sao, Kentaro, Ueda, Takuya, Sano, Isao, Miyazaki, Jun-Ichi, Gonçalves, Duarte V., Klishko, Olga K., Konopleva, Ekaterina S., Vikhrev, Ilya V., Kondakov, Alexander V., Yu. Gofarov, Mikhail, Bolotov, Ivan N., Sayenko, Elena M., Soroka, Marianna, Zieritz, Alexandra, Bogan, Arthur E., Froufe, Elsa

“…[Display omitted] •Unionidae freshwater mussels were surveyed comprehensively in Far East Asia.•Voucher specimens and tissue snips were collected for…”
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A phylogenomic analysis of turtles by Crawford, Nicholas G., Parham, James F., Sellas, Anna B., Faircloth, Brant C., Glenn, Travis C., Papenfuss, Theodore J., Henderson, James B., Hansen, Madison H., Simison, W. Brian

“…[Display omitted] •2381 Ultraconserved element (UCE) loci resolve relationships among living turtles.•The UCE phylogeny is used to test and develop a…”
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Mitochondrial phylogenomics of the Hymenoptera by Tang, Pu, Zhu, Jia-chen, Zheng, Bo-yin, Wei, Shu-jun, Sharkey, Michael, Chen, Xue-xin, Vogler, Alfried P.

“…[Display omitted] •Dated tree of major clades of Hymenoptera inferred from mitogenomes (40 newly sequenced).•Focus on poorly known basal relationships of…”
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Fifteen shades of green: The evolution of Bufotes toads revisited by Dufresnes, Christophe, Mazepa, Glib, Jablonski, Daniel, Oliveira, Ricardo Caliari, Wenseleers, Tom, Shabanov, Dmytro A., Auer, Markus, Ernst, Raffael, Koch, Claudia, Ramírez-Chaves, Héctor E., Mulder, Kevin Patrick, Simonov, Evgeniy, Tiutenko, Arthur, Kryvokhyzha, Dmytro, Wennekes, Paul L., Zinenko, Oleksandr I., Korshunov, Oleksiy V., Al-Johany, Awadh M., Peregontsev, Evgeniy A., Masroor, Rafaqat, Betto-Colliard, Caroline, Denoël, Mathieu, Borkin, Leo J., Skorinov, Dmitriy V., Pasynkova, Roza A., Mazanaeva, Lyudmila F., Rosanov, Juriy M., Dubey, Sylvain, Litvinchuk, Spartak

“…[Display omitted] •15 Bufotes species dissected by genomics and multiple genetic/biometric datasets.•Widespread mitochondrial replacements and the…”
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Adaptive radiation, correlated and contingent evolution, and net species diversification in Bromeliaceae by Givnish, Thomas J., Barfuss, Michael H.J., Ee, Benjamin Van, Riina, Ricarda, Schulte, Katharina, Horres, Ralf, Gonsiska, Philip A., Jabaily, Rachel S., Crayn, Darren M., Smith, J. Andrew C., Winter, Klaus, Brown, Gregory K., Evans, Timothy M., Holst, Bruce K., Luther, Harry, Till, Walter, Zizka, Georg, Berry, Paul E., Sytsma, Kenneth J.

“…•We trace 97 million years of bromeliad adaptation, biogeography, and species diversification.•We use these data to test an integrative model for bromeliad…”
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An enhanced target-enrichment bait set for Hexacorallia provides phylogenomic resolution of the staghorn corals (Acroporidae) and close relatives by Cowman, Peter F., Quattrini, Andrea M., Bridge, Tom C.L., Watkins-Colwell, Gregory J., Fadli, Nur, Grinblat, Mila, Roberts, T. Edward, McFadden, Catherine S., Miller, David J., Baird, Andrew H.

“…[Display omitted] •Genomic capture methods can resolve clades that lack decades of molecular marker development.•An enhanced bait setfor Hexacorallia recovers…”
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The gene tree delusion by Springer, Mark S., Gatesy, John

“…[Display omitted] •Empirical data suggest coalescence-genes are tiny owing to the recombination ratchet.•Coalescence methods have not solved difficult problems…”
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Phylogeny and polyploidy: Resolving the classification of cyprinine fishes (Teleostei: Cypriniformes) by Yang, Lei, Sado, Tetsuya, Vincent Hirt, M., Pasco-Viel, Emmanuel, Arunachalam, M., Li, Junbing, Wang, Xuzhen, Freyhof, Jörg, Saitoh, Kenji, Simons, Andrew M., Miya, Masaki, He, Shunping, Mayden, Richard L.

“…[Display omitted] •Most (117) genera and nearly half (612) of species of the Cyprininae were sampled.•Five mitochondrial genes (or mitogenomes) and cloned…”
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