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Phylogenetics [PDF]

, 2018
Describing the diversity of living beings has always instigated man. The classification proposed by Aristotle today seems naïve and unnatural, but it lasted from ancient Greece until the publication of the Linnaeus Systema Naturae in 1758. Although quite
Evanovich dos Santos, Eliane Barbosa
core   +4 more sources

Phylotranscriptomic insights into a Mesoproterozoic–Neoproterozoic origin and early radiation of green seaweeds (Ulvophyceae)

Nature Communications, 2022
“Ulvophyceae is a remarkably morphologically and ecologically diverse clade of green algae. Here, the authors reconstruct the Ulvophyceae phylogeny, showing that these algae originated earlier than expected and may have influenced biogeochemical cycles ...
Zheng Hou, Xiaoya Ma, Xuan Shi, Xi Li, Lingxiao Yang, Shuhai Xiao, Olivier De Clerck, Frederik Leliaert, Bojian Zhong   +8 more
doaj   +1 more source

Molecular phylogenetics of Melastomataceae and Memecylaceae [PDF]

, 2001
Melastomataceae are among the most abundant and diversified groups of plants throughout the tropics, but their intrafamily relationships and morphological evolution are poorly understood. Here we report the results of parsimony and maximum likelihood (ML)
Clausing, G., Renner, Susanne S.
core   +1 more source

The phylogenetics of Leucocytozoon caulleryi infecting broiler chickens in endemic areas in Indonesia [PDF]

Veterinary World, 2017
Aim: The objective of this research was to determine the species and strains of Leucocytozoon caulleryi and study the phylogenetics of L. caulleryi of broiler chickens in endemic areas in Indonesia.
Endang Suprihati, Wiwik Misaco Yuniarti
doaj   +1 more source

Accurate reconstruction of insertion-deletion histories by statistical phylogenetics [PDF]

, 2012
The Multiple Sequence Alignment (MSA) is a computational abstraction that represents a partial summary either of indel history, or of structural similarity.
A Heger, A Löytynoja, A Löytynoja, A Siepel, A Siepel, A Siepel, AG Clark, AM Moses, Art F. Y. Poon, B Knudsen, B Paten, B Rannala, Benedict Paten, C Lee, C Strope, DG Higgins, EF Moore, FA Matsen, FR Kschischang, G Lunter, Gerton Lunter, I Holmes, I Miklós, Ian Holmes, J Felsenstein, JD Thompson, JL Thorne, JL Thorne, JS Pedersen, K Katoh, K Liu, KM Wong, KS Pollard, L Gomez-Valero, L Zhu, M Larkin, M Mohri, MA Suchard, N de la Chaux, O Kamneva, O Westesson, Oscar Westesson, P Markova-Raina, R Mills, RA Cartwright, RC Edgar, RK Bradley, RK Bradley, S Nelesen, S Saccone, S Sinha, T Beissbarth, X Qu, Z Wang, Z Yang, Z Yang, Z Yang, Z Zhang   +57 more
core   +5 more sources

Rearrangement operations on unrooted phylogenetic networks [PDF]

Theory and Applications of Graphs, Vol. 6 Iss. 2 Article 6. (2019), 2019
Rearrangement operations transform a phylogenetic tree into another one and hence induce a metric on the space of phylogenetic trees. Popular operations for unrooted phylogenetic trees are NNI (nearest neighbour interchange), SPR (subtree prune and regraft), and TBR (tree bisection and reconnection).
arxiv   +1 more source

Combining morphological and genomic evidence to resolve species diversity and study speciation processes of the Pallenopsis patagonica (Pycnogonida) species complex

Frontiers in Zoology, 2019
Background Pallenopsis patagonica (Hoek, 1881) is a morphologically and genetically variable sea spider species whose taxonomic classification is challenging.
Jana S. Dömel, Till-Hendrik Macher, Lars Dietz, Sabrina Duncan, Christoph Mayer, Andrey Rozenberg, Katherine Wolcott, Florian Leese, Roland R. Melzer   +8 more
doaj   +1 more source

AWTY (are we there yet?): a system for graphical exploration of MCMC convergence in Bayesian phylogenetics

Bioinform., 2008
UNLABELLED A key element to a successful Markov chain Monte Carlo (MCMC) inference is the programming and run performance of the Markov chain.
J. Nylander, James C. Wilgenbusch, D. Warren, D. Swofford   +3 more
semanticscholar   +1 more source

The Mitochondrial Genome in Nematode Phylogenetics

Frontiers in Ecology and Evolution, 2020
In recent decades, great strides have been made using various kinds of data including molecular sequences to clarify the phylogenetic relationships of nematodes.
E. Kern, Taeho Kim, Joong-Ki Park
semanticscholar   +1 more source

Model Selection and Parameter Inference in Phylogenetics Using Nested Sampling [PDF]

Systematic Biology, 2017
&NA; Bayesian inference methods rely on numerical algorithms for both model selection and parameter inference. In general, these algorithms require a high computational effort to yield reliable estimates.
Patricio Maturana Russel, B. Brewer, S. Klaere, R. Bouckaert   +3 more
semanticscholar   +1 more source