The traditional approach to plant molecular phylogenetics involves amplifying, sequencing and analyzing one or a few genes from many species and is conducive to broad taxon sampling. An independent approach involves chloroplast genome sequencing, providing much larger amounts of data per taxon but for a smaller number of species. In principle, the two strategies can inform each other but in pra...

Evolutionary trees underpin virtually all of biology, and the wealth of new genomic data has enabled us to reconstruct them with increasing detail and confidence. While phenotypic (typically morphological) traits are becoming less important in reconstructing evolutionary trees, they still serve vital and unique roles in phylogenetics, even for living taxa for which vast amounts of genetic infor...

Motivation Biodiversity databases now comprise hundreds of thousands of sequences and trait records. For example, the Open Tree of Life includes over 1 491 000 metazoan and over 300 000 bacterial taxa. These data provide unique opportunities for analysis of phylogenetic trait distribution and reconstruction of ancestral biodiversity. However, existing tools for comparative phylogenetics scale p...

Using computational biology, we have depicted the insulin phylogenetics. We have also analyzed the sequence alignment and sequence logos formation for both the insulin chain A and B for three groups namely, the mammalian group, vertebrates group and fish group. We have also analyzed cladograms of insulin for the mammalian group. In accordance with that path lengths, matrix for distance analysis...

Molecular phylogenetics studies the hierarchical evolutionary relationships among organisms by means of molecular data. These relationships are typically described through a weighted tree, called phylogeny, whose leaves represent the observed organisms, internal vertices represent the intermediate ancestors, and the edges represent evolutionary relationships between pairs of organisms. Molecula...

Mitochondrial sequences are an important source of data in animal phylogenetics, equivalent in importance to plastid sequences in plants. However, in recent years plant systematists have begun exploring the mitochondrial genome as a source of phylogenetically useful characters. The plant mitochondrial genome is renowned for its variability in size, structure, and gene organization, but this nee...

paulyn cartwright, nathaniel m. evans, casey w. dunn, antonio c. marques, maria pia miglietta, peter schuchert and allen g. collins Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66049, USA, Department of Ecology and Evolutionary Biology, Brown University, Providence RI 02912, USA, Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo,...

Phylogenetic reconstruction is one of the fundamental problems in computational biology. The combinatorial explosion of the state space and the complexity of mathematical models impose practical limits on workable problem sizes. In this article we explore the scalability of popular algorithms under real datasets as problem dimensions grow. We furthermore develop an efficient preclassification a...

Mindell (2013) [henceforth simply “Mindell”] has provided a claim that the Tree of Life (ToL) is still useful in phylogenetics as a model, a metaphor, and a heuristic. Here I examine all three of these claims. Mindell noted that what biologists have long discussed as the ToL is in fact reticulate, and always has been. He therefore objected to simplistic declarations that there is no ToL, in the...