Computer simulations are developed and employed to examine the expected temporal distributions of nodes under a null model of stochastic lineage bifurcation and extinction. These Markovian models of phylogenetic process were constructed so as to permit direct comparisons against empirical phylogenetic trees generated from molecular or other information available solely from extant species. For ...

Branching morphogenesis is the developmental program that builds the ramified epithelial trees of various organs, including the airways of the lung, the collecting ducts of the kidney, and the ducts of the mammary and salivary glands. Even though the final geometries of epithelial trees are distinct, the molecular signaling pathways that control branching morphogenesis appear to be conserved ac...

sequences in molecular phylogenetic trees is consistent with early observations that polychaetes tend to have relatively short branches in such trees, and hence are useful taxa with which to reconstruct gene family evolution. Also it is clear that the traditional molecular model systems for protostomes (e.g. Drosophila melanogaster and Caenorhabditis elegans), which are restricted to the Ecdyso...

sequences in molecular phylogenetic trees is consistent with early observations that polychaetes tend to have relatively short branches in such trees, and hence are useful taxa with which to reconstruct gene family evolution. Also it is clear that the traditional molecular model systems for protostomes (e.g. Drosophila melanogaster and Caenorhabditis elegans), which are restricted to the Ecdyso...

A molecular phylogeny for seven taxa of enteric bacteria (Citrobacter freundii, Enterobacter cloacae, Escherichia coli, Hafnia alvei, Klebsiella oxytoca, Klebsiella pneumoniae, and Serratia plymuthica) was made from multiple isolates per taxa taken from a collection of environmental enteric bacteria. Sequences from five housekeeping genes (gapA, groEL, gyrA, ompA, and pgi) and the 16S rRNA gene...

Birth-Death (Bi-De) is an application for the Apple Macintosh which simulates the growth of phylogenetic trees using various models of lineage birth and death. The trees produced are intended to be analogous to those reconstructed from molecular sequence data. The user may define a constant birth rate and death rate or a function describing how these rates vary by time or population size. Insta...

sequences in molecular phylogenetic trees is consistent with early observations that polychaetes tend to have relatively short branches in such trees, and hence are useful taxa with which to reconstruct gene family evolution. Also it is clear that the traditional molecular model systems for protostomes (e.g. Drosophila melanogaster and Caenorhabditis elegans), which are restricted to the Ecdyso...

The concatenation method has been widely used as a means of combining data to estimate phylogenetic trees (Huelsenbeck et al. 1996a, 1996b; Glazko and Nei 2003). However, simulation studies have shown that the maximum likelihood (ML) estimate of the species tree for concatenated sequences may be statistically inconsistent if the gene trees are highly heterogeneous (Kolaczkowski and Thornton 200...

The concatenation method has been widely used as a means of combining data to estimate phylogenetic trees (Huelsenbeck et al. 1996a, 1996b; Glazko and Nei 2003). However, simulation studies have shown that the maximum likelihood (ML) estimate of the species tree for concatenated sequences may be statistically inconsistent if the gene trees are highly heterogeneous (Kolaczkowski and Thornton 200...

The reconstruction of a species phylogeny from genomic data faces two significant hurdles: 1) the trees describing the evolution of each individual gene—i.e., the gene trees—may differ from the species phylogeny and 2) the molecular sequences corresponding to each gene often provide limited information about the gene trees themselves. In this paper we consider an approach to species tree recons...