The mutation process is introduced into the colored coalescent theory. The mutation process can be viewed as an independent Poisson process running on the colored genealogical random tree generated by the colored coalescent process, with the edge lengths of the random tree serving as the time scale for the mutation process. Moving backward along the colored genealogical tree, the color of verti...

The genealogies of samples of orthologous regions from multiple species can be classified by their shapes. Using a neutral coalescent model of two species, I give exact probabilities of each of four possible genealogical shapes: reciprocal monophyly, two types of paraphyly, and polyphyly. After the divergence that forms two species, each of which has population size N, polyphyly is the most lik...

Absorption spectra of aqueous solution of ''chaotropes'' (structure maker) and ''kosmotropes'' (structure breaker) have been recorded in the mid-infrared (MIR) and terahertz (THz) spectral region. A different impact of the two groups of solutes on the absorption spectrum of water was found in the recorded THz spectra. A concentration-dependent increased absorption across the investigated THz sp...

In this article we discuss the ancestry of sequences sampled from the coalescent with recombination with constant population size 2N. We have studied a number of variables based on simulations of sample histories, and some analytical results are derived. Consider the leftmost nucleotide in the sequences. We show that the number of nucleotides sharing a most recent common ancestor (MRCA) with th...

Influenza C contributes to economic damage caused by working days lost through absence or inefficiency and may occasionally cause an acute respiratory illness in a paediatric setting. All Influenza C sequences from the NCBI Influenza Virus Resource were examined to determine the date of the most recent common ancestor (t-MRCA), the average nucleotide substitution rate, and the location of resid...

Earth's tectonic plates are generally considered to be driven largely by negative buoyancy associated with subduction of oceanic lithosphere. In this context, mid-ocean ridges (MORs) are passive plate boundaries whose divergence accommodates flow driven by subduction of oceanic slabs at trenches. We show that over the past 80 million years (My), the East Pacific Rise (EPR), Earth's dominant MOR...

Molecular Inflammation Research Center for Aging Intervention (MRCA), College of Pharmacy, Pusan National University, Busan 609-735, Republic of Korea Graduate School of Science and Engineering for Research, University of Toyama, Toyama 930-8555, Japan Faculty of Pharmaceutical Sciences, Nagasaki University, Nagasaki 852-8131, Japan Department of Physiology, The University of Texas Health Scien...

where f(t |Θ) is the probability density of the coalescent time. Assuming free recombination between loci, the full likelihood is a product of each locus likelihood. In order to determine the likelihood we must determine the density f(t |Θ) for coalescent of two samples in the IM model. Wang and Hey (2009) find the time to the MRCA by explicitly integrating over all possible sample paths in the...