1,005 research outputs found
Divergence, demography and gene loss along the human lineage
Genomic DNA sequences are an irreplaceable source for reconstructing the vanished past of living organisms. Based on updated sequence data, this paper summarizes our studies on species divergence time, ancient population size and functional loss of genes in the primate lineage leading to modern humans (Homo sapiens sapiens). The inter- and intraspecific comparisons of DNA sequences suggest that the human lineage experienced a rather severe bottleneck in the Middle Pleistocene, throughout which period the subdivided African population played a predominant role in shaping the genetic architecture of modern humans. Also, published and newly identified human-specific pseudogenes (HSPs) are enumerated in order to infer their significance for human evolution. Of the 121 candidate genes obtained, authentic HSPs turn out to comprise only 25 olfactory receptor genes, four T cell receptor genes and nine other genes. The fixation of HSPs has been too rare over the past 6–7 Myr to account for species differences between humans and chimpanzees
Statistics of selectively neutral genetic variation
Random models of evolution are instrumental in extracting rates of
microscopic evolutionary mechanisms from empirical observations on genetic
variation in genome sequences. In this context it is necessary to know the
statistical properties of empirical observables (such as the local homozygosity
for instance). Previous work relies on numerical results or assumes Gaussian
approximations for the corresponding distributions. In this paper we give an
analytical derivation of the statistical properties of the local homozygosity
and other empirical observables assuming selective neutrality. We find that
such distributions can be very non-Gaussian.Comment: 4 pages, 4 figure
AUGIST: inferring species trees while accommodating gene tree uncertainty
Summary: AUGIST (accomodating uncertainty in genealogies while inferring species tress) is a new software package for inferring species trees while accommodating uncertainty in gene genealogies. It is written for the Mesquite software system and provides sampling procedures to incorporate uncertainty in gene tree reconstruction while providing confidence estimates for inferred species trees
Blood ties: ABO is a trans-species polymorphism in primates
The ABO histo-blood group, the critical determinant of transfusion
incompatibility, was the first genetic polymorphism discovered in humans.
Remarkably, ABO antigens are also polymorphic in many other primates, with the
same two amino acid changes responsible for A and B specificity in all species
sequenced to date. Whether this recurrence of A and B antigens is the result of
an ancient polymorphism maintained across species or due to numerous, more
recent instances of convergent evolution has been debated for decades, with a
current consensus in support of convergent evolution. We show instead that
genetic variation data in humans and gibbons as well as in Old World Monkeys
are inconsistent with a model of convergent evolution and support the
hypothesis of an ancient, multi-allelic polymorphism of which some alleles are
shared by descent among species. These results demonstrate that the ABO
polymorphism is a trans-species polymorphism among distantly related species
and has remained under balancing selection for tens of millions of years, to
date, the only such example in Hominoids and Old World Monkeys outside of the
Major Histocompatibility Complex.Comment: 45 pages, 4 Figures, 4 Supplementary Figures, 5 Supplementary Table
Low thermal conductivity of the layered oxide (Na,Ca)Co_2O_4: Another example of a phonon glass and an electron crystal
The thermal conductivity of polycrystalline samples of (Na,Ca)Co_2O_4 is
found to be unusually low, 20 mW/cmK at 280 K. On the assumption of the
Wiedemann-Franz law, the lattice thermal conductivity is estimated to be 18
mW/cmK at 280 K, and it does not change appreciably with the substitution of Ca
for Na. A quantitative analysis has revealed that the phonon mean free path is
comparable with the lattice parameters, where the point-defect scattering plays
an important role. Electronically the same samples show a metallic conduction
down to 4.2 K, which strongly suggests that NaCo_2O_4 exhibits a glass-like
poor thermal conduction together with a metal-like good electrical conduction.
The present study further suggests that a strongly correlated system with
layered structure can act as a material of a phonon glass and an electron
crystal.Comment: 5 pages 3 figures, to be published in Phys. Rev.
Lack of self-averaging in neutral evolution of proteins
We simulate neutral evolution of proteins imposing conservation of the
thermodynamic stability of the native state in the framework of an effective
model of folding thermodynamics. This procedure generates evolutionary
trajectories in sequence space which share two universal features for all of
the examined proteins. First, the number of neutral mutations fluctuates
broadly from one sequence to another, leading to a non-Poissonian substitution
process. Second, the number of neutral mutations displays strong correlations
along the trajectory, thus causing the breakdown of self-averaging of the
resulting evolutionary substitution process.Comment: 4 pages, 2 figure
Fluctuating selection models and Mcdonald-Kreitman type analyses
It is likely that the strength of selection acting upon a mutation varies through time due to changes in the environment. However, most population genetic theory assumes that the strength of selection remains constant. Here we investigate the consequences of fluctuating selection pressures on the quantification of adaptive evolution using McDonald-Kreitman (MK) style approaches. In agreement with previous work, we show that fluctuating selection can generate evidence of adaptive evolution even when the expected strength of selection on a mutation is zero. However, we also find that the mutations, which contribute to both polymorphism and divergence tend, on average, to be positively selected during their lifetime, under fluctuating selection models. This is because mutations that fluctuate, by chance, to positive selected values, tend to reach higher frequencies in the population than those that fluctuate towards negative values. Hence the evidence of positive adaptive evolution detected under a fluctuating selection model by MK type approaches is genuine since fixed mutations tend to be advantageous on average during their lifetime. Never-the-less we show that methods tend to underestimate the rate of adaptive evolution when selection fluctuates
Utterance Selection Model of Language Change
We present a mathematical formulation of a theory of language change. The
theory is evolutionary in nature and has close analogies with theories of
population genetics. The mathematical structure we construct similarly has
correspondences with the Fisher-Wright model of population genetics, but there
are significant differences. The continuous time formulation of the model is
expressed in terms of a Fokker-Planck equation. This equation is exactly
soluble in the case of a single speaker and can be investigated analytically in
the case of multiple speakers who communicate equally with all other speakers
and give their utterances equal weight. Whilst the stationary properties of
this system have much in common with the single-speaker case, time-dependent
properties are richer. In the particular case where linguistic forms can become
extinct, we find that the presence of many speakers causes a two-stage
relaxation, the first being a common marginal distribution that persists for a
long time as a consequence of ultimate extinction being due to rare
fluctuations.Comment: 21 pages, 17 figure
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