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Keywords
(12)
Allele Frequency
Data Analysis
Divergence Time
Effective Population Size
Evolutionary History
Late Pleistocene
Mitochondrial Dna
Nucleotide Sequence
Population Expansion
Population Size
Effect Size
Maximum Likelihood
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Divergence Time and Population Size in the Lineage Leading to Modern Humans
Divergence Time and Population Size in the Lineage Leading to Modern Humans,10.1006/tpbi.1995.1026,Theoretical Population Biology,N. Takahata,Y. Satta
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Divergence Time and Population Size in the Lineage Leading to Modern Humans
(
Citations: 95
)
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N. Takahata
,
Y. Satta
,
J. Klein
We have developed
maximum likelihood
(ML) methods for comparisons of nucleotide sequences from unlinked genomic regions. In the case of a single species, the ML method primarily estimates the
effective population size
(Ne) under both constant size and abrupt expansion conditions. In the case of two or three species, the ML method simultaneously estimates the species
divergence time
and the effective size of ancestral populations. This allows us to trace the
evolutionary history
of the human population over the past several million years (my). Available sequences at human autosomal loci indicate Ne = 10,000 in the Late Pleistocene, a figure concordant with the results obtained from
mitochondrial DNA
sequence and allele-frequency data analysis, and there is no indication of population expansion. The ML analysis of two species shows that humans diverged from chimpanzees 4.6 my ago and that the human and chimpanzee clade diverged from the gorilla 7.2 my ago. Furthermore, the
effective population size
of humans more than 4.6 my ago is nearly 10 times larger than Ne of modern humans. The
effective population size
in the human lineage does not seem to have remained constant over the past several million pears. The ML model for three species predicts slightly different, but consistent results to those obtained by the two-species analysis.
Journal:
Theoretical Population Biology - THEOR POP BIOL
, vol. 48, no. 2, pp. 198-221, 1995
DOI:
10.1006/tpbi.1995.1026
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Citation Context
(32)
...shows the demographic model used for the simulations. Briefly, we simulated a human population with a chimp outgroup where the chimp population split from the human population 5 million years ago (assuming 25 years per generation). The ancestral human-chimp population was assumed to be of size 20,000 because previous studies have found that the ancestral human-chimp population was likely 2–10-fold larger than the current human effective population size
...
Kirk E. Lohmueller
,
et al.
Natural Selection Affects Multiple Aspects of Genetic Variation at Put...
...The variation among gene trees predicted by coalescent theory (Donnelly and Tavare 1995) and typically found in empirical studies (Chen and Li 2001; Jennings and Edwards 2005) reflects information on ancestral population sizes and divergence times in the species tree (Takahata 1989;
Takahata et al. 1995
)...
Liang Liu
,
et al.
Maximum tree: a consistent estimator of the species tree
...and the two-species maximum-likelihood (TSL) method
...
Hiromi Sawai
,
et al.
The Origin and Genetic Variation of Domestic Chickens with Special Ref...
...If any of the estimates in [26] originated from a population that had undergone a serious bottleneck in the past such as humans [
27
], the effects for these populations may mimic those found for domestication as it usually involves a reduction in effective population size, which leads to a less effective response to selection and an increase in the fixation of deleterious mutants [28-30]...
Sean MacEachern
,
et al.
Molecular evolution of the Bovini tribe (Bovidae, Bovinae): Is there e...
... To calculate the recombination parameter (
R
=4
N
e
r
) at the
TNFRSF13B
locus, we have considered an effective population size for humans of
N
e
=10 000
...
M Sazzini
,
et al.
An evolutionary approach to the medical implications of the tumor necr...
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Citations
(95)
Natural Selection Affects Multiple Aspects of Genetic Variation at Putatively Neutral Sites across the Human Genome
Kirk E. Lohmueller
,
Anders Albrechtsen
,
Yingrui Li
,
Su Yeon Kim
,
Thorfinn Korneliussen
,
Nicolas Vinckenbosch
,
Geng Tian
,
Emilia Huerta-Sanchez
,
Alison F. Feder
,
Niels Grarup
,
Torben Jørgensen
,
Tao Jiang
http://academic.research.microsoft.com/io.ashx?type=5&id=57409566&selfId1=0&selfId2=0&maxNumber=12&query=
Journal:
PLOS Genetics - PLOS GENET
, vol. 7, no. 10, 2011
Using genetic evidence to evaluate four palaeoanthropological hypotheses for the timing of Neanderthal and modern human origins
(
Citations: 13
)
Phillip Endicott
,
Simon Y. W. Ho
,
Chris Stringer
Journal:
Journal of Human Evolution - J HUM EVOL
, vol. 59, no. 1, pp. 87-95, 2010
Maximum tree: a consistent estimator of the species tree
(
Citations: 7
)
Liang Liu
,
Lili Yu
,
Dennis K. Pearl
Journal:
Journal of Mathematical Biology - J MATH BIOL
, vol. 60, no. 1, pp. 95-106, 2010
Sequence variation and genetic evolution at the human F12 locus: mapping quantitative trait nucleotides that influence FXII plasma levels
(
Citations: 1
)
F. Calafell
,
L. Almasy
,
M. Sabater-Lleal
,
A. Buil
,
C. Mordillo
,
A. Ramirez-Soriano
,
M. Sikora
,
J. C. Souto
,
J. Blangero
,
J. Fontcuberta
,
J. M. Soria
Journal:
Human Molecular Genetics - HUM MOL GENET
, vol. 19, no. 3, pp. 517-525, 2010
Lineage-Specific Differences in the Amino Acid Substitution Process
(
Citations: 2
)
Snehalata Huzurbazar
,
Grigory Kolesov
,
Steven E. Massey
,
Katherine C. Harris
,
Alexander Churbanov
,
David A. Liberles
Journal:
Journal of Molecular Biology - J MOL BIOL
, vol. 396, no. 5, pp. 1410-1421, 2010