scholarly journals An accurate genetic clock

2015 ◽  
Author(s):  
David H Hamilton
Keyword(s):  
Kin Selection ◽  
Common Ancestor ◽  
Mutation Rates ◽  
Recent Common Ancestor ◽  
Random Factor ◽  
Most Recent Common Ancestor ◽  
Wide Range ◽  
Almost All ◽  
First Time ◽  
Phylogenetic Method

Our method for ``Time to most recent common ancestor'' TMRCA of genetic trees for the first time deals with natural selection by apriori mathematics and not as a random factor. Bioprocesses such as ``kin selection'' generate a few overrepresented ``singular lineages'' while almost all other lineages terminate. This non-uniform branching gives greatly exaggerated TMRCA with current methods. Thus we introduce an inhomogenous stochastic process which will detect singular lineages by asymmetries, whose ``reduction'' then gives true TMRCA. Reduction implies younger TMRCA, with smaller errors. This gives a new phylogenetic method for computing mutation rates, with results similar to ``pedigree'' (meiosis) data. Despite these low rates, reduction implies younger TMRCA, with smaller errors. We establish accuracy by a comparison across a wide range of time, indeed this is only y-clock giving consistent results for 500-15,000 ybp. In particular we show that the dominant European y-haplotypes R1a1a $\& $ R1b1a2, expand from c3700BC, not reaching Anatolia before c3300BC. This contradicts current clocks dating R1b1a2 to either the Neolithic Near East or Paleo-Europe. However our dates match R1a1a $\& $ R1b1a2 found in Yamnaya cemetaries of c3300BC by Svante P\"{a}\"{a}bo et al, together proving R1a1a $\& $ R1b1a2 originates in the Russian Steppes.

scholarly journals An Accurate Genetic Clock

2015 ◽  
Author(s):  
David H Hamilton
Keyword(s):  
Kin Selection ◽  
Common Ancestor ◽  
Mutation Rates ◽  
Recent Common Ancestor ◽  
Random Factor ◽  
Most Recent Common Ancestor ◽  
Wide Range ◽  
Almost All ◽  
First Time ◽  
Phylogenetic Method

Our method for “Time to most recent common ancestor” TMRCA of genetic trees for the first time deals with natural selection by apriori mathematics and not as a random factor. Bioprocesses such as “kin selection” generate a few overrepresented “singular lineages” while almost all other lineages terminate. This non-uniform branching gives greatly exaggerated TMRCA with current methods. Thus we introduce an inhomogenous stochastic process which will detect singular lineages by asymmetries, whose “reduction” then gives true TMRCA. This gives a new phylogenetic method for computing mutation rates, with results similar to “pedigree” (meiosis) data. Despite these low rates, reduction implies younger TMRCA, with smaller errors. We establish accuracy by a comparison across a wide range of time, indeed this is only y-clock giving consistent results for 500-15,000 ybp. In particular we show that the dominant European Y-haplotypes R1a1a & R1b1a2, expand from c4000BC, not reaching Anatolia before c3800BC. This contradicts previous clocks dating R1b1a2 to either the Neolithic Near East or Paleo-Europe. However our dates match R1a1a & R1b1a2 found in Yamnaya cemetaries of c3300BC by Nielsen et al (2015), Pääbo et al(2015), together proving R1a1a & R1b1a2 originates in the Russian Steppes.

scholarly journals An accurate genetic clock

2015 ◽  
Author(s):  
David H Hamilton
Keyword(s):  
Stochastic Process ◽  
Kin Selection ◽  
Common Ancestor ◽  
Mutation Rates ◽  
Recent Common Ancestor ◽  
Molecular Clocks ◽  
Most Recent Common Ancestor ◽  
Wide Range ◽  
Short And Long Term

Molecular clocks give ``Time to most recent common ancestor'' TMRCA} of genetic trees. By Watson-Galton most lineages terminate, with a few overrepresented singular lineages generated by W. Hamilton's ``kin selection''. Applying current methods to this non-uniform branching produces greatly exaggerated TMRCA. We introduce an inhomogenous stochastic process which detects singular lineages by asymmetries, whose reduction gives true TMRCA. This implies a new method for computing mutation rates. Despite low rates similar to mitosis data, reduction implies younger TMRCA, with smaller errors. We establish accuracy by a comparison across a wide range of time, indeed this is only clock giving consistent results for both short and long term times. In particular we show that the dominant European y-haplotypes R1a1a & R1b1a2, expand from c3700BC, not reaching Anatolia before c3300BC. While this contradicts current clocks which date R1b1a2 to either the Neolithic Near East$ or Paleo-Europe, our dates support recent genetic analysis of ancient skeletons by Reich.

scholarly journals Quantifying the tape of life: Ancestry-based metrics provide insights and intuition about evolutionary dynamics

2018 ◽  
Author(s):  
Emily Dolson ◽  
Alexander Lalejini ◽  
Steven Jorgensen ◽  
Charles Ofria
Keyword(s):  
Evolutionary Dynamics ◽  
Common Ancestor ◽  
Optimization Problems ◽  
Mutation Rates ◽  
Recent Common Ancestor ◽  
Two Dimensional ◽  
Digital Evolution ◽  
Most Recent Common Ancestor ◽  
Long Time ◽  
Phylogenetic Divergence

Fine-scale evolutionary dynamics can be challenging to tease out when focused on broad brush strokes of whole populations over long time spans. We propose a suite of diagnostic metrics that operate on lineages and phylogenies in digital evolution experiments with the aim of improving our capacity to quantitatively explore the nuances of evolutionary histories in digital evolution experiments. We present three types of lineage measurements: lineage length, mutation accumulation, and phenotypic volatility. Additionally, we suggest the adoption of four phylogeny measurements from biology: depth of the most-recent common ancestor, phylogenetic richness, phylogenetic divergence, and phylogenetic regularity. We demonstrate the use of each metric on a set of two-dimensional, real-valued optimization problems under a range of mutation rates and selection strengths, confirming our intuitions about what they can tell us about evolutionary dynamics.

scholarly journals Quantifying the tape of life: Ancestry-based metrics provide insights and intuition about evolutionary dynamics

2018 ◽  
Author(s):  
Emily Dolson ◽  
Alexander Lalejini ◽  
Steven Jorgensen ◽  
Charles Ofria
Keyword(s):  
Evolutionary Dynamics ◽  
Common Ancestor ◽  
Optimization Problems ◽  
Mutation Rates ◽  
Recent Common Ancestor ◽  
Two Dimensional ◽  
Digital Evolution ◽  
Most Recent Common Ancestor ◽  
Long Time ◽  
Phylogenetic Divergence

Fine-scale evolutionary dynamics can be challenging to tease out when focused on broad brush strokes of whole populations over long time spans. We propose a suite of diagnostic metrics that operate on lineages and phylogenies in digital evolution experiments with the aim of improving our capacity to quantitatively explore the nuances of evolutionary histories in digital evolution experiments. We present three types of lineage measurements: lineage length, mutation accumulation, and phenotypic volatility. Additionally, we suggest the adoption of four phylogeny measurements from biology: depth of the most-recent common ancestor, phylogenetic richness, phylogenetic divergence, and phylogenetic regularity. We demonstrate the use of each metric on a set of two-dimensional, real-valued optimization problems under a range of mutation rates and selection strengths, confirming our intuitions about what they can tell us about evolutionary dynamics.

Arnebolagus, the oldest eulagomorph, and phylogenetic relationships within the Eocene Eulagomorpha new clade (Mammalia, Duplicidentata)

2020 ◽  
pp. 1-12
Author(s):  
Alexey V. Lopatin ◽  
Alexander O. Averianov
Keyword(s):  
Phylogenetic Relationships ◽  
Common Ancestor ◽  
Morphological Characters ◽  
Recent Common Ancestor ◽  
Early Eocene ◽  
Modern Aspect ◽  
Most Recent Common Ancestor ◽  
Single Tooth ◽  
Land Mammal ◽  
First Time

Abstract Arnebolagus leporinus Lopatin and Averianov, 2008, known previously from a single tooth (P3) from the early Eocene Bumban Member of Naran Bulak Formation at Tsagan-Khushu locality in Mongolia, is redescribed based on additional specimens from the type locality. Phylogenetic relationships of Eocene stem lagomorphs from Asia and North America are reconstructed for the first time based on a parsimony analysis of 54 morphological characters and 32 taxa. Two new node-based clades are proposed, stemming from the most-recent common ancestor of Lepus Linnaeus, 1758 and Dawsonolagus Li, Meng, and Wang, 2007 (Eulagomorpha new clade, ‘lagomorphs of the modern aspect’) and from the most-recent common ancestor of Lepus and Gobiolagus Burke, 1941 (Epilagomorpha new clade). Arnebolagus Lopatin and Averianov, 2008 is geologically oldest and the most plesiomorphic eulagomorph, similar to Dawsonolagus from the early Eocene Arshanto Formation of China in its weakly pronounced, unilateral hypsodonty of the upper cheek teeth and its brachyodont lower cheek teeth with separate roots. Arnebolagus is more plesiomorphic than Dawsonolagus in having two roots of P4. Arnebolagus is the oldest known eulagomorph, the only taxon known from the earliest Eocene Bumbanian Asiatic Land Mammal Age (ALMA). The other Asiatic early Eocene eulagomorphs (Dawsonolagus, Aktashmys Averianov, 1994, and Romanolagus Shevyreva, 1995) come from the Arshantan ALMA.

scholarly journals Molecular phylogeny of Hiptage (Malpighiaceae) reveals a new species from Southwest China

PhytoKeys ◽  
2019 ◽  
Vol 135 ◽  
pp. 91-104 ◽  
Author(s):  
Ke Tan ◽  
Hai-Lei Zheng ◽  
Shu-Peng Dong ◽  
Ming-Xun Ren
Keyword(s):  
New Species ◽  
Molecular Phylogeny ◽  
Internal Transcribed Spacer ◽  
Southwest China ◽  
Common Ancestor ◽  
Its Region ◽  
Recent Common Ancestor ◽  
Most Recent Common Ancestor ◽  
First Time ◽  
A New Species

Hiptage is an Asia-endemic genus of Malpighiaceae currently placed in the tetrapteroid clade, representing one of the seven inter-continent dispersions from New to Old World. A molecular phylogeny based on sequences of the internal transcribed spacer (ITS) region was recovered for the first time for the genus. Our results showed that the most recent common ancestor of Hiptage probably originated in the South Indo-China Peninsula and diversified in this region. Based on phylogenetic evidence and relevant morphological traits, we propose a new species; Hiptage incurvatum is characterised by mericarps with arcuate anterior lateral wings, two large glands on the dorsal sepals, and small glands on the remaining sepals. The new species is from Mt. Cangshan, Dali City (25°35'N, 100°02'E) in North Yunnan, Southwest China and is notable for its occurrence at high altitude, 1400 m (the highest distribution currently known for the genus). The implications of this unusual species for the dispersal and evolution of the genus are discussed.

scholarly journals Allelic Genealogies in Sporophytic Self-Incompatibility Systems in Plants

Genetics ◽  
1998 ◽  
Vol 150 (3) ◽  
pp. 1187-1198 ◽  
Author(s):  
Mikkel H Schierup ◽  
Xavier Vekemans ◽  
Freddy B Christiansen
Keyword(s):  
Dominance Hierarchy ◽  
Common Ancestor ◽  
Recent Common Ancestor ◽  
Self Incompatibility ◽  
Most Recent Common Ancestor ◽  
Dominance Interactions ◽  
Turnover Process ◽  
Neutral Gene ◽  
Interspecific Comparisons ◽  
Coalescence Times

Abstract Expectations for the time scale and structure of allelic genealogies in finite populations are formed under three models of sporophytic self-incompatibility. The models differ in the dominance interactions among the alleles that determine the self-incompatibility phenotype: In the SSIcod model, alleles act codominantly in both pollen and style, in the SSIdom model, alleles form a dominance hierarchy, and in SSIdomcod, alleles are codominant in the style and show a dominance hierarchy in the pollen. Coalescence times of alleles rarely differ more than threefold from those under gametophytic self-incompatibility, and transspecific polymorphism is therefore expected to be equally common. The previously reported directional turnover process of alleles in the SSIdomcod model results in coalescence times lower and substitution rates higher than those in the other models. The SSIdom model assumes strong asymmetries in allelic action, and the most recessive extant allele is likely to be the most recent common ancestor. Despite these asymmetries, the expected shape of the allele genealogies does not deviate markedly from the shape of a neutral gene genealogy. The application of the results to sequence surveys of alleles, including interspecific comparisons, is discussed.

scholarly journals Molecular epidemiological characteristics of echovirus 6 in mainland China: extensive circulation of genotype F from 2007 to 2018

2021 ◽  
Author(s):  
Wenjun Cheng ◽  
Tianjiao Ji ◽  
Shuaifeng Zhou ◽  
Yong Shi ◽  
Lili Jiang ◽  
...  
Keyword(s):  
Common Ancestor ◽  
Mainland China ◽  
Recent Common Ancestor ◽  
Genetic Characteristics ◽  
Most Recent Common Ancestor ◽  
Significant Difference ◽  
Echovirus 6 ◽  
Epidemiological Characteristics ◽  
Highest Posterior Density ◽  
Genotype F

AbstractEchovirus 6 (E6) is associated with various clinical diseases and is frequently detected in environmental sewage. Despite its high prevalence in humans and the environment, little is known about its molecular phylogeography in mainland China. In this study, 114 of 21,539 (0.53%) clinical specimens from hand, foot, and mouth disease (HFMD) cases collected between 2007 and 2018 were positive for E6. The complete VP1 sequences of 87 representative E6 strains, including 24 strains from this study, were used to investigate the evolutionary genetic characteristics and geographical spread of E6 strains. Phylogenetic analysis based on VP1 nucleotide sequence divergence showed that, globally, E6 strains can be grouped into six genotypes, designated A to F. Chinese E6 strains collected between 1988 and 2018 were found to belong to genotypes C, E, and F, with genotype F being predominant from 2007 to 2018. There was no significant difference in the geographical distribution of each genotype. The evolutionary rate of E6 was estimated to be 3.631 × 10-3 substitutions site-1 year-1 (95% highest posterior density [HPD]: 3.2406 × 10-3-4.031 × 10-3 substitutions site-1 year-1) by Bayesian MCMC analysis. The most recent common ancestor of the E6 genotypes was traced back to 1863, whereas their common ancestor in China was traced back to around 1962. A small genetic shift was detected in the Chinese E6 population size in 2009 according to Bayesian skyline analysis, which indicated that there might have been an epidemic around that year.

scholarly journals The Ancestry of a Sample of Sequences Subject to Recombination

Genetics ◽  
1999 ◽  
Vol 151 (3) ◽  
pp. 1217-1228 ◽  
Author(s):  
Carsten Wiuf ◽  
Jotun Hein
Keyword(s):  
Genetic Distance ◽  
Population Size ◽  
Upper Bound ◽  
Recombination Rate ◽  
Common Ancestor ◽  
Recent Common Ancestor ◽  
Sequence Length ◽  
Most Recent Common Ancestor ◽  
The Mean ◽  
Mean Time

Abstract 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 the leftmost nucleotide is ≈log(1 + 4N Lr)/4Nr when two sequences are compared, where L denotes sequence length in nucleotides, and r the recombination rate between any two neighboring nucleotides per generation. For larger samples, the number of nucleotides sharing MRCA with the leftmost nucleotide decreases and becomes almost independent of 4N Lr. Further, we show that a segment of the sequences sharing a MRCA consists in mean of 3/8Nr nucleotides, when two sequences are compared, and that this decreases toward 1/4Nr nucleotides when the whole population is sampled. A measure of the correlation between the genealogies of two nucleotides on two sequences is introduced. We show analytically that even when the nucleotides are separated by a large genetic distance, but share MRCA, the genealogies will show only little correlation. This is surprising, because the time until the two nucleotides shared MRCA is reciprocal to the genetic distance. Using simulations, the mean time until all positions in the sample have found a MRCA increases logarithmically with increasing sequence length and is considerably lower than a theoretically predicted upper bound. On the basis of simulations, it turns out that important properties of the coalescent with recombinations of the whole population are reflected in the properties of a sample of low size.

The evolutionary history and conservation value of disjunct Bartonia paniculata subsp. paniculata (Branched Bartonia) populations in Canada

Botany ◽  
2013 ◽  
Vol 91 (9) ◽  
pp. 605-613 ◽  
Author(s):  
Claudia Ciotir ◽  
Chris Yesson ◽  
Joanna Freeland
Keyword(s):  
Great Lakes ◽  
Evolutionary History ◽  
Common Ancestor ◽  
Recent Common Ancestor ◽  
Great Lakes Region ◽  
Conservation Value ◽  
Most Recent Common Ancestor ◽  
Disjunct Populations ◽  
Management Plans ◽  
Global Status

Understanding the spatial distribution of genetic diversity and its evolutionary history is an essential part of developing effective biodiversity management plans. This may be particularly true when considering the value of peripheral or disjunct populations. Although conservation decisions are often made with reference to geopolitical boundaries, many policy-makers also consider global distributions, and therefore a species’ global status may temper its regional status. Many disjunct populations can be found in the Great Lakes region of North America, including those of Bartonia paniculata subsp. paniculata, a species that has been designated as threatened in Canada but globally secure. We compared chloroplast sequences between disjunct (Canada) and core (USA) populations of B. paniculata subsp. paniculata separated by 600 km, which is the minimum distance between disjunct and core populations in this subspecies. We found that although lineages within the disjunct populations shared a relatively recent common ancestor, the genetic divergence between plants from Ontario and New Jersey was substantially greater than expected for a consubspecific comparison. A coalescence-based analysis dated the most recent common ancestor of the Canadian and US populations at approximately 534 000 years ago with the lower confidence estimate at 226 000 years ago. This substantially predates the Last Glacial Maximum and suggests that disjunct and core populations have followed independent evolutionary trajectories throughout multiple glacial–interglacial cycles. Our findings provide important insight into the diverse processes that have resulted in numerous disjunct species in the Great Lakes region and highlight a need for additional work on Canadian B. paniculata subsp. paniculata taxonomy prior to a reevaluation of its conservation value.

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