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.

Interpreting the Tape of Life: Ancestry-Based Analyses Provide Insights and Intuition about Evolutionary Dynamics

2020 ◽  
Vol 26 (1) ◽  
pp. 58-79 ◽  
Author(s):  
Emily Dolson ◽  
Alexander Lalejini ◽  
Steven Jorgensen ◽  
Charles Ofria
Keyword(s):  
Phylogenetic Trees ◽  
Evolutionary Dynamics ◽  
Fitness Landscape ◽  
Optimization Problems ◽  
Recent Common Ancestor ◽  
Digital Evolution ◽  
Most Recent Common Ancestor ◽  
Long Time ◽  
Phylogenetic Divergence ◽  
Data Visualizations

Fine-scale evolutionary dynamics can be challenging to tease out when focused on the broad brush strokes of whole populations over long time spans. We propose a suite of diagnostic analysis techniques 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: phylogenetic richness, phylogenetic divergence, phylogenetic regularity, and depth of the most-recent common ancestor. In addition to quantitative metrics, we also discuss several existing data visualizations that are useful for understanding lineages and phylogenies: state sequence visualizations, fitness landscape overlays, phylogenetic trees, and Muller plots. We examine the behavior of these metrics (with the aid of data visualizations) in two well-studied computational contexts: (1) a set of two-dimensional, real-valued optimization problems under a range of mutation rates and selection strengths, and (2) a set of qualitatively different environments in the Avida digital evolution platform. These results confirm our intuition about how these metrics respond to various evolutionary conditions and indicate their broad value.

scholarly journals Multi-year evolutionary dynamics of West Nile virus in suburban Chicago, USA, 2005–2007

2010 ◽  
Vol 365 (1548) ◽  
pp. 1871-1878 ◽  
Author(s):  
Giusi Amore ◽  
Luigi Bertolotti ◽  
Gabriel L. Hamer ◽  
Uriel D. Kitron ◽  
Edward D. Walker ◽  
...  
Keyword(s):  
West Nile Virus ◽  
Evolutionary Dynamics ◽  
Common Ancestor ◽  
Hot Spot ◽  
Viral Envelope ◽  
Recent Common Ancestor ◽  
Evolutionary Information ◽  
Envelope Gene ◽  
West Nile ◽  
Most Recent Common Ancestor

West Nile virus has evolved in concert with its expansion across North America, but little is known about the evolutionary dynamics of the virus on local scales. We analysed viral nucleotide sequences from mosquitoes collected in 2005, 2006, and 2007 from a known transmission ‘hot spot’ in suburban Chicago, USA. Within this approximately 11 × 14 km area, the viral envelope gene has increased approximately 0.1% yr −1 in nucleotide-level genetic diversity. In each year, viral diversity was higher in ‘residential’ sites characterized by dense housing than in more open ‘urban green space’ sites such as cemeteries and parks. Phylodynamic analyses showed an increase in incidence around 2005, consistent with a higher-than-average peak in mosquito and human infection rates that year. Analyses of times to most recent common ancestor suggest that WNV in 2005 and 2006 may have arisen predominantly from viruses present during 2004 and 2005, respectively, but that WNV in 2007 had an older common ancestor, perhaps indicating a predominantly mixed or exogenous origin. These results show that the population of WNV in suburban Chicago is an admixture of viruses that are both locally derived and introduced from elsewhere, containing evolutionary information aggregated across a breadth of spatial and temporal scales.

A comparison of pigmentation features among North Atlantic killer whale (Orcinus orca) populations

2014 ◽  
Vol 94 (6) ◽  
pp. 1335-1341 ◽  
Author(s):  
Pirjo Mäkeläinen ◽  
Ruth Esteban ◽  
Andrew D. Foote ◽  
Sanna Kuningas ◽  
Julius Nielsen ◽  
...  
Keyword(s):  
North Atlantic ◽  
Common Ancestor ◽  
Killer Whale ◽  
Orcinus Orca ◽  
Recent Common Ancestor ◽  
Killer Whales ◽  
Parallel Orientation ◽  
Local Populations ◽  
Most Recent Common Ancestor ◽  
Phylogenetic Divergence

Here we present a comparison of saddle and eye patch patterns of killer whales from Norwegian, Icelandic, British, Spanish and Greenlandic waters. We found only a small amount of variation in saddle patch shapes, which may reflect a recent phylogenetic divergence from the most recent common ancestor. Eye patch shapes were more variable than saddle patches in small details. Most individuals had eye patches with parallel orientation, with the exception of a small group of killer whales from the Hebrides, which, as previously reported, had sloping eye patches that sloped downward at the posterior end. This differentiation in pigmentation patterns of the Hebridean killer whales from neighbouring populations could reflect one or more of several evolutionary processes, including a deeper phylogenetic divergence, low gene flow with other local populations and drift.

scholarly journals Comprehensive evolution and molecular characteristics of a large number of SARS-CoV-2 genomes revealed its epidemic trend and possible origins

2020 ◽  
Author(s):  
Yunmeng Bai ◽  
Dawei Jiang ◽  
Jerome R Lon ◽  
Xiaoshi Chen ◽  
Meiling Hu ◽  
...  
Keyword(s):  
Common Ancestor ◽  
Neutral Evolution ◽  
Recent Common Ancestor ◽  
Molecular Characteristics ◽  
Major Haplotype ◽  
Most Recent Common Ancestor ◽  
Evolution Analysis ◽  
The World ◽  
Long Time ◽  
New Perspective

AbstractObjectivesTo reveal epidemic trend and possible origins of SARS-CoV-2 by exploring its evolution and molecular characteristics based on a large number of genomes since it has infected millions of people and spread quickly all over the world.MethodsVarious evolution analysis methods were employed.ResultsThe estimated Ka/Ks ratio of SARS-CoV-2 is 1.008 or 1.094 based on 622 or 3624 SARS-CoV-2 genomes, and the time to the most recent common ancestor (tMRCA) was inferred in late September 2019. Further 9 key specific sites of highly linkage and four major haplotypes H1, H2, H3 and H4 were found. The Ka/Ks, detected population size and development trends of each major haplotype showed H3 and H4 subgroups were going through a purify evolution and almost disappeared after detection, indicating H3 and H4 might have existed for a long time, while H1 and H2 subgroups were going through a near neutral or neutral evolution and globally increased with time. Notably the frequency of H1 was generally high in Europe and correlated to death rate (r>0.37).ConclusionsIn this study, the evolution and molecular characteristics of more than 16000 genomic sequences provided a new perspective for revealing epidemiology of SARS-CoV-2.

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 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 Origin and Phylodynamics of Rabbit Hemorrhagic Disease Virus

2009 ◽  
Vol 83 (23) ◽  
pp. 12129-12138 ◽  
Author(s):  
Peter J. Kerr ◽  
Andrew Kitchen ◽  
Edward C. Holmes
Keyword(s):  
Disease Virus ◽  
Evolutionary Dynamics ◽  
Common Ancestor ◽  
Sequence Similarity ◽  
Rabbit Hemorrhagic Disease Virus ◽  
Recent Common Ancestor ◽  
Hemorrhagic Disease ◽  
Antigenic Variant ◽  
Rabbit Hemorrhagic Disease ◽  
Most Recent Common Ancestor

ABSTRACT To determine the origin, phylogenetic relationships, and evolutionary dynamics of rabbit hemorrhagic disease virus (RHDV), we examined 210 partial and complete capsid gene nucleotide sequences. Using a Bayesian Markov chain Monte Carlo approach, we estimated that these sequences evolved at a rate of 3.9 × 10−4 to 11.9 × 10−4 nucleotide substitutions per site per year. This rate was consistent across subsets of data, was robust in response to recombination, and casts doubt on the provenance of viral strains isolated from the 1950s to the 1970s, which share strong sequence similarity to modern isolates. Using the same analysis, we inferred that the time to the most recent common ancestor for a joint group of RHDV and rabbit calicivirus sequences was <550 years ago and was <150 years ago for the RHDV isolates that have spread around the world since 1984. Importantly, multiple lineages of RHDV were clearly circulating before the major Chinese outbreak of 1984, a finding indicative of an early evolution of RHDV virulence. Four phylogenetic groups within RHDV were defined and analyzed separately. Each group shared a common ancestor in the mid-1960s or earlier, and each showed an expansion of populations starting before 1984. Notably, the group characterized by the antigenic variant RHDVa harbors the greatest genetic diversity, compatible with an elevated fitness. Overall, we contend that the high virulence of RHDV likely evolved once in the early part of the 20th century, well before the documented emergence of rabbit hemorrhagic disease in 1984.

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 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.

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