The genealogy of branching processes and the age of our most recent common ancestor

1995 ◽  
Vol 27 (2) ◽  
pp. 418-442 ◽  
Author(s):  
Neil O'Connell
Keyword(s):  
Dna Sequences ◽  
Branching Process ◽  
Common Ancestor ◽  
Branching Processes ◽  
Recent Common Ancestor ◽  
Time Interval ◽  
Weak Approximation ◽  
Family Tree ◽  
Exponential Law ◽  
Most Recent Common Ancestor

We obtain a weak approximation for the reduced family tree in a near-critical Markov branching process when the time interval considered is long; we also extend Yaglom's theorem and the exponential law to this case. These results are then applied to the problem of estimating the age of our most recent common female ancestor, using mitochondrial DNA sequences taken from a sample of contemporary humans.

The genealogy of branching processes and the age of our most recent common ancestor

1995 ◽  
Vol 27 (02) ◽  
pp. 418-442 ◽  
Author(s):  
Neil O'Connell
Keyword(s):  
Dna Sequences ◽  
Branching Process ◽  
Common Ancestor ◽  
Branching Processes ◽  
Recent Common Ancestor ◽  
Time Interval ◽  
Weak Approximation ◽  
Family Tree ◽  
Exponential Law ◽  
Most Recent Common Ancestor

We obtain a weak approximation for the reduced family tree in a near-critical Markov branching process when the time interval considered is long; we also extend Yaglom's theorem and the exponential law to this case. These results are then applied to the problem of estimating the age of our most recent common female ancestor, using mitochondrial DNA sequences taken from a sample of contemporary humans.

Coalescence on critical and subcritical multitype branching processes

2016 ◽  
Vol 53 (3) ◽  
pp. 802-817
Author(s):  
Jyy-I Hong
Keyword(s):  
Limit Distribution ◽  
Joint Distribution ◽  
Branching Process ◽  
Common Ancestor ◽  
Branching Processes ◽  
Recent Common Ancestor ◽  
Most Recent Common Ancestor ◽  
Generation Number ◽  
Multitype Branching Processes ◽  
Lines Of Descent

AbstractConsider a d-type (d<∞) Galton–Watson branching process, conditioned on the event that there are at least k≥2 individuals in the nth generation, pick k individuals at random from the nth generation and trace their lines of descent backward in time till they meet. In this paper, the limit behaviors of the distributions of the generation number of the most recent common ancestor of any k chosen individuals and of the whole population are studied for both critical and subcritical cases. Also, we investigate the limit distribution of the joint distribution of the generation number and their types.

scholarly journals Simulating trees with millions of species

2020 ◽  
Vol 36 (9) ◽  
pp. 2907-2908 ◽  
Author(s):  
Stilianos Louca
Keyword(s):  
Common Ancestor ◽  
R Package ◽  
Supplementary Information ◽  
Recent Common Ancestor ◽  
Time Interval ◽  
Simulation Tools ◽  
Parametric Bootstrapping ◽  
Most Recent Common Ancestor ◽  
Large Trees ◽  
Efficient Software

Abstract Motivation The birth-death (BD) model constitutes the theoretical backbone of most phylogenetic tools for reconstructing speciation/extinction dynamics over time. Performing simulations of reconstructed trees (linking extant taxa) under the BD model in backward time, conditioned on the number of species sampled at present day and, in some cases, a specific time interval since the most recent common ancestor (MRCA), is needed for assessing the performance of reconstruction tools, for parametric bootstrapping and for detecting data outliers. The few simulation tools that exist scale poorly to large modern phylogenies, which can comprise thousands or even millions of tips (and rising). Results Here I present efficient software for simulating reconstructed phylogenies under time-dependent BD models in backward time, conditioned on the number of sampled species and (optionally) on the time since the MRCA. On large trees, my software is 1000–10 000 times faster than existing tools. Availability and implementation The presented software is incorporated into the R package ‘castor’, which is available on The Comprehensive R Archive Network (CRAN). Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals A new time tree reveals Earth history’s imprint on the evolution of modern birds

2015 ◽  
Vol 1 (11) ◽  
pp. e1501005 ◽  
Author(s):  
Santiago Claramunt ◽  
Joel Cracraft
Keyword(s):  
Dna Sequences ◽  
Plate Tectonics ◽  
Common Ancestor ◽  
Fossil Birds ◽  
Recent Common Ancestor ◽  
Avian Evolution ◽  
Most Recent Common Ancestor ◽  
Global Cooling ◽  
Basic Features ◽  
New Time

Determining the timing of diversification of modern birds has been difficult. We combined DNA sequences of clock-like genes for most avian families with 130 fossil birds to generate a new time tree for Neornithes and investigated their biogeographic and diversification dynamics. We found that the most recent common ancestor of modern birds inhabited South America around 95 million years ago, but it was not until the Cretaceous-Paleogene transition (66 million years ago) that Neornithes began to diversify rapidly around the world. Birds used two main dispersion routes: reaching the Old World through North America, and reaching Australia and Zealandia through Antarctica. Net diversification rates increased during periods of global cooling, suggesting that fragmentation of tropical biomes stimulated speciation. Thus, we found pervasive evidence that avian evolution has been influenced by plate tectonics and environmental change, two basic features of Earth’s dynamics.

scholarly journals Target Capture Sequencing Unravels Rubus Evolution

2019 ◽  
Author(s):  
Katherine A. Carter ◽  
Aaron Liston ◽  
Nahla V. Bassil ◽  
Lawrence A. Alice ◽  
Jill M. Bushakra ◽  
...  
Keyword(s):  
North America ◽  
Dna Sequences ◽  
Common Ancestor ◽  
Recent Common Ancestor ◽  
Long Distance ◽  
Ploidy Levels ◽  
Most Recent Common Ancestor ◽  
Target Capture ◽  
Target Capture Sequencing ◽  
Capture Sequencing

AbstractBackgroundRubus (Rosaceae) comprises more than 500 species with additional commercially cultivated raspberries and blackberries. The most recent (> 100 years old) global taxonomic treatment of the genus defined 12 subgenera; two subgenera were subsequently described and some species were rearranged. Intra- and interspecific ploidy levels and hybridization make phylogenetic estimation of Rubus challenging. Our objectives were to: estimate the phylogeny of 94 geographically diverse species and 3 cultivars using chloroplast DNA sequences and target capture of approximately 1,000 low copy nuclear genes; estimate divergence times between major Rubus clades; and examine the historical biogeography of species diversification.ResultsTarget capture sequencing identified eight major groups within Rubus. Subgenus Orobatus and Subg. Anoplobatus were monophyletic, while other recognized subgenera were para- or polyphyletic. Multiple hybridization events likely occurred across the phylogeny at subgeneric levels, e.g., Subg. Rubus (blackberries) × Subg. Idaeobatus (raspberries) and Subg. Idaeobatus × Subg. Cylactis (Arctic berries) hybrids. The raspberry heritage within known cultivated blackberry hybrids was confirmed. The most recent common ancestor of the genus was most likely distributed in North America. Multiple distribution events occurred during the Miocene (about 20 Ma) from North America into Asia and Europe across the Bering land bridge and southward crossing the Panamanian Isthmus. Rubus species diversified greatly in Asia during the Miocene.ConclusionsRubus taxonomy does not reflect phylogenetic relationships and subgeneric revision is warranted. Target capture sequencing confirmed that most subgenera are para- or polyphyletic. The most recent common ancestor migrated from North America towards Asia, Europe, and Central and South America early in the Miocene then diversified. Ancestors of the genus Rubus may have migrated to Oceania by long distance bird dispersal. This phylogeny presents a roadmap for further Rubus taxonomic and phylogenetic research.

scholarly journals Estimating the Age of the Common Ancestor of a DNA Sample Using the Number of Segregating Sites

Genetics ◽  
1996 ◽  
Vol 144 (2) ◽  
pp. 829-838 ◽  
Author(s):  
Yun-Xin Fu
Keyword(s):  
Dna Sequences ◽  
Common Ancestor ◽  
Likelihood Function ◽  
Joint Probability ◽  
Recent Common Ancestor ◽  
Joint Probability Distribution ◽  
Most Recent Common Ancestor ◽  
Y Chromosomes ◽  
Point Estimators ◽  
Segregating Sites

Abstract The number of segregating sites in a sample of DNA sequences and the age of the most recent common ancestor (MRCA) of the sequences in the sample are positively correlated. The value of the former can be used to estimate the value of the latter. Using the coalescent approach, we derive in this paper the joint probability distribution of the number of segregating sites and the age of the MRCA of a sample under the neutral Wright-Fisher model. From this distribution, we are able to compute the likelihood function of the number of segregating sites and the posterior probability of the age of the MRCA of a sample. Three point estimators and one interval estimator of the age of the MRCA are developed; their relationships and properties are investigated. The estimation of the age of the MRCA of human Y chromosomes from a sample of no variation is 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.

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