The recent explosion of genomic data has underscored the need for interpretable and comprehensive analyses that can capture complex phylogenetic relationships within and across species. Recombination, reassortment and horizontal gene transfer constit
ute examples of pervasive biological phenomena that cannot be captured by tree-like representations. Starting from hundreds of genomes, we are interested in the reconstruction of potential evolutionary histories leading to the observed data. Ancestral recombination graphs represent potential histories that explicitly accommodate recombination and mutation events across orthologous genomes. However, they are computationally costly to reconstruct, usually being infeasible for more than few tens of genomes. Recently, Topological Data Analysis (TDA) methods have been proposed as robust and scalable methods that can capture the genetic scale and frequency of recombination. We build upon previous TDA developments for detecting and quantifying recombination, and present a novel framework that can be applied to hundreds of genomes and can be interpreted in terms of minimal histories of mutation and recombination events, quantifying the scales and identifying the genomic locations of recombinations. We implement this framework in a software package, called TARGet, and apply it to several examples, including small migration between different populations, human recombination, and horizontal evolution in finches inhabiting the Galapagos Islands.
We argue that in large classes of string compactifications with a MSSM-like structure substantial flavor violating SUSY-breaking soft terms are generically induced. We specify to the case of flavor dependent soft-terms in type IIB/F-theory SU(5) unif
ied models, although our results can be easily extended to other settings. The Standard Model (SM) degrees of freedom reside in a local system of 7-branes wrapping a 4-fold S in the extra dimensions. It is known that in the presence of closed string 3-form fluxes SUSY-breaking terms are typically generated. We explore the generation dependence of these soft terms and find that non-universalities arise whenever the flux varies over the 4-fold S. These non-universalities are parametrically suppressed by (M_{GUT}/M_{Pl})^{1/3}. They also arise in the case of varying open string fluxes, in this case parametrically suppressed by alpha_{GUT}^{1/2}. For a standard unification scheme with M_{GUT} = 10^{16} GeV and alpha_{rm GUT} = 1/24 these suppressions are very mild. Although limits from the kaon mass difference Delta m_K are easily obeyed for squark masses above the present LHC limits, constraints from the CP-violation parameter epsilon_K imply squark masses in the multi-TeV region. The constraints from BR(mu rightarrow egamma) turn out to be the strongest ones, with slepton masses of order ~10 TeV or heavier required to obey the experimental limits. These sfermion masses are consistent with the observed large value m_H ~ 126 GeV of the Higgs mass. We discuss under what conditions such strong limits may be relaxed allowing for SUSY particle production at LHC.
We consider 4d string compactifications in the presence of fluxes, and classify particles, strings and domain walls arising from wrapped branes which have charges conserved modulo an integer p, and whose annihilation is catalized by fluxes, through the Freed-Witten anomaly or its du
