A response to Lindsey et al. “ Wolbachia pipientis should not be split into multiple species: A response to Ramírez-Puebla et al.”

Ramírez-Puebla, Shamayim T.; Servín-Garcidueñas, Luis E.; Ormeño‐Orrillo, Ernesto; León, Arturo Vera‐Ponce de; Rosenblueth, Mónica; Delaye, Luis; Martinez, Jesse; Martı́nez-Romero, Esperanza

doi:10.1016/j.syapm.2016.03.004

Cited by 11 publications

(14 citation statements)

References 24 publications

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“…The luminosity of a subhalo (sub-subhalo) is given by the same functional form as that of a field halo, but including the dependence of the concentration parameter on the position of the subhalo (sub-subhalo) inside the host halo (subhalo). In addition to the mentioned dependences, we note that subhalos are not homogeneously distributed within the host halo (Springel et al 2008;Hellwing et al 2015;Rodríguez-Puebla et al 2016). However, we have checked that the precise spatial distribution of subhalos inside halos has only a small impact on our results (below 10%).…”

Section: Computation Of the Boostmentioning

confidence: 63%

“…In both cases, presentday (z = 0) halo catalogs are available for public download 3 and we use the results for Vmax and Rmax. Note that one may also study halo substructure properties by making use of large-scale-structure simulations such as BolshoiP (Klypin et al 2011), MultiDark (Prada et al 2012;Riebe et al 2013;Klypin et al 2016;Rodríguez-Puebla et al 2016), which in turn would allow to learn about subhalo properties up to the largest (sub)halo masses. This is left for future work.…”

Section: Description Of the Data Setsmentioning

confidence: 99%

“…Several analytical approaches based on the extended Press-Schechter theory have addressed the properties of the subhalo population in larger halos (see, e.g., Pieri et al (2008); Giocoli et al (008a, 2009);Pieri et al (2009)) and used results from early N-body cosmological simulations about the distribution of subhalos in host halos (Diemand et al 005b,a) to estimate the impact on gamma-ray searches. Also, more refined simulations in the past years have allowed us to better characterize the population and the structure of DM subhalos (Kuhlen et al 2008;Springel et al 2008;Diemand et al 2008;Hellwing et al 2015;Rodríguez-Puebla et al 2016) and different algorithms have been proposed in order to identify small structures within simulated host halos (Ghigna et al 2000;Weller et al 2005;Shaw et al 2006;Springel et al 2001;Gill et al 004a,b;Tormen & Moscardini 2004;Giocoli et al 008b, 2010;Han et al 2012;Behroozi et al 2013). However, the vast majority of this simulation work has been done for galaxy-and cluster-sized DM halos and, indeed, although a few simulations of microhalos are available (Diemand et al 005b;Anderhalden & Diemand 2013;Ishiyama et al 2013;Ishiyama 2014), simulating substructure down to the smallest predicted halo masses and up to the present time remains very challenging.…”

Section: Contextmentioning

confidence: 99%

“…These simulations have revealed in great detail the existence of a population of subhalos in larger halos, even at high redshifts. Simulations of larger volumes have also allowed us to study substructure properties at different (higher) mass scales, as Bolshoi (and BolshoiP) (Klypin et al 2011), MultiDark (Prada et al (2012), P12; Riebe et al (2013); Klypin et al (2016); Rodríguez-Puebla et al (2016)) and, more recently, Copernicus Complexio (COCO) (Hellwing et al 2015). Yet, as expected, all mentioned simulations are limited by the particle mass resolution and, indeed, are far from resolving the whole subhalo hierarchy by orders of magnitude in mass.…”

Section: Introductionmentioning

confidence: 99%

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Characterization of subhalo structural properties and implications for dark matter annihilation signals

Moliné

Sánchez‐Conde

Palomares‐Ruiz

et al. 2017

Mon. Not. R. Astron. Soc.

160

295

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A prediction of the standard ΛCDM cosmological model, also confirmed by N-body simulations, is that dark matter (DM) halos are teeming with numerous self-bound substructure, or subhalos. The precise properties of these subhalos represent important probes of the underlying cosmological model. In this work, we use data from the N-body Via Lactea II and ELVIS Milky Way-size simulations to learn about the structure of subhalos with masses 10 6 − 10 11 h −1 M . Thanks to a superb subhalo statistics, by taking a profileindependent approach, we study subhalo properties as a function of the distance to the host halo center and subhalo mass, and provide a set of fits that, including both dependences, accurately describe the subhalo structure. With this at hand, we also investigate the role of subhalos on the search for DM via its annihilation products. Indeed, previous work has shown that subhalos are expected to boost the DM signal of their host halos significantly. Yet, these works have traditionally assumed that subhalos exhibit similar structural properties than those of field halos of the same mass, while it is well known from simulations that subhalos are more concentrated. Building upon the results from our N-body data analysis, we refine the substructure boost model of Sánchez-Conde & Prada (2014). We find boost values that are a factor 2 − 3 higher than previous ones. We further refine our boost model to include unavoidable tidal stripping effects on the subhalo population. For field halos, this only introduces a moderate (∼ 20% − 30%) suppression of the boost. Yet, for subhalos like those hosting the dwarf satellite galaxies of the Milky Way, tidal stripping does play a critical role, the total boost for these objects being only at the level of a few tens of percent in the most optimistic cases. Finally, we provide a parametrization of the boost factor for field halos that can be safely applied over a wide halo mass range.

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Section: Computation Of the Boostmentioning

confidence: 63%

Section: Description Of the Data Setsmentioning

confidence: 99%

Section: Contextmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Characterization of subhalo structural properties and implications for dark matter annihilation signals

Moliné

Sánchez‐Conde

Palomares‐Ruiz

et al. 2017

Mon. Not. R. Astron. Soc.

160

295

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“…If a contig that is a part of a scaffold is not merged, the contig is placed within the resulting scaffold in a location that corresponds to the original scaffold and the gap length is recomputed. GARM was used in [30] to merge a IDBA-UD assembly with a Newbler assembly.…”

Section: Introductionmentioning

confidence: 99%

A comparative evaluation of genome assembly reconciliation tools

2017

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BackgroundThe majority of eukaryotic genomes are unfinished due to the algorithmic challenges of assembling them. A variety of assembly and scaffolding tools are available, but it is not always obvious which tool or parameters to use for a specific genome size and complexity. It is, therefore, common practice to produce multiple assemblies using different assemblers and parameters, then select the best one for public release. A more compelling approach would allow one to merge multiple assemblies with the intent of producing a higher quality consensus assembly, which is the objective of assembly reconciliation.ResultsSeveral assembly reconciliation tools have been proposed in the literature, but their strengths and weaknesses have never been compared on a common dataset. We fill this need with this work, in which we report on an extensive comparative evaluation of several tools. Specifically, we evaluate contiguity, correctness, coverage, and the duplication ratio of the merged assembly compared to the individual assemblies provided as input.ConclusionsNone of the tools we tested consistently improved the quality of the input GAGE and synthetic assemblies. Our experiments show an increase in contiguity in the consensus assembly when the original assemblies already have high quality. In terms of correctness, the quality of the results depends on the specific tool, as well as on the quality and the ranking of the input assemblies. In general, the number of misassemblies ranges from being comparable to the best of the input assembly to being comparable to the worst of the input assembly.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-017-1213-3) contains supplementary material, which is available to authorized users.

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Fifty shades of bacterial endosymbionts and some of them still remain a mystery: Wolbachia and Cardinium in oribatid mites (Acari: Oribatida)

Konecka

2022

Journal of Invertebrate Pathology

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A response to Lindsey et al. “ Wolbachia pipientis should not be split into multiple species: A response to Ramírez-Puebla et al.”

Cited by 11 publications

References 24 publications

Characterization of subhalo structural properties and implications for dark matter annihilation signals

Characterization of subhalo structural properties and implications for dark matter annihilation signals

A comparative evaluation of genome assembly reconciliation tools

Fifty shades of bacterial endosymbionts and some of them still remain a mystery: Wolbachia and Cardinium in oribatid mites (Acari: Oribatida)

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