Friday, September 23, 2022

Neanderthal Admixture Was Followed By Fitness Based Selection

Neanderthal admixture with modern humans was followed by strong fitness driven natural selection against many Neanderthal genes that made their way into the X chromosome in locations where natural selection also played a strong part in shaping great ape genetics.

We don't yet really understand, however, precisely what phenotypic traits the Neanderthal X chromosome genes selected against governed. 

We would like to know because that would help tell us what genetic traits unique to modern humans, and not found in Neanderthals or Denisovans, helped our species of hominins survive when other hominin species went extinct in the Upper Paleolithic era.
The X chromosome in non-African human populations shows less diversity and less Neanderthal introgression than expected under the standard neutral model. 
We analyzed 162 X chromosomes from human males worldwide and discovered 14 chromosomal regions where haplotypes of several hundred kilobases rapidly rose to high frequencies in non-Africans. These observations cannot be explained by neutral genetic drift in realistic demographic scenarios and are only consistent with partial selective sweeps produced by strong selection. 
Using an approach for inferring individual Neanderthal-derived haplotypes, which do not rely on an archaic reference genome, we further discover that the swept haplotypes are devoid of the archaic ancestry otherwise typical of the affected chromosomal regions. The ancient Ust’-Ishim male carries its expected proportion of these haplotypes, implying that the sweeps must have occurred between 45,000 and 55,000 years ago. 
Finally, we find that the chromosomal positions of sweeps overlap previously reported hotspots of selection in great ape evolution. We propose that this puzzling combination of observations points to a general mechanism of positive selection unique to the X chromosome.

How Did English Get To England?

The genetic differences between the ancestral (post-Bell Beaker) Celtic population of Great Britain, the people of the Atlantic Coast of Europe, and the people of Denmark and Southwestern Scandinavia are subtle. So, it takes reasonable large, and reasonably high quality samples of modern and ancient DNA to distinguish them in the course of piecing together with genetic, historical, archaeological, and linguistic evidence to form a coherent narrative of the waves of migration that gave rise to the modern British people.

The linguistic evidence supported by historical accounts long ago made clear that the English language arrived in England as a result of Anglo-Saxon migration to and conquest of Great Britain, especially in Eastern England in the early Middle Ages. This account was supported by a major study with a very large sample of moderately high quality modern DNA evidence from Britain published in 2015.

But, due to the subtly of the regional differences in population genetics between the relevant regions and a paucity of ancient DNA from the thirty or more generations earlier when it happened, it was hard to determine with confidence from that data that the Anglo-Saxon migration to England shifted more than a modestly small percentage of population genetics of Eastern England.

In this case, the language shift from a Celtic substrate to Old English in England would have been largely a case of elite dominance driven language shift, not unlike what happened in Hungary, half a millennium later.

But a new study with more ancient DNA from the relevant time period corroborated by anthropological analysis of the grave contexts of ancient DNA specimen source remains with differing levels of DNA from different regional sources, allowing scholars to distinguish between the subtly different genetic populations with more confidence have shifted that narrative considerably.

Now, it appears that in parts of Eastern England as much as three-quarters of the population's genetic ancestry (including a very similar peak 75% of Y-DNA suggesting a gender balanced migration rather than a male dominated conquest of local populations) was Anglo-Saxon, rather than being derived from the Celtic substrate in the region. This supports a different narrative of language shift due to large scale population replacement in the region. The paper states:
The history of the British Isles and Ireland is characterized by multiple periods of major cultural change, including the influential transformation after the end of Roman rule, which precipitated shifts in language, settlement patterns and material culture…The extent to which migration from continental Europe mediated these transitions is a matter of long-standing debate… 
Here we study genome-wide ancient DNA from 460 medieval northwestern Europeans—including 278 individuals from England—alongside archaeological data, to infer contemporary population dynamics. 
We identify a substantial increase of continental northern European ancestry in early medieval England, which is closely related to the early medieval and present-day inhabitants of Germany and Denmark, implying large-scale substantial migration across the North Sea into Britain during the Early Middle Ages. 
As a result, the individuals who we analysed from eastern England derived up to 76% of their ancestry from the continental North Sea zone, albeit with substantial regional variation and heterogeneity within sites. We show that women with immigrant ancestry were more often furnished with grave goods than women with local ancestry, whereas men with weapons were as likely not to be of immigrant ancestry. 
A comparison with present-day Britain indicates that subsequent demographic events reduced the fraction of continental northern European ancestry while introducing further ancestry components into the English gene pool, including substantial southwestern European ancestry most closely related to that seen in Iron Age France.

The new study also picks up a significant, but more slow and steady migration of people from across the English channel in France, in the centuries following the Anglo-Saxon migration (possibly related to the Norman Conquest).

Hat tip to Razib Khan.

Also, people in the Northern Isles of Scotland, such as Shetland and Orkney, appear from their genetics to have 16%-19% Jewish ancestry.

Tuesday, September 20, 2022

How Did Saturn Get Its Rings?

Fascinating and plausible.
Scientists propose a lost moon of Saturn, which they call Chrysalis, pulled on the planet until it ripped apart, forming rings and contributing to Saturn's tilt. . . . the team proposes that Saturn, which today hosts 83 moons, once harbored at least one more, an extra satellite that they name Chrysalis. Together with its siblings, the researchers suggest, Chrysalis orbited Saturn for several billion years, pulling and tugging on the planet in a way that kept its tilt, or "obliquity," in resonance with Neptune.
But around 160 million years ago, the team estimates, Chrysalis became unstable and came too close to its planet in a grazing encounter that pulled the satellite apart. The loss of the moon was enough to remove Saturn from Neptune's grasp and leave it with the present-day tilt.

What's more, the researchers surmise, while most of Chrysalis' shattered body may have made impact with Saturn, a fraction of its fragments could have remained suspended in orbit, eventually breaking into small icy chunks to form the planet's signature rings.

The missing satellite, therefore, could explain two longstanding mysteries: Saturn's present-day tilt and the age of its rings, which were previously estimated to be about 100 million years old -- much younger than the planet itself.
From Science Daily citing Jack Wisdom, et al., "Loss of a satellite could explain Saturn’s obliquity and young rings." 377 (6612) Science 1285 (2022). DOI: 10.1126/science.abn1234

Shape Matters

A gravitational explanation in which the inferred dark matter effect is a function of the ellipticity of the baryonic matter distribution gives rise to the same relationship.

Also, it confirms that inferred cold dark matter halos tend not to be spherically symmetric as many dark matter particle halo models, such as the NFW halo model inferred analytically, would predict, without a good reason for this being the case in a cosmology model where halos give rise to baryonic matter clustering that gives rise to galaxies, and without a good reason for the predominance of spiral shaped galaxies, both of which are natural expectations of a gravitational based explanation in which the weak gravitational fields of galaxies are strengthened when they are no spherically symmetrical.
Cold dark matter haloes are expected to be triaxial, and so appear elliptical in projection. We use weak gravitational lensing from the Canada-France Imaging Survey (CFIS) component of the Ultraviolet-Near Infrared Optical Northern Survey (UNIONS) to measure the ellipticity of the dark matter haloes around Luminous Red Galaxies (LRGs) from the Sloan Digital Sky Survey Data Release 7 (DR7) and from the CMASS and LOWZ samples of the Baryon Oscillation Spectroscopic Survey (BOSS), assuming their major axes are aligned with the stellar light. We find that DR7 LRGs with masses M∼2.5×10^13M⊙/h have halo ellipticities e=0.35±0.09. Expressed as a fraction of the galaxy ellipticity, we find fh=1.4±0.4. For BOSS LRGs, the detection is of marginal significance: e=0.17±0.10 and fh=0.1±0.4. These results are in agreement with other measurements of halo ellipticity from weak lensing and, taken together with previous results, suggest an increase of halo ellipticity of 0.10±0.05 per decade in halo mass. This trend agrees with the predictions from hydrodynamical simulations, which find that at higher halo masses, not only do dark matter haloes become more elliptical, but that the misalignment between major axis of the stellar light in the central galaxy and that of the dark matter decreases.
Bailey Robison, et al., "The shape of dark matter haloes: results from weak lensing in the Ultraviolet Near-Infrared Optical Northern Survey (UNIONS)" arXiv:2209.09088 (September 19, 2022).

Cosmology Anomalies

Rather than focus on the proposed solution, I would call attention to the fact that the standard model ΛCDM is facing three significant discrepancies with cosmology scale astronomy observations that this particular solution feels a need to address. 

Maybe there are so many discrepancies because the model is wrong.

We consider a phenomenological model of dark matter with an equation-of-state that is negative and changing at late times. We show this couples the H0 and σ8 tensions, providing an explanation for both simultaneously, while also providing an explanation for the anomalously large integrated Sachs-Wolfe (ISW) effect from cosmic voids. 

Observations of high ISW from cosmic voids may therefore be evidence that dark matter plays a significant role in the H0 and σ8 tensions. We predict the ISW from cosmic voids to be a factor of ~ 2 greater in this model than what is expected from the standard model ΛCDM.

Krishna Naidoo, et al., "A dark matter solution to the H(0) and σ(8) tensions, and the integrated Sachs-Wolfe void anomaly" arXiv:2209.08102 (September 16, 2022).

The introduction to the paper in the body text explains these anomalies:
The emergence of strong tensions in the constraints of the Hubble constant H(0) and σ(8) parameters, between early and late universe physics, have placed intense scrutiny on observations, methods and the assumptions of the standard model of cosmology ΛCDM. One of these assumptions is the presence of cold dark matter; a yet-to-be-detected massive particle that is the dominant source of gravitation in the universe. Dark matter’s interactions with known particles and forces is assumed to be very weak and the specific properties of dark matter are often assumed to manifest only on small cosmological scales. 
However, with no direct observations of dark matter, there is little we can presume about its properties, other than its gravitational effects and weak interactions with known particles. Rather than consider an endless list of dark matter model extensions we can instead consider phenomenological models that allow us to determine the general observational implications of a whole set of dark matter models, including their role in tensions and anomalies. With this in mind, we explore the implication of a subset of the generalised dark matter model, in a spatially flat universe with a cosmological constant (Λ). The equation-of-state (EoS) for dark matter (wdm) is allowed to be non-zero and evolving at late times but with null speed of sound and viscosity. For consistency with constraints from the early universe the EoS is assumed to be effectively zero at early times. We will refer to this model as evolving dark matter (eDM), to distinguish it from other models often abbreviated to WDM (such as warm dark matter), and with the full model with Λ referred to as ΛeDM. 
While the H(0) and σ(8) tensions are widely discussed in the community, a lesser known anomaly is the observation of larger than expected integrated Sachs-Wolfe [ISW] from cosmic voids (the void-ISW anomaly). This anomaly is strongest for ‘photometric’ voids, i.e. voids measured from photometric observations of galaxies which are preferentially elongated along the line-of-sight (LOS), while for ‘spectroscopic’ voids (smaller and not aligned with the LOS) the ISW is larger but to a lesser extent and remains consistent with ΛCDM. In contrast, observations of void lensing are either consistent with ΛCDM or lower than expected.

Also, kudos to the authors for resisting the inclination to create a confusing acronym for their model, when they were clearly tempted to do so.

Wikipedia explains the Integrated Sachs-Wolfe effect:

The Sachs–Wolfe effect, named after Rainer K. Sachs and Arthur M. Wolfe, is a property of the cosmic microwave background radiation (CMB), in which photons from the CMB are gravitationally redshifted, causing the CMB spectrum to appear uneven. This effect is the predominant source of fluctuations in the CMB for angular scales larger than about ten degrees.

The non-integrated Sachs–Wolfe effect is caused by gravitational redshift occurring at the surface of last scattering. The effect is not constant across the sky due to differences in the matter/energy density at the time of last scattering.
The integrated Sachs–Wolfe (ISW) effect is also caused by gravitational redshift, but it occurs between the surface of last scattering and the Earth, so it is not part of the primordial CMB. It occurs when the Universe is dominated in its energy density by something other than matter. If the Universe is dominated by matter, then large-scale gravitational potential energy wells and hills do not evolve significantly. If the Universe is dominated by radiation, or by dark energy, though, those potentials do evolve, subtly changing the energy of photons passing through them.

There are two contributions to the ISW effect. The "early-time" ISW occurs immediately after the (non-integrated) Sachs–Wolfe effect produces the primordial CMB, as photons course through density fluctuations while there is still enough radiation around to affect the Universe's expansion. Although it is physically the same as the late-time ISW, for observational purposes it is usually lumped in with the primordial CMB, since the matter fluctuations that cause it are in practice undetectable. 
Late-time integrated Sachs–Wolfe effect

The "late-time" ISW effect arises quite recently in cosmic history, as dark energy, or the cosmological constant, starts to govern the Universe's expansion. Unfortunately, the nomenclature is a bit confusing. Often, "late-time ISW" implicitly refers to the late-time ISW effect to linear/first order in density perturbations. This linear part of the effect entirely vanishes in a flat universe with only matter, but dominates over the higher-order part of the effect in a universe with dark energy. The full nonlinear (linear + higher-order) late-time ISW effect, especially in the case of individual voids and clusters, is sometimes known as the Rees–Sciama effect, since Martin Rees and Dennis Sciama elucidated the following physical picture.

Accelerated expansion due to dark energy causes even strong large-scale potential wells (superclusters) and hills (voids) to decay over the time it takes a photon to travel through them. A photon gets a kick of energy going into a potential well (a supercluster), and it keeps some of that energy after it exits, after the well has been stretched out and shallowed. Similarly, a photon has to expend energy entering a supervoid, but will not get all of it back upon exiting the slightly squashed potential hill.

A signature of the late-time ISW is a non-zero cross-correlation function between the galaxy density (the number of galaxies per square degree) and the temperature of the CMB, because superclusters gently heat photons, while supervoids gently cool them. This correlation has been detected at moderate to high significance.

A detailed analysis of how parameters such as shot noise, maximum multipole or redshift ranges can influence the significance of radio continuum surveys was presented by Rahman in 2014.

In May 2008, Granett, Neyrinck & Szapudi showed that the late-time ISW can be pinned to discrete supervoids and superclusters identified in the SDSS Luminous Red Galaxy catalog. Their ISW detection traces the localised ISW effect produced by supervoids and superclusters have on the CMB. However, the amplitude of this localised detection is controversial, as it is significantly larger than the expectations and depends on several assumptions of the analysis.

Monday, September 12, 2022

The Indo-European Languages Did Not Arise In Anatolia

Davidski at Eurogenes rightly pans, in a fifth installment of criticism, the recent Lazaridis, Alpaslan-Roodenberg et al. paper (that has lots of good new ancient DNA evidence from a critical area). The new paper wrongly interprets the data as supporting an Armenian or Anatolian origin of the Indo-European languages, when it is far more plausible that the Indo-European languages originate in Eastern Europe stating:
The debate over the location of the so called Indo-Anatolian homeland won't be decided by the persistence of any type of genetic ancestry in ancient Anatolia.

It'll be decided by a multidisciplinary study on the interactions between the ancient peoples of the North Pontic steppe, the eastern Balkans, and western Anatolia. . . .
the authors should've given us a painstaking account of the spread of different ancient Indo-European speaking groups into Anatolia and explained how, overall, their DNA was rapidly diluted to a trace amount.

However, instead they treated us to a make-believe tale about a so called Indo-Anatolian homeland in what is now Armenia.
Anatolian languages arose in Anatolia on a more elite dominance type model rather than a demic replacement model. 

Also the linguistic based estimates of the Anatolian languages divergence from other Indo-European languages grossly underestimates the role of contact with a different and stronger substrate than in most of the other cases of the spread of the Indo-European languages.

Is There Life Left In Verlinde's Emergent Gravity After All?

Eric Verlinde's paradigm of trying to derive gravity as emergent from Standard Model interactions via entanglement and entropy would, if it could be made to work, be even more reductionist than Deur's approach that seeks to explain dark matter and dark energy phenomena via vanilla General Relativity. In effect, Verlinde's approach turns the Standard Model into a theory of everything. 

Early analysis of Verlinde's proposal showed a flaw in it, but some advocates of his approach think they've fixed the problem.

I am also a fan of the transactional interpretation of quantum mechanics, so I'm heartened to see it used here.
This is a review of new developments in entropic gravity in light of the Relativistic Transactional Interpretation (RTI). A transactional approach to spacetime events can give rise in a natural way to entropic gravity (in the way originally proposed by Eric Verlinde) while also overcoming extant objections to that research program. The theory also naturally gives rise to a Cosmological Constant and to Modified Newtonian Dynamics (MOND) and thus provides a physical explanation for the phenomena historically attributed to "dark energy" and "dark matter".
A. Schlatter, R. E. Kastner, "Gravity from Transactions: A Review of Recent Developments" arXiv:2209.04025 (September 8, 2022).

Segregating Old Physics From New Physics

A new paper uses the interesting strategy of trying to make Standard Model predictions for experiments under the assumption that some of the data usually used to make Standard Model physics predictions to which experimental results are compared reflects some New Physics. The paper finds ways to ignore that "infection" of New Physics, so that the true New Physics effect can be better isolated from the true Standard Model alone prediction. 

The Standard Model (SM) does not contain by definition any new physics (NP) contributions to any observable but contains four CKM parameters which are not predicted by this model. We point out that if these four parameters are determined in a global fit that includes processes which are infected by NP, the resulting SM contributions to rare decay branching ratios cannot be considered as true SM contributions to the latter. On the other hand true SM predictions, that are free from the CKM dependence, can be obtained for suitable ratios of the K and B rare decay branching ratios to ΔMsΔMd and |εK|, all calculated within the SM. These three observables contain by now only small hadronic uncertainties and are already well measured so that rather precise true SM predictions for the ratios in question can be obtained. In this context the rapid test of NP infection in the ΔF=2 sector is provided by a |Vcb|γ plot that involves ΔMsΔMd|εK|, and the mixing induced CP-asymmetry SψKS. As with the present hadronic matrix elements this test turns out to be negative, assuming negligible NP infection in the ΔF=2 sector and setting the values of these four observables to the experimental ones, allows to obtain SM predictions for all K and B rare decay branching ratios that are most accurate to date and as a byproduct to obtain the full CKM matrix on the basis of ΔF=2 transitions alone. Using this strategy we obtain SM predictions for 26 branching ratios for rare semileptonic and leptonic K and B decays with the μ+μ pair or the νν¯ pair in the final state. Most interesting turn out to be the anomalies in the low q2 bin in B+K+μ+μ (5.1σ) and Bsϕμ+μ (4.8σ).
Andrzej J. Buras, "Standard Model Predictions for Rare K and B Decays without New Physics Infection" arXiv:2209.03968 (September 8, 2022).