Sunday, October 29, 2017

One In Ten Vascular Plants In Madagascar Have Asian Origins

Figure S3 from the paper cited below.

Ancient evidence of Asian crops in Madagascar provide another piece of evidence for discerning the details of this long distance mass migration of Austronesian people to Africa.
The prehistoric settlement of Madagascar by people from distant Southeast Asia has long captured both scholarly and public imagination, but on the ground evidence for this colonization has eluded archaeologists for decades. Our study provides the first, to our knowledge, archaeological evidence for an early Southeast Asian presence in Madagascar and reveals that this settlement extended to the Comoros. Our findings point to a complex Malagasy settlement history and open new research avenues for linguists, geneticists, and archaeologists to further study the timing and process of this population movement. They also provide insight into early processes of Indian Ocean biological exchange and in particular, Madagascar’s floral introductions, which account for one-tenth of its current vascular plant species diversity.
The Austronesian settlement of the remote island of Madagascar remains one of the great puzzles of Indo-Pacific prehistory. Although linguistic, ethnographic, and genetic evidence points clearly to a colonization of Madagascar by Austronesian language-speaking people from Island Southeast Asia, decades of archaeological research have failed to locate evidence for a Southeast Asian signature in the island’s early material record. Here, we present new archaeobotanical data that show that Southeast Asian settlers brought Asian crops with them when they settled in Africa. These crops provide the first, to our knowledge, reliable archaeological window into the Southeast Asian colonization of Madagascar. They additionally suggest that initial Southeast Asian settlement in Africa was not limited to Madagascar, but also extended to the Comoros. Archaeobotanical data may support a model of indirect Austronesian colonization of Madagascar from the Comoros and/or elsewhere in eastern Africa.
Alison Crowther, et al., "Ancient crops provide first archaeological signature of the westward Austronesian expansion" 113(24) PNAS 6635-6640 (2017) doi: 10.1073/pnas.1522714113

From the introductory body text:
One line of evidence that has been largely overlooked in archaeological investigations of Madagascar and, indeed, eastern Africa more broadly is ancient plants. However, it is estimated that some 10% of Madagascar’s flora was introduced from elsewhere, and plant introductions include a significant number of staple crops, spices, and arable weeds of Asian origin. Historically or currently important crops on Madagascar, like banana (Musa spp.), yam (Dioscorea alata), taro (Colocasia esculenta), and coconut (Cocos nucifera), are Southeast Asian cultivars. Asian rice (Oryza sativa), which was domesticated separately in East and South Asia but is the basis of traditional agriculture across much of Madagascar today, was also widely grown in Southeast Asia by the first millennium CE. Other Asian crops, like mung bean (Vigna radiata) and Asian cotton (Gossypium arboreum), are also cultivated on Madagascar. The fact that early crop introductions to Madagascar may have arrived with Austronesian settlers seems particularly feasible given that Austronesian expansion into the Pacific was linked to the spread of a similar suite of cultivars. 
To directly explore early cultivated plants on Madagascar and their potential to inform on its colonization history, we collected new archaeobotanical data from the island as well as contemporaneous sites on the African mainland coast (Kenya and Tanzania) and nearshore islands (Pemba, Zanzibar, and Mafia) and the Comoros. These data were collected from 18 sites in total, dating between approximately 650 and 1200 calibrated years (cal) CE. The archaeobotanical datasets derive primarily from recent excavations at 16 sites, during which systematic sampling for charred macrobotanical remains at high stratigraphic resolution was conducted. They are supplemented by existing records from one of the sites (Sima) as well as data from previous excavations at two other sites in the Comoros. The combined dataset includes 2,443 identified crop remains recovered from >7,430 L sediment across the sites and is supported by 48 accelerator MS (AMS) radiocarbon dates, 43 of which were obtained directly on crop seeds.
From the conclusion:
Although the presence of Asian crops that likely originate from Southeast Asia on early sites in Madagascar corresponds well with linguistic, genetic, and ethnographic evidence for a prehistoric migration of people from this region, the finding that these crops also dominate early assemblages on the Comoros is rather unexpected. In particular, the presence of Asian crops at sites in the Comoros earlier than at sites on Madagascar is of significant interest, and although sampling and preservation biases cannot be discounted, may reflect Austronesian colonization of the Comoros before Madagascar. As noted, however, Comorians today speak Bantu languages, and in addition, preliminary molecular genetic studies suggest that they possess only a small proportion of Southeast Asian ancestry. Nonetheless, the population of the Comoros is small and has been historically subject to significant population bottlenecks and Bantu input as a result of slave raiding and trading over many centuries. Thus, it is possible that the Comoros were settled at an early date by a Southeast Asian population that was later genetically and linguistically swamped. 
Direct colonization from Southeast Asia is common to many models of Madagascar’s Austronesian settlement, particularly those put forward by archaeologists and geneticists. However, linguistics have offered another perspective, with some linguists taking the view that the remarkable unity of Bantu loanwords and grammatical features throughout Malagasy dialects can only be explained through initial Austronesian settlement on the African mainland and/or the Comoros. Early Southeast Asian presence or influence on the Comoros has also been suggested on the basis of the apparent presence of several 10th or 11th century “Austronesian-type” furnaces on Mayotte as well as findings of shell-impressed pottery at early sites on the islands. These suggested Austronesian linkages, however, have been both limited and contentious. This study suggests that they deserve reinvestigation together with the argument that the Comoros may have served as a key base for Southeast Asian commercial activity in the western Indian Ocean, including an alternative slave-trading corridor. Independent linguistic, genetic, and archaeological studies are required to examine the role of the Comoros in early Indian Ocean population movements and commercial trade.

Friday, October 27, 2017

Another Problem For Particle Dark Matter Theories

The galactic cluster BCG wobble is essentially the galactic cluster scale analog to the long standing core-cusp problem with Cold Dark Matter at the galaxy scale. The press release accompanying this new paper suggests that self-interacting dark matter is the only solution, but other studies broadly rule out all astrophysically relevant parameters of SIDM models.
A striking signal of dark matter beyond the standard model is the existence of cores in the centre of galaxy clusters. Recent simulations predict that a Brightest Cluster Galaxy (BCG) inside a cored galaxy cluster will exhibit residual wobbling due to previous major mergers, long after the relaxation of the overall cluster. This phenomenon is absent with standard cold dark matter where a cuspy density profile keeps a BCG tightly bound at the centre. We test this hypothesis using cosmological simulations and deep observations of 10 galaxy clusters acting as strong gravitational lenses. Modelling the BCG wobble as a simple harmonic oscillator, we measure the wobble amplitude, Aw, in the BAHAMAS suite of cosmological hydrodynamical simulations, finding an upper limit for the CDM paradigm of Aw<2kpc at the 95% confidence limit. We carry out the same test on the data finding a non-zero amplitude of Aw=11.82+7.33.0kpc, with the observations dis-favouring Aw=0 at the 3σ confidence level. This detection of BCG wobbling is evidence for a dark matter core at the heart of galaxy clusters. It also shows that strong lensing models of clusters cannot assume that the BCG is exactly coincident with the large scale halo. While our small sample of galaxy clusters already indicates a non-zero Aw, with larger surveys, e.g. Euclid, we will be able to not only to confirm the effect but also to use it to determine whether or not the wobbling finds its origin in new fundamental physics or astrophysical process.
David Harvey, F. Courbin, J. P. Kneib, Ian G. McCarthy. "A detection of wobbling brightest cluster galaxies within massive galaxy clusters." 472(2) Monthly Notices of the Royal Astronomical Society 1972 (2017).
Using the NASA/ESA Hubble Space Telescope, astronomers have discovered that the brightest galaxies within galaxy clusters "wobble" relative to the cluster's centre of mass. This unexpected result is inconsistent with predictions made by the current standard model of dark matter. . . . 
[C]lusters have very dense cores, each containing a massive galaxy called the "brightest cluster galaxy" (BCG). The standard model of dark matter (cold dark matter model) predicts that once a galaxy cluster has returned to a "relaxed" state after experiencing the turbulence of a merging event, the BCG does not move from the cluster's centre. It is held in place by the enormous gravitational influence of dark matter. But now, a team of Swiss, French, and British astronomers have analysed ten galaxy clusters observed with the NASA/ESA Hubble Space Telescope, and found that their BCGs are not fixed at the centre as expected. 
The Hubble data indicate that they are "wobbling" around the centre of mass of each cluster long after the galaxy cluster has returned to a relaxed state following a merger. In other words, the centre of the visible parts of each galaxy cluster and the centre of the total mass of the cluster -- including its dark matter halo -- are offset, by as much as 40,000 light-years. "We found that the BCGs wobble around centre of the halos," explains David Harvey, astronomer at EPFL, Switzerland, and lead author of the paper. "This indicates that, rather than a dense region in the centre of the galaxy cluster, as predicted by the cold dark matter model, there is a much shallower central density. This is a striking signal of exotic forms of dark matter right at the heart of galaxy clusters." 
The wobbling of the BCGs could only be analysed as the galaxy clusters studied also act as gravitational lenses. . . . This effect, called strong gravitational lensing, can be used to make a map of the dark matter associated with the cluster, enabling astronomers to work out the exact position of the centre of mass and then measure the offset of the BCG from this centre. 
If this "wobbling" is not an unknown astrophysical phenomenon and in fact the result of the behaviour of dark matter, then it is inconsistent with the standard model of dark matter and can only be explained if dark matter particles can interact with each other -- a strong contradiction to the current understanding of dark matter.
 From the press release is here. Hat tip wolram.

CKM Matrix Measurements Place Strict Limits On New Physics


In the Standard Model of particle physics, sometimes a quark emits a W boson, via the weak force, and changes quark flavor. Any of the three up-type quarks can transform into any of the three down-type quarks, and visa versa, conservation of matter-energy permitting. The probability of each particular type of flavor change is governed by the three by three element CKM matrix. These probabilities are determined by observing various aspects of the weak force driven decays of hadrons (i.e. meson and baryons). 

Thus, the CKM matrix is the product of many dozens of observables, many of which provide independent measurements of the same CKM matrix element. If those independent measurements aren't consistent with each other, then the theory behind the CKM matrix is wrong, or you have a serious experimental error. As it happens, decays of a meson called a kaon are particularly important in making these measurements because these measurements of one of the lightest mesons that can experience weak force decays are particular precise.

Further, "unitarity" which is just a fancy way of saying that all probabilities of an event must add up to 100% if you have a complete description of the relevant physics, provides another test of whether the CKM matrix is complete. If there are transitions of quarks from one flavor to another (perhaps to known new quark flavors) governed by new physics, then the percentages determined by adding up the individual entries should not add up to 100%.

Thus, the unitarity of the CKM matrix which is described with a summary of the data called the "Unitary Triangle", which relies on the further assumption of the Standard Model that the nine elements of the CKM matrix are fully described by four parameters, is a good global test of the completeness and consistency of the Standard Model that can probe energy scales not otherwise reachable with direct measurements.

The New Paper

A new pre-print analyzes the extent to which the available data on the CKM matrix element values rules out beyond the Standard Model Physics.

It finds that in the most rigid model dependent analysis, that new physics are excluded up to a characteristic energy scale of about 50,000 TeV. There is no practical way that a human designed experiment could reach these energy scales from an engineering perspective. These are energy scales that haven't existed anywhere in the Universe since the early moments of the Big Bang.

If the assumptions of the model are relaxed, new physics are still excluded up to a characteristic energy scale of 114 TeV. This would take an accelerator on the order of ten times as powerful as the LHC or more to test.

To allow for new physics at a characteristic energy scale of 11 TeV which is the highest that there is a realistic chance that could be discovered at the LHC, one would have to abandon assumptions that are almost certainly correct based upon the available experimental evidence.

These limits are much more strict than the energy scale limitations established by direct searches for new particles at the LHC.

Many physicists consider the Standard Model of particle physics to be a "low energy effective theory" describing a more complete theory that is true at all energy scales. But, these CKM matrix measurements suggest that "low energy" is a term that encompasses pretty much everything that happens or has happened on a regular basis in the universe for something on the order of 13 billion years.

Tuesday, October 24, 2017

Sorghum Domestication

Sorghum was domesticated in Sudan in the 3000s BCE.
Since the 1970s, the quest for finding the origins of domesticated sorghum in Africa has remained elusive despite the fact that sorghum (Sorghum bicolor (L.) Moench. sensu stricto) is one of the world’s most important cereals. Recognized as originating from wild populations in Africa (Sorghum arundinaceum (Desv.) Stapf), however, the date and cultural context of its domestication has been controversial, with many scholars inferring an early Holocene origin in parallel with better-known cereal domestications. 
This paper presents firm evidence that the process of domesticating sorghum was present in the far eastern Sahel in the southern Atbai at an archaeological site associated with the Butana Group. Ceramic sherds recovered from excavations undertaken by the Southern Methodist University Butana Project during the 1980s from the largest Butana Group site, KG23, near Kassala, eastern Sudan, were analyzed, and examination of the plant impressions in the pottery revealed diagnostic chaff in which both domesticated and wild sorghum types were identified, thus providing archaeobotanical evidence for the beginnings of cultivation and emergence of domesticated characteristics within sorghum during the fourth millennium BC in eastern Sudan.
Frank Winchell, Chris J. Stevens, Charlene Murphy, Louis Champion, and Dorian Q Fuller , "Evidence for Sorghum Domestication in Fourth Millennium BC Eastern Sudan: Spikelet Morphology from Ceramic Impressions of the Butana Group" 58(5) Current Anthropology 673-683 (September 20, 2017).

A newspaper level account of the find can be found here.

Sudanese hands holding sorghum.
© CSI Productions / Alamy Stock Photo
Establishing the history of sorghum, Africa’s primary staple crop, has been difficult.

The earliest evidence of wild sorghum comes from short-lived hunter and gatherer camps in the Sahara dating to roughly 7,500 BCE. But, the earliest known domesticated sorghum remains dated to 2,000 – 1,700 BCE and were found in India, where it is not a native crop. Domesticated sorghum did not appear again in Sudan until the later part of the first millennium BCE, leaving a gap in knowledge of more than 5,000 years.
[The site, KG23, from which the cermaics were recovered], at roughly 120,000 square meters, was the largest site in the region and was occupied, based on radiocarbon dating, from about 3,500 BCE to 2,500 BCE.
The thick accumulation of debris in KG23’s rubbish dumps, says Winchell suggests that, “people pretty much live on that site long term and probably throughout the year.” The ancient environment around KG23 was wetter than it is today, with a small seasonal river nearby and alluvial soils suitable for crop cultivation.

. . . 
The trick to identifying domesticated sorghum is knowing what to look for, which Fuller explains, “is whether or not there is an attached torn rachis – or little stalk at the base of the spikelet.” Sorghum grains are enclosed in a spikelet and in wild sorghum, the grain pops off in the husk leaving a straight smooth scar. Domesticated sorghum, however, is propagated by human action so the plant becomes torn during threshing, leaving a small rachis stub. . . .
The team found that roughly half of the impressions were made from domestic sorghum – providing the earliest evidence of domestication for this crop. However, the other half of the plant impressions in the pottery came from wild sorghum, showing a complex picture of domestication. . . .
Based on Fuller’s work with other grains, the domestication process often took around two to three thousand years. “So, if it’s a similar rate with sorghum,” according to Fuller, “then I’d expect the process to start at least 1,000 up to 1,500 years earlier, meaning that if this site dates to 3,200 BCE, then we should be looking for sites, which have earlier stages of the process going back to 4,000 to 4,500 BCE.” . . . the Neolithic populations in Sudan figured out how to domesticate sorghum independent of earlier cereal crop domestication in Egypt and Mesopotamia.
A paper arising out of the 1980s research can be found here.

And because you knew but were afraid to ask, per Wikipedia:
Butana (Arabic: البطانة) is a region in Sudan. It is bordered by the Nile from Khartoum to Atbarah, by the Atbarah River from Atbarah to Ethiopia, by the Ethiopian border from the Atbarah River to the Blue Nile, and by the Blue Nile from Ethiopia to Khartoum. It includes most of the state of Al Qadarif plus parts of the states of Kassala, River Nile, Khartoum, Al Jazirah and Sennar. The Butana plain occupies most of Butana. The name Butana is applied to many things which come from the region, such as the Butana breed of cattle, Butana sheep, Butana goats, et cetera. Historically, it was part of Alodia and later the Funj Sultanate of Sinnar
Butana was known as "The Island of Meroe" when it was part of the Kushitic kingdom of Meroe. The city of Meroe was about halfway between Atbarah and Khartoum, on the east side of the Nileriver. There were two other major Meroitic cities in Butana, Musawwarat es-Sufra and Naqa
Today it is mainly inhabited by the Arab Bedouins of Sudan, such as the Rashaida, the Ansar, the Awazim, and other Arabian tribes.

Monday, October 23, 2017

Dark Matter Particle Theories Are Inconsistent With The Empirical Evidence: A Review Of The Literature

This was originally a post in a thread at the Physics Forums.

The fact of the matter is that there is no theory of dark matter consistent with all the data.

Every outstanding dark matter theory is contradicted by some very solid piece of empirical data. The following 36 citations set forth some of the highlights of the current crisis in dark matter theory.

There are lots of dark matter publications, but those publications are overwhelmingly ruling out variations of dark matter theory, sometimes huge classes of them such as pretty much all MACHOs, all WIMPS, all collisionless dark matter, all cold dark matter theories, and all self-interacting dark matter theories. Warm dark matter is very close to being over constrained (and general exclusions of collisionless dark matter are the nail in the coffin), and many forms of axion dark matter are ruled out.

One common theme is that it isn't possible to devise a dark matter model that simultaneously fits lamdaCDM model constraints and the tight fix of inferred dark matter distributions to baryonic matter distributions (something that modified gravity models do naturally).

* Dark matter can't have any significant coupling to Standard Model matter. This is a problem because "collisionless" dark matter that does not interact with Standard Model matter is pretty much ruled out per other citations below.

* Exclusions from Xenon-100

* Exclusions of Charming Dark Matter theories.

* Theodorus Maria Nieuwenhuizen "Subjecting dark matter candidates to the cluster test" (October 3, 2017):
Galaxy clusters, employed by Zwicky to demonstrate the existence of dark matter, pose new stringent tests. If merging clusters demonstrate that dark matter is self-interacting with cross section σ/m∼2 cm2/gr, MACHOs, primordial black holes and light axions that build MACHOs are ruled out as cluster dark matter. Recent strong lensing and X-ray gas data of the quite relaxed and quite spherical cluster A1835 allow to test the cases of dark matter with Maxwell-Boltzmann, Bose-Einstein and Fermi-Dirac distribution, next to Navarro-Frenck-White profiles. Fits to all these profiles are formally rejected at over 5σ, except in the fermionic situation. The interpretation in terms of (nearly) Dirac neutrinos with mass of 1.61+0.19−0.30 eV/c2 is consistent with results on the cluster A1689, with the WMAP, Planck and DES dark matter fractions and with the nondetection of neutrinoless double β-decay. The case will be tested in the 2018 KATRIN experiment.
A variety of searches for sterile neutrinos have also ruled out this possibility in the relevant mass range. See, e.g., and

* Exclusions for Axion Dark Matter: Renée Hlozek, David J. E. Marsh, Daniel Grin "Using the Full Power of the Cosmic Microwave Background to Probe Axion Dark Matter" (August 18, 2017).

* Combined direct dark matter detection exclusions. and

* Exclusions based on non-detection of annihilations in dwarf galaxies.

* Primordial black hole exclusions.

* Daniele Gaggero, et al., "Searching for Primordial Black Holes in the radio and X-ray sky" (Pre-Print December 1, 2016). Abstract:
We model the accretion of gas on to a population of massive primordial black holes in the Milky Way, and compare the predicted radio and X-ray emission with observational data. We show that under conservative assumptions on the accretion process, the possibility that O(10)M⊙ primordial black holes can account for all of the dark matter in the Milky Way is excluded at 4σ by a comparison with the VLA radio catalog at 1.4 GHz, and at more than 5σ by a comparison with the NuSTAR X-ray catalog (10 - 40 keV). We also propose a new strategy to identify such a population of primordial black holes with more sensitive future radio and X-ray surveys.
* Tight Warm Dark Matter parameter exclusions.

* More Warm Dark Matter parameters exclusions: Simon Birrer, Adam Amara, and Alexandre Refregier, "Lensing substructure quantification in RXJ1131-1231: A 2 keV lower bound on dark matter thermal relict mass" (January 31, 2017).
We study the substructure content of the strong gravitational lens RXJ1131-1231 through a forward modelling approach that relies on generating an extensive suite of realistic simulations. The statistics of the substructure population of halos depends on the properties of dark matter. We use a merger tree prescription that allows us to stochastically generate substructure populations whose properties depend on the dark matter particle mass. These synthetic halos are then used as lenses to produce realistic mock images that have the same features, e.g. luminous arcs, quasar positions, instrumental noise and PSF, as the data. By analysing the data and the simulations in the same way, we are able to constrain models of dark matter statistically using Approximate Bayesian Computing (ABC) techniques. This method relies on constructing summary statistics and distance measures that are sensitive to the signal being targeted. We find that using the HST data for \RXJ we are able to rule out a warm dark matter thermal relict mass below 2 keV at the 2 sigma confidence level.
* Lin Wang, Da-Ming Chen, Ran Li "The total density profile of DM halos fitted from strong lensing" (July 31, 2017). Abstract:
In cosmological N-body simulations, the baryon effects on the cold dark matter (CDM) halos can be used to solve the small scale problems in ΛCDM cosmology, such as cusp-core problem and missing satellites problem. It turns out that the resultant total density profiles (baryons plus CDM), for halos with mass ranges from dwarf galaxies to galaxy clusters, can match the observations of the rotation curves better than NFW profile. In our previous work, however, we found that such density profiles fail to match the most recent strong gravitational lensing observations. In this paper, we do the converse: we fit the most recent strong lensing observations with the predicted lensing probabilities based on the so-called (α,β,γ) double power-law profile, and use the best-fit parameters (α=3.04,β=1.39,γ=1.88) to calculate the rotation curves. We find that, at outer parts for a typical galaxy, the rotation curve calculated with our fitted density profile is much lower than observations and those based on simulations, including the NFW profile. This again verifies and strengthen the conclusions in our previous works: in ΛCDM paradigm, it is difficult to reconcile the contradictions between the observations for rotation curves and strong gravitational lensing.
As the body text explains:
It is now well established that, whatever the manners the baryon effects are included in the collisionless CDM N-body cosmological simulations, if the resultant density pro- files can match the observations of rotation curves, they cannot simultaneously predict the observations of strong gravitational lensing (under- or over-predict). And for the case of typical galaxies, the reverse is also true, namely, the SIS profile preferred by strong lensing cannot be supported by the observations of rotation curves near the centers of galaxies.
* Paolo Salucci and Nicola Turini, "Evidences for Collisional Dark Matter In Galaxies?" (July 4, 2017). Abstract:
The more we go deep into the knowledge of the dark component which embeds the stellar component of galaxies, the more we realize the profound interconnection between them. We show that the scaling laws among the structural properties of the dark and luminous matter in galaxies are too complex to derive from two inert components that just share the same gravitational field. In this paper we review the 30 years old paradigm of collisionless dark matter in galaxies. We found that their dynamical properties show strong indications that the dark and luminous components have interacted in a more direct way over a Hubble Time. The proofs for this are the presence of central cored regions with constant DM density in which their size is related with the disk length scales. Moreover we find that the quantity ρDM(r,L,RD)ρ⋆(r,L,RD) shows, in all objects, peculiarities very hardly explained in a collisionless DM scenario.
* Dark matter distributions have to closely track baryon distributions, even though there is no viable mechanism to do so: Edo van Uitert, et al., "Halo ellipticity of GAMA galaxy groups from KiDS weak lensing" (October 13, 2016).

* One of the more successful recent efforts to reproduce the baryonic Tully-Fischer relation with CDM models is L.V. Sales, et al., "The low-mass end of the baryonic Tully-Fisher relation" (February 5, 2016). It explains:
[T]he literature is littered with failed attempts to reproduce the Tully-Fisher relation in a cold dark matter-dominated universe. Direct galaxy formation simulations, for example, have for many years consistently produced galaxies so massive and compact that their rotation curves were steeply declining and, generally, a poor match to observation. Even semi-analytic models, where galaxy masses and sizes can be adjusted to match observation, have had difficulty reproducing the Tully-Fisher relation, typically predicting velocities at given mass that are significantly higher than observed unless somewhat arbitrary adjustments are made to the response of the dark halo.
The paper manages to simulate the Tully-Fisher relation only with a model that has sixteen parameters carefully "calibrated to match the observed galaxy stellar mass function and the sizes of galaxies at z = 0" and "chosen to resemble the surroundings of the Local Group of Galaxies", however, and still struggles to reproduce the one parameter fits of the MOND toy-model from three decades ago. Any data set can be described by almost any model so long as it has enough adjustable parameters.

* Dark matter can't explain bulge formation in galaxies: Alyson M. Brooks, Charlotte R. Christensen, "Bulge Formation via Mergers in Cosmological Simulations" (12 Nov 2015).
[W]e also demonstrate that it is very difficult for current stellar feedback models to reproduce the small bulges observed in more massive disk galaxies like the Milky Way. We argue that feedback models need to be improved, or an additional source of feedback such as AGN is necessary to generate the required outflows.
* Baryon effects can't save cold dark matter models.

* Cold dark matter models don't explain the astronomy data.
Evidence that Cold Dark Matter (ΛCDM), CDM+ baryons and its proposed tailored cures do not work in galaxies is staggering, and the CDM wimps (DM particles heavier than 1 GeV) are strongly disfavoured combining theory with galaxy astronomical observations.
* As of 2014, a review article ruled out rule out pretty much all cold dark matter models except "warm dark matter" (WDM) (at a keV scale mass that is at the bottom of the range permitted by the lamdaCDM model) and "self-interacting dark matter" (SIDM) (which escapes problems that otherwise plague cold dark matter models with a fifth force that only acts between dark matter particles requiring at least a beyond the Standard Model fermion and a beyond the Standard Model force carried by a new massive boson with a mass on the order of 1-100 MeV). Alyson Brooks, "Re-Examining Astrophysical Constraints on the Dark Matter Model" (July 28, 2014). As other more recent links cited here note, collisionless WDM and pretty much all SIDM models have since been ruled out.

* Dark matter annihilation has largely been ruled out as a source of FERMI signals attributed to dark matter annihilation. Samuel K. Lee, Mariangela Lisanti, Benjamin R. Safdi, Tracy R. Slatyer, and Wei Xue. "Evidence for unresolved gamma-ray point sources in the Inner Galaxy." Phys. Rev. Lett. (February 3, 2016). Millisecond pulsars were the source.

* Proposed warm dark matter annihilation signals also turned out to be false alarms. and

* The bounds on the minimum dark matter mean lifetime of 3.57*10^24 seconds. This is roughly 10^17 years. By comparison the age of the universe is roughly 1.38 * 10^9 years. This means that dark matter (if it exists) is at least as stable as anything other than a proton, which has an experimentally determined mean lifetime of at least 10^33 years. This means that all dark matter candidates that are not perfectly stable or at least metastable are ruled out. Decaying dark matter and dark matter with any significant annihilation cross section are inconsistent with observation.

* Torsten Bringmann, et al., "Strong constraints on self-interacting dark matter with light mediators" (December 2, 2016). Abstract:
Coupling dark matter to light new particles is an attractive way to combine thermal production with strong velocity-dependent self-interactions. Here we point out that in such models the dark matter annihilation rate is generically enhanced by the Sommerfeld effect, and we derive the resulting constraints from the Cosmic Microwave Background and other indirect detection probes. For the frequently studied case of s-wave annihilation these constraints exclude the entire parameter space where the self-interactions are large enough to address the small-scale problems of structure formation.
The conclusion of the paper notes that:
Models of DM with velocity-dependent self-interactions have recently received a great deal of attention for their potential to produce a number of interesting effects on astrophysical scales. We have shown in this Letter that these models face very strong constraints from the CMB and DM indirect detection. In the most natural realization of this scenario with a light vector mediator with kinetic mixing, these constraints rule out the entire parameter space where the self-scattering cross section can be relevant for astrophysical systems. These bounds remain highly relevant for a number of generalizations of the scenario, such as a different dark sector temperature and different mediator branching ratios. Clearly, future efforts to develop particle physics models for SIDM need to address these issues in order to arrive at models that provide a picture consistent with all observations in cosmology, astrophysics and particle physics.
* Dark photon parameter space (the carrier boson of the SIDM models) is also tightly constrained and all but ruled out. Yet, the properties a dark photon has to have, if there is one, are tightly experimentally established based upon cluster dynamics.

* The Bullet Cluster is a huge problem for DM. Jounghun Lee, Eiichiro Komatsu, "Bullet Cluster: A Challenge to LCDM Cosmology" (May 22, 2010). Later published in Astrophysical Journal 718 (2010) 60-65. Abstract:
To quantify how rare the bullet-cluster-like high-velocity merging systems are in the standard LCDM cosmology, we use a large-volume 27 (Gpc/h)^3 MICE simulation to calculate the distribution of infall velocities of subclusters around massive main clusters. The infall-velocity distribution is given at (1-3)R_{200} of the main cluster (where R_{200} is similar to the virial radius), and thus it gives the distribution of realistic initial velocities of subclusters just before collision. These velocities can be compared with the initial velocities used by the non-cosmological hydrodynamical simulations of 1E0657-56 in the literature. The latest parameter search carried out recently by Mastropietro and Burkert showed that the initial velocity of 3000 km/s at about 2R_{200} is required to explain the observed shock velocity, X-ray brightness ratio of the main and subcluster, and displacement of the X-ray peaks from the mass peaks. We show that such a high infall velocity at 2R_{200} is incompatible with the prediction of a LCDM model: the probability of finding 3000 km/s in (2-3)R_{200} is between 3.3X10^{-11} and 3.6X10^{-9}. It is concluded that the existence of 1E0657-56 is incompatible with the prediction of a LCDM model, unless a lower infall velocity solution for 1E0657-56 with < 1800 km/s at 2R_{200} is found.
and also

Garry W. Angus and Stacy S. McGaugh, "The collision velocity of the bullet cluster in conventional and modified dynamics" (September 2, 2007) published at MNRAS.
We consider the orbit of the bullet cluster 1E 0657-56 in both CDM and MOND using accurate mass models appropriate to each case in order to ascertain the maximum plausible collision velocity. Impact velocities consistent with the shock velocity (~ 4700km/s) occur naturally in MOND. CDM can generate collision velocities of at most ~ 3800km/s, and is only consistent with the data provided that the shock velocity has been substantially enhanced by hydrodynamical effects.
* El Gordo poses similar problems for dark matter models. Sandor M. Molnar, Tom Broadhurst. "A HYDRODYNAMICAL SOLUTION FOR THE “TWIN-TAILED” COLLIDING GALAXY CLUSTER “EL GORDO”. The Astrophysical Journal, 2015; 800 (1): 37 DOI: 10.1088/0004-637X/800/1/37

* Axion fuzzy dark matter ruled out: Vid Iršič, Matteo Viel, Martin G. Haehnelt, James S. Bolton, George D. Becker. "First Constraints on Fuzzy Dark Matter from Lyman-α Forest Data and Hydrodynamical Simulations." Physical Review Letters, 2017; 119 (3) DOI: 10.1103/PhysRevLett.119.031302

Saturday, October 21, 2017

Mexican Population Genetics

In the fifteenth century, prior to the Conquest of Mexico, Mexican territory was inhabited by many different Native groups located mainly in Mesoamerica, but also in Northern Mexico, inhabited by nomadic or semi-nomadic peoples. The Mexican population of today is the result of complex and ongoing admixture processes that began with the Conquest of Mexican territory by the Spaniards in 1521. The admixture process occurred mainly between Native Americans and Europeans, although there was a smaller contribution of the African population introduced by slave traders during the colonial period. Currently, there are 68 acknowledged Native American languages in Mexico. Native populations not only contributed very importantly to the admixture process of the Mexican population, but currently up to 21% of Mexicans identify themselves as members of one of the acknowledged Indigenous groups of Mexico. Moreover, according to a recent survey, approximately 7% of the Mexican population, that is over 7 million Mexicans, speak a Native language.
From the introduction to a new open access study of Mexican population genetics.

The sample size is small, but carefully chosen and rich:
Whole genomes of a total of 15 Mexican individuals were sequenced, including 12 NAs from six distinct ethnic groups (Tarahumara and Tepehuano from the North; Nahua, Totonaca, Zapoteca from the South; and Maya from the South-East) and a trio of Mexican Mestizos (mother, father, and offspring). NA participants were selected considering ancestry, linguistic group, geographic location, and representation of three of the main genetic clusters previously described in the NA Map of Mexico: Northern, Southern, and Mayan, as described by Moreno-Estrada et al. Estimated NA ancestry using genome-wide data was over 98% in all indigenous participants, except for both Tepehuanos who were selected for having the highest NA ancestry (91%) among those available for whole-genome sequencing (WGS).
The study reveals pre-Columbian population structure and effective population sizes.

Thursday, October 19, 2017

Early European Farmers Skipped The Baltics

In most of Europe, "Early European Farmers" genetically similar to Anatolian Neolithic farmers and modern Sardinians introduced farming. Then, their economies collapsed eventually in the Middle Neolithic during which populations were infused with hunter-gatherer ancestry, probably due to unsustainable farming practices and climate issues. Then, steppe pastoralists (mostly Indo-European) swept in resulting in major population genetic changes and a rival of societies that took on something close to their current population genetic character in the Late Neolithic/Enolithic/early Bronze Age.

But, this is not what happened in the Baltics. The Early European Farmers never arrived and their first wave of farming arrived with steppe people, according to a new ancient DNA based analysis of the question. Also, while Early European Farmers dramatically replaced local hunter-gatherer populations, Baltic Mesolithic populations had more staying power, so while they had a significant infusion of steppe ancestry into their populations, there is more continuity there between Mesolithic non-farmers and modern populations in these areas.

This could have happened in part because many Baltic hunter-gatherers were maritime fisher-gatherer populations, which are intermediate between terrestrial hunter-gatherer populations and farmers and have more staying power. It could also have happened, in part, because the crops in the Early European Farmer package were ill adapted to high latitude climates. So, the locals had more staying power while the would be incoming Neolithic migrants were at their weakest there, therefore the migration didn't happen.

Insights From Reading Selected ASHG 2017 Abstracts

The abstracts of the conference presentations at the American Society of Human Genetics Conference in Orlando, Florida for 2017 which is currently in progress is available here. It sorts by first digit of the paper number so, for example, 2, 20, 201 and 2001 are all adjacent to each other. Plenary and platform talks have numbers up to 372. Higher numbers are poster-presentations. Some notable papers:

1 African genes governing skin color

1437 Han Chinese genetics overview

2301 Russian haplotypes by geographic area (probably not, or at least not just, uniparental haplotypes).

2304 Two sources from region for mtDNA lineages in Austronesians. There is a narrative buried there that deserves to be inferred at some point if I get a chance. The abstract is as follows:
Accumulated archaeological, linguistic and genetic evidences suggest that modern Austronesian (AN)-speaking Melanesians are derived from the admixture of indigenous Non-Austronesian- (NAN-) speaking people in Near Oceania and Austronesian- (AN-) speaking people from Southeast Asia. In this study, we analyzed mitochondrial DNA (mtDNA) polymorphisms in D-loop region for two AN-speaking Melanesian populations (Munda and Kusaghe) and an AN-speaking Micronesian population (Rawaki) from New Georgia Island in the western Solomon Islands to trace the maternal lineage of AN-speaking Melanesians. The major mtDNA haplogroups in these three populations originated in Asia and the ‘Polynesian motif', which is well-characterized mtDNA marker for Polynesians, was frequently observed in the two AN-speaking Melanesian populations but not in the AN-speaking Micronesian population in New Georgia Island. Principle component analyses also revealed genetic proximity between AN-speaking Melanesians (Munda and Kusaghe) and AN-speaking Polynesians in Tonga. These results suggest that Polynesian ancestors have considerably contributed to maternal gene pool of AN-speaking Melanesians in the Solomon Islands before their expansion to Remote Oceania.
2305 Ancestral genetic components in Arabians with attention to Natufians benchmarked against ancient DNA and a Persian Gulf component that doesn't currently have an ancient DNA counterpart. It isn' clear if the Persian Gulf ghost population component is related to Caucasian hunter-gatherers and Caucasian early Neolithic, or if it is a third thing entirely. The abstract is as follows:
The extreme weather events of the Younger Dryas that left Arabia and most of the southern Levant dry drove Natufian expansion from the southern Levant to the Negev, North East Levant, and Mesopotamia while other cultures emerged in the Zagros and in Anatolia. The first Sumerian city states were established around 6 BCE, and the Dilmun culture in Arabia emerged as a major trading power connecting Sumer to the Harrupan civilization. Besides material remains, many of these cultures, including Natufians, left human remains whose genetic imformation provides geographical and chronological records of human migration and admixture starting nearly from the time of post glacial expansions to modern times. In this study, we sought to explore the population genetics of the Arabian Peninsula, identify likely ancient source populations, and investigate evidence of ancient migrations and admixture using PCA, ADMIXTURE, f3, ALDER, and LDA. ADMIXTURE identified two major contributors to the modern Arabian peninsula populations: an early expansion marked by Natufian aDNA samples, and a component Persian Gulf associated component. PCA distinguishes between the Natufian genetics and the Arabian Pensinsula group that ADMIXTURE combines. Gumuz and Somali admixture impacts the Peninsula, Egypt, and the Levant. Admixture between the Natufian genetic component and East Africa show significant negative f3 statistics admixing in Egypt, and similarly Egyptian and the Natufian genetic component admixing in East Africa in both directions. Ancient Anatolian genetics have penetrated the study region except for Yemen according to f3. While we found little gene flow as a candidate for Indo-European admixture in any direction, we did see patterns of expansions carrying Natufian genetics that marked expansion and admixture aligns with that of the proto-Semitic language.
2308 Peruvian genetics showing more diversity of indigenous ancestry than previous studies. Previous studies have shown very little continuity between ancient DNA and modern DNA in the region suggesting near total replacement in the post-Columbian era. But, this study explains why it was able to get a much richer data set, so the lack of continuity may have been, in part, a function of sampling issues in the earlier studies. The abstract is as follows:
INTRODUCTION: There are a limited number of studies from Latin America that have included native populations mainly due to geographic limitations and ethical considerations when interacting with native communities to enroll them in research studies. This project, initiated by the Peruvian National Institute of Health in 2010, represents the first major effort at studying specific native and mestizo communities across Peru, including demographic history, and population migration patterns forming the basis of precision genomic medicine for the Peruvian people. A total of 953 participants from 30 communities (13 mestizo and 17 native) were enrolled in this study, of which we have generated genotype array data for 171 and high coverage whole genome sequence data on 150. 
RESULTS: Our cohort of individuals, including the mestizos, has a much greater contribution from Native American ancestry than previous large-scale sequencing studies. We were able to construct a migration and diversity topography of Peru, which revealed that major cities harbor a high degree of genetic diversity independent of European contributions. Further, using identify-by-descent networks, we illustrate that during pre-Inca, Inca, and Spanish administration the Andean region was central to the population structure of Peru, while post-Spanish independence, the population dynamics seem to shift towards the coast, consistent with history. This is also consistent with high altitude adaptation leading to reduced gene flow into the Andes. We also demonstrate fine-scale population structure within the mestizo communities, identifying admixture between Native American communities in addition to an increase European contribution, both of which need to be considered when performing GWAS and personalized medicine programs. 
CONCLUSION: The genetic background of Native Americans has spread worldwide including in United States. It is expected that almost one million immigrants will come from Andean countries with high levels of Native American background. This population will be classified as “Hispano/Latino” in many studies in United States, but this group is a mixture of individuals with different levels of Native American ancestry and from different Native American sources. For this, we need to better understand the genetic variation and architecture of these native populations, migration patterns, and ethno geographical studies.
2309 Admixture between Finns and Estonians. The abstract is as follows:
Ancestry information at the individual level is a resource for personalized medicine, demographical and history research, and for tracing back personal history. We report a new method for quantitatively determining personal genetic ancestry based on genome-wide data.

Numerical ancestry component scores are assigned to individuals based on comparisons with reference populations. These comparisons are conducted with an existing analytical pipeline making use of genotype phasing, similarity matrix computation and our addition - multidimensional best fitting by MixFit. The method is demonstrated by studying Estonian and Finnish populations in geographical context.

We show differences in the genetic composition of these close European populations and how they have influenced each other. We determine ancestry component distribution by geographical region for Estonia and Finland to highlight how these populations have interacted with their neighbors. Sorting the individuals by the birth date allows investigation of time-dependent trends in ancestry component distribution. We perform association analyses between ancestry components and anthropometric traits and report several associations.

Our analytical methods apply to studying specific individuals but can be extended to population studies. We map the ancestral composition of Estonia and Finland in the geographical and historical context. The analytical pipeline has been published, MixFit is available at
2310 Mongolian DNA and Mongolian introgression into Finns ca. 13th century CE. Eurogenes discusses the abstract here. Basically, he argues convincing that a direct Mongolian to Finnish introgression of the magnitude suggested in impossible in historical terms and contraindicated by uniparental genetics. Instead, the Finns like have Siberian autosomal genetic admixture also appearing in the putative source population. At fault is a lack of sufficient interdisciplinary background in geneticists to realize the follow of the hypothesis as suggested to prompt them to propose a more plausible narrative. This lack of interdisciplinary background seems to be a particular problem in Chinese geneticists. The abstract is as follows:
Here, we present the whole-genome sequencing data for 386 Mongolian individuals which mainly composed of the Buryats and the Khalkha Mongols by average sequencing depth of 17X. We discovered 3.8 million novel single nucleotide polymorphisms (SNPs) which were not previously reported. Moreover, 965,663 SNPs which were rare (minor allele frequency < 0.5%) in the 1000 genome project phase 3 were low frequency or common in our dataset. Series of analysis demonstrated distinctive population structure of the Mongolians from the East Asians. We constructed robust imputation panel for Northern Asian populations which produces great imputation accuracy for rare (mean r2 of 0.82) and low frequency (mean r2 of 0.87) SNPs. We identified significant gene flow from the Buryats to the Finnish which was predicted to be occurred in 1,228 (±87) year. Moreover, 13.38% of Buryat admixture was predicted in the Finnish genome. In summary, this study illustrated advantage of whole-genome sequencing to build reference panels and to study population history.
2311 Estonian population genetics. The main distinction within Estonia is between maritime and inland populations.

2313 Malaysian indigenous populations grew rapidly more distinct despite recent (ca. 2000-4000 years) divergence due to natural selection

2314 In Kashmir, India contrary to the male dominated migrant assumption, there is great mtDNA diversity. Kashmir location put in directly in the path of many historic folk migrations. This is in contrast to other areas in India where mtDNA appears far less changed even at a quite deep time depth than Y-DNA which show male dominated influence from Indo-Aryans. One could probably use distinctions between Y-DNA and mtDNA mixes on a geographic basis to show different modes of migration/conquest. Steppe Indo-Europeans were patrilocal with high levels of female mobility at marriage over considerable distances. Kashmir may have been within the territory where this pattern prevailed, while Southern India may have had more of a male dominated military conquest model.

2315 Census population v. effective population size in two Lithuanian subpopulations, which genetic methods inaccurate assume are closer to each other than they are in reality.

2316 Evidence of natural selection related to disease resistance in Chileans

2317 Fine scale population structure in Han Chinese populations focused on haplogroups related to diseases with a 20,000 person sample size.

2322 Sardinia's population genetic stability since the Neolithic is confirmed with a set of ancient DNA from all intervening time periods with eight ancient DNA samples. Sometimes pots are people and sometimes they aren't. The abstract is as follows:
Ancient DNA (aDNA) has provided a powerful tool for assessing the temporal stability of populations within a geographic locale. In much of mainland Europe, aDNA has revealed a relatively dynamic population history from the Neolithic period through the Bronze Age. Due to their relative isolation, island populations may in general not experience the same population dynamics as mainland populations. The island population of Sardinia in particular has been hypothesized to have a relatively stable and continuous population from the early Neolithic, largely on the basis of modern Sardinian DNA. Here we directly assess continuity using genome-wide capture data (~1.2 millions SNPs) of 26 ancient humans from the island of Sardinia spanning the Neolithic, Copper Age, and Bronze Age, including individuals from the Nuragic culture. Through analyzing read-level DNA damage patterns and estimating modern contamination levels, we authenticate these ancient DNA sequences and removed outlier loci and individuals for downstream analyses. Projecting these ancient individuals on to modern axes of genetic variation, as defined by principal component analysis on a large-scale reference dataset of modern human populations from Sardinia, Europe and the Middle East, reveals no obvious temporal structure within Sardinia within this long time frame. Consistent with previous hypotheses of early migrations in Europe, we observe clustering of these ancient individuals with previously published sequences of ancient humans associated with an 'early farming' Neolithic culture. Through the application of multiple population genetic methods and exploratory data analysis tools we find that relative to mainland Europe there has been population stability within the island of Sardinia. Beyond shedding light on Sardinian population history, the relative stability we infer is important for understanding the local frequencies of disease susceptibility alleles.
2323 Decline in effective population and uniparental haplotype diversity in Native Americans quantified. Genetic diversity declined by less than census population (on the order of 50% loss of diversity v. 90% loss of census population), as one would reasonably expect. This data point is a good one to use to compare predictions about losses of genetic diversity in human populations during bottlenecks and a real world example of it.

2324 Origins of genetically Polynesian people in Brazil who died in 19th century before documented migrations redetermined using better reference sets. Original determination had been Cook Islands. The abstract doesn't tell us what the new data concluded, just that the old determination was flawed due to its limited data set. I do not like it when abstracts tease like that, rather than spilling the beans. The abstract is as follows:
In 2010, mitochondrial DNA extracted from two ancient skulls found in southern Brazil belonged to the haplogroup B4a1a1a, exclusively found in Polynesia. Radiocarbon analyses indicated that these individuals most probably died before the 19th century, prior to any registered transport of Polynesian people to South America by European vessels. Further genome-wide analyses showed a complete Polynesian ancestry for both samples, with Cook Islands as the closest source population. However, scarcity of genotyping data from modern Polynesian populations posed a major limitation for inferring a more specific place of origin for said skulls. Here, we re-analyze these ancient DNA samples using an extended reference panel that comprises over 475 genotyped samples from 18 different locations across the Pacific Ocean. With this data we explore the genetic affinities of the Botocudo skulls at a finer scale to potentially pinpoint their genetic origin, and we demonstrate the importance of assembling diverse genetic reference panels to shed light on the evolutionary past of human remains devoid of archeological context.
2353 New determination of overall mutation rate in humans. The 1.2 figure reached is on a low side within the range of estimations made in the past.

2354 Mutation rates vary across genome by type of gene. This poster presentation is more persuasive than 2353 in my view, in accord with what I know about past research on mutation rates.

2357 Easter Islanders have pre-Columbian Native American ancestry but it is derived from other Polynesian islands from which it was settled and not directly. This is at least the third investigation on the topic, with one prior study concluding that there was direct pre-Columbian Native American introgression into Easter Islanders and a subsequent paper  that is basically a rebuttal arguing that the introgression was post-Columbian. The abstract is as follows:
Reaching its easternmost extent in Easter Island less than one thousand years ago, the settlement of Polynesia represents a final chapter in the dispersal of humans across the globe. Though it occurred relatively recently, much remains unknown about this unique oceanic process in historical population genetics, including the sequences of islands settled, the timing of settlements, and the origins of the settlers. Using dense genome-wide SNP array data of 445 modern samples from seventeen key islands (or island clusters) spanning remote Oceania, we infer settlement patterns stretching across the Pacific to Easter Island, and we address the long lingering suggestion that Native Americans could have played a role in the ancient population history of Easter Island. We confirm this theory, but we show that the ancient contact with Native Americans took place in Polynesian “up stream” of Easter Island, that is, before its settlement, and that this component was then carried to Easter Island by its admixed founders. We use three different timing analyses, as well as evidence of differential origins within the Americas of distinct Native American genetic signatures that we find present in Polynesia, to support our conclusions. The isolated Polynesian islands, separated by vast Pacific distances, have provided us with a uniquely structured canvas on which to implement novel variants of ancestry deconvolution and migration analysis techniques; we will describe these techniques, which could be useful for analyzing similarly isolated populations from other understudied regions of the world. Our results demonstrate the important role that both recent and ancient admixture events have played in creating the rich diversity patterns that define modern Polynesian populations.
2359 Lakshadweep Islands of the coast of India were settled mostly from Kerala state. The abstract is as follows:
Archipelago Lakshadweep resides in a south-west part of India in the Arabian Sea. In addition to its geographical isolation, the gene pool of these islands encompasses the signatures of ancient human dispersal across the South Asian (SA) corridor. In order to reconstruct the population history of Lakshadweep population, we have analysed uniparental (mtDNA and Y chromosome) and biparental (750K autosomal loci) markers among 1359 individuals belonging to several ethnic groups of Lakshadweep Islands. We observed the overwhelming presence of mitochondrial haplogroup R30, whereas the Y chromosome major haplogroups were P267-R2a (16%), Y495-R1a2b (12%). Both mtDNA and Y chromosome signals showed a close genetic link between Lakshadweep populations with the mainland Indian populations. The allele frequency and haplotype-based autosomal analyses suggested their closest affinity with the Southern Indian state Kerala.
2360 Japan has four genetic clusters, one associated with Japanese language speakers, one associated with Ryukuan language speakers, one Korean and one Amami (an island chain between the main islands of Japan and Okinawa). Surprising. I expected an Ainu cluster. I also expected a a division within Japan between an Ainu shifted Northern Japan and a Southern Japanese cluster which were integrated under the central government at different times. And, I am surprised that Ryukuan and Amami are not in the same cluster. The abstract is as follows:
Aims the Japanese population has been known to be grouped into super-clusters, which are Mainland and Ryukyu clusters, in the population genetics. Investigation of the super-clusters in the detail was very important to perform genetic disease association studies and reveal demographic history in the Japanese population. We examined the Japanese population substructure using genome wide genotyping data from the Japan Multi-Institutional Collaborative Cohort Study (J-MICC), including south west islands of Japan. 
Methods A total of 14,539 study subjects from the 12 areas of the J-MICC study including the Ishigaki and Amami Islands were genotyped at RIKEN Center for Integrative Medicine using a HumanOmniExpressExome-8 v1.2 BeadChip array. Subjects with discordant sex information and close relationship pairs were removed. First, Principal component analysis (PCA) with J-MICC subjects, 1000 genomes East Asian (EAS), and Pan-Asian SNP (PASNP) consortium genotype data were performed to examine the population substructure of east Asian including J-MICC subjects. We also performed ADMIXTURE analysis for J-MICC subjects. 
Results PCA with J-MICC subjects, 1000 genomes EAS, and Pan-Asian EAS showed three clusters (Mainland, Ryukyu, and Korean clusters) from J-MICC subjects. Of the J-MICC subjects, 0.3% were assigned to the Korean cluster. PCA with only J-MICC subjects further indicated the Amami cluster. The Amami cluster existed closest to Ryukyu cluster, but didn’t exist closest to Korean and Taiwan populations. The result of ADMIXTURE analysis revealed that the minimum value of the cross-validation (CV) error was observed when the assumed number of ancestral populations (K) was 8. 
Conclusion We examined the population substructure of J-MICC study, and identified four sub-clusters (Mainland, Ryukyu, Amami, and Korean clusters). ADMIXTURE analysis indicated that the K=8 was minimum value of the CV error. Thus, the result suggests the possibility that more genetic clusters exist in Japanese population. These results are expected to be important information to do genetic disease association studies with the use of the Japanese population data.
2362 Genetics of Central Mexico. There was less European ancestry in a rural Mexican town than in urban areas, and was only one admixture event with European there. The abstract is as follows:
The Spanish colonization of Mexico led to the creation of new communities containing individuals who had been born in three different continents (North America, Europe, and Africa) and who came from diverse cultural and linguistic backgrounds. Major population collapses also occurred in indigenous communities following colonization of this region. While previous research has explored these events in Mexico City and other urban areas, their impact on rural populations remains unclear. In Xaltocan, a small town in central Mexico, historical documents suggest that the Spanish rarely visited the town. To better understand the demographic history of this region and the genetic effects of Spanish colonial history, we collected samples from 47 present-day residents from Xaltocan. The samples were genotyped for >600,000 genome-wide single nucleotide polymorphisms (SNPs) using the Affymetrix Axiom® Human Origins Array. Individual ancestry estimates were calculated using ADMIXTURE and RFMix. Estimates of the number and timing of admixture events at Xaltocan were calculated using TreeMix and Tracts. Past changes in population size were modeled using dadi. We find a much lower average proportion of European ancestry at Xaltocan compared to previously sampled populations in the Americas. We also find evidence that a single admixture event between European and Native American source populations affected our study population at Xaltocan.
2365 Genetics of Brittany - matches historic rather than current boundaries. Given its state of economic development, French DNA studies are rare, so it fills an important gap. Also Brittany is historically important as a source of Norman invaders to England and of Norman troops who went to Italy and participated in the Crusades. Also a good illustration of the fact that political boundaries influence mating patterns in scientifically demonstrable ways. The abstract is as follows:
The genetic structure of human populations varies throughout the world, being influenced by migration, admixture, natural selection and genetic drift. Characterising such genetic variation can provide insight into demographical history and informs research on disease association studies, especially on rare recent variants. In this study, we examine the fine-scale genetic structure of Brittany and surrounding regions of France. 
Brittany is a region in the north-west of France, historically and culturally distinctive. Genetic proximity between Bretons and Irish has been shown in [1]. Currently, administrative Brittany covers only 80% of historical Brittany. Southern limits of historical Brittany extend further than the Loire River, the biggest physical barrier in the region. Eastern limits do not coincide with any significant geographical feature, potential genetic barrier could be thus a result of cultural and historical differences. 
Methods and Results 
We genotyped 1005 individuals from North-Western France, with at least three of their grandparents born within a 15 kilometres distance using Axiom™ Precision Medicine Research Array. Principal Components analysis revealed a high correlation between geographical position and components (p-value < 2e-16). Visualisation of PC1 (0.16 % of variance) on the map points to three subpopulations: one in the south of Loire River and two in the north, one of which overlaps with historical Brittany. Partial Mantel tests confirm that genetic differentiation is not uniform. We also approximate eastern border of “genetic Brittany” based on ADMIXTURE results and test the strength of the barriers with Fst statistic. Southern border, corresponding to Loire River, is more pronounced. 
We here report both evidence for isolation by distance within at a very fine level and existence of two genetic barriers, the Loire River and the historical boundary of Brittany Duchy. Subsequently, we will verify and extend our findings with fineSTRUCTURE software and with analysis based on Identity By Descent. This fine-scale population structure may have consequence in association analyses, especially for rare variants which tend to be geographically clustered. These results support the need for a genetically matched panel of controls in gene mapping analyses in French population. 
1. Karakachoff, M. et al. Fine-scale human genetic structure in Western France. Eur J Hum Genet 23, 831–836 (2015).
2366 Genetics of Ireland - about 70% of territory is mostly Gaelic, about 30% shows admixture with Norman and Norwegian ancestry being most notable. Lines up with historical events.

2368 Genomic health of ancient hominins. The abstract is as follows:
The genomes of ancient humans, Neandertals, and Denisovans contain many alleles that influence disease risks. Using genotypes at 3180 disease-associated loci, we estimated the disease burden of 147 ancient genomes. After correcting for missing data, genetic risk scores were generated for nine disease categories and the set of all combined diseases. These genetic risk scores were used to examine the effects of different types of subsistence, geography, and sample age on the number of risk alleles in each ancient genome. On a broad scale, hereditary disease risks are similar for ancient hominins and modern-day humans, and the GRS percentiles of ancient individuals span the full range of what is observed in present day individuals. In addition, there is evidence that ancient pastoralists may have had healthier genomes than hunter-gatherers and agriculturalists. We also observed a temporal trend whereby genomes from the recent past are more likely to be healthier than genomes from the deep past. This calls into question the idea that modern lifestyles have caused genetic load to increase over time. Focusing on individual genomes, we find that the overall genomic health of the Altai Neandertal is worse than 97% of present day humans and that Ötzi the Tyrolean Iceman had a genetic predisposition to gastrointestinal and cardiovascular diseases. As demonstrated by this work, ancient genomes afford us new opportunities to diagnose past human health, which has previously been limited by the quality and completeness of remains.
2724 Brazilian slaves were almost all from Benin or Bantu with further detail as well about the pre-Benin port source of these individuals in the West African interior.

2946 Knockout disorders in Ashkenazi Jews informed by population history, including the 13th century bottleneck in that population (presumably due to pogroms related to the Crusades, although this isn't entirely clear and disease and the Little Ice Age could also have contributed either directly, or by triggering the pogroms, or both).