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:
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 www.geenivaramu.ee/en/tools/mixfit.
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:
Background
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.
Conclusion
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).

Wednesday, October 18, 2017

Neutron Star Collision Tightens Neutrino Parameter Space UPDATED

The latest big splash in physics, the observation of two neutron stars colliding into each other with both gravity waves and light, provides an independent observation of the Hubble constant that when combined with the Planck data tightens the parameter space of neutrino physics.

The sum of the three neutrino masses goes from less than 1.11 eV with Planck data alone, to less than 0.77 eV with this measurement and the Planck data combined. But, without this new data point, but combined with other data sets, the limitation was already even tighter with combinations as low as 0.11 eV, and the minimum value from neutrino oscillation data is 0.06 eV in a normal hierarchy. It isn't clear how much impact this new data point has on the earlier combination value.

The effective number of neutrino types (Neff) goes from 3.11 ± 0.25 with Planck data alone to 3.09 ± 0.25 with the addition of this measurement. But, as of 2015, the constraint with Planck data and other data sets was 3.04 ± 0.18 (even in 2014 cosmology ruled out sterile neutrinos). Neff equal to 3.046 in a case with the three Standard Model neutrinos and neutrinos with masses of 10 eV or more not counting in the calculation. It isn't entirely clear what the Neutron Star measurement of Hubble's constant adds, if anything, to the combined estimates, but it might, for example, slightly reduce the margin of error which would increase the significance by which the four neutrino case was ruled out. Neff and the Hubble constant are strongly correlated, but the combination value for Hubble's constant is very close to the new value from this observation.

So, the four neutrino case is ruled out at a more than 5.3 sigma level already, which is a threshold for a scientific discovery that there are indeed only three neutrinos with masses of 10 eV or less, ruling out the sterile neutrino hypothesis for a stable sterile neutrino of under 10 eV (when a best fit of potential anomalies from reactors predicts a sterile neutrino mass of about 1 eV also here). A 2015 pre-print on notes that:
The 95% allowed region in parameter space is Neff < 3.7, meff s < 0.52 eV from PlanckTT + lowP + lensing + BAO. This result has important consequences for the sterile neutrino interpretation of short-baseline anomalies. It has been shown that a sterile neutrino with the large mixing angles required to explain reactor anomalies would thermalize rapidly in the early Universe, yielding ∆Neff = 1. The preferred short-baseline solution then corresponds to ms of about 1 eV and ∆Neff = 1 and is strongly excluded (more than 99% confidence) by the above combination of Planck and BAO data.
UPDATE October 19, 2017

* The MINOS and MINOS+ reactor experiments rule out a light sterile neutrino, confirming the cosmology result. The abstract of a new pre-print on their results states that:

"A simultaneous fit to the charged-current muon neutrino and neutral-current neutrino energy spectra in the two detectors yields no evidence for sterile neutrino mixing using a 3+1 model. The most stringent limit to date is set on the mixing parameter sin2θ24 for most values of the sterile neutrino mass-splitting Δm241>104 eV2."

The MINOS data explores a range of values for Δm41 between the lightest mass state and the sterile neutrino mass state of 10 meV to 32,000 meV, where the bounds on the sum of the three neutrino masses from cosmology in the currently experimentally preferred normal hierarchy is 60 meV to 110 meV. For example, the MINOS data shows that:
At fixed values of ∆m241 the data provide limits on the mixing angles θ24 and θ34. At ∆m241 = 0.5 eV2, we find sin2θ24 less than [0.0050 (90% C.L.), 0.0069 (95% C.L.)] and sin2θ34 less than [0.16 (90% C.L.), 0.21 (95% C.L.)].
* Weak boson decays have long ago ruled out the possibility of a number of weakly interacting neutrinos different than three. The number of weakly interacting neutrinos of less than 45 GeV upon Z boson decay is 2.992 ± 0.007 (with a mean value 1.14 sigma from 3) which is consistent with the Standard Model, in a quantity that must have an integer value. The two neutrino and four neutrino hypotheses are ruled out at the 140+ sigma level, when a mere 5 sigma result is considered scientifically definitive.

END UPDATE

Sunday, October 15, 2017

Ancient DNA Refines New World Settlement Paradigm

Overview

new pre-print based on analysis of ancient DNA from a number of far northern populations in North America and Siberia has refined what we know about the waves of pre-Columbian migration to North American after the founding population of American entered North America from the Beringian land bridge not later than about 14,000 BCE.[1]

There is genetic variation that is found in Canada and the United States, but not in Latin America, which is not attributable to later waves of pre-Columbian migration. This was due either to founder effects in a population that rushed down the Pacific coast over a period of less than 2000 years and became ancestral to all indigenous Americans outside of Canada and the United States, or due to population structure in the original founding population of the Americas.

All pre-Columbian genetic ancestry extant in modern gene pools in the Americas (with the possible exception of part of the ancestry found in certain Amazonian tribes whose source is not well understood which is sometimes described as "Paleo-Asian" [2]) is attributable to this initial founding population (often called "First Americans" in the literature) or two main subsequent migrations from Siberia from genetically related (but not identical) Siberian populations.

The first wave of subsequent pre-Columbian migration, ca. 3500 BCE (the current pre-print makes the case for an approximate 3000 BCE date [3]) gave rise to the Paleo-Eskimos who ceased to exist as a distinct population around the time that the "Neo-Eskimos" arrived, which is also the source, a few centuries later, of the distinctive genetic ancestry of the Na-Dene people (such as the Tlingit people of Southeast Alaska, and the Apache and Navajo people of the American Southeast), which is otherwise shared with the founding population of the Americas.

The second wave sometime between 1100 BCE and 200 BCE (probably closer to 200 BCE, given the archaeological evidence) gave rise to the Neo-Eskimos such as the Inuits, after substantial admixture with people descended from the founding population of the Americas. (The Na-Dene people were not a source of admixture with the Neo-Eskimos.)

Incidentally, this three wave model had already been predicted based upon archaeological and linguistic evidence several decades before genetic evidence confirmed this model.

There have been a few other well documented instances of much more incidental pre-Columbian contact after the founding population arrived with the Americas (for example, Vikings ca. 1000 CE in Eastern Canada), but none of the other cases left any genetic legacy in the Americas. Also notably, all of those credibly documented contacts post-date the Paleo-Eskimo migration, and all but one doubtful case of a single alleged New World apple seed found in India that was carbon dated to 2000 BCE, post-date both of these migration waves. For example, the Asian War Complex arrives ca. 700 CE, about the same time as the Neo-Eskimos reach Alaska proper, an a previous major bow and arrow technology innovation arrives ca. 400 BCE around the time of first contact between pre-Neo-Eskimos from Asia and and indigenous populations in the Bering Straight. Critically, all First American populations were still isolated from all other modern humans for more than 10,000 years (a time depth that, among other things, is so great that it impossible to reconstruct a proto-Amerind language from known indigenous American languages).

The Story Of The Na-Dene

The genetic distinctiveness of the Na-Dene (a.k.a. Athabaskan) indigenous populations of North America derives from admixture of Paleo-Eskimos in Alaska ca. 3000 BCE plus or minus a few centuries (genetic and archaeological evidence suggests that they arrived ca. 3500 BCE [4], giving rise to the Saqqaq culture and started to admix several centuries later) with indigenous First Americans (whose ancestors arrived over the Beringian land bridge by not later than about 14,000 BCE). The initial admixture percentage in ancient Northern Athabaskans was roughly 25%-40%. Over time, the Paleo-Eskimo admixture percentage in the Na-Dene has been diluted to about 10%, but all Na-Dene populations have this ancestry which is almost completely absent from non-Na-Dene language speakers.

Genetic evidence also supports the Dene-Yeniseian linguistic hypothesis that the Na-Dene languages have a linguistic family relationship with the Yeniseian language family of Siberia of which the sole surviving language is the Ket language. Specifically, ancient DNA from a population in the Ust'-Belaya culture of Chukotkan in Siberia, which is ancestral to the Paleo-Eskimos, shows evidence of genetic relatedness to both the Paleo-Eskimos and a western Siberian group related to Kets. The pre-print notes that:
striking parallels in archaeological and genetic results suggest that admixture between proto-Paleo-Eskimos and Siberian lineages in Chukotka took place not long after they diverged [ca. 4300 BCE], indicating that cultural contact between these groups at this time almost certainly occurred as well. This result has implications for archaeology and historical linguistics[.]
At least two "push factors" drove Na-Dene tribes such as the Navajo to migrate to the American Southwest around 900 CE, and may have also been involved in the migration of the Tlingit Na-Dene tribes to southeastern Alaska and Pacific coastal Canada. One was the arrival of "Neo-Eskimos" (e.g. the founding population of the Inuits who were part of the Birnirk and Thule cultures) in western Alaska ca. 650 CE to 850 CE. The other was a massive volcanic ash fall ca. 900 CE. There was little or no Na-Dene genetic introgression into Neo-Eskimo populations.

In the American Southwest, there was also a "pull factor" which was the control vacuum created when the society of the ancient Puebloan people (a.k.a. the Anasazi) collapsed, in part due to a major drought associated with the Medieval Climate Anomaly (which quite possibly was related, in part, to the volcanic eruptions that took place at about the same time that the MCA began) that may have partially encouraged Na-Dene people who had already migrated to the Canadian heartland to migrate South, or may have made them more successful as a potentially competing collapsed when, or not long after, they arrived.

It is also worth noting that there were major innovations in bow and arrow technology ca. 2500 BCE, which had previously been stagnant since 10,000 BCE, which might have coincided with the arrival of the Paleo-Eskimos and the increasing prevalence of the Arctic Small Tool tradition.

The Story of the Modern Eskimos

Some members of the population the Siberian population ancestral to the Paleo-Eskimos migrated to North America. Others remained in Siberia and gave rise to a sub-population ca. 1500 BCE (about 1500 years after the first wave admixed with the Na-Dene) that was ancestral to modern "Neo-Eskimos" such as the Inuits who arrived in western Alaska ca. 650 CE to 850 CE and are known to archaeologists as the Birnirk and Thule cultures. About 43% of the modern Neo-Eskimo population's ancestry is attributable Asian migrants from this population and this population is also the source of mtDNA D2a in Neo-Eskimos.

The balance of Neo-Eskimo ancestry [5], arises from northern non-Na-Dene descendants of the first wave of migrants to North America, and in particular, from descendants of the indigenous southwestern Alaska and Kodiak Island Ocean Bay tradition (which flourished ca. 4800 BCE to 2500 BCE) in which a lot of the technological innovations involving year round maritime hunting were invented. In contrast, early "Paleo-Eskimo people used marine resources on a seasonal basis only, depended for the most part on hunting caribou and muskox, and lacked sophisticated hunting gear that allowed the later Inuit to become specialized in whaling." Thus, while the new influx of genes and their language had Asian origins, their maritime hunting technologies were made in North America.

The admixture that gave rise to the modern Neo-Eskimo population had already substantially run its course by 200 CE when ancient DNA reveals an already admixed Neo-Eskimo who was part of the Old Bering Sea culture which commenced ca. 200 BCE.

The admixture that gave rise to the ethnogenesis of the Neo-Eskimos predated the Ipiutak culture of western Alaska which emerged ca. 300 CE.

It is possible that some or all of the admixture and ethnogenesis that gave rise to the Neo-Eskimos took place in the Old Whaling culture of western Alaska (ca. 1100 BCE to 700 BCE), the Choris culture of western Alaska (ca. 700 BCE to 500 BCE) or the Norton culture of western Alaska (ca. 500 BCE to 200 BCE). There isn't enough ancient DNA data available to be more specific. Archaeological data tends to support a date at the more recent end of that range, such as the tail end of the Norton culture [6].

End notes and language from the body text of the paper supporting this summary, with editorial emphasis, additional hyperlinks to prior posts at this blog, and headings, appear below.

Saturday, October 14, 2017

Cosmological Inflation Still Bad Science UPDATED

Sabine's latest blog post explains deep problems with the theory (really an infinite class of theories) of cosmological inflation research.

Basically, it is underdetermined and can't predict anything meaningful.

UPDATE October 18, 2017

A follow up blog post explains that the flatness problem that inflation is commonly described as solving comes from an unjustified and probably unreasonable assumption about initial conditions.

END UPDATE

Friday, October 13, 2017

Back To Basics In High Energy Physics UPDATED

Usually, the headlines in physics go to people who are proposing or discovering "new Physics", but an important part of the high energy physics enterprise is constantly pushing for more precise measurements of quantities involved in plain old Standard Model physics that has been settled science for decades. Today's research results are mostly of that variety:

Top Quark Measurements:

* The DZero collaboration at the now completed Tevatron experiment released another review of its old data regarding the mass of the top quark. Bottom line:
The most precise single measurement at the Tevatron of mt = 174.98 ± 0.58(stat+JES) ± 0.49(syst) GeV is performed by the D0 Collaboration in the `+jets channel, corresponding to a relative precision of 0.43%. The combination with all other measurements from the D0 experiment results in mt = 174.95±0.40(stat)±0.63(syst) GeV. The Tevatron combination yields mt = 174.30±0.35(stat)± 0.54(syst) GeV, which corresponds to a relative precision of 0.37%.
The directly measured top quark mass according to the Particle Data Group is as follows, based upon a combined CMS measurement, a combined ATLAS measurement and a combined Tevatron measurement:

OUR AVERAGE  Error includes scale factor of 1.6.
1
 2016 T
ATLScombination of ATLAS
2
 2016 AK
CMScombination of CMS
3
 2016
TEVATevatron combination

The top quark mass measured indirectly via cross-section measurements per PDG is as follows:

OUR AVERAGE
$±$ 1
 2016 F
D0$\ell \ell$ , $\ell$+jets channels
2
 2016 AW
CMS$\mathit{e}$ + $\mu$ + ${\mathrm{E̸}}_{T}$ + $\ge$0j
3
 2015 BW
ATLS$\ell +{\mathrm{E̸}}_{T}+\ge$5j (2$\mathit{b}$-tag)
4
 2014 AY
ATLS$\mathit{p}\mathit{p}$ at $\sqrt{s}$ = 7, 8 TeV

"An extended Koide's rule estimate of the top quark mass using only the electron and muon masses as inputs, predicted a top quark mass of 173.263947 ± 0.000006 GeV", via this prior blog post, which is very close to the best fit measured value.

As previously noted in a December 16, 2016 blog post at this blog:
If the the sum of the square of the boson masses equals the sum of the square of the fermion masses equals one half of the Higgs vacuum expectation value, the implied top quark mass is 174.03 GeV if pole masses of the quarks are used, and 174.05 GeV if MS masses at typical scales are used. . . .
The expected value of the top mass from the formula that the sum of the square of each of the fundamental particle masses equals the square of the Higgs vaccum expectation value (a less stringent condition because the fermion and boson masses don't have to balance), given the global average Higgs boson mass measurement (and using a global fit value of 80.376 GeV for the W boson rather than the PDG value) is 173.73 GeV. The top quark mass can be a little lighter in this scenario because the global average measured value of the Higgs boson mass is a bit heavier than under the more stringent condition.
Both of the predictions from these phenomenological hypotheses are a bit heavier than the currently measured top quark masses as the LHC measurements have turned out to be smaller than the Tevatron measurements which are quite close to these expected values. But, the scatter in the various measurements is still broad enough that these values cannot be ruled out.

UPDATE October 18, 2017: A new review of ATLAS top quark mass measurement is available, but most, if not all are already incorporated in the PDG global weighted average:
Results of top-quark mass measurements in the di-lepton and the all-jets top-antitop decay channels with the ATLAS detector are presented. The measurements are obtained using proton-proton collisions at a centre-of-mass energy s = 8 TeV at the CERN Large Hadron Collider. The data set used corresponds to an integrated luminosity of 20.2 fb1. The top-quark mass in the di-lepton channel is measured to be 172.99 ± 0.41 (stat.) ± 0.74 (syst.) GeV. In the all-jets analysis, the top-quark mass is measured to be 173.72 ± 0.55 (stat.) ± 1.01 (syst.) GeV. In addition, the top-quark pole mass is determined from inclusive cross-section measurements in the top-antitop di-lepton decay channel with the ATLAS detector. The measurements are obtained using data at s = 7 TeV and s = 8 TeV corresponding to an integrated luminosity of 4.6 fb1 and 20.2 fb1 respectively. The top-quark pole mass is measured to be 172.9+2.52.6GeV.
Teresa Barillari, "Top-quark mass and top-quark pole mass measurements with the ATLAS detector"(October 16, 2017). END UPDATE.

* The ATLAS and CMS experiments at the Large Hadron Collider (LHC) have released a summary of their findings regarding top quark properties. Unsurprisingly, they are consistent with Standard Model expectations in all respects and strictly limit anomalies in the transition from the top quark to the bottom quark via the weak force as the accuracy of the measurement of this quantity improves. Several measurements were made and two of the easiest to summarize results were as follows:

W Boson Helicity In Top Quark Decays
The W-boson helicity fractions (left-handed, right-handed and longitudinal) are defined as FL,R,0 = ΓL,R,0/ΓTotal, where ΓL,R,0 are the partial decay widths in left-handed, right-handed, and longitudinal helicity states respectively, with ΓTotal being the total decay width. The SM next-tonext-to-leading order (NNLO) calculations [4] including the electroweak effects predict the values of FL = 0.311±0.005, FR = 0.0017±0.0001 and F0 = 0.687±0.005, for a top quark mass of 172.8±1.3 GeV.
The crude average of the CMS and ATLAS measurements (which do be exactly right should be error weighted and should include the error bars of the combined result) are as follows:

FL=0.311 (v. predicted value 0.311), FR=0.006 (v. predicted value 0.0017), and F0=0.695 (v. predicted value 0.687).

The results for FL and F0 are within the combined theoretical uncertainty of the Standard Model prediction even before considering experimental uncertainty.

The result for FR is within the experimental uncertainty of Standard Model prediction at the two sigma level. Also, keep in mind that FL, FR and F0 are not independent of each other and involve just two degrees of freedom, not three, but the crude average measurements above don't globally fit the data to reflect that fact.

Combining the ATLAS and CMS results properly, on an error weighted basis and doing a global, would give a better result, because the measurement that is closer to the predicted value has a significantly lower margin of error and because the experimental measurements of FR and F0 combined would each be reduced proportionately by a little bit in a global fit since FL+FR+F0 estimated independently slightly exceed 1.0 which must be true as a consequence of the way those variables are defined. The deviation if it was all done properly would be a bit more than one sigma.

Top Quark Decay Width

The Standard Model prediction for the top quark decay width (which as explained in a previous post at this blog is good global measure of deviations from the Standard Model) is ΓSM=1.324 GeV for mt=172.5 GeV.  The CMS measurement of the decay width of the top quark is Γt = 1.36 ± 0.02(stat)+0.14 −0.11 (syst) GeV, which agrees with the Standard Model prediction at the 0.3 sigma level.

The CMS boundary on the top mass decay width is tighter than the most recent ATLAS measurement of:
Γt = 1.76 ± 0.33 (stat.) +0.79 −0.68 (syst.) GeV = 1.76+0.86 −0.76 GeV.
The Charm Quark Mass

A previous determination of the charm quark mass at a 3 GeV energy scale was updated based upon late breaking new experimental data. Bottom line: "Our final result for the MS charm-quark mass reads mc(3 GeV) = 0.993 ± 0.008 GeV and mc(mc) = 1.279 ± 0.008 GeV."

Higgs Boson Measurements

The CMS experiment at the LHC has released its latest experimental data on decays of Higgs bosons to W bosons, to tau lepton pairs, and to muon pairs. It finds that:
the combined observed limit for 7 and 8 TeV [at the 95% confidence level] is 7.4, while the background-only expected limit is 6.5 +2.8 −1.9 . This corresponds to an observed upper limit on B(H → µµ) of 0.0016, assuming the SM cross section. The best fit value of the signal strength for a Higgs boson mass of 125 GeV is 0.8 +3.5 −3.4.
Given the large margin of error, the biggest surprise is that it is so close to the Standard Model expectation (0.059 sigma from the expected value in the Standard Model), which suggests that either the error in this measurement is probably greatly overestimated, or that CMS just got lucky, or both.

Analysis

None of the results are particularly surprising, but greater precision in these measurements of fundamental Standard Model physics quantities makes all other high energy physics work more accurate and broadly constrains all forms of beyond the Standard Model physics.